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$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:680)
Attachments
Issue Links
- relates to
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BUG-656 Tabbed Panels including Selection, Restriction Enzymes
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- Closed
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Activity
Not sure if this is an issue but if I'm not zoomed in at least 1/5 in then I get the error message
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ERROR: Residues for seq not available, search aborted.
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otherwise it works fine.
Passed on 7.0.0 (11804) Mac.
could not reproduce any exception in r11078
I see no issue with Windows
I got this error:
Exception in thread "AWT-EventQueue-0" java.util.ConcurrentModificationException
at java.util.AbstractList$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."
I did not get this exception, but it might be a matter of how many restriction sites within a region