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  • CATCH - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #563 ] Reading multiple wig files (chr1-3), one bed file (chr1)
    12/10/08 07:05
    Submitted by:
    Assigned to:
    conversion wig -> pwig
    Ticket group:
    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 *

    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(
    at data.DataSet.readSequences(
    at data.DataSet.addTrack(
    at fileControllers.FileHandlers.importDataSet(
    at fileControllers.ExtractWiggleLines.conversionPartTwo(
    at fileControllers.ExtractWiggleLines.conversionsteptwo(
    at fileManager.FileInterfaceGui.convert(
    at fileManager.FileInterfaceGui.gatherData(
    at fileManager.FileInterfaceGui.convertAndAddInCatchButtonActionPerformed(
    at fileManager.FileInterfaceGui.access$1(
    at fileManager.FileInterfaceGui$2.actionPerformed(
    at javax.swing.AbstractButton.fireActionPerformed(
    at javax.swing.AbstractButton$Handler.actionPerformed(
    at javax.swing.DefaultButtonModel.fireActionPerformed(
    at javax.swing.DefaultButtonModel.setPressed(
    at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(
    at java.awt.Component.processMouseEvent(
    at javax.swing.JComponent.processMouseEvent(
    at java.awt.Component.processEvent(
    at java.awt.Container.processEvent(
    at java.awt.Component.dispatchEventImpl(
    at java.awt.Container.dispatchEventImpl(
    at java.awt.Component.dispatchEvent(
    at java.awt.LightweightDispatcher.retargetMouseEvent(
    at java.awt.LightweightDispatcher.processMouseEvent(
    at java.awt.LightweightDispatcher.dispatchEvent(
    at java.awt.Container.dispatchEventImpl(
    at java.awt.Window.dispatchEventImpl(
    at java.awt.Component.dispatchEvent(
    at java.awt.EventQueue.dispatchEvent(
    at java.awt.EventDispatchThread.pumpOneEventForFilters(
    at java.awt.EventDispatchThread.pumpEventsForFilter(
    at java.awt.EventDispatchThread.pumpEventsForHierarchy(
    at java.awt.EventDispatchThread.pumpEvents(
    at java.awt.EventDispatchThread.pumpEvents(
    Please log in to add comments and receive followups via email.
    Comment Date By
    Fixed by returning from readSequences when there are no profiles defined in the file. 01/11/09 08:54 glyn_dk
    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.

    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)

    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);
    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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