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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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                hiralv Hiral Vora (Inactive) added a comment -

                Could not reproduce any.

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                hiralv Hiral Vora (Inactive) added a comment - Could not reproduce any.
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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.
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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.

                  People

                  • Assignee:
                    Unassigned
                    Reporter:
                    alyssa Alyssa Gulledge (Inactive)
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                    • Created:
                      Updated:
                      Resolved: