[BUG-621] GUI Test: Sequence Viewer - JIRA UNCC

Details

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

Description

Open Sequence Viewer (Whole Gene Model)

View Menu
Shortcut keystroke
Toolbar button (First enable, then use)
Right-click Menu

Open items in Sequence Viewer:

Ensure title bar accuracy
'Show cDNA' grayed out except for gene models
Whole gene model
Single exon (CDS and UTR)
Highlighted/Selected sequence
Cytoband (Human or Mouse)

View Short reads (Load a BAM file):

Open Short read sequence via View, keystroke, Toolbar button, and right-click Menu (Known issue:Selection lost with right-click Menu)
Short Read, Genomic
Short Read, Insertion (Insertion different color) and Deletion

File (Open saved file to check accuracy):

Save As Fasta
Save As Fasta (Reverse Complement)
Export Image
Close Sequence Viewer (Menu and Keystroke)

Copy (Paste into Text Editor to ensure accuracy):

Select All (Menu and Keystroke)
Copy Selected DNA Sequence
Copy DNA with lowercase...
Copy Annotated Translation
Copy Selected Translation(s)

Show

Reverse Complement (Ensure start and stop are accurately identified)
Complement
All + Translation
All - Translation

Colors/'Show cDNA' (Use Whole Gene Model):

Check both color schemes
Ensure 'Show cDNA' and 'Show genomic' work (Button switches AND function works)

Attachments

Issue Links

blocks

BUG-608 Sequence viewer bugs

Closed

Activity

Ascending order - Click to sort in descending order

Richard Linchangco (Inactive) created issue - 15/Nov/12 8:57 AM

Richard Linchangco (Inactive) made changes - 15/Nov/12 8:58 AM

Field	Original Value	New Value
Link		This issue blocks ~~BUG-608~~ [ ~~BUG-608~~ ]

Richard Linchangco (Inactive) made changes - 15/Nov/12 9:03 AM

Description

Open Sequence Viewer (Whole Gene Model)
* View Menu
* Shortcut keystroke
* Toolbar button (First enable, then use)
* Right-click Menu

Open items in Sequence Viewer:
* Whole gene model
* Single exon (CDS and UTR)
* Highlighted/Selected sequence
* Cytoband (Human or Mouse)
* Short Read, Genomic (Load a BAM file)
* Short Read, Read (Same read;Check keystroke and Toolbar button)

Richard Linchangco (Inactive) made changes - 15/Nov/12 9:27 AM

Description

Open Sequence Viewer (Whole Gene Model)
* View Menu
* Shortcut keystroke
* Toolbar button (First enable, then use)
* Right-click Menu

Open items in Sequence Viewer:
* Ensure title bar accuracy
* 'Show cDNA' grayed out except for gene models
* Whole gene model
* Single exon (CDS and UTR)
* Highlighted/Selected sequence
* Cytoband (Human or Mouse)

View Short reads (Load a BAM file):
* Open Short read sequence via View, keystroke, Toolbar button, and right-click Menu (Known issue:Selection lost with right-click Menu)
* Short Read, Genomic
* Short Read, Insertion (Insertion different color) and Deletion

File (Open saved file to check accuracy):
* Save As Fasta
* Save As Fasta (Reverse Complement)
* Export Image
* Close Sequence Viewer (Menu and Keystroke)

Copy (Paste into Text Editor to ensure accuracy):
* Select All (Menu and Keystroke)
* Copy Selected DNA Sequence
* Copy DNA with lowercase...
* Copy Annotated Translation
* Copy Selected Translation(s)

Show
* Reverse Complement (Ensure start and stop are accurately identified)
* Complement
* All + Translation
* All - Translation

Colors/'Show cDNA' (Use Whole Gene Model):
* Check both color schemes
* Ensure 'Show cDNA' and 'Show genomic' work (Button switches AND function works)

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Richard Linchangco (Inactive) added a comment - 15/Nov/12 10:58 AM

V.13526, Mac, Java 1.06.0_37

Open Sequence Viewer:

Passed
There is no Keystroke for this function yet

Open items in Sequence Viewer:

Passed

View Short Reads:

Passed
For Insertion different color is present but difficult to see at a glance. Suggestion to change to a more visible color.

File:

Passed

Copy:

Passed

Show:

Passed

Colors/'Show cDNA':

Passed

Overall:

Passed

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Richard Linchangco (Inactive) added a comment - 15/Nov/12 10:58 AM V.13526, Mac, Java 1.06.0_37 Open Sequence Viewer: Passed There is no Keystroke for this function yet Open items in Sequence Viewer: Passed View Short Reads: Passed For Insertion different color is present but difficult to see at a glance. Suggestion to change to a more visible color. File: Passed Copy: Passed Show: Passed Colors/'Show cDNA': Passed Overall: Passed

Richard Linchangco (Inactive) made changes - 15/Nov/12 10:58 AM

Assignee

Ann Loraine [ aloraine ]

Alyssa Gulledge [ alyssa ]

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Alyssa Gulledge (Inactive) added a comment - 15/Nov/12 11:33 AM

...and now, check it on windows please

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Alyssa Gulledge (Inactive) added a comment - 15/Nov/12 11:33 AM ...and now, check it on windows please

Alyssa Gulledge (Inactive) made changes - 15/Nov/12 11:33 AM

Assignee

Alyssa Gulledge [ alyssa ]

Richard Linchangco [ richard ]

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Richard Linchangco (Inactive) added a comment - 21/Nov/12 12:32 PM

V.13607, Windows XP Professional, Java 1.06.0_32

Please see 2 FAIL regarding the Main Toolbar

Open Sequence Viewer:

From 'View' Menu-PASSED
From Keystroke-No available keystroke
From Main Toolbar-FAIL
- When adding to toolbar: Preferences > Shortcuts
  - 'View Genomic Sequence in Sequence Viewer...' and 'View Read Sequence in Sequence Viewer...' are NOT added to toolbar when check box is selected
  - Appears that there are a set limit of spaces for main toolbar, when tools already in the bar are de-selected, the newly requested tools appear
  - Throws NegativeArraySizeException (attached to bottom of comment)
  - PASSES when tool does appear in main toolbar though
From Right-Click Menu-PASSED

Open Items in Sequence Viewer:

Title Bar-PASSED
'Show cDNA' only for Gene models-PASSED
Whole Gene Models-PASSED
Single Exons (CDS and UTR)-PASSED
Highlighted/Selected sequence-PASSED
Cytoband-PASSED
- Human tested, cannot locate Cytobands from IGB Quickload for any M. musculus genomes

View Short Reads:

Open Short Read Sequence:
- From 'View' Menu-PASSED
- From Keystroke-No available keystroke
- From Main Toolbar-FAIL
  - Same issue as above
  - PASSES when tool does appear in main toolbar though
- From Right-Click Menu-PASSED
'View Read/Genomic Sequence in Sequence Viewer...':
- 'View Read Seq...'-PASSED
- 'View Genomic Seq...'-PASSED
Short Read Sequence in Seq Viewer... Insertion and Deletion:
- Insertion-PASSED
  - Insert is white in black and yellow color scheme
  - Insert is black in white and blue color scheme
    - Colors could be more obvious
- Deletion-PASSED
  - Deletions appear as underscores where bases are missing
  - This is adequate and obvious

'File':

'Save As Fasta'-PASSED
'Save As Fasta (Reverse Complement)'-PASSED
'Export Image'-PASSED
'Close Seqeuence Viewer'-PASSED
- Keystroke works as well

'Copy':

'Select All'-PASSED
- Keystroke works as well
'Copy Selected DNA Sequence'-PASSED
'Copy DNA with lowercase introns and start/stop codons-PASSED
'Copy Annotated Translated'-PASSED

'Show':

'Reverse Complement'-PASSED
'Complement'-PASSED
'+1 to +3'-PASSED
'~~1 to -3'~~PASSED
'All +'-PASSED
'ALL 'PASSED

'Colors'/'Show cDNA':

'Yellow on Black'-PASSED
'Blue on White'-PASSED
'Show cDNA'-PASSED
'Show genomic'-PASSED

Toolbar Sequence Viewer Exception:
Exception in thread "AWT-EventQueue-0" java.lang.NegativeArraySizeException
at com.affymetrix.genoviz.datamodel.Sequence.getResidues(Sequence.java:237)
at com.affymetrix.genoviz.widget.neoseq.WrapSequence.drawResidues(WrapSequence.java:232)
at com.affymetrix.genoviz.widget.neoseq.WrapSequence.drawResidues(WrapSequence.java:110)
at com.affymetrix.genoviz.widget.neoseq.WrapFontColors.draw(WrapFontColors.java:51)
at com.affymetrix.genoviz.bioviews.Glyph.drawTraversal(Glyph.java:128)
at com.affymetrix.genoviz.bioviews.Glyph.drawChildren(Glyph.java:169)
at com.affymetrix.genoviz.bioviews.Glyph.drawTraversal(Glyph.java:129)
at com.affymetrix.genoviz.widget.neoseq.WrapSequence.drawTraversal(WrapSequence.java:450)
at com.affymetrix.genoviz.bioviews.Glyph.drawChildren(Glyph.java:169)
at com.affymetrix.genoviz.bioviews.Glyph.drawTraversal(Glyph.java:129)
at com.affymetrix.genoviz.glyph.RootGlyph.drawTraversal(RootGlyph.java:74)
at com.affymetrix.genoviz.bioviews.View.normalDraw(View.java:450)
at com.affymetrix.genoviz.bioviews.View.draw(View.java:359)
at com.affymetrix.genoviz.bioviews.View.componentPainted(View.java:869)
at com.affymetrix.genoviz.awt.NeoCanvas.postPaintEvent(NeoCanvas.java:72)
at com.affymetrix.genoviz.awt.NeoCanvas.paintComponent(NeoCanvas.java:47)
at javax.swing.JComponent.paint(Unknown Source)
at java.awt.GraphicsCallback$PaintCallback.run(Unknown Source)
at sun.awt.SunGraphicsCallback.runOneComponent(Unknown Source)
at sun.awt.SunGraphicsCallback.runComponents(Unknown Source)
at java.awt.Container.paint(Unknown Source)
at com.affymetrix.genoviz.widget.NeoMap.paint(NeoMap.java:1235)
at java.awt.GraphicsCallback$PaintCallback.run(Unknown Source)
at sun.awt.SunGraphicsCallback.runOneComponent(Unknown Source)
at sun.awt.SunGraphicsCallback.runComponents(Unknown Source)
at java.awt.Container.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at javax.swing.JLayeredPane.paint(Unknown Source)
at javax.swing.JComponent.paintChildren(Unknown Source)
at javax.swing.JComponent.paintToOffscreen(Unknown Source)
at javax.swing.BufferStrategyPaintManager.paint(Unknown Source)
at javax.swing.RepaintManager.paint(Unknown Source)
at javax.swing.JComponent.paint(Unknown Source)
at java.awt.GraphicsCallback$PaintCallback.run(Unknown Source)
at sun.awt.SunGraphicsCallback.runOneComponent(Unknown Source)
at sun.awt.SunGraphicsCallback.runComponents(Unknown Source)
at java.awt.Container.paint(Unknown Source)
at java.awt.Window.paint(Unknown Source)
at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source)
at javax.swing.RepaintManager.prePaintDirtyRegions(Unknown Source)
at javax.swing.RepaintManager.access$700(Unknown Source)
at javax.swing.RepaintManager$ProcessingRunnable.run(Unknown Source)
at java.awt.event.InvocationEvent.dispatch(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$000(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.awt.EventQueue$1.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)

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Richard Linchangco (Inactive) added a comment - 21/Nov/12 12:32 PM V.13607, Windows XP Professional, Java 1.06.0_32 Please see 2 FAIL regarding the Main Toolbar Open Sequence Viewer : From 'View' Menu- PASSED From Keystroke-No available keystroke From Main Toolbar- FAIL When adding to toolbar: Preferences > Shortcuts 'View Genomic Sequence in Sequence Viewer...' and 'View Read Sequence in Sequence Viewer...' are NOT added to toolbar when check box is selected Appears that there are a set limit of spaces for main toolbar, when tools already in the bar are de-selected, the newly requested tools appear Throws NegativeArraySizeException (attached to bottom of comment) PASSES when tool does appear in main toolbar though From Right-Click Menu- PASSED Open Items in Sequence Viewer : Title Bar- PASSED 'Show cDNA' only for Gene models- PASSED Whole Gene Models- PASSED Single Exons (CDS and UTR)- PASSED Highlighted/Selected sequence- PASSED Cytoband- PASSED Human tested, cannot locate Cytobands from IGB Quickload for any M. musculus genomes View Short Reads : Open Short Read Sequence : From 'View' Menu- PASSED From Keystroke-No available keystroke From Main Toolbar- FAIL Same issue as above PASSES when tool does appear in main toolbar though From Right-Click Menu- PASSED 'View Read/Genomic Sequence in Sequence Viewer...' : 'View Read Seq...'- PASSED 'View Genomic Seq...'- PASSED Short Read Sequence in Seq Viewer... Insertion and Deletion : Insertion- PASSED Insert is white in black and yellow color scheme Insert is black in white and blue color scheme Colors could be more obvious Deletion- PASSED Deletions appear as underscores where bases are missing This is adequate and obvious 'File' : 'Save As Fasta'- PASSED 'Save As Fasta (Reverse Complement)'- PASSED 'Export Image'- PASSED 'Close Seqeuence Viewer'- PASSED Keystroke works as well 'Copy' : 'Select All'- PASSED Keystroke works as well 'Copy Selected DNA Sequence'- PASSED 'Copy DNA with lowercase introns and start/stop codons- PASSED 'Copy Annotated Translated'- PASSED 'Show' : 'Reverse Complement'- PASSED 'Complement'- PASSED '+1 to +3'- PASSED ' 1 to -3' PASSED 'All +'- PASSED 'ALL ' PASSED 'Colors'/'Show cDNA' : 'Yellow on Black'- PASSED 'Blue on White'- PASSED 'Show cDNA'- PASSED 'Show genomic'- PASSED Toolbar Sequence Viewer Exception : Exception in thread "AWT-EventQueue-0" java.lang.NegativeArraySizeException at com.affymetrix.genoviz.datamodel.Sequence.getResidues(Sequence.java:237) at com.affymetrix.genoviz.widget.neoseq.WrapSequence.drawResidues(WrapSequence.java:232) at com.affymetrix.genoviz.widget.neoseq.WrapSequence.drawResidues(WrapSequence.java:110) at com.affymetrix.genoviz.widget.neoseq.WrapFontColors.draw(WrapFontColors.java:51) at com.affymetrix.genoviz.bioviews.Glyph.drawTraversal(Glyph.java:128) at com.affymetrix.genoviz.bioviews.Glyph.drawChildren(Glyph.java:169) at com.affymetrix.genoviz.bioviews.Glyph.drawTraversal(Glyph.java:129) at com.affymetrix.genoviz.widget.neoseq.WrapSequence.drawTraversal(WrapSequence.java:450) at com.affymetrix.genoviz.bioviews.Glyph.drawChildren(Glyph.java:169) at com.affymetrix.genoviz.bioviews.Glyph.drawTraversal(Glyph.java:129) at com.affymetrix.genoviz.glyph.RootGlyph.drawTraversal(RootGlyph.java:74) at com.affymetrix.genoviz.bioviews.View.normalDraw(View.java:450) at com.affymetrix.genoviz.bioviews.View.draw(View.java:359) at com.affymetrix.genoviz.bioviews.View.componentPainted(View.java:869) at com.affymetrix.genoviz.awt.NeoCanvas.postPaintEvent(NeoCanvas.java:72) at com.affymetrix.genoviz.awt.NeoCanvas.paintComponent(NeoCanvas.java:47) at javax.swing.JComponent.paint(Unknown Source) at java.awt.GraphicsCallback$PaintCallback.run(Unknown Source) at sun.awt.SunGraphicsCallback.runOneComponent(Unknown Source) at sun.awt.SunGraphicsCallback.runComponents(Unknown Source) at java.awt.Container.paint(Unknown Source) at com.affymetrix.genoviz.widget.NeoMap.paint(NeoMap.java:1235) at java.awt.GraphicsCallback$PaintCallback.run(Unknown Source) at sun.awt.SunGraphicsCallback.runOneComponent(Unknown Source) at sun.awt.SunGraphicsCallback.runComponents(Unknown Source) at java.awt.Container.paint(Unknown Source) at javax.swing.JComponent.paintChildren(Unknown Source) at javax.swing.JComponent.paint(Unknown Source) at javax.swing.JComponent.paintChildren(Unknown Source) at javax.swing.JComponent.paint(Unknown Source) at javax.swing.JLayeredPane.paint(Unknown Source) at javax.swing.JComponent.paintChildren(Unknown Source) at javax.swing.JComponent.paintToOffscreen(Unknown Source) at javax.swing.BufferStrategyPaintManager.paint(Unknown Source) at javax.swing.RepaintManager.paint(Unknown Source) at javax.swing.JComponent.paint(Unknown Source) at java.awt.GraphicsCallback$PaintCallback.run(Unknown Source) at sun.awt.SunGraphicsCallback.runOneComponent(Unknown Source) at sun.awt.SunGraphicsCallback.runComponents(Unknown Source) at java.awt.Container.paint(Unknown Source) at java.awt.Window.paint(Unknown Source) at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source) at javax.swing.RepaintManager.paintDirtyRegions(Unknown Source) at javax.swing.RepaintManager.prePaintDirtyRegions(Unknown Source) at javax.swing.RepaintManager.access$700(Unknown Source) at javax.swing.RepaintManager$ProcessingRunnable.run(Unknown Source) at java.awt.event.InvocationEvent.dispatch(Unknown Source) at java.awt.EventQueue.dispatchEventImpl(Unknown Source) at java.awt.EventQueue.access$000(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.awt.EventQueue$1.run(Unknown Source) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(Unknown Source) at java.awt.EventQueue.dispatchEvent(Unknown Source) at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source) at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.pumpEvents(Unknown Source) at java.awt.EventDispatchThread.run(Unknown Source)

Richard Linchangco (Inactive) made changes - 21/Nov/12 12:33 PM

Assignee

Richard Linchangco [ richard ]

Alyssa Gulledge [ alyssa ]

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Alyssa Gulledge (Inactive) added a comment - 26/Nov/12 8:57 AM

Bug ~~IGBC-618~~ created for the shortcut issue (seems to be more of a shortcut issue than a viewer issue)

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Alyssa Gulledge (Inactive) added a comment - 26/Nov/12 8:57 AM Bug IGBC-618 created for the shortcut issue (seems to be more of a shortcut issue than a viewer issue)

Alyssa Gulledge (Inactive) made changes - 26/Nov/12 8:57 AM

Status	Open [ 1 ]	Resolved [ 5 ]
Assignee	Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 26/Nov/12 8:57 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

People

Assignee:

Unassigned

Reporter:

Richard Linchangco (Inactive)

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Dates

Created:

15/Nov/12 8:57 AM

Updated:

26/Nov/12 8:57 AM

Resolved:

26/Nov/12 8:57 AM