Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Critical
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Resolution: Fixed
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Labels:None
Description
Clear and run IGB at starting size!!
A thaliana, chr 1, search set to residue.
Problem 1. enter 'GATC' and search. The search shows a blank image window. After any type of resize, it shows some of the image. If you go to the data screen and load a new file (with the load function) the image resolves, but shows incorrect green flowing out of the coordinate axis. It should be a solid bar in coordinate axis.
Problem 2. If you THEN clear and re-search for the same term, it loads the sequence again (for the new file?) even though it is clearly loaded.
Revisit problem 1. After the reload, it still shows the search results incorrectly.
Attachments
Issue Links
- is blocked by
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BUG-648 Search bugs
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- Closed
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Activity
Can you reproduce this?
| Field | Original Value | New Value |
|---|---|---|
| Assignee | Hiral Vora [ hiralv ] | David Norris [ david ] |
| Assignee | David Norris [ david ] | Hiral Vora [ hiralv ] |
Fixed in r9691.
| Assignee | Hiral Vora [ hiralv ] | Alyssa Gulledge [ alyssa ] |
| Comment | [ I am running 9691, but I am still seeing the same issue... ] |
| Status | Open [ 1 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Assignee | Fuquan Wang [ fwang4 ] |
Passed on 7.0.0 (11884) Mac.
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Fuquan Wang [ fwang4 ] | |
| Resolution | Fixed [ 1 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Resolved [ 5 ] | Reopened [ 4 ] |
| Status | Reopened [ 4 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Status | Reopened [ 4 ] | Closed [ 6 ] |
| Resolution | Fixed [ 1 ] |
| Resolution | Fixed [ 1 ] | |
| Status | Closed [ 6 ] | Reopened [ 4 ] |
| Assignee | Tarun Santosh [ tkanapar ] |
| Assignee | Tarun Santosh [ tkanapar ] | Alyssa Gulledge [ alyssa ] |
Version 15385 - error:
java.lang.NullPointerException
java.util.concurrent.ExecutionException: java.lang.NullPointerException
at java.util.concurrent.FutureTask$Sync.innerGet(FutureTask.java:252)
at java.util.concurrent.FutureTask.get(FutureTask.java:111)
at javax.swing.SwingWorker.get(SwingWorker.java:602)
at com.affymetrix.igb.search.SearchView$SearchAction$1.finished(SearchView.java:166)
at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:41)
at javax.swing.SwingWorker$5.run(SwingWorker.java:737)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:832)
at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:112)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:842)
at javax.swing.Timer.fireActionPerformed(Timer.java:312)
at javax.swing.Timer$DoPostEvent.run(Timer.java:244)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:251)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:733)
at java.awt.EventQueue.access$200(EventQueue.java:103)
at java.awt.EventQueue$3.run(EventQueue.java:694)
at java.awt.EventQueue$3.run(EventQueue.java:692)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:703)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)
Caused by: java.lang.NullPointerException
at com.affymetrix.igb.view.factories.DefaultTierGlyph.addChild(DefaultTierGlyph.java:132)
at com.affymetrix.igb.IGB.searchForRegexInResidues(IGB.java:459)
at com.affymetrix.igb.IGBServiceImpl.searchForRegexInResidues(IGBServiceImpl.java:204)
at com.affymetrix.igb.search.SearchModeResidue.search(SearchModeResidue.java:240)
at com.affymetrix.igb.search.SearchModeResidue.search(SearchModeResidue.java:196)
at com.affymetrix.igb.search.SearchView$SearchAction$1.runInBackground(SearchView.java:130)
at com.affymetrix.igb.search.SearchView$SearchAction$1.runInBackground(SearchView.java:125)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:61)
at javax.swing.SwingWorker$1.call(SwingWorker.java:296)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at javax.swing.SwingWorker.run(SwingWorker.java:335)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1145)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:615)
at java.lang.Thread.run(Thread.java:724)
| Assignee | Alyssa Gulledge [ alyssa ] | Hiral Vora [ hiralv ] |
Fixed in r15386.
| Assignee | Hiral Vora [ hiralv ] | Alyssa Gulledge [ alyssa ] |
| Status | Reopened [ 4 ] | Resolved [ 5 ] |
| Assignee | Alyssa Gulledge [ alyssa ] | |
| Resolution | Fixed [ 1 ] |
| Status | Resolved [ 5 ] | Closed [ 6 ] |
Actually - it doesn't matter the starting size - it ALWAYS seems to go to a black screen after searching, although any change to window size (including thw WHOLE frame) will cause it to draw some mishmash of what should be there...