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  1. Bug Repository
  2. BUG-497

set color by score range is broken

          Details

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

            Description

            also, it throws an npe:

            Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 256
            at com.affymetrix.igb.tiers.TrackStyle.getScoreColor(TrackStyle.java:1072)
            at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.getSymColor(AnnotationGlyphFactory.java:362)
            at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.determineGlyph(AnnotationGlyphFactory.java:220)
            at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.determinePGlyph(AnnotationGlyphFactory.java:176)
            at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.addToTier(AnnotationGlyphFactory.java:158)
            at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.addLeafsToTier(AnnotationGlyphFactory.java:121)
            at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.addLeafsToTier(AnnotationGlyphFactory.java:118)
            at com.affymetrix.igb.viewmode.AnnotationGlyphFactory.getViewModeGlyph(AnnotationGlyphFactory.java:570)
            at com.affymetrix.igb.shared.TierGlyph.setViewModeGlyph(TierGlyph.java:103)
            at com.affymetrix.igb.shared.TierGlyph.setInfo(TierGlyph.java:472)
            at com.affymetrix.igb.view.TrackView.addAnnotationGlyphs(TrackView.java:232)
            at com.affymetrix.igb.view.TrackView.addTracks(TrackView.java:153)
            at com.affymetrix.igb.view.SeqMapView.addAnnotationTracks(SeqMapView.java:1246)
            at com.affymetrix.igb.view.SeqMapView.addGlyphs(SeqMapView.java:988)
            at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:805)
            at com.affymetrix.igb.view.SeqMapView.updatePanel(SeqMapView.java:2721)
            at com.affymetrix.igb.action.SeqMapViewActionA.refreshMap(SeqMapViewActionA.java:88)
            at com.affymetrix.igb.action.SetColorByScoreAction.updateColorByScore(SetColorByScoreAction.java:71)
            at com.affymetrix.igb.action.SetColorByScoreAction.actionPerformed(SetColorByScoreAction.java:77)
            at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)
            at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)
            at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
            at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
            at javax.swing.AbstractButton.doClick(AbstractButton.java:389)
            at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)
            at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)
            at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)
            at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
            at java.awt.Component.processMouseEvent(Component.java:6375)
            at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
            at java.awt.Component.processEvent(Component.java:6140)
            at java.awt.Container.processEvent(Container.java:2083)
            at java.awt.Component.dispatchEventImpl(Component.java:4737)
            at java.awt.Container.dispatchEventImpl(Container.java:2141)
            at java.awt.Component.dispatchEvent(Component.java:4565)
            at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4619)
            at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4280)
            at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4210)
            at java.awt.Container.dispatchEventImpl(Container.java:2127)
            at java.awt.Window.dispatchEventImpl(Window.java:2482)
            at java.awt.Component.dispatchEvent(Component.java:4565)
            at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:684)
            at java.awt.EventQueue.access$000(EventQueue.java:85)
            at java.awt.EventQueue$1.run(EventQueue.java:643)
            at java.awt.EventQueue$1.run(EventQueue.java:641)
            at java.security.AccessController.doPrivileged(Native Method)
            at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
            at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
            at java.awt.EventQueue$2.run(EventQueue.java:657)
            at java.awt.EventQueue$2.run(EventQueue.java:655)
            at java.security.AccessController.doPrivileged(Native Method)
            at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
            at java.awt.EventQueue.dispatchEvent(EventQueue.java:654)
            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.lang.NullPointerException
            at com.affymetrix.genoviz.bioviews.Scene.removeGlyph(Scene.java:391)
            at com.affymetrix.genoviz.widget.NeoMap.removeItem(NeoMap.java:1021)
            at com.affymetrix.igb.tiers.AffyTieredMap.removeItem(AffyTieredMap.java:277)
            at com.affymetrix.igb.tiers.AffyTieredMap.removeTier(AffyTieredMap.java:296)
            at com.affymetrix.igb.tiers.AffyLabelledTierMap.removeTier(AffyLabelledTierMap.java:251)
            at com.affymetrix.igb.view.SeqMapView.copyMapTierGlyphs(SeqMapView.java:973)
            at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:779)
            at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:727)
            at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:713)
            at com.affymetrix.igb.view.SeqMapView.seqSelectionChanged(SeqMapView.java:2370)
            at com.affymetrix.genometryImpl.GenometryModel.fireSeqSelectionEvent(GenometryModel.java:208)
            at com.affymetrix.genometryImpl.GenometryModel.setSelectedSeq(GenometryModel.java:188)
            at com.affymetrix.genometryImpl.GenometryModel.setSelectedSeq(GenometryModel.java:171)
            at com.affymetrix.igb.view.SeqGroupView.valueChanged(SeqGroupView.java:348)
            at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:167)
            at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:137)
            at javax.swing.DefaultListSelectionModel.setValueIsAdjusting(DefaultListSelectionModel.java:668)
            at com.jidesoft.grid.JideTable$24.setValueIsAdjusting(Unknown Source)
            at javax.swing.plaf.basic.BasicTableUI$Handler.setValueIsAdjusting(BasicTableUI.java:923)
            at javax.swing.plaf.basic.BasicTableUI$Handler.mouseReleased(BasicTableUI.java:1136)
            at java.awt.AWTEventMulticaster.mouseReleased(AWTEventMulticaster.java:272)
            at java.awt.Component.processMouseEvent(Component.java:6375)
            at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
            at java.awt.Component.processEvent(Component.java:6140)
            at java.awt.Container.processEvent(Container.java:2083)
            at java.awt.Component.dispatchEventImpl(Component.java:4737)
            at java.awt.Container.dispatchEventImpl(Container.java:2141)
            at java.awt.Component.dispatchEvent(Component.java:4565)
            at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4619)
            at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4280)
            at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4210)
            at java.awt.Container.dispatchEventImpl(Container.java:2127)
            at java.awt.Window.dispatchEventImpl(Window.java:2482)
            at java.awt.Component.dispatchEvent(Component.java:4565)
            at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:684)
            at java.awt.EventQueue.access$000(EventQueue.java:85)
            at java.awt.EventQueue$1.run(EventQueue.java:643)
            at java.awt.EventQueue$1.run(EventQueue.java:641)
            at java.security.AccessController.doPrivileged(Native Method)
            at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
            at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
            at java.awt.EventQueue$2.run(EventQueue.java:657)
            at java.awt.EventQueue$2.run(EventQueue.java:655)
            at java.security.AccessController.doPrivileged(Native Method)
            at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
            at java.awt.EventQueue.dispatchEvent(EventQueue.java:654)
            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)

              Attachments

                Issue Links

                relates to

                Task - A task that needs to be done. BUG-682 Style elements

                • Blocker - Blocks development and/or testing work, production could not run.
                • Closed

                  Activity

                  Ascending order - Click to sort in descending order
                  alyssa Alyssa Gulledge (Inactive) created issue -
                  lfrohman Lance Frohman (Inactive) made changes -
                  Field Original Value New Value
                  Assignee Hiral Vora [ hiralv ] Lance Frohman [ lfrohman ]
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                  lfrohman Lance Frohman (Inactive) added a comment -

                  Please give the steps to reproduce.

                  Show
                  lfrohman Lance Frohman (Inactive) added a comment - Please give the steps to reproduce.
                  Hide
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                  lfrohman Lance Frohman (Inactive) added a comment - - edited
                  • open A. thal.
                  • Go down to our labs data, open one of the junction files. {IGB Quickload > RNA-Seq > Loraine Lab > Mixed Cold > Juncs > Control, junctions}
                  • Zoom in to one or two genes {chr1 : 11,460,272 - 11,460,840}

                    until you can see the number range (the score should be showing over each glyph (if not, set the glyph label to score in the track adjuster tab).

                  • {Load Data button}
                  • Right click track, select Change... then select Set range of color by score.
                  • Set the upper score to be higher than the scores you see (ie, if 45 is the highest score, use 50). {90}
                  • THEN apply the function (right menu>change>color by score) - main view freaks out, and OutofBounds shows up.
                  Show
                  lfrohman Lance Frohman (Inactive) added a comment - - edited open A. thal. Go down to our labs data, open one of the junction files. {IGB Quickload > RNA-Seq > Loraine Lab > Mixed Cold > Juncs > Control, junctions} Zoom in to one or two genes {chr1 : 11,460,272 - 11,460,840} until you can see the number range (the score should be showing over each glyph (if not, set the glyph label to score in the track adjuster tab). {Load Data button} Right click track, select Change... then select Set range of color by score. Set the upper score to be higher than the scores you see (ie, if 45 is the highest score, use 50). {90} THEN apply the function (right menu>change>color by score) - main view freaks out, and OutofBounds shows up.
                  Hide
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                  lfrohman Lance Frohman (Inactive) added a comment -

                  fixed
                  rev 12205

                  Show
                  lfrohman Lance Frohman (Inactive) added a comment - fixed rev 12205
                  lfrohman Lance Frohman (Inactive) made changes -
                  Assignee Lance Frohman [ lfrohman ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Open [ 1 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Project IGB 7.0 [ 10140 ] Bug Repository [ 10030 ]
                  Key IGBC-388 BUG-497
                  richard Richard Linchangco (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-682 [ BUG-682 ]
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  The function works, but should only accept integers, not decimals.

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - The function works, but should only accept integers, not decimals.
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Will score always be integer?

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Will score always be integer?
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  I guess it is possible that it will not be... so I guess it should be left alone.

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - I guess it is possible that it will not be... so I guess it should be left alone.
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]

                    People

                    • Assignee:
                      Unassigned
                      Reporter:
                      alyssa Alyssa Gulledge (Inactive)
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                      Dates

                      • Created:
                        Updated:
                        Resolved: