[BUG-359] Sliced View improvements; specifically for ORF view - JIRA UNCC

Details

Type: Bug
Status: Closed (View Workflow)
Priority: Major
Resolution: Fixed
Labels:
None

Description

Sliced View can be improved in 2 ways.

1. The background color for ORF view should be changeable. We can change stop and dynamic orf colors, but the background is always gray - we need access to colors (specifically white) so that it can be used for publication. The BG color box can easily be added to Preference > other > ORF analyzer.

2. When 'Analyze ORFs' box is selected, it should AUTOMATICALLY change Slice buffer to '0' and become grayed out/unchangeable. This will make using the ORF analyzer much easier and much more obvious.

Attachments

Issue Links

relates to

BUG-661 Sliced View

Closed

Activity

Ascending order - Click to sort in descending order

Hide

Permalink

Nick Ren (Inactive) added a comment - 27/Feb/12 4:58 AM

Fixed in truck version 10477.

Show

Nick Ren (Inactive) added a comment - 27/Feb/12 4:58 AM Fixed in truck version 10477.

7 older comments

Hide

Permalink

Alyssa Gulledge (Inactive) added a comment - 04/Apr/12 5:00 AM

Currently, if I try to change the color of any of the elements (BG, stop, orf) they throw:

Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException
at java.util.AbstractList$Itr.checkForComodification(AbstractList.java:372)
at java.util.AbstractList$Itr.next(AbstractList.java:343)
at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:185)
at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:166)
at com.affymetrix.igb.tiers.AffyLabelledTierMap.packTiers(AffyLabelledTierMap.java:148)
at com.affymetrix.igb.tiers.AffyTieredMap.repack(AffyTieredMap.java:159)
at com.affymetrix.igb.view.OrfAnalyzer$2$1.actionPerformed(OrfAnalyzer.java:305)
at com.affymetrix.igb.view.SeqMapView.preserveSelectionAndPerformAction(SeqMapView.java:798)
at com.affymetrix.igb.view.OrfAnalyzer$2.run(OrfAnalyzer.java:310)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677)
at java.awt.EventQueue.access$000(EventQueue.java:85)
at java.awt.EventQueue$1.run(EventQueue.java:638)
at java.awt.EventQueue$1.run(EventQueue.java:636)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:647)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException
at java.util.AbstractList$Itr.checkForComodification(AbstractList.java:372)
at java.util.AbstractList$Itr.next(AbstractList.java:343)
at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:211)
at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:166)
at com.affymetrix.igb.tiers.AffyLabelledTierMap.packTiers(AffyLabelledTierMap.java:148)
at com.affymetrix.igb.tiers.AffyTieredMap.repack(AffyTieredMap.java:159)
at com.affymetrix.igb.view.OrfAnalyzer$2$1.actionPerformed(OrfAnalyzer.java:305)
at com.affymetrix.igb.view.SeqMapView.preserveSelectionAndPerformAction(SeqMapView.java:798)
at com.affymetrix.igb.view.OrfAnalyzer$2.run(OrfAnalyzer.java:310)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677)
at java.awt.EventQueue.access$000(EventQueue.java:85)
at java.awt.EventQueue$1.run(EventQueue.java:638)
at java.awt.EventQueue$1.run(EventQueue.java:636)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:647)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException
at java.util.AbstractList$Itr.checkForComodification(AbstractList.java:372)
at java.util.AbstractList$Itr.next(AbstractList.java:343)
at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:211)
at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:166)
at com.affymetrix.igb.tiers.AffyLabelledTierMap.packTiers(AffyLabelledTierMap.java:148)
at com.affymetrix.igb.tiers.AffyTieredMap.repack(AffyTieredMap.java:159)
at com.affymetrix.igb.view.OrfAnalyzer$2$1.actionPerformed(OrfAnalyzer.java:305)
at com.affymetrix.igb.view.SeqMapView.preserveSelectionAndPerformAction(SeqMapView.java:798)
at com.affymetrix.igb.view.OrfAnalyzer$2.run(OrfAnalyzer.java:310)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677)
at java.awt.EventQueue.access$000(EventQueue.java:85)
at java.awt.EventQueue$1.run(EventQueue.java:638)
at java.awt.EventQueue$1.run(EventQueue.java:636)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:647)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

Show

Alyssa Gulledge (Inactive) added a comment - 04/Apr/12 5:00 AM Currently, if I try to change the color of any of the elements (BG, stop, orf) they throw: Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException at java.util.AbstractList$Itr.checkForComodification(AbstractList.java:372) at java.util.AbstractList$Itr.next(AbstractList.java:343) at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:185) at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:166) at com.affymetrix.igb.tiers.AffyLabelledTierMap.packTiers(AffyLabelledTierMap.java:148) at com.affymetrix.igb.tiers.AffyTieredMap.repack(AffyTieredMap.java:159) at com.affymetrix.igb.view.OrfAnalyzer$2$1.actionPerformed(OrfAnalyzer.java:305) at com.affymetrix.igb.view.SeqMapView.preserveSelectionAndPerformAction(SeqMapView.java:798) at com.affymetrix.igb.view.OrfAnalyzer$2.run(OrfAnalyzer.java:310) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677) at java.awt.EventQueue.access$000(EventQueue.java:85) at java.awt.EventQueue$1.run(EventQueue.java:638) at java.awt.EventQueue$1.run(EventQueue.java:636) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:647) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException at java.util.AbstractList$Itr.checkForComodification(AbstractList.java:372) at java.util.AbstractList$Itr.next(AbstractList.java:343) at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:211) at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:166) at com.affymetrix.igb.tiers.AffyLabelledTierMap.packTiers(AffyLabelledTierMap.java:148) at com.affymetrix.igb.tiers.AffyTieredMap.repack(AffyTieredMap.java:159) at com.affymetrix.igb.view.OrfAnalyzer$2$1.actionPerformed(OrfAnalyzer.java:305) at com.affymetrix.igb.view.SeqMapView.preserveSelectionAndPerformAction(SeqMapView.java:798) at com.affymetrix.igb.view.OrfAnalyzer$2.run(OrfAnalyzer.java:310) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677) at java.awt.EventQueue.access$000(EventQueue.java:85) at java.awt.EventQueue$1.run(EventQueue.java:638) at java.awt.EventQueue$1.run(EventQueue.java:636) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:647) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException at java.util.AbstractList$Itr.checkForComodification(AbstractList.java:372) at java.util.AbstractList$Itr.next(AbstractList.java:343) at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:211) at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:166) at com.affymetrix.igb.tiers.AffyLabelledTierMap.packTiers(AffyLabelledTierMap.java:148) at com.affymetrix.igb.tiers.AffyTieredMap.repack(AffyTieredMap.java:159) at com.affymetrix.igb.view.OrfAnalyzer$2$1.actionPerformed(OrfAnalyzer.java:305) at com.affymetrix.igb.view.SeqMapView.preserveSelectionAndPerformAction(SeqMapView.java:798) at com.affymetrix.igb.view.OrfAnalyzer$2.run(OrfAnalyzer.java:310) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677) at java.awt.EventQueue.access$000(EventQueue.java:85) at java.awt.EventQueue$1.run(EventQueue.java:638) at java.awt.EventQueue$1.run(EventQueue.java:636) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:647) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)

Hide

Permalink

Alyssa Gulledge (Inactive) added a comment - 04/Apr/12 5:01 AM

However, every other aspect finally seems to be working GREAT!

Show

Alyssa Gulledge (Inactive) added a comment - 04/Apr/12 5:01 AM However, every other aspect finally seems to be working GREAT!

Hide

Permalink

Alyssa Gulledge (Inactive) added a comment - 30/Apr/12 5:23 AM

Currently in v. 11279, just trying to open sliced view at all throws:

Exception in thread "pool-13-thread-1" java.lang.NullPointerException
at com.affymetrix.genometryImpl.util.GeneralUtils.stripEndings(GeneralUtils.java:72)
at com.affymetrix.genometryImpl.parsers.FileTypeHolder.getFileTypeHandlerForURI(FileTypeHolder.java:442)
at com.affymetrix.igb.viewmode.MapViewModeHolder.getAutoloadFactory(MapViewModeHolder.java:118)
at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:831)
at com.affymetrix.igb.view.AltSpliceSeqMapView.getTrack(AltSpliceSeqMapView.java:73)
at com.affymetrix.igb.view.TrackView.addAnnotationGlyphs(TrackView.java:230)
at com.affymetrix.igb.view.TrackView.addTracks(TrackView.java:153)
at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1121)
at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:894)
at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:727)
at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:287)
at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:652)
at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:56)
at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:639)
at com.affymetrix.igb.view.AltSpliceSeqMapView.sliceAndDiceNow(AltSpliceSeqMapView.java:255)
at com.affymetrix.igb.view.AltSpliceSeqMapView.access$200(AltSpliceSeqMapView.java:29)
at com.affymetrix.igb.view.AltSpliceSeqMapView$3.run(AltSpliceSeqMapView.java:121)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:680)

Show

Alyssa Gulledge (Inactive) added a comment - 30/Apr/12 5:23 AM Currently in v. 11279, just trying to open sliced view at all throws: Exception in thread "pool-13-thread-1" java.lang.NullPointerException at com.affymetrix.genometryImpl.util.GeneralUtils.stripEndings(GeneralUtils.java:72) at com.affymetrix.genometryImpl.parsers.FileTypeHolder.getFileTypeHandlerForURI(FileTypeHolder.java:442) at com.affymetrix.igb.viewmode.MapViewModeHolder.getAutoloadFactory(MapViewModeHolder.java:118) at com.affymetrix.igb.view.SeqMapView.getTrack(SeqMapView.java:831) at com.affymetrix.igb.view.AltSpliceSeqMapView.getTrack(AltSpliceSeqMapView.java:73) at com.affymetrix.igb.view.TrackView.addAnnotationGlyphs(TrackView.java:230) at com.affymetrix.igb.view.TrackView.addTracks(TrackView.java:153) at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1121) at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:894) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:727) at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:287) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:652) at com.affymetrix.igb.view.AltSpliceSeqMapView.setAnnotatedSeq(AltSpliceSeqMapView.java:56) at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:639) at com.affymetrix.igb.view.AltSpliceSeqMapView.sliceAndDiceNow(AltSpliceSeqMapView.java:255) at com.affymetrix.igb.view.AltSpliceSeqMapView.access$200(AltSpliceSeqMapView.java:29) at com.affymetrix.igb.view.AltSpliceSeqMapView$3.run(AltSpliceSeqMapView.java:121) at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:680)

Hide

Permalink

Hiral Vora (Inactive) added a comment - 10/May/12 11:55 AM

Fixed.

Show

Hiral Vora (Inactive) added a comment - 10/May/12 11:55 AM Fixed.

Hide

Permalink

Fuquan Wang (Inactive) added a comment - 05/Jun/12 6:09 AM

Passed on 7.0.0 (11804) Mac.

Show

Fuquan Wang (Inactive) added a comment - 05/Jun/12 6:09 AM Passed on 7.0.0 (11804) Mac.

People

Assignee:

Unassigned

Reporter:

Alyssa Gulledge (Inactive)

Votes:

0 Vote for this issue

Watchers:

0 Start watching this issue

Dates

Created:

26/Jan/12 8:40 AM

Updated:

02/Jan/13 5:58 AM

Resolved:

02/Jan/13 5:58 AM