Mac v9938

Sliced view tab sub-panel

-Horizantal slider for zooming in and out works accurately
-Vertical slider for zooming in and out works accurately
-Slice by selection checkbox works accurately
-Move tool works fine
-select tool works fine
-Analyze ORFs checkbox works fine
-Min ORF length slider also works fine.

Sliced buffer text field

-When I tried to enter the alphabets instead of numbers it just throws an exception in the console but does not alert the user that he has entered the wrong data Reported as a bug (IGBB-266)

Windows v9994

• Horizontal and Vertical zoom
• Rt click options
• Collapse
• Center at zoom stripe
• Scroll bars
• Coordinate range text field
• Select & move tools
• Activate analyze ORFs
  • Colors do not auto update (IGBB-275)
• Min ORF length
• Slice by selection
• Slice buffer text field
  • Entering letters OR digit longer than 10 digits throws error (IGBB-266)

Passed Windows v11840

• Activate analyze ORFs
  • Colors are hard to see (Improvement reported and moved to repository BUG-411)

V.13782, Mac, Java 1.7.0_10

FAILED please see sections labeled thus

'Sliced View' Tab:

Chromosome and nucleotide range/Search field : PASSED

• Located in top left corner of tab, displaying what is selected
  • Nucleotide range of window dependent on if a single read section is clicked (Default of 0-75 bases when 'Slice Buffer' is at default 100 with 'Analyze ORFs' inactive)
  • If multiple reads are selected, the range varies to thousands
• Inputting a different chromosome and range in the format: chr# : 0-# will load that entire chromosome into the main viewer and blank the 'Sliced View' viewer
• Inputting a range of 0-1 will default to a range of 0-65 nucleotides when 'Slice Buffer' is at default 100 with 'Analyze ORFs' inactive
• Inputting any symbols, letters, or numbers begins a search through the sequences for that query
  • A progress bar and the number of times the query is found is displayed on the bottom left of the main window

'Select'/'Move' : PASSED

• Perform same functions as in the main viewer
• 'Select' will choose an exon, intron, or whole read or gene model
• 'Move', when the viewer is zoomed in, will allow user to shift viewer window left and right.

Zoom (Horizontal and Vertical) : PASSED

• Horizontal zoom will zoom in when slider is moved from left to right and vice versa
  • Zoom centers window on selected nucleotide region
• Vertical zoom will zoom in when slider is moved from top to bottom and vice versa
  • Zoom centers on selected exon, intron, read, or gene model

'Slice by Selection' : PASSED

• Checked by default so when a read or reads or gene models are selected in the main viewer, they are centered and loaded into the 'Sliced View' viewer
• Unchecking the 'Slice by Selection' option means when selecting a read in the main viewer, the 'Sliced View' viewer will not navigate and fixate on that read.

'Slice Buffer' : FAILED

• Default for 'Slice Buffer' is set to 100
• Letters and symbols are not recognized as input and are not allowed to be put in the text field
• Numerically the 'Slice Buffer' will do nothing if there are more than 10 digits input
  • Otherwise 'Slice Buffer' will reload with the number range selected.
  • Will act the same as the main viewer when a 'Slice Buffer' larger than the size of the genome is selected
• When 'Analyze ORFs' is checked, the 'Slice Buffer' is set to 0, creating a default span size for 0-75 nucleotides.
• Unchecking 'Analyze ORFs' will revert the 'Slice Buffer' back to whatever it was set to prior to checking 'Analyze ORFs'
• If 'Analyze ORFs' is checked and there is no number in 'Slice Buffer' an Exception is thrown in the Java console and the ORF tracks do not appear in the 'Sliced View' viewer. (SEE EXCEPTION 1 below)

'Analyze ORFs' : FAILED

• Default state is unchecked
• Checking 'Analyze ORFs' brings up two tracks on top and bottom of the 'Sliced View' Tab in a dark grey
  • ORF Tracks display STOP codons and 'Dynamic ORFs'
    • Defaults are red for STOP and green for 'Dynamic ORFs' (lines)
    • Colors for ORFs and their background can be changed from 'Preferences' > 'Other Options' > 'ORF Analyzer (Sliced View tab)'
• 'Min ORF Length:' is a slider next to 'Analyze ORFs' PASSED
  • Slide left to right to increase minimum ORF size and vice versa
    • Absolute minimum is 10 and absolute maximum is 500
  • If minimum is decreased, more green 'Dynamic ORFs' lines will be drawn in ORF tracks
• Issue when loading new data and having 'Analyze ORFs' active
  • ORF tracks disappear and must inactivate and reactivate in order to bring them back (noted in IGBC-877)

Resizing the 'Sliced View' Tab : FAILED

• Resizing the 'Sliced View' Tab to a smaller size and then resizing it again to a larger size (performed by clicking the area directly above all tabs) causes vertical zooming
  • Vertical zoom does not revert back when resizing to a larger size, giving the impression that tracks have disappeared. This is unexpected behavior
    • Preferably the vertical zoom should remain proportional to the 'Sliced View' tab window size.

Exceptions
Exception 1

Exception in thread "AWT-EventQueue-0" java.lang.NumberFormatException: For input string: ""
at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
at java.lang.Integer.parseInt(Integer.java:504)
at java.lang.Integer.parseInt(Integer.java:527)
at com.affymetrix.igb.view.OrfAnalyzer.actionPerformed(OrfAnalyzer.java:117)
at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018)
at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341)
at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402)
at javax.swing.JToggleButton$ToggleButtonModel.setPressed(JToggleButton.java:308)
at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:252)
at java.awt.Component.processMouseEvent(Component.java:6505)
at javax.swing.JComponent.processMouseEvent(JComponent.java:3321)
at java.awt.Component.processEvent(Component.java:6270)
at java.awt.Container.processEvent(Container.java:2229)
at java.awt.Component.dispatchEventImpl(Component.java:4861)
at java.awt.Container.dispatchEventImpl(Container.java:2287)
at java.awt.Component.dispatchEvent(Component.java:4687)
at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492)
at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422)
at java.awt.Container.dispatchEventImpl(Container.java:2273)
at java.awt.Window.dispatchEventImpl(Window.java:2719)
at java.awt.Component.dispatchEvent(Component.java:4687)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:723)
at java.awt.EventQueue.access$200(EventQueue.java:103)
at java.awt.EventQueue$3.run(EventQueue.java:682)
at java.awt.EventQueue$3.run(EventQueue.java:680)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
at java.awt.EventQueue$4.run(EventQueue.java:696)
at java.awt.EventQueue$4.run(EventQueue.java:694)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:693)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)

Fixed exception in r13838.