[BUG-343] Exception on Console by Map sites button click in Restriction sites tab - JIRA UNCC

Details

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

BUG-656 Tabbed Panels including Selection, Restriction Enzymes

Closed

Activity

Ascending order - Click to sort in descending order

Anuj Puram (Inactive) created issue - 27/Jan/12 9:28 AM

Anuj Puram (Inactive) made changes - 27/Jan/12 9:28 AM

Field	Original Value	New Value
Assignee		Alyssa Gulledge [ alyssa ]

Anuj Puram (Inactive) made changes - 27/Jan/12 9:30 AM

Summary	Exception on Console by Multiple selection of residue in Restriction sites tab	Exception on Console by Multiple selection of enzymes in Restriction sites tab
Description	When I tried to select a lot of residues 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$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:680)	When I tried to select a lot of enzymes in the Restriction sites tab and clicked on Map sites button the following exception is thrown in the console Exception in thread "pool-13-thread-2" java.lang.OutOfMemoryError: Java heap space at java.nio.HeapByteBuffer.<init>(HeapByteBuffer.java:39) at java.nio.ByteBuffer.allocate(ByteBuffer.java:312) at com.affymetrix.genometryImpl.util.TwoBitIterator.parse(TwoBitIterator.java:196) at com.affymetrix.genometryImpl.util.TwoBitIterator.substring(TwoBitIterator.java:176) at com.affymetrix.genometryImpl.symloader.TwoBit.getRegionResidues(TwoBit.java:88) at com.affymetrix.igb.general.ResidueLoading.GetQuickLoadResidues(ResidueLoading.java:219) at com.affymetrix.igb.general.ResidueLoading.getQuickLoadResidues(ResidueLoading.java:171) at com.affymetrix.igb.general.ResidueLoading.getResidues(ResidueLoading.java:86) at com.affymetrix.igb.view.load.GeneralLoadUtils.loadResidues(GeneralLoadUtils.java:992) at com.affymetrix.igb.view.load.GeneralLoadView.loadResidues(GeneralLoadView.java:230) at com.affymetrix.igb.view.load.GeneralLoadView.loadResidues(GeneralLoadView.java:223) at com.affymetrix.igb.action.LoadResidueAction.actionPerformed(LoadResidueAction.java:75) at com.affymetrix.igb.restrictions.RestrictionControlView$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)

Anuj Puram (Inactive) made changes - 27/Jan/12 9:32 AM

Summary	Exception on Console by Multiple selection of enzymes in Restriction sites tab	Exception on Console by Map sites button click in Restriction sites tab
Description	When I tried to select a lot of 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$Worker.run(ThreadPoolExecutor.java:908) at java.lang.Thread.run(Thread.java:680)	When I tried to select an enzymes in the Restriction sites tab and clicked on Map sites button the following exception is thrown in the console Exception in thread "pool-13-thread-2" java.lang.OutOfMemoryError: Java heap space at java.nio.HeapByteBuffer.<init>(HeapByteBuffer.java:39) at java.nio.ByteBuffer.allocate(ByteBuffer.java:312) at com.affymetrix.genometryImpl.util.TwoBitIterator.parse(TwoBitIterator.java:196) at com.affymetrix.genometryImpl.util.TwoBitIterator.substring(TwoBitIterator.java:176) at com.affymetrix.genometryImpl.symloader.TwoBit.getRegionResidues(TwoBit.java:88) at com.affymetrix.igb.general.ResidueLoading.GetQuickLoadResidues(ResidueLoading.java:219) at com.affymetrix.igb.general.ResidueLoading.getQuickLoadResidues(ResidueLoading.java:171) at com.affymetrix.igb.general.ResidueLoading.getResidues(ResidueLoading.java:86) at com.affymetrix.igb.view.load.GeneralLoadUtils.loadResidues(GeneralLoadUtils.java:992) at com.affymetrix.igb.view.load.GeneralLoadView.loadResidues(GeneralLoadView.java:230) at com.affymetrix.igb.view.load.GeneralLoadView.loadResidues(GeneralLoadView.java:223) at com.affymetrix.igb.action.LoadResidueAction.actionPerformed(LoadResidueAction.java:75) at com.affymetrix.igb.restrictions.RestrictionControlView$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)

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Alyssa Gulledge (Inactive) added a comment - 30/Jan/12 5:50 AM

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."

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Alyssa Gulledge (Inactive) added a comment - 30/Jan/12 5:50 AM 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."

Alyssa Gulledge (Inactive) made changes - 30/Jan/12 5:50 AM

Assignee

Alyssa Gulledge [ alyssa ]

Hiral Vora [ hiralv ]

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Katharine Kubiak (Inactive) added a comment - 31/Jan/12 12:07 PM

I see no issue with Windows

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Katharine Kubiak (Inactive) added a comment - 31/Jan/12 12:07 PM I see no issue with Windows

Hiral Vora (Inactive) made changes - 01/Feb/12 7:05 AM

Project	IGB 6.7 [ 10040 ]	IGB 7.0 [ 10140 ]
Key	~~IGBB-282~~	~~IGBC-54~~

Hiral Vora (Inactive) made changes - 01/Feb/12 7:05 AM

Assignee

Hiral Vora [ hiralv ]

Hiral Vora (Inactive) made changes - 13/Apr/12 7:09 AM

Assignee

Anuj Puram [ anuj ]

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Anuj Puram (Inactive) added a comment - 13/Apr/12 7:17 AM

could not reproduce any exception in r11078

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Anuj Puram (Inactive) added a comment - 13/Apr/12 7:17 AM could not reproduce any exception in r11078

Anuj Puram (Inactive) made changes - 13/Apr/12 7:17 AM

Assignee

Anuj Puram [ anuj ]

Alyssa Gulledge [ alyssa ]

Alyssa Gulledge (Inactive) made changes - 18/Apr/12 7:16 AM

Status	Open [ 1 ]	Resolved [ 5 ]
Assignee	Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 18/Apr/12 7:16 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

Alyssa Gulledge (Inactive) made changes - 18/Apr/12 7:17 AM

Project	IGB 7.0 [ 10140 ]	Bug Repository [ 10030 ]
Key	~~IGBC-54~~	~~BUG-343~~

Fuquan Wang (Inactive) made changes - 05/Jun/12 9:57 AM

Resolution	Fixed [ 1 ]
Status	Closed [ 6 ]	Reopened [ 4 ]
Assignee		Fuquan Wang [ fwang4 ]

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Fuquan Wang (Inactive) added a comment - 05/Jun/12 10:04 AM

Passed on 7.0.0 (11804) Mac.

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Fuquan Wang (Inactive) added a comment - 05/Jun/12 10:04 AM Passed on 7.0.0 (11804) Mac.

Fuquan Wang (Inactive) made changes - 05/Jun/12 10:04 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee	Fuquan Wang [ fwang4 ]
Resolution		Fixed [ 1 ]

Richard Linchangco (Inactive) made changes - 13/Nov/12 9:43 AM

Resolution	Fixed [ 1 ]
Status	Resolved [ 5 ]	Reopened [ 4 ]

Alyssa Gulledge (Inactive) made changes - 12/Dec/12 9:55 AM

Link

This issue relates to ~~BUG-656~~ [ ~~BUG-656~~ ]

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darius added a comment - 14/Dec/12 5:24 AM

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
-------------------------------------------------------
ERROR: Residues for seq not available, search aborted.
-------------------------------------------------------
otherwise it works fine.

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darius added a comment - 14/Dec/12 5:24 AM 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 ------------------------------------------------------- ERROR: Residues for seq not available, search aborted. ------------------------------------------------------- otherwise it works fine.

darius made changes - 14/Dec/12 5:24 AM

Assignee

Alyssa Gulledge [ alyssa ]

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Alyssa Gulledge (Inactive) added a comment - 17/Dec/12 4:21 AM

I did not get this exception, but it might be a matter of how many restriction sites within a region

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Alyssa Gulledge (Inactive) added a comment - 17/Dec/12 4:21 AM I did not get this exception, but it might be a matter of how many restriction sites within a region

Alyssa Gulledge (Inactive) made changes - 17/Dec/12 4:21 AM

Status	Reopened [ 4 ]	Resolved [ 5 ]
Assignee	Alyssa Gulledge [ alyssa ]
Resolution		Fixed [ 1 ]

Alyssa Gulledge (Inactive) made changes - 17/Dec/12 4:21 AM

Status

Resolved [ 5 ]

Closed [ 6 ]

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Reporter:

Anuj Puram (Inactive)

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Dates

Created:

27/Jan/12 9:28 AM

Updated:

17/Dec/12 4:21 AM

Resolved:

17/Dec/12 4:21 AM