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  • CATCH - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #563 ] Reading multiple wig files (chr1-3), one bed file (chr1)
    Date:
    12/10/08 07:05
    Submitted by:
    glyn_dk
    Assigned to:
    glyn_dk
    Category:
    conversion wig -> pwig
    Priority:
    5
    Ticket group:
    reproducible
    Resolution:
    Resolved
    Summary:
    Reading multiple wig files (chr1-3), one bed file (chr1)
    Original submission:
    (running: CATCH3 svn revision 205 on catch1-desktop)
    Thes files listed below are the ones that I sent to Richard in a previous mail.

    peaktrack_example_chr1.bed *
    peaktrack_example_chr2.bed
    peaktrack_example_chr3.bed

    ERDD_T7_BR1_chr1.wig *
    ERDD_T7_BR1_chr2.wig *
    ERDD_T7_BR1_chr3.wig *
    ERDD_T7_BR2_chr1.wig *
    ERDD_T7_BR2_chr2.wig *
    ERDD_T7_BR2_chr3.wig *
    ERDD_T7_BR3_chr1.wig *
    ERDD_T7_BR3_chr2.wig *
    ERDD_T7_BR3_chr3.wig *

    When adding all the wig files and only one bed file (indicated by star *), I get an exception:
    Exception in thread "AWT-EventQueue-0"
    java.lang.ArrayIndexOutOfBoundsException: -1
    at java.util.ArrayList.remove(ArrayList.java:390)
    at data.DataSet.readSequences(DataSet.java:416)
    at data.DataSet.addTrack(DataSet.java:292)
    at fileControllers.FileHandlers.importDataSet(FileHandlers.java:45)
    at fileControllers.ExtractWiggleLines.conversionPartTwo(ExtractWiggleLines.java:68)
    at fileControllers.ExtractWiggleLines.conversionsteptwo(ExtractWiggleLines.java:57)
    at fileManager.FileInterfaceGui.convert(FileInterfaceGui.java:395)
    at fileManager.FileInterfaceGui.gatherData(FileInterfaceGui.java:429)
    at fileManager.FileInterfaceGui.convertAndAddInCatchButtonActionPerformed(FileInterfaceGui.java:449)
    at fileManager.FileInterfaceGui.access$1(FileInterfaceGui.java:447)
    at fileManager.FileInterfaceGui$2.actionPerformed(FileInterfaceGui.java:154)
    at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)
    at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)
    at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)
    at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)
    at java.awt.Component.processMouseEvent(Component.java:6041)
    at javax.swing.JComponent.processMouseEvent(JComponent.java:3265)
    at java.awt.Component.processEvent(Component.java:5806)
    at java.awt.Container.processEvent(Container.java:2058)
    at java.awt.Component.dispatchEventImpl(Component.java:4413)
    at java.awt.Container.dispatchEventImpl(Container.java:2116)
    at java.awt.Component.dispatchEvent(Component.java:4243)
    at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4322)
    at java.awt.LightweightDispatcher.processMouseEvent(Container.java:3986)
    at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3916)
    at java.awt.Container.dispatchEventImpl(Container.java:2102)
    at java.awt.Window.dispatchEventImpl(Window.java:2440)
    at java.awt.Component.dispatchEvent(Component.java:4243)
    at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)
    at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:273)
    at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:183)
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:173)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:168)
    at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:160)
    at java.awt.EventDispatchThread.run(EventDispatchThread.java:121)
    Please log in to add comments and receive followups via email.
    Followups
    Comment Date By
    Fixed by returning from readSequences when there are no profiles defined in the file. 01/11/09 08:54 glyn_dk
    Berry:
    Unfortunately I don't know how to deal with this one. The bug is caused by the ERDD_T7_BR1_chr2.wig * file, after I/O is done and this is run:

    if (seqpositions.size() < 2) {
    // the sequence must have at least two measuring points
    // remove the sequence from the sequencenames, reference positions
    seqnames.remove(seqnames.size() - 1);
    refposList.remove(refposList.size() - 1);

    What the meaning of the code around here is and what might cause this issue, I unfortunately do not know.


    Fiona:
    I think this will have to be rewritten to fix the bug...
    (and I am probably the one who has to rewrite it)
    I guess that the bug is caused by some window for which the wig file
    has less than two measuring points, but why it is not handled right. I don't know.

    QuickFIX: catch any exception, and notify the user which file CATCH
    had problems reading.
    (then the user has the possibility to deselect the problematic file
    and continue with other files)

    Berry:
    QuickFix implemented.

    String errorMessage = "The following file has encountered a known bug:nn" + files[filei] + "nn" +
    "This bug will be fixed as soon as possible. For now, please deselect this file and try again.";
    JOptionPane.showMessageDialog(null, errorMessage, "Error", JOptionPane.ERROR_MESSAGE);
    return;
    01/05/09 09:34 glyn_dk
    No results for "Dependent on ticket"
    No results for "Dependent on Task"
    No other tickets are dependent on this ticket
    Ticket change history
    Field Old value Date By
    status_id Pending 01/11/09 08:54 glyn_dk
    assigned_to unset 01/11/09 08:54 glyn_dk
    resolution_id Not Resolved 01/11/09 08:54 glyn_dk
    close_date 12/31/69 19:00 01/11/09 08:54 glyn_dk
    status_id Unset 01/05/09 09:34 glyn_dk
    resolution_id Unset 01/05/09 09:34 glyn_dk

     

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