Test: Create an intron glyph for genoviz-sdk (ArrowHeadGlyph)

To begin testing this issue:
Step 1: Please clone genoviz-sdk repo to you local system (I don't think forking this repo is necessary for testing).
Step 2: Open the project in a Java IDE (I recommend IntelliJ)

There are two parts to this testing - testing the demo class and testing the glyph class. Genoviz-sdk is a java library so both the testing happens at the Java class level - so in some cases the code needs to be changed and then the GUI should be checked to see if the corresponding changes are appearing correctly

The glyph class that needs to be tested is IntronGlyph.java (genoviz_sdk/src/main/java/com/affymetrix/genoviz/glyph/IntronGlyph.java). The class generates an arrow in the GUI (NeoMap), where the arrow-head is in the middle of the arrow shaft(see attached image, IntronGlyph).

To test if the IntronGlyph appears correctly:
Step 1: Open GlyphTestMap.java (genovizTutorial/src/main/java/com/affymetrix/genoviz/tutorial/GlyphTestMap.java)
Step 2: In line 37, a string array, 'glyphtypes', is declared. Add "com.affymetrix.genoviz.glyph.IntronGlyph" to the array.
Step 3: Run GlyphTestMap.java.
Step 4: In the GUI, select 'com.affymetrix.genoviz.glyph.IntronGlyph' from the dropdown on top of the window and click on 'Add Glyph' button
Step 5: Change the start,end and color values to your liking and see how if the glyph behaves as expected.

Repeat the same steps for SimpleMap4 (same folder path) and SimpleSelectableMap (same folder path). In SimpleMap4, change the zoom level by moving the slider on the left side of the window(green background). In SimpleSelectableMap, click on the arrows and check if the boundary boxes appear correctly.

The demo class that needs testing is BedSequenceDemo.class (genovizTutorial/src/main/java/com/affymetrix/genoviz/tutorial/BedSequenceDemo.java). The class reads a bed file provided in the data folder (genovizTutorial/src/main/resources/data) and renders the sequences using IntronGlyph and SequenceGlyph(rectangles) types.

Step 1: Run BedSequenceDemo.class (path above). See if the sequences are being rendered.
Step 2: In the zoomed out level, observe if the arrowheads are do not appear and only lines connecting rectangles. No arrowheads is correct result.
Step 3: Click and release on any of the glyphs generated on the map and see if the zoom stripe appears (grey vertical line going down the map intersecting the point you clicked)
Step 4: Scroll up to see if the map zooms at the stripe. As you zoom in see if the arrow heads start to appear when there is enough space between the rectangles.
Step 5: Click on any of the glyphs and check if the glyph is getting highlighted red
Step 6: Test if the sliders in the window are work as expected as well

While testing please be mindful that the errors could be very minute when rendering the glyphs in the map. If there are slight inconsistencies, please take a screenshot and add to this issue. Use "TAIR10 mRNA" image and other images in IGBF-2865 for reference.

Test result for IntronGlyph file

• After adding 'com.affymetrix.genoviz.glyph.IntronGlyph" in the String array and executing the file I am getting the error " Could not intronGlyp.java". Its happening for all the files 3 files, GlyphTestMap, SimpleMap4, SimpleSelectableMap. For the rest of the array values the start - end color values and zoom level are working good. Check attached snapshots 'IntronGlyph', 'SimpleMap4 'and 'SimpleSelectable'.

Test result for BedSequenceDemo file

• After executing BedSequenceDemo the output window was blank with just zoom in-out arrowheads and slider bar. They seems to working fine but with no output. Please check 'BedSequence' snapshot.

Test result for IntronGlyph file on IntelliJ IDE.

• After adding 'com.affymetrix.genoviz.glyph.IntronGlyph" in the String array and executing the file GlyphTestMap the glyph behave as expected. The color values and start and end values reflected in the glyph. The zoom level are working good for all the files. I repeated the same steps for SimpleMap4.java and SimpleSelectableMap.java. The glyph behaved as expected. Please check the snapshot 'Intron1' , 'Intron2', 'Intron3'.

Test result for BedSequenceDemo file on IntelliJ IDE.

• After executing BedSequenceDemo the output window was blank with just zoom in-out arrowheads and slider bar. I am getting java null pointer exception error and java.net.MalformedURLException: unknown protocol: c error in the output. Please check 'BedSequenceDemo' and 'Bed1' snapshot.

Solution to the error mentioned in 'BedSequenceDemo' and 'Bed1' snapshot.

I changed the absolute path below

For BedSequenceDemo.java file :

 String bedUrl = "C:\\genoviz-sdk\\genovizTutorial\\src\\main\\resources\\data\\AraportBedFile.bed"; 

For BedFileParser.java file :

 String urlpath = "C:\\genoviz-sdk\\genovizTutorial\\src\\main\\resources\\data\\AraportBedFile.bed"; 

to file path as below in both BedSequenceDemo.java and BedFileParser.java files respectively.

 String bedUrl ="file:///C:/genoviz-sdk/genovizTutorial/src/main/resources/data/AraportBedFile.bed"; 

 String urlpath ="file:///C:/genoviz-sdk/genovizTutorial/src/main/resources/data/AraportBedFile.bed"; 

In absolute path it takes "C:" drive as a URL protocol which causes the problem.

Also, for plugin error mentioned in 'PluginError' snapshot, I added maven version in the pom.xml file which resolved the error. Please check 'Pluginresolve' snapshot. Plugin error is kind of a warning which doesn't affect the output but it may come in the future though if we don't add the maven version which we are using in the pom.xml file.

After this change I am getting expected out.

• Arrowheads do not appear in zoomed out level and only lines connecting rectangles can be seen.
• After clicking and releasing on any of the glyphs generated on the map, the zoom stripe appears which is grey vertical line going down the map intersecting the point which has been clicked.
• After scrolling up, the map zooms at the stripe. After zoom in, the arrow heads start to appear when there is enough space between the rectangles.
• Glyphs are getting highlighted after they are clicked.
• Sliders in the window are working as expected.
• Refer 'Bed2' snapshot for output.

Karthik Raveendran Please check and you can push the change.

Absolute Path issue has been fixed Commit

Please submit PR.

PR submitted

Change looks fine. Merged. Moving to Needs Testing.

Test results after performing above mentioned steps:

• Arrowheads do not appear in zoomed out level and only lines connecting rectangles can be seen.
• After clicking and releasing on any of the glyphs generated on the map, the zoom stripe appears which is grey vertical line going down the map intersecting the point which has been clicked.
• After scrolling up, the map zooms at the stripe. After zoom in, the arrow heads start to appear when there is enough space between the rectangles.
• Glyphs are getting highlighted after they are clicked.
• Sliders in the window are working as expected.
• Refer 'Bed2' snapshot for output.

Closing the issue.