[Next-Generation Sequencing Book]

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[ 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.
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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
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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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