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  • BIRCH: Comprehensive bioinfo. system - Support tickets

    Submit | Open tickets | Closed tickets

    [ Ticket #1199 ] Cut and paste in a multiple alignment deletes gaps
    Date:
    03/15/15 19:56
    Submitted by:
    B_Fristensky
    Assigned to:
    B_Fristensky
    Category:
    bioLegato
    Priority:
    8
    Ticket group:
    Bug
    Resolution:
    Resolved
    Summary:
    Cut and paste in a multiple alignment deletes gaps
    Original submission:
    The subject pretty much says it. If you have a multiple alignment in a sequence canvas, select by name, and cut one sequence from one row and past it to a different row, the gaps are lost.
    Please log in to add comments and receive followups via email.
    Followups
    Comment Date By
    It turned out that GenBank2008.java:translateSequence, line 214, had the following:

    parray[1].replaceAll("[^a-zA-Z]", ""));

    The decision to not allow gaps in GenBank files was based
    on the mistaken belief that they weren't in the official
    format definition in the NCBI Release Notes. However, it turns out that the Release Notes say nothing whatsoever about which characters are legal, so the gap character has been added.

    parray[1].replaceAll("[^a-zA-Z-]", ""));
    04/13/15 11:36 B_Fristensky
    Just to make the point, both Cut/Paste and Copy/Paste fail to preserve the gaps. However, when calling either Copy or Cut, a System.out.println(result.toString()) added in line 1ine 1513 of SequenceCanvas.java copyClipboard does print out a sequence in GenBank format with gaps. So the gaps must be lost during the Paste step. 04/09/15 12:47 B_Fristensky
    Interestingly, CopyOut and PasteIn DO preserve gaps. The contents of .blpalign_clipboard, for example, clearly show gaps. It is worthy of note that CopyOut saves files in GDE format. What do the internal Copy and Paste functions do? 04/09/15 12:41 B_Fristensky
    During a copy and paste, no error messages are sent to the console. 04/09/15 12:09 B_Fristensky
    This is also true with CopyOut and PasteIn, as well as with Extract. 03/16/15 17:12 B_Fristensky
    I don't know for a fact that this is related to 1198, but it's an odd coincidence. 03/15/15 19:57 B_Fristensky

    1 - 1 of 1

    Dependent on ticket
    encryption certificate expired
       

    1 - 1 of 1

    Dependent on Task
    Add geSignatures method
       
    No other tickets are dependent on this ticket
    Ticket change history
    Field Old value Date By
    status_id Pending 04/13/15 11:36 B_Fristensky
    resolution_id Not Resolved 04/13/15 11:36 B_Fristensky
    close_date 12/31/69 19:00 04/13/15 11:36 B_Fristensky
    priority 6 03/16/15 17:13 B_Fristensky
    priority 5 03/15/15 19:57 B_Fristensky
    assigned_to unset 03/15/15 19:57 B_Fristensky
    resolution_id Unset 03/15/15 19:57 B_Fristensky

     

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