Deleting graphs throws NPE

should be fixed
this was difficult to track down since it
was intermittent. I believe what was happening was that because there are multiple
threads to delete and draw tracks, IGB was drawing the deleted track before it was set to not visible.

Still seeing it in v.11822

Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 1
at com.affymetrix.genometryImpl.symmetry.GraphSym.getGraphYCoord(GraphSym.java:270)
at com.affymetrix.genometryImpl.symmetry.GraphSym.copyGraphYCoords(GraphSym.java:283)
at com.affymetrix.genometryImpl.symmetry.GraphSym.normalizeGraphYCoords(GraphSym.java:293)
at com.affymetrix.igb.shared.AbstractGraphGlyph.copyYCoords(AbstractGraphGlyph.java:143)
at com.affymetrix.igb.shared.GraphGlyphUtils.getPercents2Scores(GraphGlyphUtils.java:139)
at com.affymetrix.igb.shared.GraphGlyphUtils.getPercentForValue(GraphGlyphUtils.java:166)
at com.affymetrix.igb.trackAdjuster.GraphVisibleBoundsSetter.initPercents(GraphVisibleBoundsSetter.java:309)
at com.affymetrix.igb.trackAdjuster.GraphVisibleBoundsSetter.setGraphs(GraphVisibleBoundsSetter.java:189)
at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.resetGraphAndRangePanel(TrackAdjusterTab.java:499)
at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.refreshSelection(TrackAdjusterTab.java:310)
at com.affymetrix.igb.trackAdjuster.TrackAdjusterTab.trackstylePropertyChanged(TrackAdjusterTab.java:808)
at com.affymetrix.igb.shared.TrackstylePropertyMonitor.firePropertyChanged(TrackstylePropertyMonitor.java:47)
at com.affymetrix.igb.shared.TrackstylePropertyMonitor.tableChanged(TrackstylePropertyMonitor.java:29)
at javax.swing.table.AbstractTableModel.fireTableChanged(AbstractTableModel.java:280)
at javax.swing.table.AbstractTableModel.fireTableDataChanged(AbstractTableModel.java:182)
at com.affymetrix.igb.view.load.DataManagementTableModel.createVirtualFeatures(DataManagementTableModel.java:91)
at com.affymetrix.igb.view.load.GeneralLoadView$5.run(GeneralLoadView.java:448)
at com.affymetrix.genometryImpl.util.ThreadUtils.runOnEventQueue(ThreadUtils.java:29)
at com.affymetrix.igb.view.load.GeneralLoadView.refreshDataManagementTable(GeneralLoadView.java:444)
at com.affymetrix.igb.view.load.GeneralLoadView.refreshDataManagementView(GeneralLoadView.java:456)
at com.affymetrix.igb.view.load.GeneralLoadView$8.finished(GeneralLoadView.java:676)
at com.affymetrix.genometryImpl.thread.CThreadWorker.done(CThreadWorker.java:41)
at javax.swing.SwingWorker$5.run(SwingWorker.java:717)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.run(SwingWorker.java:814)
at sun.swing.AccumulativeRunnable.run(AccumulativeRunnable.java:95)
at javax.swing.SwingWorker$DoSubmitAccumulativeRunnable.actionPerformed(SwingWorker.java:824)
at javax.swing.Timer.fireActionPerformed(Timer.java:291)
at javax.swing.Timer$DoPostEvent.run(Timer.java:221)
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)

left something out of last fix
should be fixed now

Katie - I really need you to beat on this one... I have loaded graphs, then moved them, then made depth graphs, and sometimes after all of that deleting throws the error again. See if you can get it to show up...

I kept getting the issue below, but now Im not getting any issues

Are you using RNA-Seq > Loraine Lab > Mixed Cold? Because it seems that there is an issue with the 'Cold' treatments for both the READS and the GRAPHS every time I try to load I get an exception, but not with 'Control' treatments.

java.net.BindException: Address already in use: connect
at java.net.PlainSocketImpl.socketConnect(Native Method)
at java.net.PlainSocketImpl.doConnect(Unknown Source)
at java.net.PlainSocketImpl.connectToAddress(Unknown Source)
at java.net.PlainSocketImpl.connect(Unknown Source)
at java.net.SocksSocketImpl.connect(Unknown Source)
at java.net.Socket.connect(Unknown Source)
at java.net.Socket.connect(Unknown Source)
at sun.net.NetworkClient.doConnect(Unknown Source)
at sun.net.www.http.HttpClient.openServer(Unknown Source)
at sun.net.www.http.HttpClient.openServer(Unknown Source)
at sun.net.www.http.HttpClient.<init>(Unknown Source)
at sun.net.www.http.HttpClient.New(Unknown Source)
at sun.net.www.http.HttpClient.New(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.plainConnect(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.connect(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
at org.broad.tribble.util.HTTPHelper.openInputStreamForRange(HTTPHelper.java:99)
at org.broad.tribble.util.SeekableHTTPStream.read(SeekableHTTPStream.java:129)
at org.broad.tribble.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:321)
at org.broad.tribble.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:309)
at org.broad.tribble.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:284)
at org.broad.tribble.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:96)
at org.broad.tribble.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:130)
at org.broad.tribble.source.tabix.TabixReader.readLine(TabixReader.java:149)
at org.broad.tribble.source.tabix.TabixReader$Iterator.next(TabixReader.java:341)
at org.broad.tribble.source.tabix.TabixLineReader$TabixIteratorToLineReader.readLine(TabixLineReader.java:111)
at com.affymetrix.genometryImpl.symloader.Wiggle$2.next(Wiggle.java:196)
at com.affymetrix.genometryImpl.symloader.Wiggle$2.next(Wiggle.java:185)
at com.affymetrix.genometryImpl.symloader.Wiggle.parse(Wiggle.java:227)
at com.affymetrix.genometryImpl.symloader.Wiggle.processLines(Wiggle.java:210)
at com.affymetrix.genometryImpl.symloader.SymLoaderTabix.getRegion(SymLoaderTabix.java:147)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.getRegion(QuickLoadSymLoader.java:257)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadAndAddSymmetries(QuickLoadSymLoader.java:134)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadSymmetriesThread(QuickLoadSymLoader.java:108)
at com.affymetrix.genometryImpl.quickload.QuickLoadSymLoader.loadFeatures(QuickLoadSymLoader.java:94)
at com.affymetrix.genometryImpl.quickload.QuickloadServerType.loadFeatures(QuickloadServerType.java:386)
at com.affymetrix.igb.view.load.GeneralLoadUtils.loadFeaturesForSym(GeneralLoadUtils.java:816)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:756)
at com.affymetrix.igb.view.load.GeneralLoadUtils$3.runInBackground(GeneralLoadUtils.java:751)
at com.affymetrix.genometryImpl.thread.CThreadWorker.doInBackground(CThreadWorker.java:59)
at javax.swing.SwingWorker$1.call(Unknown Source)
at java.util.concurrent.FutureTask$Sync.innerRun(Unknown Source)
at java.util.concurrent.FutureTask.run(Unknown Source)
at javax.swing.SwingWorker.run(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(Unknown Source)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source)
at java.lang.Thread.run(Unknown Source)

passed finally

Passed 7.0.0 (11959)

Passed V.13740, Mac, Java 1.6.0_33

Graph tracks were rearranged in the main viewer, track labels were modified, different colors for 'FG' and 'BG' were selected, track label font size was changed, and multiple tracks were selected for deletion via the 'Delete Graph' button under 'Graph' Tab and no errors appeared in the Java console.