TPP:4.7.0 SVN Log

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Changes since 4.6.3 release

Last Generated Wed Feb 5 2014


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r6252 | eng_jk | 2013-07-24 15:35:06 -0700 (Wed, 24 Jul 2013) | 2 lines

correct Comet filtering options; update some of the horrendous layout

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r6253 | slagelwa | 2013-07-25 14:49:09 -0700 (Thu, 25 Jul 2013) | 2 lines

Cleanup/touch ups

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r6254 | slagelwa | 2013-07-29 11:34:36 -0700 (Mon, 29 Jul 2013) | 2 lines

Merged r6220:HEAD of 4.6.3 branch back into trunk

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r6255 | slagelwa | 2013-07-30 13:45:46 -0700 (Tue, 30 Jul 2013) | 2 lines

Fixing Valgrind reported "Mismatched free() / delete / delete []" problem 

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r6256 | real_procopio | 2013-07-31 16:32:20 -0700 (Wed, 31 Jul 2013) | 10 lines

[Petunia] Added utility to edit Tandem parameters files:
- Page allows users to change values, delete them, and add new ones
- Include "I'm feeling lucky" google link to GPM for each parameter for extra help
- User is able to save parameters under a different file name
- No longer requiring that Tandem params filenames end in ".xml"; instead Petunia can recognize it from its contents
- Added ability to list files by wildcard, not just by filename extension/ending
- Use a different color when choosing files vs. browsing
- Moved s3 and basicauth code to more relevant spots


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r6257 | slagelwa | 2013-08-01 12:22:59 -0700 (Thu, 01 Aug 2013) | 5 lines

Upgraded to r33 of X!Tandem (first beta of 2013.02.01.1 of X! Tandem)
by checking it out of their subversion repository and applying 
creative use of diff/path.


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r6258 | slagelwa | 2013-08-01 12:27:20 -0700 (Thu, 01 Aug 2013) | 5 lines

Upgraded to r50 of X!Tandem (Jackhammer X! Tandem 2013.06.15)
by checking it out of their subversion repository and applying 
creative use of diff/path.


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r6259 | slagelwa | 2013-08-01 12:30:35 -0700 (Thu, 01 Aug 2013) | 5 lines

Upgraded to r51 of X!Tandem (Jackhammer updates)
by checking it out of their subversion repository and applying 
creative use of diff/path.


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r6260 | real_procopio | 2013-08-01 18:40:30 -0700 (Thu, 01 Aug 2013) | 1 line

[Petunia] Flag duplicated parameters and non-existent default files in edit Tandem params page; also added link to top-level Tandem API at GPM
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r6261 | slagelwa | 2013-08-02 14:47:21 -0700 (Fri, 02 Aug 2013) | 3 lines

Small change to use absolute paths for all file
references in the tandem parameters.

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r6262 | real_procopio | 2013-08-05 18:26:10 -0700 (Mon, 05 Aug 2013) | 1 line

[PepXMLViewer] Display friendly 'spectrum' link when no matched ions information is available from pepXML
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r6263 | real_procopio | 2013-08-05 18:30:07 -0700 (Mon, 05 Aug 2013) | 1 line

[PepXMLViewer] Display MSGF+ and (correct) Myrimatch search scores, and add filter options.  Also some minor reformatting of filters for PeptideProphet and OMSSA
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r6264 | slagelwa | 2013-08-06 10:53:04 -0700 (Tue, 06 Aug 2013) | 2 lines

Fix the name of our own software

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r6265 | slagelwa | 2013-08-06 11:00:26 -0700 (Tue, 06 Aug 2013) | 2 lines

Include comet.exe in installer

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r6266 | real_procopio | 2013-08-06 16:55:24 -0700 (Tue, 06 Aug 2013) | 1 line

[Petunia] Add ability to launch Comet
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r6267 | real_procopio | 2013-08-08 18:43:12 -0700 (Thu, 08 Aug 2013) | 1 line

[Petunia] Add ppm (-a) option to XPRESS; minor text changes to ASAP and XPRESS entry fields
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r6268 | eng_jk | 2013-08-09 15:34:17 -0700 (Fri, 09 Aug 2013) | 2 lines

get rid of old/deprecated Comet references

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r6269 | eng_jk | 2013-08-09 17:11:22 -0700 (Fri, 09 Aug 2013) | 5 lines

PepXField.cxx: remove a deprecated comet url entry
add esoteric -E option to XpressPeptideParser to force reported start/end points to be MS1 scans; for external user; not needed by TPP
change comment styles from /* */ to //


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r6270 | real_procopio | 2013-08-09 17:47:11 -0700 (Fri, 09 Aug 2013) | 1 line

[tpp_models] Get rid of 'qw as parentheses is deprecated' warnings
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r6271 | slagelwa | 2013-08-23 16:14:43 -0700 (Fri, 23 Aug 2013) | 12 lines

Added the following additional parameters for TPP's version
of X!Tandem:

   tpp list path, peptide
   tpp list path, saps
   tpp list path, mods

so that you no longer need to use a taxonomy.xml file and 
instead can simply include the fasta database file path in
the params file.


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r6272 | henryhlam | 2013-08-29 19:40:15 -0700 (Thu, 29 Aug 2013) | 1 line

[InteractParser] Check missing protein_descr to prevent seg fault in OMISSA fix

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r6274 | real_procopio | 2013-09-03 18:27:40 -0700 (Tue, 03 Sep 2013) | 1 line

[ProtXMLViewer] Intial commit (alpha) of new protXML viewer.  It is *much* faster, uses an index to retrieve selected entries, uses simple graphical elements, and has a clean interface.  Still need to add more info, quantitation, etc
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r6275 | slagelwa | 2013-09-05 11:08:29 -0700 (Thu, 05 Sep 2013) | 4 lines

Fixed an issue with testing comet on Windows platform.  Added
logging and cleaned up (again) mapping file paths from win32
to unix and back.

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r6276 | eng_jk | 2013-09-05 12:09:03 -0700 (Thu, 05 Sep 2013) | 2 lines

add DCT's fix so that InteractParser will write out proper closing tags when last spectrum_query of input file has blank search result.

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r6277 | slagelwa | 2013-09-06 13:32:06 -0700 (Fri, 06 Sep 2013) | 4 lines

Added "no enzyme" (OMSSA) and "no cleavage" (Myrimatch) as alternatives
to the "nonspecific" enzyme entry.


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r6278 | slagelwa | 2013-09-06 13:43:42 -0700 (Fri, 06 Sep 2013) | 5 lines

* Added comet-pepxml.cgi to Windows installer so it gets installed.
* Fixed the link in the PepXMLViewer to use the pep.xml file instead
  of using the basename location of the input spectrum
* Uses '/' then a '\' when separating the file from the spectrum

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r6279 | eng_jk | 2013-09-09 10:28:10 -0700 (Mon, 09 Sep 2013) | 2 lines

initialize pointer

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r6280 | henryhlam | 2013-09-09 16:05:57 -0700 (Mon, 09 Sep 2013) | 1 line

[SpectraST] Spectral dataset fingerprinting option
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r6281 | slagelwa | 2013-09-12 10:33:22 -0700 (Thu, 12 Sep 2013) | 6 lines

Authors of IO::Compress::Zip renamed the option FilterEnvelope to 
FilterContainer without making it backwards compatible.  Changed to use the
more recent rendition and also added a minimum version of IO::Compress::Zip
allowed.


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r6282 | slagelwa | 2013-09-16 15:44:30 -0700 (Mon, 16 Sep 2013) | 4 lines

RNA-Seq functionality for TPP.  This check in contains a "perlified" version
of the bash script Zhi wrote (rnaseqpdb.pl) and the additional perl libraries
and script dependencies.

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r6283 | slagelwa | 2013-09-17 15:14:27 -0700 (Tue, 17 Sep 2013) | 2 lines

Releasing 2.3 so I can finish up 2.4

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r6284 | slagelwa | 2013-09-18 08:55:25 -0700 (Wed, 18 Sep 2013) | 3 lines

Rolling back Henry's most recent check in as its breaking the
nightly builds.

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r6285 | slagelwa | 2013-09-20 09:50:03 -0700 (Fri, 20 Sep 2013) | 3 lines

Now with RNA-Seq functionality (alpha)


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r6286 | slagelwa | 2013-09-20 09:51:47 -0700 (Fri, 20 Sep 2013) | 2 lines

Building new image, so moving fixme to build process

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r6287 | slagelwa | 2013-09-20 14:11:59 -0700 (Fri, 20 Sep 2013) | 11 lines

Zhi recently reported an segmentation fault occurring in Spectrast that appeared
to be happening in mzParser.  While investigating the issue I noticed that
about a year ago the author of Czran had made a memory reallocation fix  (the
code that this module is based on).  So I simply applied the same fix to our
version.

While the new code seems to correct the segmentation fault at first glance I'm
not certain why this would be the case.  I would think that the bug's only harm
is that it allocates more memory than necessary and leaves unused memory behind.


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r6288 | henryhlam | 2013-09-23 01:28:26 -0700 (Mon, 23 Sep 2013) | 1 line

[SpectraST] Re-submitting spectral dataset fingerprinting option
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r6289 | henryhlam | 2013-09-23 02:00:41 -0700 (Mon, 23 Sep 2013) | 1 line

[SpectraST] This should fix the compile warning of the previous check-in.
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r6290 | dshteyn | 2013-09-23 10:09:42 -0700 (Mon, 23 Sep 2013) | 1 line

get_prot.pl: filter by probability and any filter out filter_out string
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r6291 | dshteyn | 2013-09-23 11:19:29 -0700 (Mon, 23 Sep 2013) | 1 line

compareProts_ClusterHM.pl: tool for building heatmaps comparing different ProteinProphet results.
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r6292 | dshteyn | 2013-09-23 11:34:49 -0700 (Mon, 23 Sep 2013) | 1 line

paths
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r6293 | slagelwa | 2013-09-23 14:15:33 -0700 (Mon, 23 Sep 2013) | 2 lines

Use perl in users path as default 

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r6294 | dshteyn | 2013-10-01 13:44:26 -0700 (Tue, 01 Oct 2013) | 1 line

Adding installation of compareProts_ClusterHM.pl
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r6295 | dshteyn | 2013-10-01 14:11:18 -0700 (Tue, 01 Oct 2013) | 1 line

d3-328.js: required for compareProts_ClusterHM.pl
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r6296 | dshteyn | 2013-10-01 16:27:37 -0700 (Tue, 01 Oct 2013) | 1 line

compareProts_ClusterHM.pl installer update
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r6297 | dshteyn | 2013-10-02 10:07:11 -0700 (Wed, 02 Oct 2013) | 1 line

compareProts_ClusterHM.pl installation
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r6298 | dshteyn | 2013-10-02 15:58:32 -0700 (Wed, 02 Oct 2013) | 1 line

InterProphetParser: fix bug with DECOY= option found by Joe
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r6299 | slagelwa | 2013-10-02 16:22:10 -0700 (Wed, 02 Oct 2013) | 6 lines

Made the target perl_paths a phony target.  There happens to be a directory
with the same name as the target in top level directory.  After the first build
this means that the target will usually never get run again as the timestamp
of the dependencies will likely always be newer than the directory.


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r6300 | slagelwa | 2013-10-03 17:27:44 -0700 (Thu, 03 Oct 2013) | 2 lines

Might as well enable running of comet on the cloud.

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r6301 | dshteyn | 2013-10-04 15:23:55 -0700 (Fri, 04 Oct 2013) | 1 line

xinteract:  Allow xinteract to keep running even if -nI is used to disable InteractParser, for using xinteract on previously interacted files (e.g. to do Quantitation separately with xinteract)
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r6302 | slagelwa | 2013-10-04 15:28:52 -0700 (Fri, 04 Oct 2013) | 3 lines

Instead of requiring a version try to do the right thing based 
on the version.

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r6303 | slagelwa | 2013-10-09 14:18:13 -0700 (Wed, 09 Oct 2013) | 2 lines

Adding usage reporting and costing scripts to amztpp

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r6304 | dshteyn | 2013-10-14 11:16:34 -0700 (Mon, 14 Oct 2013) | 1 line

Usage statement formatting.  Improved colors and different scale in Heatmap.
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r6305 | real_procopio | 2013-10-14 15:11:47 -0700 (Mon, 14 Oct 2013) | 1 line

[Petunia] Add new options and handling to run the compare proteins with heatmap utility
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r6306 | real_procopio | 2013-10-15 17:30:00 -0700 (Tue, 15 Oct 2013) | 1 line

[Petunia] Added ability to terminate a running job
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r6307 | slagelwa | 2013-10-17 16:47:58 -0700 (Thu, 17 Oct 2013) | 17 lines

Replaced gcc 4.7 patch to boost with a new patch that addresses gcc 4.8 issues:

* Issue with conflict with the macro TIME_UTC which is a new macro defined
in C11.  So we renamed it TIME_UTC_.  For more information see:

   https://svn.boost.org/trac/boost/ticket/6940
   https://bugzilla.redhat.com/show_bug.cgi?id=825039
   https://bbs.archlinux.org/viewtopic.php?pid=1126374 

* Build issues with threads under MingW.  From what I can tell the macro name
used in the threading test may have changed again. For more information see:

   https://svn.boost.org/trac/boost/ticket/6165
   https://svn.boost.org/trac/boost/changeset/76594
   https://svn.boost.org/trac/boost/attachment/ticket/6165/boost-1.48.0-gcc47-winthreads.patch


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r6308 | slagelwa | 2013-10-17 16:58:26 -0700 (Thu, 17 Oct 2013) | 14 lines

gcc 4.8 was complaining about fprintf() of a time_t typed variable using
a long int.  Unfortunately there is no specification as to what the actual
primitive data type is for time_t.  For the meantime type cast it as a 
unsigned long long and print that out.  But we have to use two different
formats, as Mingw/Win32 passes the call to a Window's library that doesn't
support C99's "%llu" format.

See also:

http://stackoverflow.com/questions/2792551/what-primitive-data-type-is-time-t
http://sourceforge.net/mailarchive/message.php?msg_id=23004498
http://stackoverflow.com/questions/2467418/portable-way-to-deal-with-64-32-bit-time-t


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r6309 | real_procopio | 2013-10-18 14:33:56 -0700 (Fri, 18 Oct 2013) | 1 line

[Petunia] Properly kill all Linux session jobs (where fork actually works!)
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r6310 | real_procopio | 2013-10-18 14:42:30 -0700 (Fri, 18 Oct 2013) | 1 line

[Petunia] Oops! Wrong perl...
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r6311 | slagelwa | 2013-10-18 16:10:10 -0700 (Fri, 18 Oct 2013) | 4 lines

Latest MingW (with gcc 4.8) links using -lpthread but the linker doesn't
find the library now.  Being more specific works though.


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r6312 | slagelwa | 2013-10-18 16:17:39 -0700 (Fri, 18 Oct 2013) | 12 lines

Linker under MingW/gcc 4.8 was complaining about undefined references to some
zlib routines.  While ZLIB_LIB is included in SYSLIBS it occurs before 
HDF5_LIB in the link command. Since not all linkers keep all references in
memory when using the gcc compiler its practice to order your dependencies
from left to right.  Presumbably the HDF5 library uses something from zlib so
it should be left of the zlib library.

I don't know why this worked before and doesn't under gcc 4.8.  Perhaps the 
new version of the linker is more aggressively removing references that aren't
used from its global list.


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r6313 | eng_jk | 2013-10-21 13:42:29 -0700 (Mon, 21 Oct 2013) | 2 lines

pick up changes through r57 of Lorikeet code; major difference is the ions labeled in spectrum should improve

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r6314 | dshteyn | 2013-10-21 15:24:51 -0700 (Mon, 21 Oct 2013) | 1 line

Cast to avoid imprecise calculation
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r6315 | dshteyn | 2013-10-21 15:34:46 -0700 (Mon, 21 Oct 2013) | 1 line

Correct issue with filter_in option.  Allow filters to contain '|' character for matching multiple strings.
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r6316 | mhoopmann | 2013-10-21 16:13:41 -0700 (Mon, 21 Oct 2013) | 1 line

Making HDF5/mz5 support opt-in with the following declaration at compile time: MZP_MZ5
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r6317 | mhoopmann | 2013-10-25 11:07:49 -0700 (Fri, 25 Oct 2013) | 1 line

Added support for reading data compressed with MS-Numpress. Also simplified binary data reading to a single function.
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r6318 | mhoopmann | 2013-10-25 11:10:20 -0700 (Fri, 25 Oct 2013) | 1 line

Included stdint.h for linux compilation.
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r6319 | mhoopmann | 2013-10-28 10:48:54 -0700 (Mon, 28 Oct 2013) | 1 line

Updated Makefile to compile MSNumpress for reading numpress-compressed mzML files. I think... Who knows what I did or if I did it right? The Makefile looks very obfuscated...
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r6320 | mhoopmann | 2013-10-29 15:13:25 -0700 (Tue, 29 Oct 2013) | 1 line

Making explicit casts when changing data types to silence compiler warnings.
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r6321 | dshteyn | 2013-10-30 12:15:04 -0700 (Wed, 30 Oct 2013) | 1 line

indexmzXML: Allow more upto 100K scans per mzXML file
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r6322 | slagelwa | 2013-10-30 12:51:13 -0700 (Wed, 30 Oct 2013) | 2 lines

Added MSNumpress to libmzparser archive

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r6323 | real_procopio | 2013-11-01 16:07:25 -0700 (Fri, 01 Nov 2013) | 1 line

[TPP Models] Fixed tick marks for nmc and ntt models; fixed minor filename bug; added placeholder in code for inserting decoy-based analysis results; added quantitation summary and parameters to 'Run Options' tab.
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r6324 | real_procopio | 2013-11-04 17:48:24 -0800 (Mon, 04 Nov 2013) | 1 line

[Petunia] Remove access to PepC due to lack of use and support
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r6325 | real_procopio | 2013-11-05 10:25:20 -0800 (Tue, 05 Nov 2013) | 1 line

[Lorikeet] Add precursor m/z info back to header
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r6326 | slagelwa | 2013-11-05 14:43:32 -0800 (Tue, 05 Nov 2013) | 4 lines

Updated boost to version 1.54.0.  Several of the changes
were supplied by David Trudgian.


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r6327 | slagelwa | 2013-11-05 15:57:57 -0800 (Tue, 05 Nov 2013) | 3 lines

Applied David Trudgian's recent changes to support clang 5.0/MacOSX


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r6328 | dshteyn | 2013-11-06 12:17:39 -0800 (Wed, 06 Nov 2013) | 1 line

xinteract: Fix BUG with -MONO option being incorrectly parsed as a PTMProphet command.
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r6329 | dshteyn | 2013-11-06 16:23:52 -0800 (Wed, 06 Nov 2013) | 1 line

InteractParser: -N (no reference option), better usage statement, Use NativeSpectrumID to find the index of spectra from ABI files and use index+1 as the scan number.
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r6330 | dshteyn | 2013-11-06 17:02:43 -0800 (Wed, 06 Nov 2013) | 1 line

PeptideProphetParser: print usage and exit when envoked without arguments.
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r6331 | slagelwa | 2013-11-07 00:13:47 -0800 (Thu, 07 Nov 2013) | 7 lines

Patch for building boost 1.54 under mingw.  This patch comes from:

https://svn.boost.org/trac/boost/ticket/8762
https://svn.boost.org/trac/boost/changeset/86460
http://risc.blogspot.com/2013/08/so-you-want-to-build-boost-1.html


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r6332 | dshteyn | 2013-11-07 09:52:42 -0800 (Thu, 07 Nov 2013) | 1 line

xinteract: BUGFIX pep.xml was being appended twice due to typo.
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r6333 | dshteyn | 2013-11-07 12:00:41 -0800 (Thu, 07 Nov 2013) | 1 line

InteractParser: write directory to inputfile tag when the file path is not absolute.
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r6334 | dshteyn | 2013-11-07 12:02:27 -0800 (Thu, 07 Nov 2013) | 1 line

PeptideProphetParser:  write directory to inputfile tag when the file path is not absolute, and check for extension...add one if needed.
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r6335 | real_procopio | 2013-11-07 17:27:40 -0800 (Thu, 07 Nov 2013) | 1 line

[TPP models] Bugfix: create full filepaths when generating models for all files in a given directory
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r6336 | dshteyn | 2013-11-08 08:32:58 -0800 (Fri, 08 Nov 2013) | 1 line

InteractParser: fix typo.
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r6337 | slagelwa | 2013-11-08 12:17:09 -0800 (Fri, 08 Nov 2013) | 2 lines

Patch inserted DCT's change twice

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r6338 | slagelwa | 2013-11-11 11:16:53 -0800 (Mon, 11 Nov 2013) | 2 lines

Removing Pepc from TPP.

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r6339 | henryhlam | 2013-11-13 22:39:43 -0800 (Wed, 13 Nov 2013) | 1 line

[PeptideProphet] Change to SpectraST's parametric model: Generalized Gaussian for positives, EVD for negatives. Option to optimize f-value function.
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r6340 | henryhlam | 2013-11-14 01:16:32 -0800 (Thu, 14 Nov 2013) | 1 line

[SpectraST] Update Makefile dependency
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r6341 | real_procopio | 2013-11-18 16:02:21 -0800 (Mon, 18 Nov 2013) | 1 line

[protxmlviewer] Remove confusing 'confidence' metric; deal with it in new viewer
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r6342 | real_procopio | 2013-11-19 12:07:25 -0800 (Tue, 19 Nov 2013) | 1 line

[ProtXMLViewer] Add to the installer
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r6343 | slagelwa | 2013-11-19 12:48:56 -0800 (Tue, 19 Nov 2013) | 5 lines

Replacing updateAllPaths.pl with a new script that
parses the XML and updates attributes on the element
based on the element name.


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r6344 | slagelwa | 2013-11-19 14:16:36 -0800 (Tue, 19 Nov 2013) | 2 lines

Updating installer for updateAllPaths.pl <=> updatepaths.pl

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r6345 | real_procopio | 2013-11-19 15:43:31 -0800 (Tue, 19 Nov 2013) | 1 line

[ProtXMLViewer] Add to the installer - part 2
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r6346 | real_procopio | 2013-11-19 17:58:28 -0800 (Tue, 19 Nov 2013) | 1 line

[Petunia] Added auto page refresh when submitting a job in Linux (avoids accidental job resubmission if refreshing the jobs page); added link to beta ProtXMLViewer; use clear wording when user needs to select a directory vs a file
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r6347 | real_procopio | 2013-11-19 18:06:59 -0800 (Tue, 19 Nov 2013) | 1 line

[ProtXMLViewer] Corrected path to perl; removed unused code
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r6348 | henryhlam | 2013-11-20 01:55:06 -0800 (Wed, 20 Nov 2013) | 1 line

[SpectraST] First SpectraST 5.0 check-in. More to come. Potentially unstable initially. Includes new scoring function and some minor new features.
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r6349 | dshteyn | 2013-11-20 10:56:25 -0800 (Wed, 20 Nov 2013) | 1 line

Memory bug submitted by Henry fixed.
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r6350 | dshteyn | 2013-11-20 10:57:26 -0800 (Wed, 20 Nov 2013) | 1 line

Memory bug submitted by Henry fixed.
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r6351 | slagelwa | 2013-11-20 16:30:27 -0800 (Wed, 20 Nov 2013) | 2 lines

Added message about replacing original file

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r6352 | slagelwa | 2013-11-22 16:02:10 -0800 (Fri, 22 Nov 2013) | 4 lines

Addressed several issues found on the win32 platform.  Better
handling of xml-stylesheet.  Touched up the documentation a
little.

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r6353 | slagelwa | 2013-11-22 16:06:15 -0800 (Fri, 22 Nov 2013) | 3 lines

Now uses new updatepaths.pl script.  Also updated the
form to use the new options to updatpaths.

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r6354 | dshteyn | 2013-11-25 12:23:45 -0800 (Mon, 25 Nov 2013) | 1 line

InteractParser: BUGFIX write closing tags when last spectrum query is empty.
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r6355 | slagelwa | 2013-11-25 16:03:20 -0800 (Mon, 25 Nov 2013) | 2 lines

Updating Apache to from 2.2.8 to 2.2.25

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r6356 | slagelwa | 2013-11-25 16:09:22 -0800 (Mon, 25 Nov 2013) | 2 lines

bzip not gzip the apache module

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r6357 | slagelwa | 2013-12-11 11:09:14 -0800 (Wed, 11 Dec 2013) | 2 lines

Don't warn about amino acid codes if it is a stop ('*') code

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r6358 | henryhlam | 2013-12-12 02:00:27 -0800 (Thu, 12 Dec 2013) | 1 line

[SpectraST] Fix uninitialized variable bug for no-binning option.
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r6359 | slagelwa | 2013-12-19 09:03:42 -0800 (Thu, 19 Dec 2013) | 4 lines

Fix buffer overrun issue when charge states are outside the max allowed.  
Recently ran into this on some Thermo LTQ data that had just a couple of 
charge states assigned to spectrum that were...large, like > 100.  

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r6360 | slagelwa | 2013-12-19 10:19:33 -0800 (Thu, 19 Dec 2013) | 2 lines

Lets not be off by one in our range check

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r6361 | real_procopio | 2013-12-23 15:29:10 -0800 (Mon, 23 Dec 2013) | 1 line

[Petunia] Added option to run xinteract on each individual input file (i.e. not combine them into a single interact.*.xml) -- requested feature
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r6362 | slagelwa | 2014-01-02 15:02:51 -0800 (Thu, 02 Jan 2014) | 2 lines

Silence the error message if lsb_release isn't found

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r6363 | slagelwa | 2014-01-03 09:34:27 -0800 (Fri, 03 Jan 2014) | 3 lines

Added useSGE and useSudo options to run commands as authenticated user
and/or to run on SGE .

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r6364 | eng_jk | 2014-01-03 13:13:03 -0800 (Fri, 03 Jan 2014) | 2 lines

add some context to esoteric message that rampOpenFile reports when input XML file not present

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r6365 | dshteyn | 2014-01-03 13:53:41 -0800 (Fri, 03 Jan 2014) | 1 line

ShowXIC.cgi - tool for visualizing Single Ion Current traces
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r6366 | dshteyn | 2014-01-03 13:55:15 -0800 (Fri, 03 Jan 2014) | 1 line

PepXMLViewer: New feature, MZratio now is a link to the new ShowXIC.cgi tool.
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r6367 | dshteyn | 2014-01-03 13:56:51 -0800 (Fri, 03 Jan 2014) | 1 line

ShowXIC.cgi - tool for visualizing Single Ion Current traces
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r6368 | slagelwa | 2014-01-03 14:06:26 -0800 (Fri, 03 Jan 2014) | 3 lines

Make a better guess as to the linux platform
we're on.

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r6369 | slagelwa | 2014-01-03 16:18:36 -0800 (Fri, 03 Jan 2014) | 3 lines

Warn if WEBSERVER_ROOT isn't set and we are being
run by a web server. 

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r6370 | henryhlam | 2014-01-06 01:20:20 -0800 (Mon, 06 Jan 2014) | 1 line

[SpectraST] Retention time normalization with landmark peptides.
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r6371 | dshteyn | 2014-01-06 10:10:36 -0800 (Mon, 06 Jan 2014) | 1 line

ShowXIC.cgi - tool for visualizing Single Ion Current traces
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r6372 | dshteyn | 2014-01-06 14:58:24 -0800 (Mon, 06 Jan 2014) | 1 line

PTMProphet: improve modification recognition and performance on N-glyco capture data.
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r6373 | henryhlam | 2014-01-06 22:16:57 -0800 (Mon, 06 Jan 2014) | 1 line

[SpectraST] Flag RT landmark peptides in Remark field; print iRT in MRM table.
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r6374 | slagelwa | 2014-01-07 14:20:22 -0800 (Tue, 07 Jan 2014) | 34 lines

Addresses the issues brought up by http://www.viva64.com/en/b/0212/

1. Henry must've fixed this issue
2. Fixed fairly serious issue with dereferencing null pointers in ASAPRatio.
   Also uncommented out the line that allocated an array of pepDataStrct as without
   this we are again dereferencing a null pointer (and potentially modifying
   memory)
3. Replaced empty() with clear() in Parsers/Parser/Tag.cxx
4. Fixed problems with constructor initializations in MascotConverter.cxx,
    ASAPRatioPeptideParser.cxx CruxDiscrimFunction.cxx 
    DiscrimValmMxtureDistr.cxx MascotDiscrimFunction.cxx 
    MascotScoreParser.cxx tandemdiscrimfunction.cxx TandemKScoredF.cxx
    TandemNativedF.cxx 
5. Corrected minor issue in InterProphet by making the test conjuction
6. Fixed ASAPRatio issue with assigning the ratio twice to the same value
   instead of the 2nd element.
7. Corrected significant issue with comparing a unsigned and signed int 
   in ProteinProphet.  Looks like Henry already fixed the similar issue in
   Spectrast
8. Its an odd loop, but I think the intend is correct.  We're setting one of 
   two different references to true based on a conditional.
9. Already fixed in RTCalculator.  Fixed in cgi_pep3d and AsapRatio by casting
   as double.
10. Fixed what appeared to be a significant typo when setting peptide max 
   probability in ProteinProphet for "pep6/pep7".
11. Already fixed
12. Already fixed
13. DCT commented out the noop statement already found in MixtureModel.cxx
    Corrected delete with delete[] where pointed out. The last issue is in 
    ProteoWizard code therefore not changed.

Everything compiles but I haven't run tests yet.


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r6375 | slagelwa | 2014-01-07 15:50:31 -0800 (Tue, 07 Jan 2014) | 2 lines

We have a name

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r6376 | real_procopio | 2014-01-07 19:24:55 -0800 (Tue, 07 Jan 2014) | 12 lines

[ProtXMLViewer] Many changes, including:
- Display protein annotation via AJAX call, with show/hide divs
- Added display, sorting, and filtering by pct_spectrum_ids
- Added link to protein sequence viewer (comet)
- Display ntt and pre-nsp prob in peptide view, graphically, and text via mouse-over
- Gray out peptide probability histograms for those that are not contributing evidence
- New graphical cues for uniquely mapping sequences, and ntt in sequences view
- Rewrote filtering logic to accommodate multiple entities per field (e.g. peptides)
- Now using indistinguishable entries when filtering
- Corrected entry count bug
- Added link to MODELS file, if present
- Rounded corners on tabs
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r6377 | henryhlam | 2014-01-07 23:09:28 -0800 (Tue, 07 Jan 2014) | 1 line

[SpectraST] Fix to RT normalization -- allow negative iRT values.
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r6378 | slagelwa | 2014-01-08 16:37:42 -0800 (Wed, 08 Jan 2014) | 5 lines

Added "build" of Mayu and installation on linux.  Now off to shower
to try to shake this feeling of dirty after what how I implemented
this.


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r6379 | slagelwa | 2014-01-09 11:52:22 -0800 (Thu, 09 Jan 2014) | 2 lines

Added Mayu to Windows installer

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r6380 | slagelwa | 2014-01-09 16:24:12 -0800 (Thu, 09 Jan 2014) | 3 lines

Should now handle updating files that came from an OS
other than the one currently on.

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r6381 | slagelwa | 2014-01-09 16:29:10 -0800 (Thu, 09 Jan 2014) | 7 lines

Reverting back to using -lpthread instead of -lpthread-dll.  Everything
I've read about mingw pthreads indicates that this is the proper linker
flag to use.  I think that some of the linker problems we've encountered
across different mingw versions is related to gcc and that the order of
libraries/*.o files when linking can be important.


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r6382 | mhoopmann | 2014-01-14 10:18:40 -0800 (Tue, 14 Jan 2014) | 1 line

Updating MSNumpress to latest release (contains bugfixes related to memory allocation and access).
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r6383 | mhoopmann | 2014-01-14 12:08:20 -0800 (Tue, 14 Jan 2014) | 1 line

Added explicit recasts in a few places to silence warnings (so TPP can build).
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r6384 | real_procopio | 2014-01-14 17:44:15 -0800 (Tue, 14 Jan 2014) | 1 line

[Petunia] Added simple interface to Mayu; small bugfix: align speclibs panes to top of table
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r6385 | henryhlam | 2014-01-14 22:24:23 -0800 (Tue, 14 Jan 2014) | 1 line

[SpectraST] Rudimentary outlier removal for RT normalization (linear regression mode)
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r6386 | mhoopmann | 2014-01-15 11:35:51 -0800 (Wed, 15 Jan 2014) | 1 line

Fixed memory allocation error when decoding numpressed data. Also catching numpress exceptions and notifying user, should they occur.
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r6387 | real_procopio | 2014-01-15 13:34:09 -0800 (Wed, 15 Jan 2014) | 1 line

[Mayu] 'csv' stands for comma-separated values. Mayu was lying about this, and Excel did not like it. Fixed.
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r6388 | real_procopio | 2014-01-15 14:40:40 -0800 (Wed, 15 Jan 2014) | 1 line

[Lorikeet] Updating to r61. Label iTraq/TMT peaks; Label precursor ion and m/z; Label immonium ions.
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r6389 | real_procopio | 2014-01-16 17:48:52 -0800 (Thu, 16 Jan 2014) | 1 line

[plot-msms] New 'Isobaric' url variable sets appropriate flag in Lorikeet to label iTraq/TMT peaks; add revision info to file
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r6390 | real_procopio | 2014-01-16 18:14:23 -0800 (Thu, 16 Jan 2014) | 1 line

[PepXMLViewer] Add 'Isobaric' parameter which makes Lorikeet label iTraq/TMT peaks
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r6391 | real_procopio | 2014-01-21 19:20:04 -0800 (Tue, 21 Jan 2014) | 1 line

[ProtXMLViewer] Auto-scroll main window to last clicked-on protein entry when switching tabs; fix bug with indexing of last protein entry; no-wrap column head row; fixed division-by-zero bug when no entries have contributing spectra; minor code clean-up
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r6392 | dshteyn | 2014-01-22 15:36:38 -0800 (Wed, 22 Jan 2014) | 1 line

Add start scan back as a sortable column.  Allow iProphet results to link out to the correct search_summary thereby allowing to a link on each spectrum to display the results depending on the best scoring search engine.
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r6393 | real_procopio | 2014-01-22 18:30:46 -0800 (Wed, 22 Jan 2014) | 1 line

[ProtXMLViewer] Added NSP values to peptide view; Enabled 'Restore' button; Minor changes to column row; code formatting change for subroutines
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r6394 | eng_jk | 2014-01-24 11:30:34 -0800 (Fri, 24 Jan 2014) | 2 lines

cleanup xpress options usage statement

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r6395 | dshteyn | 2014-01-24 13:34:48 -0800 (Fri, 24 Jan 2014) | 1 line

iProphet: Added optional LENGTH model, and reporting of estimated number of corrects. KDModel:  added more flexibility in bandwidth control.
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r6396 | dshteyn | 2014-01-24 13:37:59 -0800 (Fri, 24 Jan 2014) | 1 line

iModelParser.cgi:  added display of iProphet estimates of total correct PSM and total correct peptides in the results.
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r6397 | dshteyn | 2014-01-27 10:04:44 -0800 (Mon, 27 Jan 2014) | 1 line

If PTMProphet was enabled, run quantitation on the ptm results.
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r6398 | dshteyn | 2014-01-27 10:07:34 -0800 (Mon, 27 Jan 2014) | 1 line

PTMProphet: handle static terminal modifications, whether of not the mod is writtten in the modified_peptide attribute of pepXML file.
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r6399 | slagelwa | 2014-01-28 12:26:02 -0800 (Tue, 28 Jan 2014) | 10 lines

Upgraded Proteowizard to 3.0.5533: 

   * Now uses the minimal distributed source tarball from
     pwiz's TeamCity.  
   * Updated instructions on how to do furture upgrades.
   * Updated how versions are generated to use the revision number
     assigned in Proteowizard as major/minor versions aren't used.
   * Removed Version(h|c)pp files and added a svn:ignore on these. 


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r6400 | slagelwa | 2014-01-28 13:43:24 -0800 (Tue, 28 Jan 2014) | 4 lines

Only the Version.cpp files are generated so I'm adding
back in the Version.hpp files.


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r6401 | slagelwa | 2014-01-29 09:30:42 -0800 (Wed, 29 Jan 2014) | 5 lines

Adding set of files that were missed in the r6399 checkin.
Could be that some "endline" errors occurred when adding this 
files to svn.


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