Details
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Type:
Bug
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Fixed
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Labels:None
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Environment:
Mac OS
Description
When I tried to select an enzymes in the Restriction sites tab and clicked on Map sites button the following exception is thrown in the console
Exception in thread "pool-13-thread-2" java.lang.OutOfMemoryError: Java heap space
at java.nio.HeapByteBuffer.<init>(HeapByteBuffer.java:39)
at java.nio.ByteBuffer.allocate(ByteBuffer.java:312)
at com.affymetrix.genometryImpl.util.TwoBitIterator.parse(TwoBitIterator.java:196)
at com.affymetrix.genometryImpl.util.TwoBitIterator.substring(TwoBitIterator.java:176)
at com.affymetrix.genometryImpl.symloader.TwoBit.getRegionResidues(TwoBit.java:88)
at com.affymetrix.igb.general.ResidueLoading.GetQuickLoadResidues(ResidueLoading.java:219)
at com.affymetrix.igb.general.ResidueLoading.getQuickLoadResidues(ResidueLoading.java:171)
at com.affymetrix.igb.general.ResidueLoading.getResidues(ResidueLoading.java:86)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadResidues(GeneralLoadUtils.java:992)
at com.affymetrix.igb.view.load.GeneralLoadView.loadResidues(GeneralLoadView.java:230)
at com.affymetrix.igb.view.load.GeneralLoadView.loadResidues(GeneralLoadView.java:223)
at com.affymetrix.igb.action.LoadResidueAction.actionPerformed(LoadResidueAction.java:75)
at com.affymetrix.igb.restrictions.RestrictionControlView$GlyphifyMatchesThread.run(RestrictionControlView.java:261)
at java.lang.Thread.run(Thread.java:680)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:680)
Attachments
Issue Links
- relates to
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BUG-656 Tabbed Panels including Selection, Restriction Enzymes
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- Closed
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Activity
I see no issue with Windows
could not reproduce any exception in r11078
Passed on 7.0.0 (11804) Mac.
Not sure if this is an issue but if I'm not zoomed in at least 1/5 in then I get the error message
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ERROR: Residues for seq not available, search aborted.
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otherwise it works fine.
I did not get this exception, but it might be a matter of how many restriction sites within a region
I got this error:
Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException
at java.util.AbstractList$Itr.checkForComodification(AbstractList.java:372)
at java.util.AbstractList$ListItr.set(AbstractList.java:409)
at java.util.Collections.sort(Collections.java:163)
at com.affymetrix.igb.shared.TierGlyph.sortChildren(TierGlyph.java:254)
at com.affymetrix.igb.shared.TierGlyph.initForSearching(TierGlyph.java:140)
at com.affymetrix.igb.shared.TierGlyph.pack(TierGlyph.java:321)
at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:186)
at com.affymetrix.igb.tiers.AffyTieredMap.packTiers(AffyTieredMap.java:166)
at com.affymetrix.igb.tiers.AffyLabelledTierMap.packTiers(AffyLabelledTierMap.java:144)
at com.affymetrix.igb.tiers.AffyTieredMap.repack(AffyTieredMap.java:159)
at com.affymetrix.igb.view.SeqMapView.setAnnotatedSeq(SeqMapView.java:728)
at com.affymetrix.igb.action.LoadResidueAction$1.run(LoadResidueAction.java:85)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677)
at java.awt.EventQueue.access$000(EventQueue.java:85)
at java.awt.EventQueue$1.run(EventQueue.java:638)
at java.awt.EventQueue$1.run(EventQueue.java:636)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:647)
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)
To reproduce, load A. thal, chr1. In RE select AflIII, AscI, Bce83I and BsePI. Then select map. sequence loads fine, but it freaks out because there are SOOOOO many hits by those 4 enzymes. Perhaps some kind of warning "Too many hits in the selected region. Please chose a smaller area and try again."