Targets
    Occurrences of 'http://' in Directory D:\REPOS\kkorey-igb
Found Occurrences  (1,278 usages found)
    Unclassified occurrence  (298 usages found)
        affymetrix-common  (22 usages found)
              (19 usages found)
                NOTICES.txt  (19 usages found)
                    7      http://jetty.mortbay.org/jetty/
                    10      http://www.apache.org/licenses/LICENSE-2.0    
                    17      http://www.affymetrix.com/support/developer/fusion/index.affx
                    22      http://www.gnu.org/copyleft/lesser.html
                    29      http://java.sun.com/developer/techDocs/hi/repository/
                    41      http://java.freehep.org/vectorgraphics/index.html
                    50      http://sourceforge.net/projects/picard/
                    58      http://www.jidesoft.com/
                    67      http://felix.apache.org/site/index.html
                    79      http://commons.apache.org/
                    86      http://www.servlets.com/index.tea
                    95      http://emma.sourceforge.net/index.html
                    102      http://www.antlr.org/
                    108      http://jackson.codehaus.org/
                    114      http://rabbit-hole.blogspot.com/2006/04/decoratingoverpainting-swing.html
                    120      http://jdotsoft.com
                    126      http://http://www.aqute.biz/Bnd/Bnd
                    132      http://code.google.com/p/bigwig
                    133      http://code.google.com/p/tribble
            images  (3 usages found)
                picture_credits.txt  (3 usages found)
                    2 m_musculus.png				| http://www.flickr.com/photos/hthg1983/2237614948/
                    4 a_thaliana.png 				| http://commons.wikimedia.org/wiki/File:Arabidopsis_thaliana-flower.jpg
                    5 d_melanogaster.png			| http://eol.org/data_objects/9676872
        bam  (2 usages found)
            data.bam  (2 usages found)
                README.txt  (2 usages found)
                    4 The Java library is called sam/picard (http://picard.sourceforge.net/javadoc).
                    37 http://lookseq.svn.sourceforge.net/viewvc/lookseq/bam_c/render_image.cpp
        bed  (4 usages found)
            data.bed  (4 usages found)
                bed_01.bed  (1 usage found)
                    1 track name="Bed Test File" description="Test bed file" color=255,255,0 itemRgb="on" useScore=0 url="http://www.google.com/search?q=$$"
                bed_02.bed  (1 usage found)
                    1 track name="Bed Test File" description="Test bed file" color=255,255,0 itemRgb="on" useScore=0 url="http://www.google.com/search?q=$$"
                bed_03.bed  (1 usage found)
                    1 track name="Bed Test File" description="Test bed file" color=255,255,0 itemRgb="on" useScore=0 url="http://www.google.com/search?q=$$"
                bedDetailExample.bed  (1 usage found)
                    1 track name=HbVar type=bedDetail description="HbVar custom track" db=hg19 visibility=3 url="http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?display_format=page&mode=output&i=$$"
        das  (167 usages found)
            data.das1  (167 usages found)
                das1-sample-hg10.dasxml  (3 usages found)
                    6     <GFF version="1.0" href="http://genome.cse.ucsc.edu/cgi-bin/das/hg10/features">
                    18                 <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr22:20012405-20012900&amp;db=hg10">Link to UCSC Browser for the feature</LINK>
                    20                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr22:20012405-20012900&amp;db=hg10">Link to UCSC Browser</LINK>
                das1-sample-hg18.dasxml  (164 usages found)
                    6     <GFF version="1.0" href="http://genome.cse.ucsc.edu/cgi-bin/das/hg18/features">
                    17                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    30                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    43                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    56                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    69                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    82                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    95                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    108                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    121                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    134                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    147                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    160                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    173                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    186                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    199                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    212                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    225                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    238                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    251                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    264                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74394408-74618331&amp;db=hg18">Link to UCSC Browser</LINK>
                    277                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73128640-73197707&amp;db=hg18">Link to UCSC Browser</LINK>
                    290                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73128640-73197707&amp;db=hg18">Link to UCSC Browser</LINK>
                    303                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73128640-73197707&amp;db=hg18">Link to UCSC Browser</LINK>
                    316                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73128640-73197707&amp;db=hg18">Link to UCSC Browser</LINK>
                    329                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73128640-73197707&amp;db=hg18">Link to UCSC Browser</LINK>
                    342                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73128640-73197707&amp;db=hg18">Link to UCSC Browser</LINK>
                    355                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73128640-73197707&amp;db=hg18">Link to UCSC Browser</LINK>
                    368                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73128640-73197707&amp;db=hg18">Link to UCSC Browser</LINK>
                    381                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73128640-73197707&amp;db=hg18">Link to UCSC Browser</LINK>
                    394                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73128640-73197707&amp;db=hg18">Link to UCSC Browser</LINK>
                    407                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73128640-73197707&amp;db=hg18">Link to UCSC Browser</LINK>
                    420                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73128640-73197707&amp;db=hg18">Link to UCSC Browser</LINK>
                    433                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73128640-73197707&amp;db=hg18">Link to UCSC Browser</LINK>
                    446                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73128640-73197707&amp;db=hg18">Link to UCSC Browser</LINK>
                    459                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73539898-73756681&amp;db=hg18">Link to UCSC Browser</LINK>
                    472                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73539898-73756681&amp;db=hg18">Link to UCSC Browser</LINK>
                    485                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73539898-73756681&amp;db=hg18">Link to UCSC Browser</LINK>
                    498                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73539898-73756681&amp;db=hg18">Link to UCSC Browser</LINK>
                    511                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    524                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    537                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    550                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    563                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    576                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    589                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    602                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    615                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    628                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    641                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    654                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    667                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    680                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    693                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    706                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    719                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    732                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    745                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    758                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    771                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73514273-73756762&amp;db=hg18">Link to UCSC Browser</LINK>
                    784                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:72881119-72980288&amp;db=hg18">Link to UCSC Browser</LINK>
                    797                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:72881119-72980288&amp;db=hg18">Link to UCSC Browser</LINK>
                    810                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:72881119-72980288&amp;db=hg18">Link to UCSC Browser</LINK>
                    823                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:72881119-72980288&amp;db=hg18">Link to UCSC Browser</LINK>
                    836                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:72881119-72980288&amp;db=hg18">Link to UCSC Browser</LINK>
                    849                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:72881119-72980288&amp;db=hg18">Link to UCSC Browser</LINK>
                    862                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:72881119-72980288&amp;db=hg18">Link to UCSC Browser</LINK>
                    875                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:72881119-72980288&amp;db=hg18">Link to UCSC Browser</LINK>
                    888                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:72881119-72980288&amp;db=hg18">Link to UCSC Browser</LINK>
                    901                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:72881119-72980288&amp;db=hg18">Link to UCSC Browser</LINK>
                    914                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:72881119-72980288&amp;db=hg18">Link to UCSC Browser</LINK>
                    927                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:72881119-72980288&amp;db=hg18">Link to UCSC Browser</LINK>
                    940                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73111607-73112040&amp;db=hg18">Link to UCSC Browser</LINK>
                    953                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73059109-73060641&amp;db=hg18">Link to UCSC Browser</LINK>
                    966                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73059109-73060641&amp;db=hg18">Link to UCSC Browser</LINK>
                    979                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73059109-73060641&amp;db=hg18">Link to UCSC Browser</LINK>
                    992                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73059109-73060641&amp;db=hg18">Link to UCSC Browser</LINK>
                    1005                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73059109-73060641&amp;db=hg18">Link to UCSC Browser</LINK>
                    1018                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73059109-73060641&amp;db=hg18">Link to UCSC Browser</LINK>
                    1031                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73059109-73060641&amp;db=hg18">Link to UCSC Browser</LINK>
                    1044                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73059109-73060641&amp;db=hg18">Link to UCSC Browser</LINK>
                    1057                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73059109-73060641&amp;db=hg18">Link to UCSC Browser</LINK>
                    1070                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73059109-73060641&amp;db=hg18">Link to UCSC Browser</LINK>
                    1083                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73059109-73060641&amp;db=hg18">Link to UCSC Browser</LINK>
                    1096                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73059109-73060641&amp;db=hg18">Link to UCSC Browser</LINK>
                    1109                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73089142-73107313&amp;db=hg18">Link to UCSC Browser</LINK>
                    1122                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73089142-73107313&amp;db=hg18">Link to UCSC Browser</LINK>
                    1135                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73089142-73107313&amp;db=hg18">Link to UCSC Browser</LINK>
                    1148                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73089142-73107313&amp;db=hg18">Link to UCSC Browser</LINK>
                    1161                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73108241-73108890&amp;db=hg18">Link to UCSC Browser</LINK>
                    1174                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73112532-73113172&amp;db=hg18">Link to UCSC Browser</LINK>
                    1187                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73112532-73113172&amp;db=hg18">Link to UCSC Browser</LINK>
                    1200                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73112532-73113172&amp;db=hg18">Link to UCSC Browser</LINK>
                    1213                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73180313-73180935&amp;db=hg18">Link to UCSC Browser</LINK>
                    1226                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73180313-73180935&amp;db=hg18">Link to UCSC Browser</LINK>
                    1239                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73180313-73180935&amp;db=hg18">Link to UCSC Browser</LINK>
                    1252                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73180313-73180935&amp;db=hg18">Link to UCSC Browser</LINK>
                    1265                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73180313-73180935&amp;db=hg18">Link to UCSC Browser</LINK>
                    1278                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73180313-73180935&amp;db=hg18">Link to UCSC Browser</LINK>
                    1291                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73180313-73180935&amp;db=hg18">Link to UCSC Browser</LINK>
                    1304                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73180313-73180935&amp;db=hg18">Link to UCSC Browser</LINK>
                    1317                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73180313-73180935&amp;db=hg18">Link to UCSC Browser</LINK>
                    1330                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73180313-73180935&amp;db=hg18">Link to UCSC Browser</LINK>
                    1343                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73194112-73195159&amp;db=hg18">Link to UCSC Browser</LINK>
                    1356                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73196948-73199034&amp;db=hg18">Link to UCSC Browser</LINK>
                    1369                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73196948-73199034&amp;db=hg18">Link to UCSC Browser</LINK>
                    1382                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73199168-73201039&amp;db=hg18">Link to UCSC Browser</LINK>
                    1395                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73199168-73201039&amp;db=hg18">Link to UCSC Browser</LINK>
                    1408                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73199168-73201039&amp;db=hg18">Link to UCSC Browser</LINK>
                    1421                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73199168-73201039&amp;db=hg18">Link to UCSC Browser</LINK>
                    1434                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73193889-73194657&amp;db=hg18">Link to UCSC Browser</LINK>
                    1447                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73193889-73194657&amp;db=hg18">Link to UCSC Browser</LINK>
                    1460                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73193889-73194657&amp;db=hg18">Link to UCSC Browser</LINK>
                    1473                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73193889-73194657&amp;db=hg18">Link to UCSC Browser</LINK>
                    1486                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73193889-73194657&amp;db=hg18">Link to UCSC Browser</LINK>
                    1499                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73193889-73194657&amp;db=hg18">Link to UCSC Browser</LINK>
                    1512                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73529212-73530655&amp;db=hg18">Link to UCSC Browser</LINK>
                    1525                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73529212-73530655&amp;db=hg18">Link to UCSC Browser</LINK>
                    1538                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73529212-73530655&amp;db=hg18">Link to UCSC Browser</LINK>
                    1551                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73529212-73530655&amp;db=hg18">Link to UCSC Browser</LINK>
                    1564                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73529212-73530655&amp;db=hg18">Link to UCSC Browser</LINK>
                    1577                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73529212-73530655&amp;db=hg18">Link to UCSC Browser</LINK>
                    1590                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73529212-73530655&amp;db=hg18">Link to UCSC Browser</LINK>
                    1603                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73529212-73530655&amp;db=hg18">Link to UCSC Browser</LINK>
                    1616                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73624825-73626604&amp;db=hg18">Link to UCSC Browser</LINK>
                    1629                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73624825-73626604&amp;db=hg18">Link to UCSC Browser</LINK>
                    1642                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73624825-73626604&amp;db=hg18">Link to UCSC Browser</LINK>
                    1655                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73624825-73626604&amp;db=hg18">Link to UCSC Browser</LINK>
                    1668                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73624825-73626604&amp;db=hg18">Link to UCSC Browser</LINK>
                    1681                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73624825-73626604&amp;db=hg18">Link to UCSC Browser</LINK>
                    1694                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73622087-73622819&amp;db=hg18">Link to UCSC Browser</LINK>
                    1707                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73622087-73622819&amp;db=hg18">Link to UCSC Browser</LINK>
                    1720                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73622087-73622819&amp;db=hg18">Link to UCSC Browser</LINK>
                    1733                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73694860-73697643&amp;db=hg18">Link to UCSC Browser</LINK>
                    1746                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73694860-73697643&amp;db=hg18">Link to UCSC Browser</LINK>
                    1759                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73694860-73697643&amp;db=hg18">Link to UCSC Browser</LINK>
                    1772                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73694860-73697643&amp;db=hg18">Link to UCSC Browser</LINK>
                    1785                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73694860-73697643&amp;db=hg18">Link to UCSC Browser</LINK>
                    1798                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73694860-73697643&amp;db=hg18">Link to UCSC Browser</LINK>
                    1811                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73669645-73671682&amp;db=hg18">Link to UCSC Browser</LINK>
                    1824                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73669645-73671682&amp;db=hg18">Link to UCSC Browser</LINK>
                    1837                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73759272-73759736&amp;db=hg18">Link to UCSC Browser</LINK>
                    1850                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74131645-74137450&amp;db=hg18">Link to UCSC Browser</LINK>
                    1863                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74131645-74137450&amp;db=hg18">Link to UCSC Browser</LINK>
                    1876                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74131645-74137450&amp;db=hg18">Link to UCSC Browser</LINK>
                    1889                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:74642797-74644551&amp;db=hg18">Link to UCSC Browser</LINK>
                    1902                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:75552411-75554635&amp;db=hg18">Link to UCSC Browser</LINK>
                    1915                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:75552411-75554635&amp;db=hg18">Link to UCSC Browser</LINK>
                    1928                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:75552411-75554635&amp;db=hg18">Link to UCSC Browser</LINK>
                    1941                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:75552411-75554635&amp;db=hg18">Link to UCSC Browser</LINK>
                    1954                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:75552411-75554635&amp;db=hg18">Link to UCSC Browser</LINK>
                    1967                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:75547154-75547810&amp;db=hg18">Link to UCSC Browser</LINK>
                    1980                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:75804122-75804611&amp;db=hg18">Link to UCSC Browser</LINK>
                    1993                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:75804122-75804611&amp;db=hg18">Link to UCSC Browser</LINK>
                    2006                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:75799389-75803931&amp;db=hg18">Link to UCSC Browser</LINK>
                    2019                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:75799389-75803931&amp;db=hg18">Link to UCSC Browser</LINK>
                    2032                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:75799389-75803931&amp;db=hg18">Link to UCSC Browser</LINK>
                    2045                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:75796170-75799058&amp;db=hg18">Link to UCSC Browser</LINK>
                    2058                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:75796170-75799058&amp;db=hg18">Link to UCSC Browser</LINK>
                    2071                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:75796170-75799058&amp;db=hg18">Link to UCSC Browser</LINK>
                    2084                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:75796170-75799058&amp;db=hg18">Link to UCSC Browser</LINK>
                    2097                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:75796170-75799058&amp;db=hg18">Link to UCSC Browser</LINK>
                    2110                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:75796170-75799058&amp;db=hg18">Link to UCSC Browser</LINK>
                    2123                     <LINK href="http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:75796170-75799058&amp;db=hg18">Link to UCSC Browser</LINK>
        externalView  (5 usages found)
              (5 usages found)
                ensemblURLs  (5 usages found)
                    1 mm9	http://may2010.archive.ensembl.org/Mus_musculus
                    2 mm10    http://dec2011.archive.ensembl.org/Mus_musculus
                    3 hg19	http://may2010.archive.ensembl.org/Homo_sapiens
                    4 hg38    http://useast.ensembl.org/Homo_sapiens/
                    5 dm3	http://may2010.archive.ensembl.org/Drosophila_melanogaster
        genometry  (9 usages found)
            data.bed  (4 usages found)
                bed_01.bed  (1 usage found)
                    1 track name="Bed Test File" description="Test bed file" color=255,255,0 itemRgb="on" useScore=0 url="http://www.google.com/search?q=$$"
                bed_02.bed  (1 usage found)
                    1 track name="Bed Test File" description="Test bed file" color=255,255,0 itemRgb="on" useScore=0 url="http://www.google.com/search?q=$$"
                bed_03.bed  (1 usage found)
                    1 track name="Bed Test File" description="Test bed file" color=255,255,0 itemRgb="on" useScore=0 url="http://www.google.com/search?q=$$"
                bedDetailExample.bed  (1 usage found)
                    1 track name=HbVar type=bedDetail description="HbVar custom track" db=hg19 visibility=3 url="http://globin.bx.psu.edu/cgi-bin/hbvar/query_vars3?display_format=page&mode=output&i=$$"
            data.das2  (3 usages found)
                test2.das2xml  (3 usages found)
                    3     xmlns="http://biodas.org/documents/das2"
                    4     xmlns:xlink="http://www.w3.org/1999/xlink" 
                    5     xml:base="http://www.bioviz.org/das2/genome/A_thaliana_TAIR8/" >
            data.gff1  (1 usage found)
                GFF1_example.gff  (1 usage found)
                    9 track name="Track A" url="http://www.google.com/search?q=$$" useScore=1 color=200,0,0 visibility=2 
            data.gff3  (1 usage found)
                GFF3_canonical_example.gff3  (1 usage found)
                    5 # http://song.sourceforge.net/gff3.shtml
        igb  (9 usages found)
              (2 usages found)
                Apache_License.html  (2 usages found)
                    9 http://www.apache.org/licenses/
                    201 http://www.apache.org/licenses/LICENSE-2.0
            documentation  (3 usages found)
                How_to_create_a_QuickLoad_directory.html  (3 usages found)
                    13 <br /><a href="http://bioviz.org/quickload/">http://bioviz.org/quickload/</a>
                    38 <a href="http://bioviz.org/quickload/">http://bioviz.org/quickload/</a> as a guide to create your own.</br>
                    134 <li>A web site: "http://netaffxdas.affymetrix.com/quickload_data/"
            formats  (4 usages found)
                igb_data_formats.html  (4 usages found)
                    40 <td>XML formats returned from DAS servers. See <a href="http://www.biodas.org/wiki/Main_Page">http://www.biodas.org</a>.
                    163 http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml
                    168 http://genes.cs.wustl.edu/GTF2.html
                    173 http://song.sourceforge.net/gff3-jan04.shtml
        igb-project  (57 usages found)
              (18 usages found)
                NOTICES.txt  (10 usages found)
                    6      http://www.affymetrix.com/support/developer/fusion/index.affx
                    11      http://www.gnu.org/copyleft/lesser.html
                    18      http://java.sun.com/developer/techDocs/hi/repository/
                    30      http://java.freehep.org/vectorgraphics/index.html
                    39      http://sourceforge.net/projects/picard/
                    47      http://www.jidesoft.com/
                    56      http://felix.apache.org/site/index.html
                    68      http://commons.apache.org/
                    74      http://jackson.codehaus.org/
                    80      http://rabbit-hole.blogspot.com/2006/04/decoratingoverpainting-swing.html
                README.md  (8 usages found)
                    7 To get IGB, clone this repository or download an [IGB installer for your platform](http://bioviz.org/igb/download.html).
                    11 * [BioViz Web site](http://www.bioviz.org) with platform-specific installers
                    16 * [IGB Jira Issue Tracker site](http://jira.transvar.org) describes development plans
                    17 * Article describing [Integrated Genome Browser: Visual analytics platform for genomics](http://bioinformatics.oxfordjournals.org/content/early/2016/04/04/bioinformatics.btw069.long) 
                    44 IGB and IGB Apps use [semantic versioning](http://semver.org/). 
                    55 Visit the [Bioviz help page](http://bioviz.org/igb/help.html)
                    72 1. Fork the [team repository](http://www.bitbucket.org/lorainelab/integrated-genome-browser).
                    80 * Blog post titled [Using the Fork-and-Branch Git Workflow](http://blog.scottlowe.org/2015/01/27/using-fork-branch-git-workflow/)
            distribution  (3 usages found)
                igb.install4j  (3 usages found)
                    4 "http://b
                    17       <variable name="codeBaseUrl" value="http://eos.transvar.org/igb/" description="A variable holding the url location of the lateset IGB installers and update information" category="" />
                    1007                                 <string>http://bioviz.org/igb/news.html</string>
            galaxy  (7 usages found)
                bam.xml  (1 usage found)
                    3 >http://b
                bb.xml  (1 usage found)
                    4 >http://b
                bed.xml  (1 usage found)
                    14 http://b
                bedgraph.xml  (1 usage found)
                    14 http://b
                bigwig.xml  (1 usage found)
                    4 >http://b
                gtf.xml  (1 usage found)
                    14 http://b
                wig.xml  (1 usage found)
                    4 >http://b
            optionalPlugins\23andMe-snp-converter\src\test\resources  (1 usage found)
                sample23andMe.txt  (1 usage found)
                    13 # http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9606
            optionalPlugins\23andMe-snp-converter\target\test-classes  (1 usage found)
                sample23andMe.txt  (1 usage found)
                    13 # http://www.ncbi.nlm.nih.gov/mapview/map_search.cgi?taxid=9606
            optionalPlugins\protannot\src\test\resources\diff_motifs  (13 usages found)
                bad.paxml  (1 usage found)
                    3 <dnaseq seq="chr17" version="hg19" xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" xs:noNamespaceSchemaLocation="protannot.xsd">
                good.paxml  (1 usage found)
                    3 <dnaseq seq="chr17" version="hg19" xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" xs:noNamespaceSchemaLocation="protannot.xsd">
                STARD3.sample.paxml  (11 usages found)
                    3 <dnaseq seq="chr17" version="hg19" xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" xs:noNamespaceSchemaLocation="protannot.xsd">
                    9         <descriptor type="URL">http://www.ncbi.nlm.nih.gov/nuccore/NM_001165937.1</descriptor>
                    67                 <descriptor type="URL">http://www.ebi.ac.uk/interpro/IEntry?ac=IPR000799</descriptor>
                    99                 <descriptor type="URL">http://www.ebi.ac.uk/interpro/IEntry?ac=IPR002913</descriptor>
                    111                 <descriptor type="URL">http://www.ebi.ac.uk/interpro/IEntry?ac=IPR019498</descriptor>
                    123                 <descriptor type="URL">http://www.ebi.ac.uk/interpro/ISearch?query=tmhmm</descriptor>
                    143         <descriptor type="URL">http://www.ncbi.nlm.nih.gov/nuccore/NM_001165938.1</descriptor>
                    198                 <descriptor type="URL">http://www.ebi.ac.uk/interpro/IEntry?ac=IPR000799</descriptor>
                    230                 <descriptor type="URL">http://www.ebi.ac.uk/interpro/IEntry?ac=IPR002913</descriptor>
                    242                 <descriptor type="URL">http://www.ebi.ac.uk/interpro/IEntry?ac=IPR019498</descriptor>
                    258                 <descriptor type="URL">http://www.ebi.ac.uk/interpro/ISearch?query=tmhmm</descriptor>
            optionalPlugins\protannot\target\test-classes\diff_motifs  (13 usages found)
                bad.paxml  (1 usage found)
                    3 <dnaseq seq="chr17" version="hg19" xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" xs:noNamespaceSchemaLocation="protannot.xsd">
                good.paxml  (1 usage found)
                    3 <dnaseq seq="chr17" version="hg19" xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" xs:noNamespaceSchemaLocation="protannot.xsd">
                STARD3.sample.paxml  (11 usages found)
                    3 <dnaseq seq="chr17" version="hg19" xmlns:xs="http://www.w3.org/2001/XMLSchema-instance" xs:noNamespaceSchemaLocation="protannot.xsd">
                    9         <descriptor type="URL">http://www.ncbi.nlm.nih.gov/nuccore/NM_001165937.1</descriptor>
                    67                 <descriptor type="URL">http://www.ebi.ac.uk/interpro/IEntry?ac=IPR000799</descriptor>
                    99                 <descriptor type="URL">http://www.ebi.ac.uk/interpro/IEntry?ac=IPR002913</descriptor>
                    111                 <descriptor type="URL">http://www.ebi.ac.uk/interpro/IEntry?ac=IPR019498</descriptor>
                    123                 <descriptor type="URL">http://www.ebi.ac.uk/interpro/ISearch?query=tmhmm</descriptor>
                    143         <descriptor type="URL">http://www.ncbi.nlm.nih.gov/nuccore/NM_001165938.1</descriptor>
                    198                 <descriptor type="URL">http://www.ebi.ac.uk/interpro/IEntry?ac=IPR000799</descriptor>
                    230                 <descriptor type="URL">http://www.ebi.ac.uk/interpro/IEntry?ac=IPR002913</descriptor>
                    242                 <descriptor type="URL">http://www.ebi.ac.uk/interpro/IEntry?ac=IPR019498</descriptor>
                    258                 <descriptor type="URL">http://www.ebi.ac.uk/interpro/ISearch?query=tmhmm</descriptor>
            tools\LuceneIndexing  (1 usage found)
                buildAndTest.sh  (1 usage found)
                    9 wget http://mirrors.gigenet.com/apache//felix/org.apache.felix.main.distribution-4.2.1.tar.gz
        main  (1 usage found)
            main  (1 usage found)
                hs_err_pid11535.log  (1 usage found)
                    14 #   http://bugreport.java.com/bugreport/crash.jsp
        plugins-manager  (3 usages found)
              (3 usages found)
                README.md  (3 usages found)
                    1 (http://b
                    36 The fastest way to get started is to serve JavaScript from the CDN (also available on [cdnjs](https://cdnjs.com/libraries/react) and [jsdelivr](http://www.jsdelivr.com/#!react)):
                    47 If you'd like to use [bower](http://bower.io), it's as easy as:
        synonym-lookup  (16 usages found)
              (16 usages found)
                synonyms.txt  (16 usages found)
                    24 C_elegans_Aug_2004	http://www.wormbase.org/genome/C_elegans/WS130	http://www.wormbase.org/genome/C_elegans/WS130/
                    30 C_elegans_Mar_2004	http://www.wormbase.org/genome/C_elegans/WS120	http://www.wormbase.org/genome/C_elegans/WS120/
                    31 C_elegans_Mar_2005	ce3	http://www.wormbase.org/genome/C_elegans/WS140	http://www.wormbase.org/genome/C_elegans/WS140/
                    33 C_elegans_May_2003	http://www.wormbase.org/genome/C_elegans/WS100	http://www.wormbase.org/genome/C_elegans/WS100/
                    35 C_elegans_Nov_2005	http://www.wormbase.org/genome/C_elegans/WS150	http://www.wormbase.org/genome/C_elegans/WS150/
                    36 C_elegans_Oct_2003	http://www.wormbase.org/genome/C_elegans/WS110	http://www.wormbase.org/genome/C_elegans/WS110/
                    105 H_sapiens_Apr_2003	http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B33	http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B33/
                    109 H_sapiens_Jul_2003	http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B34.1	http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B34.1/
                    110 H_sapiens_Jul_2003	http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B34.2	http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B34.2/
                    111 H_sapiens_Jul_2003	http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B34.3	http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B34.3/
                    114 H_sapiens_Mar_2006	http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B36.1	http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B36.1/
                    116 H_sapiens_May_2004	http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B35.1	http://www.ncbi.nlm.nih.gov/genome/H_sapiens/B35.1/
                    139 M_musculus_Aug_2005	http://www.ncbi.nlm.nih.gov/genome/M_musculus/35.1	http://www.ncbi.nlm.nih.gov/genome/M_musculus/35.1/
                    144 M_musculus_Mar_2005	http://www.ncbi.nlm.nih.gov/genome/M_musculus/34.1	http://www.ncbi.nlm.nih.gov/genome/M_musculus/34.1/
                    146 M_musculus_May_2004	http://www.ncbi.nlm.nih.gov/genome/M_musculus/33.1	http://www.ncbi.nlm.nih.gov/genome/M_musculus/33.1/
                    148 M_musculus_Oct_2003	http://www.ncbi.nlm.nih.gov/genome/M_musculus/32.1	http://www.ncbi.nlm.nih.gov/genome/M_musculus/32.1/
        update  (3 usages found)
              (3 usages found)
                updates.xml  (3 usages found)
                    6 <link>http://bioviz.org/igb/download.html</link>
                    11 <link>http://bioviz.org/igb/download.html</link>
                    16 <link>http://bioviz.org/igb/download.html</link>
    Usage in GUI form  (2 usages found)
        igb  (1 usage found)
            com.affymetrix.igb.prefs  (1 usage found)
                AddDataProvider.form  (1 usage found)
                    130 <AuxValue name="JavaCodeGenerator_CreateCodeCustom" type="java.lang.String" value="new JRPTextField(&quot;ServerPrefsView_url&quot;, &quot;http://&quot;)"/>
        plugins-manager  (1 usage found)
            org.lorainelab.igb.plugin.manager.repos.view  (1 usage found)
                AddBundleRepositoryFrame.form  (1 usage found)
                    106 <AuxValue name="JavaCodeGenerator_CreateCodeCustom" type="java.lang.String" value="new JRPTextField(&quot;ServerPrefsView_url&quot;, &quot;http://&quot;)"/>
    Usage in comments  (577 usages found)
        org  (1 usage found)
            lorainelab  (1 usage found)
                igb  (1 usage found)
                    error  (1 usage found)
                        reporter  (1 usage found)
                            manager  (1 usage found)
                                org.lorainelab.igb.error.reporter.manager  (1 usage found)
                                    ErrorReportingAppender.java  (1 usage found)
                                        humanReadableByteCount(long, boolean)  (1 usage found)
                                            81 //credit http://stackoverflow.com/questions/3758606/how-to-convert-byte-size-into-human-readable-format-in-java
        affymetrix-common  (1 usage found)
            com.affymetrix.common  (1 usage found)
                PreferenceUtils.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
        bookmark  (19 usages found)
            com.affymetrix.igb.bookmarks  (14 usages found)
                BookMarkCommandLine.java  (1 usage found)
                    gotoBookmark()  (1 usage found)
                        62 // If the command line contains a parameter "-href http://..." where
                BookmarkController.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                BookmarkHttpRequestHandler.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                BookmarkIcon.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                BookmarkList.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                BookmarkManagerView.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                BookmarkMenuItem.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                BookmarksParser.java  (2 usages found)
                    parseSimpleHTML(BookmarkList, File)  (1 usage found)
                        315 * format now. Any line that contains "http://" will be parsed as a
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                BookmarkTreeCellRenderer.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                BookmarkUnibrowControlServlet.java  (1 usage found)
                    7 * The license is also available at http://www.opensource.org/licenses/cpl.php
                Separator.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                SimpleBookmarkServer.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                UrlLoaderThread.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
            com.affymetrix.igb.bookmarks.action  (1 usage found)
                BookmarkActionManager.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
            com.affymetrix.igb.bookmarks.model  (4 usages found)
                Bookmark.java  (4 usages found)
                    parseParameters(URL)  (1 usage found)
                        131 * the url is http://www.abc.com/page?x=3&z&y=4&y=5 then the resulting Map
                    constructURL(String, ListMultimap<String, String>)  (2 usages found)
                        211 * @param url_base The beginning part of a url, like "http://www.xxx.com" or
                        212 * even "http://www.xxx.com?x=1&y=2".
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
        cache  (1 usage found)
            org.lorainelab.igb.cache.disk  (1 usage found)
                RemoteFileDiskCacheService.java  (1 usage found)
                    sortByComparator(Map<String, BigInteger>)  (1 usage found)
                        775 * http://www.mkyong.com/java/how-to-sort-a-map-in-java/
        das  (23 usages found)
            org.lorainelab.igb.das  (1 usage found)
                DasSymloader.java  (1 usage found)
                    getRegion(SeqSpan)  (1 usage found)
                        49 //e.g. http://genome.cse.ucsc.edu/cgi-bin/das/hg38/features?type=altLocations;segment=chr1%3A1%2C14422303;
            org.lorainelab.igb.das.model.dsn  (5 usages found)
                DasDsn.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                Description.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                Dsn.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                ObjectFactory.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
                Source.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
            org.lorainelab.igb.das.model.ep  (3 usages found)
                DasEp.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                EntryPoints.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                Segment.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
            org.lorainelab.igb.das.model.gff  (10 usages found)
                DasGff.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                Feature.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                Gff.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                Group.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                Link.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                Method.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                Note.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                Segment.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                Target.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                Type.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
            org.lorainelab.igb.das.model.types  (4 usages found)
                DasTypes.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                Gff.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                Segment.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                Type.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
        das2  (19 usages found)
            org.lorainelab.igb.das2  (1 usage found)
                SimpleDas2Feature.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
            org.lorainelab.igb.das2.model.segments  (6 usages found)
                Segments.java  (6 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
                    69 *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
                    70 *       &lt;attribute name="uri" type="{http://www.w3.org/2001/XMLSchema}string" />
                    71 *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
                    72 *       &lt;attribute name="length" type="{http://www.w3.org/2001/XMLSchema}int" />
                    73 *       &lt;attribute name="reference" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
            org.lorainelab.igb.das2.model.sources  (6 usages found)
                Capability.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
                Coordinates.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
                Maintainer.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
                Source.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
                Sources.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
                Version.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
            org.lorainelab.igb.das2.model.types  (1 usage found)
                Types.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
            org.lorainelab.igb.das2.parser  (5 usages found)
                Das2FeatureSaxParser.java  (5 usages found)
                    parse(InputSource, String, GenomeVersion, boolean)  (1 usage found)
                        216 //      reader.setFeature("http://xml.org/sax/features/string-interning", true);
                    writeAnnotations(Collection<? extends SeqSymmetry>, BioSeq, String, OutputStream)  (1 usage found)
                        663 //	pw.println("<!DOCTYPE DAS2FEATURE SYSTEM \"http://www.biodas.org/dtd/das2feature.dtd\"> ");
                    11 * http://www.opensource.org/licenses/cpl.php
                    54 * Spec for this format is at http://biodas.org/documents/das2/das2_get.html * DTD is at
                    55 * http://www.biodas.org/dtd/das2feature.dtd ???
        genometry  (119 usages found)
            com.affymetrix.genometry  (6 usages found)
                GenometryConstants.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                MutableSeqSpan.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                Scored.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                SeqSpan.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                SharedProbesetInfo.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                SupportsCdsSpan.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
            com.affymetrix.genometry.comparator  (2 usages found)
                AlphanumComparator.java  (2 usages found)
                    6  * The Alphanum Algorithm is discussed at http://www.DaveKoelle.com
                    41 * Source : http://www.davekoelle.com/files/AlphanumComparator.java
            com.affymetrix.genometry.operator  (1 usage found)
                GraphMultiplexer.java  (1 usage found)
                    7  *  http://www.opensource.org/licenses/CPL
            com.affymetrix.genometry.parsers  (30 usages found)
                AbstractPSLParser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                BedParser.java  (2 usages found)
                    11 * http://www.opensource.org/licenses/cpl.php
                    53 *  From http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED
                Bprobe1Parser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                BrptParser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                BrsParser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                BsnpParser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                ChromInfoParser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                CytobandParser.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                ExonArrayDesignParser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                FastaParser.java  (4 usages found)
                    oldparse(InputStream, BioSeq, int)  (1 usage found)
                        300 // see http://en.wikipedia.org/wiki/Fasta_format
                    readFASTA(File, int, int)  (1 usage found)
                        375 * Sequence range is specified in interbase format. (See http://www.biodas.org/documents/das2/das2_get.html.)
                    BlockUntilSkipped(BufferedInputStream, int)  (1 usage found)
                        580 // (See http://java.sun.com/j2se/1.5.0/docs/api/java/io/InputStream.html#skip(long) .)
                    11 * http://www.opensource.org/licenses/cpl.php
                FishClonesParser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                GFF3Parser.java  (2 usages found)
                    11 * http://www.opensource.org/licenses/cpl.php
                    50 *  See http://song.sourceforge.net/gff3.shtml.
                GFFParser.java  (2 usages found)
                    11 * http://www.opensource.org/licenses/cpl.php
                    137 // According to http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml
                LiftParser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                NibbleResiduesParser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                PSLParser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                SAMWriter.java  (3 usages found)
                    29 * http://samtools.sourceforge.net/
                    30 * http://genome.sph.umich.edu/wiki/SAM
                    31 * http://samtools.sourceforge.net/SAM1.pdf
                SimpleBedParser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                TabDelimitedParser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                TrackLineParser.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                VarParser.java  (2 usages found)
                    11 * http://www.opensource.org/licenses/cpl.php
                    32 * A parser designed to parse genomic variants data from http://projects.tcag.ca/variation/
            com.affymetrix.genometry.parsers.gchp  (11 usages found)
                AffyChpColumnData.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                AffyChpColumnType.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                AffyChpParameter.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                AffyCnChpParser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                AffyDataGroup.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                AffyDataSet.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                AffyDataType.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                AffyGenericChpFile.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                AffyGenericDataHeader.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                AffySingleChromData.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                ChromLoadPolicy.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
            com.affymetrix.genometry.parsers.graph  (9 usages found)
                BgrParser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                CntParser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                GrParser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                ScoredIntervalParser.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                ScoredMapParser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                WiggleParser.java  (4 usages found)
                    parseDataLine(String[], WiggleData, Map<String, WiggleData>, String, int)  (1 usage found)
                        231 current_start -= 1;	// This is because fixedStep and variableStep sequences are 1-indexed.  See http://genome.ucsc.edu/goldenPath/help/wiggle.html
                    parseDataLine(String[], WiggleData, Map<String, WiggleData>, String, int, int)  (1 usage found)
                        261 current_start -= 1;	// This is because fixedStep and variableStep formats are 1-indexed.  See http://genome.ucsc.edu/goldenPath/help/wiggle.html
                    31 * See http://genome.ucsc.edu/google/goldenPath/help/wiggle.html
                    32 * See http://gmod.org/wiki/GBrowse/Uploading_Wiggle_Tracks for test data.
            com.affymetrix.genometry.span  (3 usages found)
                MutableDoubleSeqSpan.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                SimpleMutableSeqSpan.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                SimpleSeqSpan.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
            com.affymetrix.genometry.style  (10 usages found)
                DefaultStateProvider.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                DefaultTrackStyle.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                GraphState.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                HeatMap.java  (3 usages found)
                    toString()  (2 usages found)
                        87 //				// http://www.unicode.org/charts/PDF/U2580.pdf
                        88 //				// http://en.wikipedia.org/wiki/Box-drawing_character
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                ITrackStyle.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                ITrackStyleExtended.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                SimpleTrackStyle.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                StateProvider.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
            com.affymetrix.genometry.symloader  (3 usages found)
                GFF.java  (1 usage found)
                    63 // According to http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml
                Wiggle.java  (2 usages found)
                    parseDataLine(String[], WiggleData, Map<String, WiggleData>, String, int, int, int)  (1 usage found)
                        357 current_start -= 1;	// This is because fixedStep and variableStep sequences are 1-indexed.  See http://genome.ucsc.edu/goldenPath/help/wiggle.html
                    parseDataLine(String[], WiggleData, Map<String, WiggleData>, String, int, int, int, ...)  (1 usage found)
                        391 current_start -= 1;	// This is because fixedStep and variableStep formats are 1-indexed.  See http://genome.ucsc.edu/goldenPath/help/wiggle.html
            com.affymetrix.genometry.symmetry  (5 usages found)
                DerivedSeqSymmetry.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                IndexedSym.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                MutableSeqSymmetry.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                SimpleSeqSymmetry.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                TypedSym.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
            com.affymetrix.genometry.symmetry.impl  (29 usages found)
                EfficientProbesetSymA.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                EfficientSnpSym.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                GFF3Sym.java  (2 usages found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                    42 * See http://song.sourceforge.net/gff3.shtml
                IndexedSingletonSym.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                LeafSingletonSymmetry.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                LeafTrioSeqSymmetry.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                MutableSingletonSeqSymmetry.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                Psl3Sym.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                ScoredContainerSym.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                ScoredSingletonSym.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                SearchableSeqSymmetry.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                SeqSymmetry.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                SeqSymmetryConverter.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                SeqSymSummarizer.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                SimpleDerivedSeqSymmetry.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                SimpleMutableSeqSymmetry.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                SimpleSymWithProps.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                SingletonSeqSymmetry.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                SingletonSymWithIntId.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                SingletonSymWithProps.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                TypeContainerAnnot.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                UcscBedSym.java  (2 usages found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                    28 *  From http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED
                UcscGeneSym.java  (2 usages found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                    37 * from http://genome.cse.ucsc.edu/goldenPath/gbdDescriptions.html#RefFlat:
                UcscGffSym.java  (2 usages found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                    22 * http://genome.ucsc.edu/goldenPath/help/customTrack.html#GTF
                UcscPslSym.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
            com.affymetrix.genometry.util  (10 usages found)
                DisplayUtils.java  (1 usage found)
                    scrollToVisible(JTable, int, int)  (1 usage found)
                        33 * See http://javaalmanac.com/egs/javax.swing.table/Vis.html
                DNAUtils.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                ErrorHandler.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                FileDropHandler.java  (1 usage found)
                    importData(TransferSupport)  (1 usage found)
                        45 // Workaround for Linux -- see http://bugs.sun.com/view_bug.do?bug_id=4899516, for example
                GeneralUtils.java  (2 usages found)
                    httpExists(String)  (1 usage found)
                        536      * from http://stackoverflow.com/questions/4596447/java-check-if-file-exists-on-remote-server-using-its-url
                    asSortedList(Collection<T>)  (1 usage found)
                        631 * http://stackoverflow.com/questions/740299/how-do-i-sort-a-set-to-a-list-in-java
                IgbStringUtils.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                LocalUrlCacher.java  (1 usage found)
                    getInputStream(String, int, boolean, Map<String, String>, Map<String, List<String>>, boolean, boolean)  (1 usage found)
                        169 * 'http://www.transvar.org?=/contents.txt' will return a html page
                UniFileChooser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                UniFileFilter.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
        igb  (58 usages found)
              (4 usages found)
                Apache_License.html  (1 usage found)
                    2 <!-- saved from url=http://www.apache.org/licenses/LICENSE-2.0.txt  -->
                igb_stylesheet.dtd  (2 usages found)
                    8   SYSTEM ID: http://genoviz.sourceforge.net/formats/stylesheets/igb_stylesheet_0_1.dtd
                    12     "http://genoviz.sourceforge.net/formats/stylesheets/igb_stylesheet_0_1.dtd"
                igb_system_stylesheet.xml  (1 usage found)
                    9     "http://genoviz.sourceforge.net/formats/stylesheets/igb_stylesheet_0_1.dtd"
            com.affymetrix.igb  (4 usages found)
                IGB.java  (2 usages found)
                    humanReadableByteCount(long, boolean)  (1 usage found)
                        218 //credit http://stackoverflow.com/questions/3758606/how-to-convert-byte-size-into-human-readable-format-in-java
                    7 * The license is also available at http://www.opensource.org/licenses/cpl.php
                IGBConstants.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                IgbServiceImpl.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
            com.affymetrix.igb.action  (8 usages found)
                CanonicalizeTracksAction.java  (1 usage found)
                    9  *  http://www.opensource.org/licenses/CPL
                ColorSchemeChoiceAction.java  (2 usages found)
                    ColorSchemeChoiceAction()  (1 usage found)
                        58 * Mark James of <a href="http://www.famfamfam.com/about/">Fam Fam Fam</a>.
                    9  *  http://www.opensource.org/licenses/CPL
                LoadFileAction.java  (1 usage found)
                    7 * The license is also available at http://www.opensource.org/licenses/cpl.php
                RunScriptAction.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                SeqMapToggleAction.java  (1 usage found)
                    7  *  http://www.opensource.org/licenses/CPL
                SetSummaryThresholdAction.java  (1 usage found)
                    7  *  http://www.opensource.org/licenses/CPL
                ZoomingRepackAction.java  (1 usage found)
                    9  *  http://www.opensource.org/licenses/CPL
            com.affymetrix.igb.glyph  (5 usages found)
                CodonGlyph.java  (1 usage found)
                    getEffectiveContrastColor(Color)  (1 usage found)
                        216      * Credit: http://24ways.org/2010/calculating-color-contrast
                EdgeMatchAdjuster.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                GlyphEdgeMatcher.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                GraphSelectionManager.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                GraphTierGlyph.java  (1 usage found)
                    12 * The license is also available at http://www.opensource.org/licenses/cpl.php
            com.affymetrix.igb.parsers  (1 usage found)
                ChpParser.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
            com.affymetrix.igb.prefs  (2 usages found)
                IgbPreferencesLoadingOrchestrator.java  (1 usage found)
                    139 List<String> URL_IGNORE_LIST = ImmutableList.of("http://www.ensembl.org/das/dsn/", "http://bioviz.org/cached/", "http://genome.cse.ucsc.edu/cgi-bin/das/dsn/");
                PreferencesPanel.java  (1 usage found)
                    7 * The license is also available at http://www.opensource.org/licenses/cpl.php
            com.affymetrix.igb.shared  (3 usages found)
                ColorSchemeAction.java  (2 usages found)
                    ColorSchemeAction()  (1 usage found)
                        51 * James of <a href="http://www.famfamfam.com/about/">Fam Fam Fam</a>.
                    7  *  http://www.opensource.org/licenses/CPL
                OpenURIAction.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
            com.affymetrix.igb.stylesheet  (10 usages found)
                AssociationElement.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                ChildrenElement.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                DrawableElement.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                ElseElement.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                MatchElement.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                PropertyMap.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                StyleElement.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                Stylesheet.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                XmlAppender.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                XmlStylesheetParser.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
            com.affymetrix.igb.tiers  (5 usages found)
                AffyLabelledTierMap.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                AffyTieredMap.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                SeqMapViewPopup.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                TextStroke.java  (2 usages found)
                    8  http://www.apache.org/licenses/LICENSE-2.0
                    31 * Ref: http://www.jhlabs.com/java/java2d/strokes/
            com.affymetrix.igb.util  (3 usages found)
                ConfigurableStreamHandlerFactory.java  (1 usage found)
                    4  * http://stackoverflow.com/questions/861500/url-to-load-resources-from-the-classpath-in-java
                ReplaceFilterInputStream.java  (1 usage found)
                    1 // http://denis-zhdanov.blogspot.com/2009/09/convenient-input-stream-data.html
                ServiceUtils.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
            com.affymetrix.igb.view  (6 usages found)
                AltSpliceView.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                GlyphResizer.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
                LawrencianZoomer.java  (1 usage found)
                    9  *  http://www.opensource.org/licenses/CPL
                MapRangeBox.java  (1 usage found)
                    7 * The license is also available at http://www.opensource.org/licenses/cpl.php
                OrfAnalyzer.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                UnibrowHairline.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
            com.affymetrix.igb.view.factories  (3 usages found)
                AnnotationGlyphFactory.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                MapTierGlyphFactoryI.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                ProbeSetGlyphFactory.java  (1 usage found)
                    createGlyphs(RootSeqSymmetry, ITrackStyleExtended, SeqMapViewExtendedI, BioSeq)  (1 usage found)
                        505 // http://sourceforge.net/tracker/?func=detail&aid=3213610&group_id=129420&atid=714744
            com.affymetrix.igb.view.load  (2 usages found)
                FeatureTreeView.java  (2 usages found)
                    getState()  (1 usage found)
                        312 //Ref : http://www.javalobby.org/java/forums/t19857.html
                    505      * http://www.experts-exchange.com/Programming/Languages/Java/Q_23851420.html
            com.affymetrix.igb.view.welcome  (1 usage found)
                GeneConfiguration.java  (1 usage found)
                    scaleImage(BufferedImage, int)  (1 usage found)
                        178 * from http://stackoverflow.com/questions/1324106/jai-change-jpeg-resolution
            OSGI-INF  (1 usage found)
                component.xml  (1 usage found)
                    4 <!-- xmlns="http://www.osgi.org/xmlns/scr/v1.0.0" -->
        igb-genoviz-extensions  (3 usages found)
            org.lorainelab.igb.genoviz.extensions  (3 usages found)
                GraphGlyphUtils.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                GraphVisibleBoundsSetter.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                SmartRubberBand.java  (1 usage found)
                    11 * http://www.opensource.org/licenses/cpl.php
        igb-preferences  (1 usage found)
              (1 usage found)
                igbDefaultPrefs.xml  (1 usage found)
                    115 <!-- see http://www.ncbi.nlm.nih.gov/projects/collab/db_xref.html to support more --> 
        igb-project  (279 usages found)
              (1 usage found)
                bitbucket-pipelines.yml  (1 usage found)
                    3 # Team: IGB (http://bioviz.org)
            developmentPlugins\FindAnnotations\src\main\java\com\gene\findannotations  (1 usage found)
                FindAnnotationsGUI.java  (1 usage found)
                    main(String[])  (1 usage found)
                        102          * For details see http://download.oracle.com/javase/tutorial/uiswing/lookandfeel/plaf.html 
            developmentPlugins\SearchModeLucene\src\main\java\com\gene\searchmodelucene  (1 usage found)
                SearchModeLucene.java  (1 usage found)
                    getName()  (1 usage found)
                        62 ////		String uri = args.length > 1 ? args[0] : "http://localhost/Bed/bed_01.bed";
            optionalPlugins\protannot\src\main\java\org\lorainelab\igb\protannot  (3 usages found)
                ProtAnnotAction.java  (3 usages found)
                    checkArguments(String, String)  (3 usages found)
                        859 //eg http:// or https://
                        862 //eg http://protannot.bioviz.org/samples/
                        876 //eg http://protannot.bioviz.org/samples
            optionalPlugins\protannot\src\main\java\org\lorainelab\igb\protannot\interproscan\appl\model  (19 usages found)
                ObjectFactory.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                ParameterType.java  (5 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    25 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    27 *         &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
                    28 *         &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
                    29 *         &lt;element name="type" type="{http://www.w3.org/2001/XMLSchema}string"/>
                PropertiesType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    25 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                PropertyType.java  (4 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    25 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    27 *         &lt;element name="key" type="{http://www.w3.org/2001/XMLSchema}string"/>
                    28 *         &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string"/>
                ValuesType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    26 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                ValueType.java  (5 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    25 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    27 *         &lt;element name="label" type="{http://www.w3.org/2001/XMLSchema}string"/>
                    28 *         &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string"/>
                    29 *         &lt;element name="defaultValue" type="{http://www.w3.org/2001/XMLSchema}string"/>
            optionalPlugins\protannot\src\main\java\org\lorainelab\igb\protannot\interproscan\model  (238 usages found)
                BlastProDomLocationType.java  (4 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    25 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}LocationType">
                    28 *       &lt;attribute name="evalue" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
                    29 *       &lt;attribute name="score" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
                BlastProDomMatchType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}MatchType">
                CoilsLocationType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}LocationType">
                CoilsMatchType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}MatchType">
                EntryType.java  (11 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    28 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    30 *         &lt;element name="go-xref" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}GoXrefType" maxOccurs="unbounded" minOccurs="0"/>
                    31 *         &lt;element name="pathway-xref" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}PathwayXrefType" maxOccurs="unbounded" minOccurs="0"/>
                    33 *       &lt;attribute name="abstract" type="{http://www.w3.org/2001/XMLSchema}string" />
                    34 *       &lt;attribute name="ac" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                    35 *       &lt;attribute name="created" type="{http://www.w3.org/2001/XMLSchema}string" />
                    36 *       &lt;attribute name="desc" type="{http://www.w3.org/2001/XMLSchema}string" />
                    37 *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
                    38 *       &lt;attribute name="type" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}EntryTypeType" />
                    39 *       &lt;attribute name="updated" type="{http://www.w3.org/2001/XMLSchema}string" />
                EntryTypeType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    22 *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
                FingerPrintsLocationType.java  (5 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    25 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}LocationType">
                    28 *       &lt;attribute name="motifNumber" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
                    29 *       &lt;attribute name="pvalue" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
                    30 *       &lt;attribute name="score" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
                FingerPrintsMatchType.java  (4 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    25 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}MatchType">
                    28 *       &lt;attribute name="evalue" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
                    29 *       &lt;attribute name="graphscan" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                GoCategoryType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    22 *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
                GoXrefType.java  (3 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    25 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}XrefType">
                    28 *       &lt;attribute name="category" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}GoCategoryType" />
                HmmBoundsType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    22 *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
                Hmmer2LocationType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}HmmerLocationType">
                Hmmer2MatchType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}HmmerMatchType">
                Hmmer3LocationType.java  (4 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    25 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}HmmerLocationType">
                    28 *       &lt;attribute name="env-end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
                    29 *       &lt;attribute name="env-start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
                Hmmer3MatchType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}HmmerMatchType">
                HmmerLocationType.java  (7 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    26 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}LocationType">
                    29 *       &lt;attribute name="score" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
                    30 *       &lt;attribute name="evalue" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
                    31 *       &lt;attribute name="hmm-start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
                    32 *       &lt;attribute name="hmm-end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
                    33 *       &lt;attribute name="hmm-length" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
                HmmerMatchType.java  (4 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    26 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}MatchType">
                    29 *       &lt;attribute name="evalue" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
                    30 *       &lt;attribute name="score" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
                KeyGen.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                LevelType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    22 *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
                Location.java  (4 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    25 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    28 *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
                    29 *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
                LocationsType.java  (14 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    27 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    29 *         &lt;element name="blastprodom-location" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}BlastProDomLocationType" maxOccurs="unbounded" minOccurs="0"/>
                    30 *         &lt;element name="coils-location" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}CoilsLocationType" maxOccurs="unbounded" minOccurs="0"/>
                    31 *         &lt;element name="fingerprints-location" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}FingerPrintsLocationType" maxOccurs="unbounded" minOccurs="0"/>
                    32 *         &lt;element name="hmmer2-location" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}Hmmer2LocationType" maxOccurs="unbounded" minOccurs="0"/>
                    33 *         &lt;element name="hmmer3-location" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}Hmmer3LocationType" maxOccurs="unbounded" minOccurs="0"/>
                    34 *         &lt;element name="panther-location" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}PantherLocationType" maxOccurs="unbounded" minOccurs="0"/>
                    35 *         &lt;element name="patternscan-location" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}PatternScanLocationType" maxOccurs="unbounded" minOccurs="0"/>
                    36 *         &lt;element name="phobius-location" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}PhobiusLocationType" maxOccurs="unbounded" minOccurs="0"/>
                    37 *         &lt;element name="profilescan-location" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}ProfileScanLocationType" maxOccurs="unbounded" minOccurs="0"/>
                    38 *         &lt;element name="signalp-location" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}SignalPLocationType" maxOccurs="unbounded" minOccurs="0"/>
                    39 *         &lt;element name="superfamilyhmmer3-location" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}SuperFamilyHmmer3LocationType" maxOccurs="unbounded" minOccurs="0"/>
                    40 *         &lt;element name="tmhmm-location" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}TMHMMLocationType" maxOccurs="unbounded" minOccurs="0"/>
                LocationType.java  (4 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    26 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    29 *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
                    30 *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
                MatchesType.java  (14 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    27 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    29 *         &lt;element name="coils-match" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}CoilsMatchType" maxOccurs="unbounded" minOccurs="0"/>
                    30 *         &lt;element name="fingerprints-match" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}FingerPrintsMatchType" maxOccurs="unbounded" minOccurs="0"/>
                    31 *         &lt;element name="hmmer2-match" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}Hmmer2MatchType" maxOccurs="unbounded" minOccurs="0"/>
                    32 *         &lt;element name="hmmer3-match" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}Hmmer3MatchType" maxOccurs="unbounded" minOccurs="0"/>
                    33 *         &lt;element name="panther-match" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}PantherMatchType" maxOccurs="unbounded" minOccurs="0"/>
                    34 *         &lt;element name="patternscan-match" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}PatternScanMatchType" maxOccurs="unbounded" minOccurs="0"/>
                    35 *         &lt;element name="phobius-match" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}PhobiusMatchType" maxOccurs="unbounded" minOccurs="0"/>
                    36 *         &lt;element name="blastprodom-match" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}BlastProDomMatchType" maxOccurs="unbounded" minOccurs="0"/>
                    37 *         &lt;element name="profilescan-match" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}ProfileScanMatchType" maxOccurs="unbounded" minOccurs="0"/>
                    38 *         &lt;element name="signalp-match" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}SignalPMatchType" maxOccurs="unbounded" minOccurs="0"/>
                    39 *         &lt;element name="superfamilyhmmer3-match" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}SuperFamilyHmmer3MatchType" maxOccurs="unbounded" minOccurs="0"/>
                    40 *         &lt;element name="tmhmm-match" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}TMHMMMatchType" maxOccurs="unbounded" minOccurs="0"/>
                MatchType.java  (4 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    26 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    28 *         &lt;element ref="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}signature"/>
                    29 *         &lt;element name="locations" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}locationsType" minOccurs="0"/>
                ModelsType.java  (3 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    26 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    28 *         &lt;element name="model" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}ModelType" maxOccurs="unbounded" minOccurs="0"/>
                ModelType.java  (6 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    25 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    28 *       &lt;attribute name="ac" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                    29 *       &lt;attribute name="desc" type="{http://www.w3.org/2001/XMLSchema}string" />
                    30 *       &lt;attribute name="md5" type="{http://www.w3.org/2001/XMLSchema}string" />
                    31 *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
                NucleicAcidMatchesType.java  (3 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    27 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    29 *         &lt;element ref="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}nucleotide-sequence" maxOccurs="unbounded" minOccurs="0"/>
                NucleotideSequenceStrandType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    22 *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
                NucleotideSequenceType.java  (3 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    26 *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
                    27 *       &lt;attribute name="md5" type="{http://www.w3.org/2001/XMLSchema}string" />
                NucleotideSequenceXrefType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}XrefType">
                NucleotideType.java  (5 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    27 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    29 *         &lt;element name="sequence" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}NucleotideSequenceType" minOccurs="0"/>
                    30 *         &lt;element name="xref" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}NucleotideSequenceXrefType" maxOccurs="unbounded"/>
                    31 *         &lt;element ref="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}orf" maxOccurs="unbounded"/>
                ObjectFactory.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                OrfType.java  (6 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    25 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    27 *         &lt;element ref="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}protein" minOccurs="0"/>
                    29 *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
                    30 *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
                    31 *       &lt;attribute name="strand" use="required" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}NucleotideSequenceStrandType" />
                package-info.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                PantherLocationType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}LocationType">
                PantherMatchType.java  (5 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    25 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}MatchType">
                    28 *       &lt;attribute name="evalue" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
                    29 *       &lt;attribute name="familyName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                    30 *       &lt;attribute name="score" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
                PathwayDatabase.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    22 *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
                PathwayXrefType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}XrefType">
                PatternScanLocationType.java  (4 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    26 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}LocationType">
                    28 *         &lt;element name="alignment" type="{http://www.w3.org/2001/XMLSchema}string"/>
                    30 *       &lt;attribute name="level" use="required" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}LevelType" />
                PatternScanMatchType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}MatchType">
                PersistenceConversion.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                PhobiusFeatureType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    22 *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
                PhobiusLocationType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}LocationType">
                PhobiusMatchType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}MatchType">
                ProfileScanLocationType.java  (4 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    26 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}LocationType">
                    28 *         &lt;element name="alignment" type="{http://www.w3.org/2001/XMLSchema}string"/>
                    30 *       &lt;attribute name="score" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
                ProfileScanMatchType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}MatchType">
                ProteinMatchesType.java  (3 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    26 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    28 *         &lt;element ref="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}protein" maxOccurs="unbounded" minOccurs="0"/>
                ProteinType.java  (6 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    27 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    29 *         &lt;element name="sequence" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}SequenceType" minOccurs="0"/>
                    30 *         &lt;element name="xref" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}ProteinXrefType" maxOccurs="unbounded" minOccurs="0"/>
                    31 *         &lt;element name="super-match" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}SuperMatchType" maxOccurs="unbounded" minOccurs="0"/>
                    32 *         &lt;element name="matches" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}matchesType"/>
                ProteinXrefType.java  (3 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    25 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}XrefType">
                    28 *       &lt;attribute name="desc" type="{http://www.w3.org/2001/XMLSchema}string" />
                ReleaseType.java  (4 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    27 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    29 *         &lt;element ref="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}entry" maxOccurs="unbounded" minOccurs="0"/>
                    31 *       &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                SequenceType.java  (3 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    26 *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
                    27 *       &lt;attribute name="md5" type="{http://www.w3.org/2001/XMLSchema}string" />
                SignalPLocationType.java  (3 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    25 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}LocationType">
                    28 *       &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}double" />
                SignalPMatchType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}MatchType">
                SignalPOrganismType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    22 *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
                SignatureLibraryReleaseType.java  (5 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    27 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    29 *         &lt;element ref="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}signature" maxOccurs="unbounded" minOccurs="0"/>
                    31 *       &lt;attribute name="library" use="required" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}SignatureLibraryType" />
                    32 *       &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                SignatureLibraryType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    23 *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
                SignatureType.java  (16 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    28 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    30 *         &lt;element name="abstract" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
                    31 *         &lt;element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
                    32 *         &lt;element name="xref" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}SignatureXrefType" maxOccurs="unbounded" minOccurs="0"/>
                    33 *         &lt;element name="deprecated-ac" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
                    34 *         &lt;element ref="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}entry" minOccurs="0"/>
                    35 *         &lt;element name="models" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}modelsType" minOccurs="0"/>
                    36 *         &lt;element ref="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}signature-library-release" minOccurs="0"/>
                    38 *       &lt;attribute name="ac" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                    39 *       &lt;attribute name="created" type="{http://www.w3.org/2001/XMLSchema}string" />
                    40 *       &lt;attribute name="desc" type="{http://www.w3.org/2001/XMLSchema}string" />
                    41 *       &lt;attribute name="md5" type="{http://www.w3.org/2001/XMLSchema}string" />
                    42 *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
                    43 *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
                    44 *       &lt;attribute name="updated" type="{http://www.w3.org/2001/XMLSchema}string" />
                SignatureXrefType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}XrefType">
                SuperFamilyHmmer3LocationType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}LocationType">
                SuperFamilyHmmer3MatchType.java  (3 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    25 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}MatchType">
                    28 *       &lt;attribute name="evalue" use="required" type="{http://www.w3.org/2001/XMLSchema}double" />
                SuperMatchType.java  (4 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    27 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    29 *         &lt;element ref="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}entry"/>
                    30 *         &lt;element name="location" type="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}location" maxOccurs="unbounded"/>
                TMHMMLocationType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}LocationType">
                TMHMMMatchType.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    24 *     &lt;extension base="{http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5}MatchType">
                TmhmmSignature.java  (2 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    22 *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
                XrefType.java  (5 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    26 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    29 *       &lt;attribute name="db" type="{http://www.w3.org/2001/XMLSchema}string" />
                    30 *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                    31 *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
            optionalPlugins\protannot\src\main\java\org\lorainelab\igb\protannot\model  (14 usages found)
                Dnaseq.java  (14 usages found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
                    639 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    640 *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
                    641 *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
                    758 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
                    763 *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
                    764 *                 &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
                    770 *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
                    771 *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
                    882 *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
                    883 *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" default="0" />
                    884 *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}nonNegativeInteger" />
                    983 *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
                    984 *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
            tools\LuceneIndexing\conf  (2 usages found)
                config.properties  (2 usages found)
                    9 #   http://www.apache.org/licenses/LICENSE-2.0
                    102 #obr.repository.url=http://felix.apache.org/obr/releases.xml
        igbScript  (2 usages found)
            com.gene.igbscript  (2 usages found)
                IGBScriptEngine.java  (1 usage found)
                    44 * http://today.java.net/pub/a/today/2006/09/21/making-scripting-languages-jsr-223-aware.html
                IGBScriptEngineFactory.java  (1 usage found)
                    18 * http://today.java.net/pub/a/today/2006/09/21/making-scripting-languages-jsr-223-aware.html
        igbSwingExt  (1 usage found)
            com.affymetrix.igb.swing  (1 usage found)
                MenuUtil.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
        keybinding-registry  (5 usages found)
            org.lorainelab.igb.keystrokes  (4 usages found)
                KeyStrokeEditPanel.java  (3 usages found)
                    keyStroke2String(KeyStroke)  (1 usage found)
                        311 * http://javaalmanac.com/egs/javax.swing/Key2Str.html
                    getKeyText(int)  (1 usage found)
                        349 * http://javaalmanac.com/egs/javax.swing/Key2Str.html
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                KeyStrokesView.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
            org.lorainelab.igb.keystrokes.model  (1 usage found)
                KeyStrokeViewTableModel.java  (1 usage found)
                    7  *  http://www.opensource.org/licenses/CPL
        main  (3 usages found)
              (2 usages found)
                config.properties  (2 usages found)
                    9 #   http://www.apache.org/licenses/LICENSE-2.0
                    155 #obr.repository.url=http://felix.apache.org/obr/releases.xml
            com.affymetrix.main  (1 usage found)
                Main.java  (1 usage found)
                    13 * The license is also available at http://www.opensource.org/licenses/cpl.php
        plugins-manager  (29 usages found)
            pluginInfoTemplateResources  (29 usages found)
                JSXTransformer.js  (29 usages found)
                    442  * @author   Feross Aboukhadijeh <feross@feross.org> <http://feross.org>
                    7145 // see http://wiki.ecmascript.org/doku.php?id=harmony:const
                    7146 // and http://wiki.ecmascript.org/doku.php?id=harmony:let
                    7519 // http://wiki.ecmascript.org/doku.php?id=proposals:iterators_and_generators&s=each
                    10044  * http://opensource.org/licenses/BSD-3-Clause
                    10055  * http://opensource.org/licenses/BSD-3-Clause
                    10154  * http://opensource.org/licenses/BSD-3-Clause
                    10300  * http://opensource.org/licenses/BSD-3-Clause
                    10344  * http://opensource.org/licenses/BSD-3-Clause
                    10427  * http://opensource.org/licenses/BSD-3-Clause
                    10906  * http://opensource.org/licenses/BSD-3-Clause
                    11288  * http://opensource.org/licenses/BSD-3-Clause
                    11661  * http://opensource.org/licenses/BSD-3-Clause
                    11868 * see: http://github.com/jrburke/amdefine for details
                    12174 * http://www.apache.org/licenses/LICENSE-2.0
                    12262 * http://www.apache.org/licenses/LICENSE-2.0
                    12563 * http://www.apache.org/licenses/LICENSE-2.0
                    13273 * http://www.apache.org/licenses/LICENSE-2.0
                    13542 * http://www.apache.org/licenses/LICENSE-2.0
                    14132 * http://www.apache.org/licenses/LICENSE-2.0
                    14414 * http://www.apache.org/licenses/LICENSE-2.0
                    14485 * http://www.apache.org/licenses/LICENSE-2.0
                    14540 * http://www.apache.org/licenses/LICENSE-2.0
                    14648 * http://www.apache.org/licenses/LICENSE-2.0
                    14668 * http://people.mozilla.org/~jorendorff/es6-draft.html#sec-12.1.9
                    14724 * http://people.mozilla.org/~jorendorff/es6-draft.html#sec-12.2.6
                    14806 * http://www.apache.org/licenses/LICENSE-2.0
                    14998 * http://www.apache.org/licenses/LICENSE-2.0
                    15074 * http://www.apache.org/licenses/LICENSE-2.0
        propertyView  (2 usages found)
            com.affymetrix.igb.property  (2 usages found)
                JTableCutPasteAdapter.java  (2 usages found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                    33 * http://www.javaworld.com/javaworld/javatips/jw-javatip77.html Copyright (c)
        quickload  (1 usage found)
            org.lorainelab.igb.quickload.model.annots  (1 usage found)
                AnnotsRootElement.java  (1 usage found)
                    3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
        restrictionSites  (1 usage found)
            com.affymetrix.igb.restrictions  (1 usage found)
                RestrictionControlView.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
        thresholding  (5 usages found)
            com.affymetrix.igb.thresholding  (5 usages found)
                GraphScoreThreshSetter.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                MaxGapThresholder.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                MinRunThresholder.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                MinScoreThresholder.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
                PercentThresholder.java  (1 usage found)
                    8 * The license is also available at http://www.opensource.org/licenses/cpl.php
        window-service  (4 usages found)
            com.affymetrix.igb.window.service.def  (4 usages found)
                JTabbedTrayHorizontalPane.java  (1 usage found)
                    createTabbedPane(String, int)  (1 usage found)
                        32 * http://www.jroller.com/santhosh/date/20050617#adobe_like_tabbedpane_in_swing
                JTabbedTrayPane.java  (2 usages found)
                    JTabbedTrayPane(String, TabState, JComponent, int, int, double)  (2 usages found)
                        104 // http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4465870
                        105 // http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4499556
                VerticalTextIcon.java  (1 usage found)
                    18 * http://www.jroller.com/santhosh/date/20050617#adobe_like_tabbedpane_in_swing
    Usage in string constants  (263 usages found)
        bam  (3 usages found)
            org.lorainelab.igb.bam  (3 usages found)
                BAM.java  (2 usages found)
                    init()  (1 usage found)
                        169 + "Please validate your BAM files (see http://picard.sourceforge.net/command-line-overview.shtml#ValidateSamFile). "
                    writeAnnotations(BioSeq, int, int, DataOutputStream, boolean)  (1 usage found)
                        355 + "Please validate your BAM files and contact the Picard project at http://picard.sourceforge.net."
                SAM.java  (1 usage found)
                    init()  (1 usage found)
                        59 + "Please validate your BAM files (see http://picard.sourceforge.net/command-line-overview.shtml#ValidateSamFile). "
        bookmark  (6 usages found)
            com.affymetrix.igb.bookmarks  (4 usages found)
                BookmarkConstants.java  (1 usage found)
                    45 public static final String DEFAULT_SERVLET_URL = "http://localhost:" + DEFAULT_SERVER_PORT + "/" + SERVLET_NAME;
                BookmarkHttpRequestHandler.java  (2 usages found)
                    remoteFileExists(String)  (1 usage found)
                        135 url = url.replace("http://", "https://");
                    getWelcomeMessage()  (1 usage found)
                        174 + "      <a class='btn btn-primary' href='http://localhost:7085/UnibrowControl?bringIGBToFront=true'>Click to go to IGB</a>"
                BookmarksParser.java  (1 usage found)
                    parseSimpleHTML(BookmarkList, File)  (1 usage found)
                        330 int uindex = line.indexOf("http://");
            plugins\Bookmark\src\test\com\affymetrix\igb\bookmarks  (2 usages found)
                BookMarkTest.java  (2 usages found)
                    testParseQueryString()  (1 usage found)
                        27 String url = "http://localhost?x=3&z&y=4&y=5";
                    constructURLTest()  (1 usage found)
                        47 assertEquals("http://localhost:7085/IGBControl?seqid=testSeqID&version=C_briggsae_Jan_2007&start=0&end=1000", bookmarkUrl);
        cache  (11 usages found)
            com.lorainelab.cache.disk  (11 usages found)
                RemoteFileCacheServiceTest.java  (11 usages found)
                    testGetCacheStatus()  (1 usage found)
                        55 URL url = new URL("http://bioviz.org/quickload/A_thaliana_Jan_2004/chr2.bnib");
                    testEnforceEvictionPolicies()  (4 usages found)
                        71 remoteFileService.getFilebyUrl(new URL("http://igbquickload.org/A_gambiae_Feb_2003/A_gambiae_Feb_2003.2bit"), false);
                        84 remoteFileService.getFilebyUrl(new URL("http://igbquickload.org/A_gambiae_Feb_2003/A_gambiae_Feb_2003.2bit"), false);
                        85 remoteFileService.getFilebyUrl(new URL("http://igbquickload.org/A_lyrata_Apr_2011/A_lyrata_Apr_2011.2bit"), false);
                        86 remoteFileService.getFilebyUrl(new URL("http://igbquickload.org/A_thaliana_Jan_2004/chr2.bnib"), false);
                    testGetFilebyUrl()  (3 usages found)
                        97 Optional<InputStream> is = remoteFileService.getFilebyUrl(new URL("http://igbquickload.org/A_gambiae_Feb_2003/A_gambiae_Feb_2003.2bit"), false);
                        98 remoteFileService.getFilebyUrl(new URL("http://igbquickload.org/A_lyrata_Apr_2011/A_lyrata_Apr_2011.2bit"), false);
                        99 remoteFileService.getFilebyUrl(new URL("http://igbquickload.org/A_thaliana_Jan_2004/chr2.bnib"), false);
                    testFileSizeLimit()  (1 usage found)
                        107 Optional<InputStream> is = remoteFileService.getFilebyUrl(new URL("http://localhost/index.html"), false);
                    testClearCacheByUrl()  (1 usage found)
                        123 URL url = new URL("http://igbquickload.org/A_gambiae_Feb_2003/A_gambiae_Feb_2003.2bit");
                    testGetCacheSize()  (1 usage found)
                        133 URL url = new URL("http://igbquickload.org/A_gambiae_Feb_2003/A_gambiae_Feb_2003.2bit");
        das  (10 usages found)
            com.lorainelab.das  (8 usages found)
                DasDataProviderTest.java  (1 usage found)
                    17 private final static String UCSC_DAS_URL = "http://genome.cse.ucsc.edu/cgi-bin/das/dsn";
                DASFeatureParserTest.java  (2 usages found)
                    testLinks()  (1 usage found)
                        81 assertEquals("http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr3:73089142-73107313&db=hg18", link);
                    testParse()  (1 usage found)
                        143 assertEquals("http://genome.ucsc.edu/cgi-bin/hgTracks?position=chr22:20012405-20012900&db=hg10", link);
                DasServerInfoTest.java  (5 usages found)
                    retrieveDnaTest()  (1 usage found)
                        44 String contextRoot = "http://genome.cse.ucsc.edu:80/cgi-bin/das/hg38";
                    retrieveDasEpResponseTest()  (1 usage found)
                        52 String contextRoot = "http://genome.cse.ucsc.edu:80/cgi-bin/das/hg38";
                    retrieveDasTypesResponseTest()  (1 usage found)
                        65 String contextRoot = "http://genome.cse.ucsc.edu:80/cgi-bin/das/hg38";
                    retrieveDasFeatureResponseTest()  (1 usage found)
                        78 String contextRoot = "http://genome.cse.ucsc.edu:80/cgi-bin/das/hg38";
                    27 private final String UCSC_DAS_URL = "http://genome.cse.ucsc.edu/cgi-bin/das/dsn/";
            org.lorainelab.igb.das.utils  (2 usages found)
                DasServerUtils.java  (2 usages found)
                    createSaxSource(InputStream)  (2 usages found)
                        208 spf.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
                        209 spf.setFeature("http://xml.org/sax/features/validation", false);
        das2  (9 usages found)
            com.lorainelab.das2  (2 usages found)
                Das2DataProviderTest.java  (1 usage found)
                    20 public static String DAS2_URL = "http://bioserver.hci.utah.edu:8080/DAS2DB";
                Das2ServerUtilsTest.java  (1 usage found)
                    22 public static String DAS2_URL = "http://bioserver.hci.utah.edu:8080/DAS2DB";
            org.lorainelab.igb.das2.parser  (5 usages found)
                Das2FeatureSaxParser.java  (5 usages found)
                    parse(InputSource, String, GenomeVersion, boolean)  (3 usages found)
                        217 reader.setFeature("http://xml.org/sax/features/validation", false);
                        218 reader.setFeature("http://apache.org/xml/features/validation/dynamic", false);
                        219 reader.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
                    writeAnnotations(Collection<? extends SeqSymmetry>, BioSeq, String, OutputStream)  (1 usage found)
                        667 pw.println("    xmlns:xlink=\"http://www.w3.org/1999/xlink\" ");
                    71 public static final String DAS2_NAMESPACE = "http://biodas.org/documents/das2";
            org.lorainelab.igb.das2.utils  (2 usages found)
                Das2ServerUtils.java  (2 usages found)
                    createSaxSource(InputStream)  (2 usages found)
                        111 spf.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
                        112 spf.setFeature("http://xml.org/sax/features/validation", false);
        externalView  (7 usages found)
            com.affymetrix.igb.external  (7 usages found)
                UCSCLoader.java  (3 usages found)
                    getUrlForView(Loc, int)  (1 usage found)
                        32 return "http://genome.ucsc.edu/cgi-bin/hgTracks?" + width + "db=" + loc.db + "&position=" + loc.chr + ":" + loc.start + "-" + loc.end;
                    27 private static final String fileNameBaseUrl = "http://genome.ucsc.edu/trash/hgt/";
                    28 private static final String sideNameBaseUrl = "http://genome.ucsc.edu/trash/hgtSide/";
                UCSCView.java  (2 usages found)
                    UCSCHelper(Window, String)  (2 usages found)
                        96 "http://g
                        127 ucscInfo.addActionListener(e -> GeneralUtils.browse("http://genome.ucsc.edu/cgi-bin/cartDump"));
                UCSCViewAction.java  (2 usages found)
                    51 private static final String UCSC_DAS_URL = "http://genome.cse.ucsc.edu/cgi-bin/das/";
                    52 private static final String UCSC_URL = "http://genome.ucsc.edu/cgi-bin/hgTracks?";
        feedback  (1 usage found)
            org.lorainelab.igb.feedback  (1 usage found)
                FeedbackMenuProvider.java  (1 usage found)
                    37 private static final String BIOVIZ_HELP_PAGE = "http://bioviz.org/igb/help.html";
        frameManager  (2 usages found)
              (2 usages found)
                bundle.properties  (2 usages found)
                    4 default_url=http://bioviz.org/igb/
                    6 instruction_page=http://wiki.transvar.org/confluence/display/igbman/Configuring+Web+links+%28LinkOuts%29+to+external+sites
        genometry  (15 usages found)
              (1 usage found)
                annots.xsd  (1 usage found)
                    2 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
            com.affymetrix.genometry.event  (1 usage found)
                ReportBugAction.java  (1 usage found)
                    actionPerformed(ActionEvent)  (1 usage found)
                        36 GeneralUtils.browse("http://sourceforge.net/p/genoviz/bugs/");
            com.affymetrix.genometry.parsers  (5 usages found)
                TrackLineParserTest.java  (2 usages found)
                    testSetTrackProperties()  (2 usages found)
                        29 String str = "track foo=bar this=\"that\" color=123,100,10 useScore=1 ignore= ignore2 nothing=\"\" url=\"http://www.foo.bar?x=y&this=$$\"";
                        40 assertEquals("http://www.foo.bar?x=y&this=$$", tlp.getTrackLineContent().get("url"));
                TwoBitNewTest.java  (1 usage found)
                    35 String url = "http://test.bioviz.org/testdata/";
                TwoBitParser.java  (1 usage found)
                    main(String[])  (1 usage found)
                        299 URI uri = URI.create("http://test.bioviz.org/testdata/nblocks.2bit");
                TwoBitParserTest.java  (1 usage found)
                    36 String url = "http://test.bioviz.org/testdata/";
            com.affymetrix.genometry.parsers.useq.apps  (4 usages found)
                Text2USeq.java  (1 usage found)
                    printDocs()  (1 usage found)
                        1064 + "      see http://genome.ucsc.edu/FAQ/FAQreleases#release1\n"
                USeq2UCSCBig.java  (1 usage found)
                    printDocs()  (1 usage found)
                        363 + "       from http://hgdownload.cse.ucsc.edu/admin/exe/\n"
                Wig2USeq.java  (2 usages found)
                    processArgs(String[])  (1 usage found)
                        612 USeqUtilities.printExit("\nError: you must supply a genome version. Goto http://genome.ucsc.edu/cgi-"
                    printDocs()  (1 usage found)
                        635 + "      http://genome.ucsc.edu/FAQ/FAQreleases\n"
            com.affymetrix.genometry.util  (4 usages found)
                GeneralUtils.java  (1 usage found)
                    convertStreamNameToValidURLName(String)  (1 usage found)
                        216 return "http://" + streamName;
                XMLUtils.java  (3 usages found)
                    nonValidatingFactory()  (3 usages found)
                        34 setFeature(factory, "http://xml.org/sax/features/validation");
                        35 setFeature(factory, "http://apache.org/xml/features/validation/dynamic");
                        36 setFeature(factory, "http://apache.org/xml/features/nonvalidating/load-external-dtd");
        igb  (50 usages found)
              (4 usages found)
                default_user_stylesheet.xml  (1 usage found)
                    3 "http://genoviz.sourceforge.net/formats/stylesheets/igb_stylesheet_0_1.dtd"
                igb.properties  (1 usage found)
                    298 quickstart=http://wiki.transvar.org/confluence/display/igbman/Quick+Start
                igb_system_stylesheet.xml  (2 usages found)
                    2 <!DOCTYPE IGB_STYLESHEET SYSTEM "http://genoviz.sourceforge.net/formats/stylesheets/igb_stylesheet_0_1.dtd"
                    18 dtd="http://genoviz.sourceforge.net/formats/stylesheets/igb_stylesheet_0_1.dtd">
            com.affymetrix.igb  (1 usage found)
                IGB.java  (1 usage found)
                    105 private static final String COUNTER_URL = "http://www.igbquickload.org/igb/counter";
            com.affymetrix.igb.action  (2 usages found)
                DocumentationAction.java  (1 usage found)
                    actionPerformed(ActionEvent)  (1 usage found)
                        41 GeneralUtils.browse("http://wiki.transvar.org/confluence/display/igbman");
                RequestFeatureAction.java  (1 usage found)
                    actionPerformed(ActionEvent)  (1 usage found)
                        42 GeneralUtils.browse("http://sourceforge.net/p/genoviz/feature-requests/");
            com.affymetrix.igb.prefs  (2 usages found)
                AddDataProvider.java  (2 usages found)
                    init(boolean, String, DataProvider)  (1 usage found)
                        122 urlText.setText("http://");
                    initComponents()  (1 usage found)
                        156 urlText = new JRPTextField("ServerPrefsView_url", "http://");
            com.affymetrix.igb.stylesheet  (1 usage found)
                Stylesheet.java  (1 usage found)
                    appendXML(String, StringBuffer)  (1 usage found)
                        138 sb.append(indent).append("<IGB_STYLESHEET\n").append(indent).append("version='0.1\'\n").append(indent).append("dtd='http://genoviz.sourceforge.net/formats/stylesheets/igb_stylesheet_0_1.dtd' "
            com.affymetrix.igb.util  (1 usage found)
                BugOrFeatureRequestForm.java  (1 usage found)
                    16 private static String URL = "http://bioviz.org/bugreporter/report";
            documentation  (20 usages found)
                How_to_create_a_QuickLoad_directory.html  (4 usages found)
                    13 <br /><a href="http://bioviz.org/quickload/">http://bioviz.org/quickload/</a>
                    38 <a href="http://bioviz.org/quickload/">http://bioviz.org/quickload/</a> as a guide to create your own.</br>
                    108 An incomplete list of formats supported by IGB can be found <a href="http://sourceforge.net/apps/trac/genoviz/wiki/File%20Formats">here</a>.<br />
                    119 Instructions for creating a bnib file can be found <a href="http://sourceforge.net/apps/trac/genoviz/wiki/Converting%20FASTA%20to%20BNIB">here</a>.<br />
                sample_bookmarks.html  (16 usages found)
                    12 <DT><A HREF="http://localhost:7085/IGBControl?version=H_sapiens_Mar_2006&seqid=chr17&start=43966897&end=44063310">Region of homeoboxes</A>
                    13 <DT><A HREF="http://localhost:7085/IGBControl?version=H_sapiens_Mar_2006&seqid=chr10&start=102905000&end=104995000">q24.32 on chr10</A>
                    16 "http://l
                    21 <DT><A HREF="http://localhost:7085/IGBControl?version=D_melanogaster_Apr_2004&seqid=chr3R&start=8216261&end=8359982">D_melanogaster_Apr_2004, a region on chr3R</A>
                    25 <DT><A HREF="http://localhost:7085/IGBControl?seqid=chr5&start=100000&end=200000">No genome specified, chr5:100,000-200,000</A>
                    27 <DT><A HREF="http://localhost:7085/IGBControl?version=H_sapiens_Mar_2006">Only genome specified: H_sapiens_Mar_2006</A>
                    28 <DT><A HREF="http://localhost:7085/IGBControl?version=H_sapiens_May_2004">Only genome specified: H_sapiens_May_2004</A>
                    30 <DT><A HREF="http://localhost:7085/IGBControl?seqid=chr18">Only chromosome specified: chr18</A>
                    31 <DT><A HREF="http://localhost:7085/IGBControl?seqid=chr22">Only chromosome specified: chr22</A>
                    32 <DT><A HREF="http://localhost:7085/IGBControl?seqid=chr3R">Only chromosome specified: chr3R</A>
                    37 "http://l
                    38 "http://l
                    39 "http://l
                    40 "http://l
                    41 "http://l
                    42 "http://l
            formats  (17 usages found)
                igb_data_formats.html  (17 usages found)
                    12 "http://s
                    19 See <a href="http://genome.ucsc.edu/goldenPath/help/customTrack.html#BED">BED format description</a> for more details.
                    27 <a href="http://sourceforge.net/docman/display_doc.php?docid=27770&group_id=129420">.bnib</a> format.
                    40 <td>XML formats returned from DAS servers. See <a href="http://www.biodas.org/wiki/Main_Page">http://www.biodas.org</a>.
                    42 See <a href="http://www.biodas.org/documents/spec.html">DAS/1 specification</a> and
                    43 <a href="http://biodas.org/documents/das2/das2_protocol.html">DAS/2 specification</a></td>
                    48 <td>Sequence data in a simple ASCII format.  See <a href="http://en.wikipedia.org/wiki/FASTA_format">here</a>.
                    50 these <a href="http://sourceforge.net/docman/display_doc.php?docid=27770&group_id=129420">instructions</a> to convert to the internal ".bnib" format.
                    59 The original GFF format is <a href="http://www.sanger.ac.uk/Software/formats/GFF">GFF1</a>.
                    60 A variant called <a href="http://genome.ucsc.edu/goldenPath/help/customTrack.html#GTF">GTF</a> is also used.
                    61 <a href="http://song.sourceforge.net/gff3-jan04.shtml">GFF3</a> has been proposed
                    76 <td>An alignment format developed by UCSC.  Please see the <a href="http://genome.ucsc.edu/goldenPath/help/customTrack.html#PSL">PSL format description</a> for more details.
                    82 <td>A tabular format, described <a href="http://sourceforge.net/docman/display_doc.php?docid=33332&group_id=129420">here</a>, 
                    97 <td>USeq is a binary indexed format used to display graph and annotation data. Please see the <a href="http://useq.sourceforge.net/">USEQ SourceForge page</a> for more details.</td>
                    102 <td><a href="http://genome.ucsc.edu/goldenPath/help/wiggle.html">Wiggle</a> 
                    110 "http://g
                    124 The full specification is available at <a href="http://genome.ucsc.edu/goldenPath/help/customTrack.html#PSL">UCSC</a>.
            help  (2 usages found)
                org.lorainelab.igb.AboutIGB.html  (2 usages found)
                    12 To find out more, visit <a href="http://bioviz.org/">BioViz.org</a>.
                    17 <a href="http://www.ncbi.nlm.nih.gov/pubmed/19654113">The Integrated Genome 
        igb-preferences  (75 usages found)
              (75 usages found)
                igbDefaultPrefs.json  (26 usages found)
                    7 "url": "http://lorainelab-quickload.scidas.org/rnaseq",
                    14 "url": "http://igbquickload.org/quickload",
                    16 "mirror": "http://lorainelab-quickload.scidas.org/quickload",
                    22 "url": "http://igbquickload.org/blueberry",
                    24 "mirror": "http://lorainelab-quickload.scidas.org/blueberry",
                    30 "url": "http://igbquickload.org/soyseq",
                    32 "mirror": "http://lorainelab-quickload.scidas.org/soyseq",
                    38 "url": "http://genome.cse.ucsc.edu/cgi-bin/das",
                    46 "url": "http://bioserver.hci.utah.edu:8080/DAS2DB",
                    54 "url": "http://lorainelab-quickload.scidas.org/bar",
                    62 "url": "http://bioviz.org/igbserver",
                    68 "url": "http://eos.transvar.org/igb_plugins",
                    77 "url": "http://www.google.com/search?q=$$",
                    86 "url": "http://www.ncbi.nlm.nih.gov/nuccore/$$",
                    94 "url": "http://www.arabidopsis.org/servlets/TairObject?type=gene&name=$$",
                    102 "url": "http://dictybase.org/gene/$$",
                    109 "url": "http://www.dictybase.org/db/cgi-bin/search/search.pl?query=$$",
                    116 "url": "http://www.genedb.org/genedb/Search?name=$$&organism=pombe&desc=yes&wildcard=yes&searchId=Search",
                    123 "url": "http://www.maizesequence.org/Zea_mays/Transcript/Transcript?t=$$",
                    130 "url": "http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=$$",
                    144 "url": "http://www.affymetrix.com/analysis/netaffx/exon/probe_set.affx?pk=$$",
                    151 "url": "http://www.affymetrix.com/analysis/netaffx/exon/transcript.affx?pk=$$",
                    159 "url": "http://flybase.org/.bin/fbidq.html?$$",
                    167 "url": "http://dictybase.org/db/cgi-bin/search/search.pl?query=$$",
                    175 "url": "http://www.ncbi.nlm.nih.gov/gene/$$",
                    182 "url": "http://www.ncbi.nlm.nih.gov/gquery?term=$$",
                igbDefaultPrefs.json  (26 usages found)
                    7 "url": "http://lorainelab-quickload.scidas.org/rnaseq",
                    14 "url": "http://igbquickload.org/quickload",
                    16 "mirror": "http://lorainelab-quickload.scidas.org/quickload",
                    22 "url": "http://igbquickload.org/blueberry",
                    24 "mirror": "http://lorainelab-quickload.scidas.org/blueberry",
                    30 "url": "http://igbquickload.org/soyseq",
                    32 "mirror": "http://lorainelab-quickload.scidas.org/soyseq",
                    38 "url": "http://genome.cse.ucsc.edu/cgi-bin/das",
                    46 "url": "http://bioserver.hci.utah.edu:8080/DAS2DB",
                    54 "url": "http://lorainelab-quickload.scidas.org/bar",
                    62 "url": "http://bioviz.org/igbserver",
                    68 "url": "http://eos.transvar.org/igb_plugins",
                    77 "url": "http://www.google.com/search?q=$$",
                    86 "url": "http://www.ncbi.nlm.nih.gov/nuccore/$$",
                    94 "url": "http://www.arabidopsis.org/servlets/TairObject?type=gene&name=$$",
                    102 "url": "http://dictybase.org/gene/$$",
                    109 "url": "http://www.dictybase.org/db/cgi-bin/search/search.pl?query=$$",
                    116 "url": "http://www.genedb.org/genedb/Search?name=$$&organism=pombe&desc=yes&wildcard=yes&searchId=Search",
                    123 "url": "http://www.maizesequence.org/Zea_mays/Transcript/Transcript?t=$$",
                    130 "url": "http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=$$",
                    144 "url": "http://www.affymetrix.com/analysis/netaffx/exon/probe_set.affx?pk=$$",
                    151 "url": "http://www.affymetrix.com/analysis/netaffx/exon/transcript.affx?pk=$$",
                    159 "url": "http://flybase.org/.bin/fbidq.html?$$",
                    167 "url": "http://dictybase.org/db/cgi-bin/search/search.pl?query=$$",
                    175 "url": "http://www.ncbi.nlm.nih.gov/gene/$$",
                    182 "url": "http://www.ncbi.nlm.nih.gov/gquery?term=$$",
                igbDefaultPrefs.xml  (23 usages found)
                    6 <server type="quickload" name="IGB Quickload" url="http://igbquickload.org/quickload/" order="0" default="true" enabled="true" mirror="http://bioviz.org/quickload/"/>
                    7 <server type="quickload" name="Pollen" url="http://www.igbquickload.org/pollen" order="1" default="true" enabled="true" mirror="http://bioviz.org/pollen/"/>
                    8 <server type="quickload" name="Cytokinin" url="http://www.igbquickload.org/cyto" order="2" default="true" enabled="true" mirror="http://bioviz.org/cytopub/"/>
                    9 <server type="quickload" name="Blueberry" url="http://www.igbquickload.org/blueberry" order="3" default="true" enabled="true" mirror="http://bioviz.org/berrypub/"/>
                    10 <server type="das" name="UCSC" url="http://genome.cse.ucsc.edu/cgi-bin/das/dsn" order="5" default="true" enabled="false"/>
                    11 <server type="das" name="Ensembl" url="http://www.ensembl.org/das/dsn" order="6" default="true" enabled="false"/>
                    12 <server type="quickload" name="BioVizServerCache" url="http://bioviz.org/cached/" enabled="true" primary="true" order="7" default="true"/>
                    22 <repository name="BioViz" url="http://bioviz.org/igbserver" enabled="true" default="true"/>
                    24 <repository name="BioViz development" url="http://eos.transvar.org/igb_plugins" enabled="false" default="true"/>
                    37 url="http://www.google.com/search?q=$$"
                    46 url="http://www.ncbi.nlm.nih.gov/nuccore/$$"
                    57 url="http://www.arabidopsis.org/servlets/TairObject?type=gene&amp;name=$$"
                    66 url="http://dictybase.org/gene/$$"
                    71 url="http://www.dictybase.org/db/cgi-bin/search/search.pl?query=$$"
                    78 url="http://www.genedb.org/genedb/Search?name=$$&amp;organism=pombe&amp;desc=yes&amp;wildcard=yes&amp;searchId=Search"
                    87 url="http://www.maizesequence.org/Zea_mays/Transcript/Transcript?t=$$"
                    94 url="http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=$$" 
                    106 url="http://www.affymetrix.com/analysis/netaffx/exon/probe_set.affx?pk=$$"
                    111 url="http://www.affymetrix.com/analysis/netaffx/exon/transcript.affx?pk=$$"
                    118 url="http://flybase.org/.bin/fbidq.html?$$"
                    123 url="http://dictybase.org/db/cgi-bin/search/search.pl?query=$$"
                    128 url="http://www.ncbi.nlm.nih.gov/gene/$$"
                    136 url="http://www.ncbi.nlm.nih.gov/gquery?term=$$"
        igb-project  (55 usages found)
              (2 usages found)
                build.gradle  (1 usage found)
                    25 url 'http://maven.ej-technologies.com/repository'
                nb-configuration.xml  (1 usage found)
                    9 <properties xmlns="http://www.netbeans.org/ns/maven-properties-data/1">
            developmentPlugins\FindAnnotations\src\main\resources\docs  (1 usage found)
                FindAnnotations.html  (1 usage found)
                    18 If you feel like the plugin has a defect, you can fill out a bug report in <a href="http://sourceforge.net/tracker/?group_id=129420&atid=714744">SourceForge Genoviz</a>.
            developmentPlugins\NCBIPrimer\src\main\java\apollo\analysis  (1 usage found)
                RemotePrimerBlastNCBI.java  (1 usage found)
                    28 private static final String PRIMER_BLAST_URL = "http://www.ncbi.nlm.nih.gov/tools/primer-blast/primertool.cgi";
            developmentPlugins\OverlapAnnotationOperator\src\main\resources\docs  (1 usage found)
                OverlapAnnotationOperator.html  (1 usage found)
                    21 If you feel like the plugin has a defect, you can fill out a bug report in <a href="http://sourceforge.net/tracker/?group_id=129420&atid=714744">SourceForge Genoviz</a>.
            developmentPlugins\SampleSelection\src\main\resources\docs  (1 usage found)
                SampleSelection.html  (1 usage found)
                    33 If you feel like the plugin has a defect, you can fill out a bug report in <a href="http://sourceforge.net/tracker/?group_id=129420&atid=714744">SourceForge Genoviz</a>.
            developmentPlugins\TallyHandler\src\main\resources\docs  (1 usage found)
                TallyHandler.html  (1 usage found)
                    27 If you feel like the plugin has a defect, you can fill out a bug report in <a href="http://sourceforge.net/tracker/?group_id=129420&atid=714744">SourceForge Genoviz</a>.
            developmentPlugins\TranscriptIsoform\src\main\resources\docs  (1 usage found)
                TranscriptIsoform.html  (1 usage found)
                    29 If you feel like the plugin has a defect, you can fill out a bug report in <a href="http://sourceforge.net/tracker/?group_id=129420&atid=714744">SourceForge Genoviz</a>.
            doc  (5 usages found)
                useqArchiveFormat.html  (5 usages found)
                    31 The Java code for reading and writing useq data is distributed through the <a href="http://genoviz.sourceforge.net">GenoViz</a> and 
                    32 <a href="http://useq.sourceforge.net">USeq</a> sourceforge projects.  
                    33 The <a href="http://igb.bioviz.org">Integrated Genome Browser</a> and <a href="http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2">GenoPub</a> 
                    49 Use the <a href="http://useq.sourceforge.net/cmdLnMenus.html#Text2USeq">Text2USeq</a> application to convert text genomic data formats into USeq archives.
                    50 Likewise, use the <a href="http://useq.sourceforge.net/cmdLnMenus.html#USeq2Text">USeq2Text</a> application to covert USeq archives into 6 
            optionalPlugins\protannot\src\main\java\org\lorainelab\igb\protannot  (5 usages found)
                ProtAnnotAction.java  (4 usages found)
                    checkArguments(String, String)  (1 usage found)
                        883 + "\n eg. http://protannot.bioviz.org/samples/");
                    getAboutAction()  (1 usage found)
                        1471 + "http://www.bioviz.org/protannot\n";
                    build_url(Properties)  (2 usages found)
                        1576 return "http://www.ebi.ac.uk/interpro/entry/" + val;
                        1584 return "http://www.ncbi.nlm.nih.gov:80/entrez/query.fcgi?cmd=Retrieve&db=nucleotide&list_uids=" + val + "&dopt=GenBank";
                ProtAnnotService.java  (1 usage found)
                    showSetupModal()  (1 usage found)
                        475 Desktop.getDesktop().browse(new URI("http://www.ebi.ac.uk/interpro/about.html"));
            optionalPlugins\protannot\src\main\java\org\lorainelab\igb\protannot\interproscan  (3 usages found)
                InterProscanServiceRest.java  (1 usage found)
                    48 private static final String INTERPROSCAN_BASE_URL = "http://www.ebi.ac.uk/Tools/services/rest/iprscan5";
                InterProscanTranslator.java  (2 usages found)
                    generateUrlFromAc(String)  (2 usages found)
                        160 return new URL("http://www.ebi.ac.uk/interpro/entry/" + ac);
                        162 return new URL("http://www.google.com/search?q=" + ac);
            optionalPlugins\protannot\src\main\java\org\lorainelab\igb\protannot\interproscan\model  (19 usages found)
                ObjectFactory.java  (18 usages found)
                    createNucleotideSequenceMatches(NucleicAcidMatchesType)  (1 usage found)
                        431 @XmlElementDecl(namespace = "http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", name = "nucleotide-sequence-matches")
                    createProteinMatches(ProteinMatchesType)  (1 usage found)
                        440 @XmlElementDecl(namespace = "http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", name = "protein-matches")
                    createNucleotideSequence(NucleotideType)  (1 usage found)
                        449 @XmlElementDecl(namespace = "http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", name = "nucleotide-sequence")
                    createSignature(SignatureType)  (1 usage found)
                        458 @XmlElementDecl(namespace = "http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", name = "signature")
                    createInterproRelease(ReleaseType)  (1 usage found)
                        467 @XmlElementDecl(namespace = "http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", name = "interpro-release")
                    createProtein(ProteinType)  (1 usage found)
                        476 @XmlElementDecl(namespace = "http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", name = "protein")
                    createSignatureLibraryRelease(SignatureLibraryReleaseType)  (1 usage found)
                        485 @XmlElementDecl(namespace = "http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", name = "signature-library-release")
                    createEntry(EntryType)  (1 usage found)
                        494 @XmlElementDecl(namespace = "http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", name = "entry")
                    createOrf(OrfType)  (1 usage found)
                        503 @XmlElementDecl(namespace = "http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", name = "orf")
                    34 private final static QName _NucleotideSequenceMatches_QNAME = new QName("http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", "nucleotide-sequence-matches");
                    35 private final static QName _ProteinMatches_QNAME = new QName("http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", "protein-matches");
                    36 private final static QName _NucleotideSequence_QNAME = new QName("http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", "nucleotide-sequence");
                    37 private final static QName _Signature_QNAME = new QName("http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", "signature");
                    38 private final static QName _InterproRelease_QNAME = new QName("http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", "interpro-release");
                    39 private final static QName _Protein_QNAME = new QName("http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", "protein");
                    40 private final static QName _SignatureLibraryRelease_QNAME = new QName("http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", "signature-library-release");
                    41 private final static QName _Entry_QNAME = new QName("http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", "entry");
                    42 private final static QName _Orf_QNAME = new QName("http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", "orf");
                package-info.java  (1 usage found)
                    8 @javax.xml.bind.annotation.XmlSchema(namespace = "http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
            optionalPlugins\protannot\src\main\java\org\lorainelab\igb\protannot\model  (2 usages found)
                InterProScanTableModel.java  (1 usage found)
                    131 private static final String BASE_URL = "http://www.ebi.ac.uk/Tools/services/rest/iprscan5/result/";
                ProtannotParser.java  (1 usage found)
                    addDescriptorsToMrna(SeqSymmetry, MRNA)  (1 usage found)
                        267 mrna.addDescriptor("URL", "http://www.google.com/search?q=" + ((BasicSeqSymmetry) sym).getID());
            optionalPlugins\protannot\src\main\resources\org\lorainelab\igb\protannot  (1 usage found)
                protannot.xsd  (1 usage found)
                    2 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
            optionalPlugins\protannot\src\test\resources  (2 usages found)
                sample1.xml  (1 usage found)
                    3 <protein-matches xmlns="http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5">
                sample2.xml  (1 usage found)
                    2 <protein-matches xmlns="http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5">
            optionalPlugins\protannot\src\test\resources\diff_motifs  (1 usage found)
                InterProtScanResponse.xml  (1 usage found)
                    1 <protein-matches xmlns="http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5">
            optionalPlugins\protannot\target\classes\org\lorainelab\igb\protannot  (1 usage found)
                protannot.xsd  (1 usage found)
                    2 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
            optionalPlugins\protannot\target\test-classes  (2 usages found)
                sample1.xml  (1 usage found)
                    3 <protein-matches xmlns="http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5">
                sample2.xml  (1 usage found)
                    2 <protein-matches xmlns="http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5">
            optionalPlugins\protannot\target\test-classes\diff_motifs  (1 usage found)
                InterProtScanResponse.xml  (1 usage found)
                    1 <protein-matches xmlns="http://www.ebi.ac.uk/interpro/resources/schemas/interproscan5">
            tools\LuceneIndexing\docs  (5 usages found)
                readme.html  (5 usages found)
                    3 This is a batch utility that is used to create <a href="http://lucene.apache.org">Apache Lucene</a> indexes
                    5 are to be used with the <a href="http://research-pub.gene.com/igb_plugins/docs/LuceneIndexing.html">SearchModeLucene IGB plugin</a>.<br/>
                    7 unzip the <a href="http://research-pub.gene.com/igb_plugins/util/LuceneIndexing.zip">LuceneIndexing.zip</a> file to a new directory.<br/>
                    11 <li><a href="http://www.oracle.com/technetwork/java/javase/downloads/index.html">java</a> must be installed</li>
                    12 <li><a href="http://ant.apache.org/">Apache ant</a> must be installed</li>
        main  (1 usage found)
              (1 usage found)
                config.properties  (1 usage found)
                    159 org.amdatu.remote.discovery.configured.endpoints=http://reporting.bioviz.org/org.amdatu.remote.discovery.configured
        ncbiBlast  (2 usages found)
            apollo.analysis  (2 usages found)
                completeTestBlast.xml  (1 usage found)
                    2 <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
                testBlast.xml  (1 usage found)
                    2 <!DOCTYPE BlastOutput PUBLIC "-//NCBI//NCBI BlastOutput/EN" "http://www.ncbi.nlm.nih.gov/dtd/NCBI_BlastOutput.dtd">
        plugins-manager  (6 usages found)
              (1 usage found)
                PluginConfigurationPanel.fxml  (1 usage found)
                    13 <VBox prefHeight="541.0" prefWidth="885.0" xmlns="http://javafx.com/javafx/8.0.60" xmlns:fx="http://javafx.com/fxml/1">
            org.lorainelab.igb.plugin.manager.repos.view  (2 usages found)
                AddBundleRepositoryFrame.java  (2 usages found)
                    init(boolean, PluginRepository)  (1 usage found)
                        91 urlText.setText("http://");
                    initComponents()  (1 usage found)
                        116 urlText = new JRPTextField("ServerPrefsView_url", "http://");
            pluginInfoTemplateResources  (1 usage found)
                JSXTransformer.js  (1 usage found)
                    317 'http://facebook.github.io/react/docs/tooling-integration.html#jsx'
            pluginInfoTemplateResources.fonts  (2 usages found)
                fontawesome-webfont.svg  (2 usages found)
                    2 <!DOCTYPE svg PUBLIC "-//W3C//DTD SVG 1.1//EN" "http://www.w3.org/Graphics/SVG/1.1/DTD/svg11.dtd" >
                    3 <svg xmlns="http://www.w3.org/2000/svg" xmlns:xlink="http://www.w3.org/1999/xlink" version="1.1">
        quickload  (7 usages found)
              (1 usage found)
                annots.xsd  (1 usage found)
                    2 <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema">
            org.lorainelab.igb.quickload.util  (2 usages found)
                AnnotsParser.java  (2 usages found)
                    createSaxSource(InputStream)  (2 usages found)
                        60 spf.setFeature("http://apache.org/xml/features/nonvalidating/load-external-dtd", false);
                        61 spf.setFeature("http://xml.org/sax/features/validation", false);
            org.lorainelab.igb.quickload.utils  (4 usages found)
                QuickloadDataProviderTest.java  (3 usages found)
                    setup()  (2 usages found)
                        27 dataProvider = new QuickloadDataProvider("http://igbquickload.org/", "igbquickload", 1);
                        29 dataProvider.setMirrorUrl("http://bioviz.org/quickload/");
                    checkMirrorUrl()  (1 usage found)
                        65 assertTrue(dataProvider.getMirrorUrl().get().equals("http://bioviz.org/quickload/"));
                QuickloadUtilsTest.java  (1 usage found)
                    contentsTxtParserTest()  (1 usage found)
                        20 Assert.assertTrue(CharStreams.toString(new InputStreamReader(getInputStream(new URI("http://igbquickload.org/contents.txt")))).contains("A_thaliana_Jun_2009"));
        survey  (1 usage found)
              (1 usage found)
                survey.properties  (1 usage found)
                    3 surveys=http://bioviz.org/igb/releases/surveys.xml
        update  (1 usage found)
              (1 usage found)
                updates.properties  (1 usage found)
                    1 updates=http://bioviz.org/igb/releases/updates.xml
        weblinks  (1 usage found)
              (1 usage found)
                bundle.properties  (1 usage found)
                    6 instruction_page=http://wiki.transvar.org/confluence/display/igbman/Configuring+Web+links+%28LinkOuts%29+to+external+sites
    Occurrence in XML descriptor  (138 usages found)
        org  (3 usages found)
            lorainelab  (3 usages found)
                igb  (3 usages found)
                    error  (1 usage found)
                        reporter  (1 usage found)
                            manager  (1 usage found)
                                plugins\org.lorainelab.igb.error.reporter.manager  (1 usage found)
                                    pom.xml  (1 usage found)
                                        1 "http://m
                    menu  (2 usages found)
                        api  (2 usages found)
                            core\menu-api  (2 usages found)
                                pom.xml  (2 usages found)
                                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        affymetrix-common  (1 usage found)
            core\common  (1 usage found)
                pom.xml  (1 usage found)
                    2 "http://m
        annotation-tab  (2 usages found)
            plugins\AnnotationTab  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        apollo-library  (2 usages found)
            plugins\ApolloLibrary  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        bam  (2 usages found)
            plugins\bam  (2 usages found)
                pom.xml  (2 usages found)
                    2 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    3 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        bed  (2 usages found)
            plugins\bed  (2 usages found)
                pom.xml  (2 usages found)
                    2 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    3 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        bigBedHandler  (2 usages found)
            plugins\BigBedHandler  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        bigWigHandler  (2 usages found)
            plugins\BigWigHandler  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        bookmark  (2 usages found)
            plugins\Bookmark  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        cache  (1 usage found)
            plugins\cache  (1 usage found)
                pom.xml  (1 usage found)
                    2 "http://m
        cache-api  (1 usage found)
            plugins\cache-api  (1 usage found)
                pom.xml  (1 usage found)
                    2 "http://m
        console-gui  (2 usages found)
            plugins\ConsoleGui  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        context-menu-service  (2 usages found)
            core\context-menu-service  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        das  (2 usages found)
            core\das  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        das2  (2 usages found)
            core\das2  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        external-sort  (2 usages found)
            plugins\external-sort  (2 usages found)
                pom.xml  (2 usages found)
                    2 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    3 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        externalView  (2 usages found)
            plugins\ExternalView  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        feedback  (2 usages found)
            plugins\feedback  (2 usages found)
                pom.xml  (2 usages found)
                    2 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    3 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        frameManager  (2 usages found)
            core\frameManager  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        genometry  (2 usages found)
            core\genometry  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        graphTab  (2 usages found)
            plugins\GraphTab  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        heatmap-editor  (2 usages found)
            core\heatmap-editor  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        igb  (2 usages found)
            core\igb  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        igb-genoviz-extensions  (2 usages found)
            core\igb-genoviz-ext  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        igb-javafx-util  (2 usages found)
            core\igb-javafx-util  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        igb-preferences  (2 usages found)
            core\igb-preferences  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        igb-project  (36 usages found)
              (5 usages found)
                pom.xml  (5 usages found)
                    2 "http://m
                    62 <url>http://maven.bioviz.org/repo1</url>
                    66 <url>http://maven.bioviz.org/repo2</url>
                    70 <url>http://maven.bioviz.org/repo3</url>
                    77 <url>http://maven.bioviz.org/repo3</url>
            core\taglets  (1 usage found)
                pom.xml  (1 usage found)
                    2 "http://m
            developmentPlugins\FindAnnotations  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
            developmentPlugins\NCBIPrimer  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
            developmentPlugins\OverlapAnnotationOperator  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
            developmentPlugins\ParentOperators  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
            developmentPlugins\SampleSelection  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
            developmentPlugins\SearchModeLucene  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
            developmentPlugins\SearchModeSymmetryFilter  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
            developmentPlugins\TallyHandler  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
            developmentPlugins\TranscriptIsoform  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
            optionalPlugins\23andMe-snp-converter  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
            optionalPlugins\geometric-mean  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
            optionalPlugins\igb-command-socket  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
            optionalPlugins\merge-annotation-operator  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
            optionalPlugins\protannot  (2 usages found)
                pom.xml  (2 usages found)
                    2 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    3 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
            optionalPlugins\tutorial-helper  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        igb-services  (2 usages found)
            core\igb-services-api  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        igbScript  (2 usages found)
            plugins\IGBScript  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        igbSwingExt  (2 usages found)
            core\igb-swing-ext  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        image-exporter  (2 usages found)
            plugins\image-exporter  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        keybinding-registry  (2 usages found)
            plugins\Keybinding-registry  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        keyWordSearch  (2 usages found)
            plugins\KeyWordSearch  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        logging-config  (2 usages found)
            core\logging-config  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        main  (1 usage found)
            main  (1 usage found)
                pom.xml  (1 usage found)
                    2 "http://m
        narrowpeak  (2 usages found)
            plugins\narrowpeak  (2 usages found)
                pom.xml  (2 usages found)
                    2 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    3 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        ncbiBlast  (2 usages found)
            plugins\NCBIBlast  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        paired-data-preprocessor  (2 usages found)
            plugins\PairedEndDataPreprocessor  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        plugins-manager  (2 usages found)
            plugins\plugin-manager  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        propertyView  (2 usages found)
            plugins\PropertyView  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        quickload  (2 usages found)
            core\quickload  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        restrictionSites  (2 usages found)
            plugins\RestrictionSites  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        searchModelIdOrProps  (2 usages found)
            plugins\SearchModeIdOrProps  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        searchView  (2 usages found)
            plugins\SearchView  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        sequenceViewer  (2 usages found)
            plugins\SequenceViewer  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        session-manager  (2 usages found)
            plugins\session-manager  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        shared-lib-wrapper  (1 usage found)
            core\shared-lib-wrapper  (1 usage found)
                pom.xml  (1 usage found)
                    2 "http://m
        survey  (2 usages found)
            plugins\Survey  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        synonym-lookup  (2 usages found)
            core\synonym-lookup  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        thresholding  (2 usages found)
            plugins\Thresholding  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        track-operations-panel  (2 usages found)
            plugins\track-operations-panel  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        update  (2 usages found)
            plugins\Update  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        weblinks  (2 usages found)
            core\weblinks  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
        window-service  (2 usages found)
            core\window-service  (2 usages found)
                pom.xml  (2 usages found)
                    1 <project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
                    2 xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
Usages in generated code  (48 usages found)
    Usage in comments  (43 usages found)
        plugins-manager  (43 usages found)
            pluginInfoTemplateResources  (43 usages found)
                bootstrap.min.css  (1 usage found)
                    2  * Bootstrap v3.3.5 (http://getbootstrap.com)
                font-awesome.min.css  (2 usages found)
                    2  *  Font Awesome 4.4.0 by @davegandy - http://fontawesome.io - @fontawesome
                    3  *  License - http://fontawesome.io/license (Font: SIL OFL 1.1, CSS: MIT License)
                pluginInfoTemplateResources.css  (1 usage found)
                    2  * Bootstrap v3.3.5 (http://getbootstrap.com)
                react.min.js  (39 usages found)
                    453 * http://www.w3.org/TR/2013/WD-DOM-Level-3-Events-20131105/#events-inputevents.
                    563 * individual properties. See http://bugs.jquery.com/ticket/12385.
                    1510 * @see http://jsperf.com/key-exists
                    1511 * @see http://jsperf.com/key-missing
                    1866 * @see http://jsperf.com/extract-nodename
                    3342 // Microdata support. See http://schema.org/docs/gs.html
                    3374 // http://www.w3.org/TR/html5/forms.html#dom-fs-encoding
                    3948 * @see http://www.quirksmode.org/blog/archives/2010/09/click_event_del.html
                    3972 // @see http://www.quirksmode.org/dom/events/tests/scroll.html
                    3989 // @see http://www.quirksmode.org/blog/archives/2008/04/delegating_the.html
                    4020 * @see http://www.quirksmode.org/dom/events/scroll.html
                    6562 // http://www.w3.org/TR/REC-xml/#NT-Name
                    6728 * @see http://jsperf.com/obj-vs-arr-iteration
                    6818 // See: <http://www.w3.org/TR/html-polyglot/#newlines-in-textarea-and-pre>
                    6819 // See: <http://www.w3.org/TR/html5/syntax.html#element-restrictions>
                    6820 // See: <http://www.w3.org/TR/html5/syntax.html#newlines>
                    6822 //  from <http://www.w3.org/TR/html5/syntax.html#parsing-main-inbody>
                    7514 * @see http://www.w3.org/TR/2012/WD-html5-20121025/the-input-element.html
                    10890 // http://jsperf.com/emptying-a-node
                    14690 // @see http://www.w3.org/TR/html5/index.html#events-0
                    14801 * @see http://www.w3.org/TR/clipboard-apis/
                    14841 * @see http://www.w3.org/TR/DOM-Level-3-Events/#events-compositionevents
                    14879 * @see http://www.w3.org/TR/DOM-Level-3-Events/
                    14921 * @see http://www.w3.org/TR/DOM-Level-3-Events/
                    15095 * @see http://www.w3.org/TR/DOM-Level-3-Events/
                    15133 * @see http://www.w3.org/TR/2013/WD-DOM-Level-3-Events-20131105
                    15176 * @see http://www.w3.org/TR/DOM-Level-3-Events/
                    15261 * @see http://www.w3.org/TR/DOM-Level-3-Events/
                    15334 * @see http://www.w3.org/TR/touch-events/
                    15381 * @see http://www.w3.org/TR/DOM-Level-3-Events/
                    15440 * @see http://www.w3.org/TR/DOM-Level-3-Events/
                    15874 // http://www.thespanner.co.uk/2007/11/26/ultimate-xss-css-injection/
                    16285 * @see http://www.w3.org/TR/DOM-Level-3-Events/#keys-Modifiers
                    16338 // @see http://www.quirksmode.org/js/events_properties.html
                    16625 // @see http://dom.spec.whatwg.org/#dom-domimplementation-hasfeature
                    16681 * @see http://www.whatwg.org/specs/web-apps/current-work/multipage/the-input-element.html#input-type-attr-summary
                    17523 * http://www.apache.org/licenses/LICENSE-2.0
                    17700 * (http://www.andismith.com/blog/2012/02/modernizr-prefixed/), an `-ms` prefix
                    18257 * As Modernizr suggests (http://modernizr.com/docs/#prefixed), an `ms` prefix
    Usage in string constants  (5 usages found)
        plugins-manager  (5 usages found)
            pluginInfoTemplateResources  (5 usages found)
                highlight.min.js  (1 usage found)
                    1 "http://w
                react.min.js  (4 usages found)
                    3188 hasSVG = implementation && implementation.hasFeature && implementation.hasFeature('http://www.w3.org/TR/SVG11/feature#BasicStructure', '1.1');
                    13853 xlink: 'http://www.w3.org/1999/xlink',
                    13854 xml: 'http://www.w3.org/XML/1998/namespace'
                    18097 var svgWrap = [1, '<svg xmlns="http://www.w3.org/2000/svg">', '</svg>'];