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  1. Bugs That Are No Longer Relevant
  2. OLD-111

Edit>optimize all tracks throws exception

          Details

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

            Description

            the 'all' button in annotation panel seems to workfine.

            Exception in thread "AWT-EventQueue-0" java.lang.ClassCastException: com.affymetrix.igb.view.factories.DefaultTierGlyph cannot be cast to com.affymetrix.igb.shared.GraphGlyph
            at com.affymetrix.igb.action.ZoomingRepackAction.actionPerformed(ZoomingRepackAction.java:78)
            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 com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:95)
            at java.awt.MenuItem.processActionEvent(MenuItem.java:650)
            at java.awt.MenuItem.processEvent(MenuItem.java:609)
            at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:343)
            at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:331)
            at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:707)
            at java.awt.EventQueue.access$400(EventQueue.java:82)
            at java.awt.EventQueue$2.run(EventQueue.java:663)
            at java.awt.EventQueue$2.run(EventQueue.java:661)
            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$3.run(EventQueue.java:677)
            at java.awt.EventQueue$3.run(EventQueue.java:675)
            at java.security.AccessController.doPrivileged(Native Method)
            at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
            at java.awt.EventQueue.dispatchEvent(EventQueue.java:674)
            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)

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                alyssa Alyssa Gulledge (Inactive) created issue -
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                hiralv Hiral Vora (Inactive) added a comment -

                Fixed in r13060.

                Show
                hiralv Hiral Vora (Inactive) added a comment - Fixed in r13060.
                hiralv Hiral Vora (Inactive) made changes -
                Field Original Value New Value
                Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
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                alyssa Alyssa Gulledge (Inactive) added a comment -

                Still some misbehavior... load A. thal, go to this range chr5 : 3,815,759 - 3,825,281. Load RNA-seq>lab>mixed>LL, both tracks. Make all single track. You should see a single model gene and a 4 high model gene in TAIR10 track, and each LL track has a stack of 3 high (in different spots). Do the following (always return tracks to Max depth 10 via the annotation tab)

                1) if you select all tracks and use the 'all' button in the Annotations tab, the track labels become unattached, and jump up showing black space, even though the tracks resize properly.

                2) if you select all tracks and use the 'optimal' option in the Edit menu, the track labels AND the tracks jump up showing black space, even though the tracks resize.

                3) if you select all tracks and right-click menu > Adj Max Expand > 'optimal' button, the track labels become unattached, and jump up showing black space, even though the tracks resize properly (as with annotation tab button).

                4) if you select all tracks and right-click menu > Adj Max Expand > put in '4' and go, the track labels become unattached, and jump up showing black space, even though the tracks resize properly (as with annotation tab button).

                5) if you select all tracks and enter 4 in the box, hit go button in the Annotations tab, and here everything works.

                Show
                alyssa Alyssa Gulledge (Inactive) added a comment - Still some misbehavior... load A. thal, go to this range chr5 : 3,815,759 - 3,825,281. Load RNA-seq>lab>mixed>LL, both tracks. Make all single track. You should see a single model gene and a 4 high model gene in TAIR10 track, and each LL track has a stack of 3 high (in different spots). Do the following (always return tracks to Max depth 10 via the annotation tab) 1) if you select all tracks and use the 'all' button in the Annotations tab, the track labels become unattached, and jump up showing black space, even though the tracks resize properly. 2) if you select all tracks and use the 'optimal' option in the Edit menu, the track labels AND the tracks jump up showing black space, even though the tracks resize. 3) if you select all tracks and right-click menu > Adj Max Expand > 'optimal' button, the track labels become unattached, and jump up showing black space, even though the tracks resize properly (as with annotation tab button). 4) if you select all tracks and right-click menu > Adj Max Expand > put in '4' and go, the track labels become unattached, and jump up showing black space, even though the tracks resize properly (as with annotation tab button). 5) if you select all tracks and enter 4 in the box, hit go button in the Annotations tab, and here everything works.
                alyssa Alyssa Gulledge (Inactive) made changes -
                Assignee Alyssa Gulledge [ alyssa ] Hiral Vora [ hiralv ]
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                hiralv Hiral Vora (Inactive) added a comment -

                Could not reproduce any.

                Show
                hiralv Hiral Vora (Inactive) added a comment - Could not reproduce any.
                hiralv Hiral Vora (Inactive) made changes -
                Assignee Hiral Vora [ hiralv ] 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-542 BUG-568
                richard Richard Linchangco (Inactive) made changes -
                Resolution Fixed [ 1 ]
                Status Closed [ 6 ] Reopened [ 4 ]
                alyssa Alyssa Gulledge (Inactive) made changes -
                Link This issue relates to BUG-658 [ BUG-658 ]
                alyssa Alyssa Gulledge (Inactive) made changes -
                Project Bug Repository [ 10030 ] Bugs That Are No Longer Relevant [ 10041 ]
                Key BUG-568 OLD-111
                alyssa Alyssa Gulledge (Inactive) made changes -
                Link This issue relates to BUG-658 [ BUG-658 ]
                hiralv Hiral Vora (Inactive) made changes -
                Status Reopened [ 4 ] Closed [ 6 ]
                Resolution Fixed [ 1 ]

                  People

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

                    • Created:
                      Updated:
                      Resolved: