TPP:4.7.0 SVN Log
From SPCTools
[edit]
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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