Issue 69: "Pick Children" causes exception when there is only a peptide list (no proteins)

issues
Status:closed
Assigned To:Guest
Type:Defect
Area:Skyline
Priority:3
Milestone:1.2
Opened:2011-07-11 by Nathan Manes
Changed:2011-08-24 by Brendan MacLean
Resolved:2011-08-24 by Brendan MacLean
Resolution:Fixed
Closed:2011-08-24 by Brendan MacLean
2011-07-11 Nathan Manes
Title»"Pick Children" causes exception when there is only a peptide list (no proteins)
Assigned To»Nathan Manes
Type»Defect
Area»Skyline
Priority»3
Milestone»1.2
Skyline can in silico digest proteins or work with a simple list of peptides. If there are only peptides (no proteins), then there are no "children" (peptides resulting from in silico digestion). Right-clicking on "peptides1" (top-left of attached file) causes an exception. Ideally, this should not be click-able. I didn't know who to assign this issue to so I assigned it to myself.
 
 Bug PeptideList-PickChildren.png

2011-07-14 Brendan MacLean
Assigned ToNathan Manes»Brendan MacLean

2011-07-16 Brendan MacLean
Title"Pick Children" causes exception when there is only a peptide list (no proteins)»**"Pick Children" causes exception when there is only a peptide list (no proteins)
Hi Nathan,
Thanks for the report, and especially for posting the message with the stack trace. It was very helpful, in identifying the code at fault. It turns out that I intentionally enabled the use of the peptide picker on peptide lists in v0.7, because it can actually be useful with variable modifications. This was pointed out and essentially requested during the development of v0.7. It worked just fine in all my testing, but apparently I never tested it with a document that had a library and peptide ranking by a score in the library.

This was the route problem. In showing the picker, Skyline was attempting to rank peptides by values in the library, which is only valid for FASTA backed proteins, and not peptide lists.

I have made the ranking dependent on not being a peptide list, which fixes this error. This fix will be in the first v1.1 patch release.

Again, thanks for taking the time to report the issue.

--Brendan

2011-08-24 Brendan MacLean
resolve as Fixed
Title**"Pick Children" causes exception when there is only a peptide list (no proteins)»"Pick Children" causes exception when there is only a peptide list (no proteins)
Statusopen»resolved
Assigned ToBrendan MacLean»Nathan Manes
Fixed and released.

2011-08-24 Brendan MacLean
close
Statusresolved»closed
Assigned ToNathan Manes»Guest