TPP:4.6.3 SVN Log

From SPCTools

Jump to: navigation, search

Changes since 4.6.2 release

------------------------------------------------------------------------
r6248 | dshteyn | 2013-07-22 11:29:54 -0700 (Mon, 22 Jul 2013) | 1 line

compareProts.pl: fix issue with single quotes and switch to webserver path without the host.
------------------------------------------------------------------------
r6246 | dshteyn | 2013-07-19 11:49:41 -0700 (Fri, 19 Jul 2013) | 1 line

compareProts.pl: should be less prone to errors on different windows shell.
------------------------------------------------------------------------
r6245 | slagelwa | 2013-07-19 11:25:59 -0700 (Fri, 19 Jul 2013) | 2 lines

d3.js was missing from Windows installer, making new RC release

------------------------------------------------------------------------
r6244 | slagelwa | 2013-07-18 15:00:45 -0700 (Thu, 18 Jul 2013) | 3 lines

There are some subtleties with MingW and the .exe extension that I wasn't fully aware of. 


------------------------------------------------------------------------
r6242 | slagelwa | 2013-07-17 11:02:21 -0700 (Wed, 17 Jul 2013) | 3 lines

* Bumped RC version to RC5
* Updated comet build to just skip installation if MacOSX

------------------------------------------------------------------------
r6240 | slagelwa | 2013-07-17 10:47:40 -0700 (Wed, 17 Jul 2013) | 5 lines

Added a simple "AJAXPing" call that implements a simple JSONP handle so that TWA
can check on the status of a EC2 instance and connect to it. That way we can
reduce the amount of polling that's done to when loading the iFrame in TWA>


------------------------------------------------------------------------
r6238 | slagelwa | 2013-07-15 11:01:30 -0700 (Mon, 15 Jul 2013) | 3 lines

Adding get_prots.pl to the Windows installer so that it'll get installed.


------------------------------------------------------------------------
r6237 | dshteyn | 2013-07-11 17:30:59 -0700 (Thu, 11 Jul 2013) | 1 line

protxml2html.pl: fix problem with GAGGLE Results not showing up when enabled
------------------------------------------------------------------------
r6234 | real_procopio | 2013-06-27 16:41:02 -0700 (Thu, 27 Jun 2013) | 1 line

[Petunia] Merging changes from commit#6224: mostly page and code formatting
------------------------------------------------------------------------
r6233 | slagelwa | 2013-06-27 13:43:22 -0700 (Thu, 27 Jun 2013) | 3 lines

Be a little less rigorous about checking the amino acid codes.


------------------------------------------------------------------------
r6231 | slagelwa | 2013-06-26 10:12:18 -0700 (Wed, 26 Jun 2013) | 3 lines

Bumping RC version


------------------------------------------------------------------------
r6230 | dshteyn | 2013-06-25 16:40:13 -0700 (Tue, 25 Jun 2013) | 1 line

get_prot.pl filter_out feature didn't filter out...fixed
------------------------------------------------------------------------
r6229 | dshteyn | 2013-06-25 16:22:43 -0700 (Tue, 25 Jun 2013) | 1 line

Should work under https or http
------------------------------------------------------------------------
r6228 | dshteyn | 2013-06-25 16:18:18 -0700 (Tue, 25 Jun 2013) | 1 line

Make it work on linux or windows
------------------------------------------------------------------------
r6227 | dshteyn | 2013-06-25 11:52:34 -0700 (Tue, 25 Jun 2013) | 1 line

Proper quote escape to work on linux and windows.
------------------------------------------------------------------------
r6226 | dshteyn | 2013-06-25 10:14:00 -0700 (Tue, 25 Jun 2013) | 1 line

wrong perl path
------------------------------------------------------------------------
r6225 | dshteyn | 2013-06-25 10:05:59 -0700 (Tue, 25 Jun 2013) | 1 line

get_prots.pl copy to bin
------------------------------------------------------------------------
r6223 | dshteyn | 2013-06-24 16:30:14 -0700 (Mon, 24 Jun 2013) | 1 line

Wrong path to perl
------------------------------------------------------------------------
r6222 | slagelwa | 2013-06-24 12:59:14 -0700 (Mon, 24 Jun 2013) | 3 lines

Proteowizard dlls have changed.  Used DependencyWalker to update list of
dlls to package with TPP.

------------------------------------------------------------------------
r6221 | slagelwa | 2013-06-24 09:53:41 -0700 (Mon, 24 Jun 2013) | 3 lines

Merging David's last set of changes on the trunk into the 4.6.3 branch at his request.


------------------------------------------------------------------------
r6220 | slagelwa | 2013-06-21 12:04:19 -0700 (Fri, 21 Jun 2013) | 2 lines

Set the version and RC number

------------------------------------------------------------------------
r6219 | slagelwa | 2013-06-21 10:28:43 -0700 (Fri, 21 Jun 2013) | 9 lines

[branch 4.6.3] creating a 4-6-3 branch from revision r6212 of the trunk

* Using new branch point instead of 4-6 branch to reduce merging 
  conflicts/issues

* Also using revision prior to last set of most recent check ins as
  that work isn't quite ready for production


------------------------------------------------------------------------
r6212 | slagelwa | 2013-06-19 08:29:27 -0700 (Wed, 19 Jun 2013) | 3 lines

Updating COMET_VERSION to reflect latest version


------------------------------------------------------------------------
r6211 | slagelwa | 2013-06-18 14:58:32 -0700 (Tue, 18 Jun 2013) | 2 lines

Updating to 2013.01 rev. 0 version of comet

------------------------------------------------------------------------
r6210 | slagelwa | 2013-06-17 12:46:48 -0700 (Mon, 17 Jun 2013) | 7 lines

* Updated how spot/ec2 instance statuses are reported
* Added a Myrimatch command line "parameter".  The latest versions of
  Myrimatch no longer contain a parameter for the number of cpu's to use.  This
  can now only be specified on the command line of the program.
* Left out Comet test scripts from check-in.


------------------------------------------------------------------------
r6209 | henryhlam | 2013-06-14 21:12:43 -0700 (Fri, 14 Jun 2013) | 1 line

[SpectraST] Different m/z tolerance for alignment and annotation; By default don't print top hits with zero f-value.
------------------------------------------------------------------------
r6208 | slagelwa | 2013-06-13 10:50:17 -0700 (Thu, 13 Jun 2013) | 4 lines

Moved the old sequest.params file to sequest27.params to indicate its the old
template.  Then added the new sequest template.


------------------------------------------------------------------------
r6207 | slagelwa | 2013-06-10 15:54:07 -0700 (Mon, 10 Jun 2013) | 3 lines

Added back in s3cmd stuff.  


------------------------------------------------------------------------
r6206 | slagelwa | 2013-06-10 10:23:52 -0700 (Mon, 10 Jun 2013) | 2 lines

Accidently did in perl path

------------------------------------------------------------------------
r6205 | slagelwa | 2013-06-07 15:37:28 -0700 (Fri, 07 Jun 2013) | 2 lines

Removing Comet2XML from Windows installer

------------------------------------------------------------------------
r6204 | eng_jk | 2013-06-07 10:54:03 -0700 (Fri, 07 Jun 2013) | 2 lines

get rid of Comet2XML

------------------------------------------------------------------------
r6203 | slagelwa | 2013-06-06 11:23:56 -0700 (Thu, 06 Jun 2013) | 6 lines

* Revised S3 sync functionality so that it handles going both
  up and down more gracefully.
* Disabled use of Amazon account management to write s3cfg
  files. S3 sync now only available if one manually configures
  it. (TWA does this for users btw) 

------------------------------------------------------------------------
r6202 | dshteyn | 2013-06-05 10:47:31 -0700 (Wed, 05 Jun 2013) | 1 line

BUGFIX: fixed problem with FPKM model being used when not selected.
------------------------------------------------------------------------
r6201 | dshteyn | 2013-06-04 15:28:17 -0700 (Tue, 04 Jun 2013) | 1 line

BUGFIX: InteractParser generated some bad results on Comet data with missing search_hits.
------------------------------------------------------------------------
r6200 | slagelwa | 2013-06-04 10:53:39 -0700 (Tue, 04 Jun 2013) | 2 lines

Development snapshot

------------------------------------------------------------------------
r6199 | slagelwa | 2013-06-04 09:35:35 -0700 (Tue, 04 Jun 2013) | 12 lines

Added checking for valid amino acid codes in fasta sequences.  

X!Tandem expects the codes to be capital letters which it uses in a lookup table.  If
they aren't it ends up reading invalid memory.  For now it just emits a warning when
invalid codes are seen (which is outputted prior to the inevitable core dump).  We try
to only output output the warning once so as to not overwhelm the output with millions
of messages but due to the way the threading is implemented you'll likely see the
warning printed once for each thread. 

For now the check confirms that the code is one of A-Z, but not U, O, J, or X.


------------------------------------------------------------------------
r6198 | dshteyn | 2013-05-31 12:40:23 -0700 (Fri, 31 May 2013) | 1 line

 PTMProphet:  handling of various odds mods.  iProphet: FPKM. ProteinProphet: FPKM
------------------------------------------------------------------------
r6197 | dshteyn | 2013-05-31 12:39:38 -0700 (Fri, 31 May 2013) | 1 line

InteractParser: large memory issue bug.
------------------------------------------------------------------------
r6196 | dshteyn | 2013-05-31 12:34:36 -0700 (Fri, 31 May 2013) | 1 line

RTCatalog: use XICs to compute RT stats.
------------------------------------------------------------------------
r6195 | dshteyn | 2013-05-31 12:33:21 -0700 (Fri, 31 May 2013) | 1 line

RefreshParser: treat in sequence stop codons as tryptic sites, count and output num_tot_proteins.
------------------------------------------------------------------------
r6194 | mhoopmann | 2013-05-29 13:13:54 -0700 (Wed, 29 May 2013) | 1 line

Added filter line to scan header output.
------------------------------------------------------------------------
r6193 | mhoopmann | 2013-05-29 13:04:07 -0700 (Wed, 29 May 2013) | 1 line

Added filter line and centroid status to ramp interface for mzML, mzXML, and mz5.
------------------------------------------------------------------------
r6192 | eng_jk | 2013-05-28 13:14:50 -0700 (Tue, 28 May 2013) | 2 lines

add util to grab the uniprot proteomes databases and append contaminants

------------------------------------------------------------------------
r6191 | slagelwa | 2013-05-17 22:39:07 -0700 (Fri, 17 May 2013) | 5 lines

Added s3cmd syncing of tppdata on a node (configured through the EC2 userdata
scripts).  Also slightly better checking of EC2 states in TWA.  Also fixed
and/or updated a few things in the ec2 creation scripts.


------------------------------------------------------------------------
r6190 | slagelwa | 2013-05-15 23:23:28 -0700 (Wed, 15 May 2013) | 6 lines

Addresses a compiler issue iwth latest  Windows/MingW and Ubuntu. With Linux g++ version 4.1.2 the overloaded 
constructor construct is allowed but with g++ 4.6.2 it complains about having a constructor call itself. 
Regardless its unnecessary to have both constructors since the definition is assigning a default value to the
last parameter anyhow.


------------------------------------------------------------------------
r6189 | slagelwa | 2013-05-15 16:02:06 -0700 (Wed, 15 May 2013) | 2 lines

First pass at adding S3 sync functionality to Petunia interface

------------------------------------------------------------------------
r6188 | dshteyn | 2013-05-15 11:50:40 -0700 (Wed, 15 May 2013) | 1 line

PTMProphet: fix reporting of mods on peptides with an n-terminal mod.
------------------------------------------------------------------------
r6187 | dshteyn | 2013-05-15 10:51:26 -0700 (Wed, 15 May 2013) | 1 line

PTMProphet: further improve handling and reporting of unusual or unknown mods.
------------------------------------------------------------------------
r6186 | dshteyn | 2013-05-15 10:47:38 -0700 (Wed, 15 May 2013) | 1 line

SpectraST: BUG not reading usernmods correctly FIXED
------------------------------------------------------------------------
r6185 | slagelwa | 2013-05-13 13:14:52 -0700 (Mon, 13 May 2013) | 6 lines

Merging in r6013 fix on 4.6 branch for 4.6.2 that didn't
make it to trunk.  Also should address similar issue 
under Ubuntu.  Essentially the constructor was overloadded
to call itself, unnecessarily.


------------------------------------------------------------------------
r6184 | dshteyn | 2013-05-09 11:14:52 -0700 (Thu, 09 May 2013) | 1 line

decoyFastaGenerator.pl :  adding an index to the Decoy protein names to make them unique (for MyriMatch indexing)
------------------------------------------------------------------------
r6183 | eng_jk | 2013-05-07 14:00:52 -0700 (Tue, 07 May 2013) | 2 lines

parse 'r' for rapid scan in filter line; add Velos Pro instrument

------------------------------------------------------------------------
r6182 | dshteyn | 2013-04-30 11:02:43 -0700 (Tue, 30 Apr 2013) | 1 line

PTMProphet:  fixing bug with handling of unusual mods.
------------------------------------------------------------------------
r6181 | slagelwa | 2013-04-09 15:28:49 -0700 (Tue, 09 Apr 2013) | 23 lines

* Now supports Comet!

* Updated VM::EC2 dependency to include a version as some of the older versions
  had bugs we had to implement workarounds for and those have since been removed
  as they are incompatible with the recent versions of VM::EC2.

* No longer base64 the user-data bootstrap script when starting spot instances.
  VM::EC2 now does this for you (see previous statement).

* Added apt-get update to the bootstrap script to update the ubuntu
  repositories before updating the image

* Removed Cwd::realpath call on all S3 put of files.  Problem is when
  we use the realpath(or its alias, abs_path) it resolves both ".." and more
  importantly *links*. So what happens is that if you have a path in a 
  parameters file the happens to have links in it the phys path to the file gets  
  used.  Then on the server end when you run a search it can't find the file 
  it read from in the parameter file.

  So instead of globably applying a physical path instead do it explictly before
  calling put() -- but only if its needed.


------------------------------------------------------------------------
r6180 | dshteyn | 2013-04-09 14:20:26 -0700 (Tue, 09 Apr 2013) | 1 line

SpectraST change for PTMProphet: recongnize Lys4 mod.
------------------------------------------------------------------------
r6179 | slagelwa | 2013-04-05 14:36:10 -0700 (Fri, 05 Apr 2013) | 3 lines

Added the option of using basic authentication from the browser
instead of its own user authentication scheme.

------------------------------------------------------------------------
r6178 | slagelwa | 2013-04-03 09:47:53 -0700 (Wed, 03 Apr 2013) | 4 lines

It seems that newer xsltproc programs check the validity of the xsl and
require the params directive for a template to be before any variables.


------------------------------------------------------------------------
r6177 | eng_jk | 2013-04-02 13:35:01 -0700 (Tue, 02 Apr 2013) | 2 lines

update getdb scripts

------------------------------------------------------------------------
r6176 | slagelwa | 2013-04-01 11:48:24 -0700 (Mon, 01 Apr 2013) | 6 lines

* Added parameter checking to qcomet
* Runs interactparser on myrimatch output
* Updated myrimatch parameters
* Removed /hpc/bin/perl reference in qmascot


------------------------------------------------------------------------
r6175 | dshteyn | 2013-03-29 13:06:52 -0700 (Fri, 29 Mar 2013) | 1 line

PTMProphet:  terminal mods specified with uppercase characters in the pepXML needed to be lowercased first so that they don't appear on N and C amino acids.
------------------------------------------------------------------------
r6174 | eng_jk | 2013-03-29 12:37:31 -0700 (Fri, 29 Mar 2013) | 2 lines

forgot to delete these lines before 6173 checkin

------------------------------------------------------------------------
r6173 | eng_jk | 2013-03-29 12:35:13 -0700 (Fri, 29 Mar 2013) | 4 lines

Simple workarounds for Dta input and fixPath() horribleness.
This workaround allows the programs to still display spectra from mzXML input when Dta directory exists but Dta file does not.
In this scenario, fixPath() overwrites input file with directory and thus the program never gets to test mzXML input.

------------------------------------------------------------------------
r6172 | dshteyn | 2013-03-29 12:21:13 -0700 (Fri, 29 Mar 2013) | 1 line

PTMProphet: fix issues with handling of peptides with n-terminal mods (e.g. iTRAQ)
------------------------------------------------------------------------
r6171 | dshteyn | 2013-03-28 14:24:49 -0700 (Thu, 28 Mar 2013) | 1 line

RTCalc: bugfix in memory with artificial neural network usage.
------------------------------------------------------------------------
r6170 | dshteyn | 2013-03-27 16:27:08 -0700 (Wed, 27 Mar 2013) | 1 line

iProphet: NSP model was broken.
------------------------------------------------------------------------
r6169 | dshteyn | 2013-03-27 16:24:03 -0700 (Wed, 27 Mar 2013) | 1 line

PTMProphet: Change the algorithm to detect unspecified modiciation, previous had a bug that would invalidate some peptides with valid mods.
------------------------------------------------------------------------
r6168 | slagelwa | 2013-03-27 14:04:29 -0700 (Wed, 27 Mar 2013) | 2 lines

Include the actual binaries

------------------------------------------------------------------------
r6167 | slagelwa | 2013-03-27 14:01:48 -0700 (Wed, 27 Mar 2013) | 6 lines

Adding Comet to TPP.  Instead of building from source and dealing with those
complications instead take advanatage of the fact that binaries are already
build, released, and maintained by the developers of Comet and have no 
system dependencies.


------------------------------------------------------------------------
r6166 | dshteyn | 2013-03-26 16:55:54 -0700 (Tue, 26 Mar 2013) | 1 line

PTMProphet: fix out putting of options to pepXML, throw a warning and skip peptides with unspecified variable mods instead of silently removing unspecified mod.
------------------------------------------------------------------------
r6165 | slagelwa | 2013-03-25 15:09:54 -0700 (Mon, 25 Mar 2013) | 1 line

Fixed what looked to be a typo.
------------------------------------------------------------------------
r6164 | slagelwa | 2013-03-25 11:25:51 -0700 (Mon, 25 Mar 2013) | 4 lines

Added XPRESS schema change for Patrick. New attribute "ppmtol" which
specifies whether or nott the masstol is in ppm (1) or daltons (0). 


------------------------------------------------------------------------
r6163 | slagelwa | 2013-03-25 10:40:08 -0700 (Mon, 25 Mar 2013) | 2 lines

Sloppy cut&paster.

------------------------------------------------------------------------
r6162 | slagelwa | 2013-03-25 10:38:57 -0700 (Mon, 25 Mar 2013) | 9 lines

Get rid of "flashy" console on Windows.

The background client process was causing a console window 
to briefly popup.  The problem lies deep within LWP::UserAgent.
I put it a nasty hack to keep the window from showing.  This 
hack could present problems for users with alternative character
sets.


------------------------------------------------------------------------
r6161 | ppatrick | 2013-03-25 06:40:09 -0700 (Mon, 25 Mar 2013) | 2 lines

Added support for ppm tolerance (-a) to XPRESS.

------------------------------------------------------------------------
r6160 | real_procopio | 2013-03-21 14:33:28 -0700 (Thu, 21 Mar 2013) | 1 line

[plot-msms] Do not error if dta file itself cannot be found, as its path may still be valid.
------------------------------------------------------------------------
r6159 | slagelwa | 2013-03-18 14:42:37 -0700 (Mon, 18 Mar 2013) | 2 lines

Removing said file from r6158

------------------------------------------------------------------------
r6158 | slagelwa | 2013-03-18 14:35:46 -0700 (Mon, 18 Mar 2013) | 5 lines

No longer calls the shell script find_arch.sh to determine the name of the Linux
distribution but instead uses the standard lsb_release command.  In the case
where this command fails fall back on the word 'unknown'.


------------------------------------------------------------------------
r6157 | henryhlam | 2013-03-15 06:23:39 -0700 (Fri, 15 Mar 2013) | 1 line

[SpectraST] Fix minor bug in similarity clustering; Other immaterial changes.
------------------------------------------------------------------------
r6156 | slagelwa | 2013-03-13 11:42:31 -0700 (Wed, 13 Mar 2013) | 5 lines

Increased buffer sizes to accommodate long paths otherwise we get 
buffer overruns and have a bad day.  Also removed a spurious 
debugging statement I left in.


------------------------------------------------------------------------
r6155 | dshteyn | 2013-03-12 12:54:53 -0700 (Tue, 12 Mar 2013) | 1 line

InteractParser: had extra closing tags left over from original enzyme entry
------------------------------------------------------------------------
r6154 | slagelwa | 2013-03-11 14:53:33 -0700 (Mon, 11 Mar 2013) | 4 lines

Fixes issue with trying to view mz*ML files with no MS1 spectrum by
initializing bounding ranges before reading scans from file and then
checking that there is indeed a range.

------------------------------------------------------------------------
r6153 | dshteyn | 2013-03-11 11:03:16 -0700 (Mon, 11 Mar 2013) | 1 line

InteractParser: when enzyme is given on the commandline it should overwrite the sample_enzyme in the pepXML file.
------------------------------------------------------------------------
r6152 | real_procopio | 2013-03-08 16:56:24 -0800 (Fri, 08 Mar 2013) | 1 line

[Petunia] Added PTMProphet to xinteract page; Added NOFPKM option to iProphet; and of course we had to change the default file name extension of iProphet files from 'iproph' to 'ipro'.  Yea...  Someone should test this since I am going on vacation...NOW!
------------------------------------------------------------------------
r6151 | slagelwa | 2013-03-08 15:12:37 -0800 (Fri, 08 Mar 2013) | 3 lines

Now validates interprophet pep.xml


------------------------------------------------------------------------
r6150 | dshteyn | 2013-03-08 15:07:41 -0800 (Fri, 08 Mar 2013) | 1 line

Sequest model:  expect score not implemented...disable by default.
------------------------------------------------------------------------
r6149 | dshteyn | 2013-03-08 15:06:57 -0800 (Fri, 08 Mar 2013) | 1 line

iProphet: save peptideprophet analysis_summary tags and report in iProphet pep.xml for schema validation.
------------------------------------------------------------------------
r6148 | dshteyn | 2013-03-08 15:06:04 -0800 (Fri, 08 Mar 2013) | 1 line

xinteract: options to run PTMProphet.
------------------------------------------------------------------------
r6147 | dshteyn | 2013-03-08 14:22:52 -0800 (Fri, 08 Mar 2013) | 1 line

iProphet: auto-disable models without data
------------------------------------------------------------------------
r6146 | dshteyn | 2013-03-08 12:54:35 -0800 (Fri, 08 Mar 2013) | 1 line

iProphet: FPKM model, pep.xml output enhancement to improve schema compliance, etc... 
------------------------------------------------------------------------
r6145 | dshteyn | 2013-03-08 12:52:59 -0800 (Fri, 08 Mar 2013) | 1 line

PTMProphet: improved handling of bad input, also adding pep.xml tags to validate against schema.
------------------------------------------------------------------------
r6144 | dshteyn | 2013-03-07 11:25:43 -0800 (Thu, 07 Mar 2013) | 1 line

xinteract: put quotes around decoy_tag incase it contains characters interpreted by shell, submitted by Frank Liu
------------------------------------------------------------------------
r6143 | slagelwa | 2013-03-06 20:17:18 -0800 (Wed, 06 Mar 2013) | 26 lines

In the herculean effort to try to get pep.xml to actually validate against its
TPP schema I identified and corrected the following issues.  These changes by
no means fix all of the validation problems in the format at this point but it
did validate a pep.xml file created in part of the demo2009 tutorial.

   * Cosmetic change.  I moved the interact_summary, libra_result, and 
     libra_summary elements above the comment that says "the types used by 
     above elements".  I'm guessing these were added at a later date and just
     appended to the bottom of the file so I figured I'd honor the comments 
     wishes...

   * Changed the search engine type COMET to Comet, as that's what seems to be
     used.

   * Added attribute charge_est_correct to the roc_error_data element with a
     annotation "Confidence in estimation of the charge state".  I'm assuming 
     this is correct and that this attribute is optional and is not required.

   * Added optional search_engine attribute (via engineType) to 
     msms_run_summary.  

   * Added the '^' symbol to the enumeration of allowable terminal symbols.  We
     should probably reevaluate this as some search engines allow you to choose
     your character and I'm not sure if that's a factor in this list.


------------------------------------------------------------------------
r6142 | slagelwa | 2013-03-06 11:07:14 -0800 (Wed, 06 Mar 2013) | 4 lines

Fixed invalid schema definitions for roc_error_data.  This schema definition
file is now valid.


------------------------------------------------------------------------
r6141 | real_procopio | 2013-03-05 19:07:48 -0800 (Tue, 05 Mar 2013) | 1 line

[Petunia] Add new -X -Q -G (remove precursor, iTRAQ, TMT peaks) options, and clarify 'all' scans option in MzXML2Search
------------------------------------------------------------------------
r6140 | real_procopio | 2013-03-05 18:31:39 -0800 (Tue, 05 Mar 2013) | 1 line

[MzXML2Search] Update usage statement
------------------------------------------------------------------------
r6139 | real_procopio | 2013-03-05 16:23:00 -0800 (Tue, 05 Mar 2013) | 1 line

[Pep3D] Stop using old Pep3D spectrum viewer; link to Lorikeet instead.Also required adding the precursorCharge to the cid/peptide data structure.
------------------------------------------------------------------------
r6138 | real_procopio | 2013-03-05 15:49:40 -0800 (Tue, 05 Mar 2013) | 9 lines

[plot-msms-js]

- Added support for displaying unidentified spectra
- Added support for passing an mz[X]ML file + scan number and charge in the URL; no need to construct a fake .dta name
- If precursor m/z is passed, then do not compute it from sequence and charge
- Added check for File or Dta passed from URL to avoid cryptic error message downstream
- Display error messages on the screen where users can read them (and not within the html code)
- Added page title and (common TPP) footer with version info

------------------------------------------------------------------------
r6137 | slagelwa | 2013-03-05 15:44:54 -0800 (Tue, 05 Mar 2013) | 15 lines

I noticed that the pepXML schema wasn't validating and that
there were a number of changes done to 117 that should probably 
have been rolled out as a v118.  Therefore:

* Added a README to remind people to increment versions
* Created a new pepXML_v118. I made this from a copy of r5616 
  of pepXML_v117 as Jimmy's last set of changes made some
  formatting/whitespace alternations that I wanted to back out.
  I then re-merged Jimmy's changes into this.  
* Touched pepXML_v117 so that this comment appears on it.
* Fixed a validation issue introduced with the last change.

The new schema still isn't validating correctly, fyi.


------------------------------------------------------------------------
r6136 | dshteyn | 2013-03-05 15:17:56 -0800 (Tue, 05 Mar 2013) | 1 line

iProphet: fix bug introduced with NSP value caching.
------------------------------------------------------------------------
r6135 | dshteyn | 2013-03-05 13:47:51 -0800 (Tue, 05 Mar 2013) | 1 line

iProphet: passing wrong hashtable fixed.
------------------------------------------------------------------------
r6134 | dshteyn | 2013-03-05 13:07:53 -0800 (Tue, 05 Mar 2013) | 1 line

iProphet: Fast NSP computation from caching... Log space summation of doubles to deal with rounding issue.
------------------------------------------------------------------------
r6133 | slagelwa | 2013-03-04 17:05:44 -0800 (Mon, 04 Mar 2013) | 7 lines

GCC 4.6.2 (MingW) was complaining about const char * vs char *.  The exact error message was:

   Visualization/Comet/comet-pepxml/comet-pepxml.cxx: In function 'int main()':
   Visualization/Comet/comet-pepxml/comet-pepxml.cxx:112:60: error: deprecated conversion from string constant to 'char*' [-Werror=write-strings]

Instead of disabling the error using no-write-strings,  it seemed better to just make the 2nd argument to GET_VAL be a const char *.  Then the only other change that was needed wash the funky cast needed on the static strings returned.  If anyone has a better way please change.

------------------------------------------------------------------------
r6132 | slagelwa | 2013-03-04 15:54:30 -0800 (Mon, 04 Mar 2013) | 4 lines

Reimplemented the changes in r6130. This time without the
whitespace/tab changes.


------------------------------------------------------------------------
r6131 | slagelwa | 2013-03-04 15:49:31 -0800 (Mon, 04 Mar 2013) | 1 line

reverting back to 6129 as my editor did somethign funny with whitespace
------------------------------------------------------------------------
r6130 | slagelwa | 2013-03-04 15:03:00 -0800 (Mon, 04 Mar 2013) | 6 lines

Corrects and issue between const char * and char * pointers that was 
seen in gcc version 4.4.  Not seen in 4.1 gcc nor 4.6.2.  Regardless one
probably shouldn't be changing a const string even if the compiler
lets you.  (And yes, I also don't like doing pointer math myself).


------------------------------------------------------------------------
r6129 | dshteyn | 2013-03-04 14:52:20 -0800 (Mon, 04 Mar 2013) | 1 line

follow-up commit
------------------------------------------------------------------------
r6128 | dshteyn | 2013-03-04 14:48:54 -0800 (Mon, 04 Mar 2013) | 1 line

PTMProphet: using clean function from spectrast, also better error reporting and a bugfix.
------------------------------------------------------------------------
r6127 | slagelwa | 2013-03-04 13:18:36 -0800 (Mon, 04 Mar 2013) | 11 lines

The MingW g++ compiler (version 4.6.2) was complaining about a vector
intialization. It wasn't a problem in our earlier CentOS (version 4.1.2) 
compiler.

I believe that the two parameter vector constructor in std::vector expects the 
second parameter to be a reference. I guess its possible that older versions
of the compiler didn't check that NULL wasn't a reference.

Anyhow hopefully Henry can take a look at this and make sure it works.


------------------------------------------------------------------------
r6126 | dshteyn | 2013-03-02 14:00:57 -0800 (Sat, 02 Mar 2013) | 1 line

InterProphetParser: bugfix, order of elements affected the computed probabilities (very slightly but noticeably), fixed.
------------------------------------------------------------------------
r6125 | henryhlam | 2013-03-02 04:37:40 -0800 (Sat, 02 Mar 2013) | 1 line

[SpectraST] Follow-up to last check-in: Makefile for compiling SpectraST independent of the rest of TPP (needs GSL installed in /usr/lib)
------------------------------------------------------------------------
r6124 | henryhlam | 2013-03-02 04:16:18 -0800 (Sat, 02 Mar 2013) | 1 line

[SpectraST] Updated denoiser; Factorize code in SpectraSTSpLibImporter; Two new filtering options for searching; Set Makefile dependency to all headers; Fix bug introduced in last revision in SpectraSTPeakList::simplify and SpectraSTPeakList::getNthLargestPeak; SpectraSTPeakList::clean for use in PTMProphet
------------------------------------------------------------------------
r6123 | slagelwa | 2013-02-27 16:57:39 -0800 (Wed, 27 Feb 2013) | 11 lines

* Use default !perl on bin/ scripts so that Makefile.pl fills 
  them with the correct location of perl on a install
* No longer renames .pep.xml output with a myrimatch, omssa,
  tandem, or inspect substring.  This proved to problematic
  with the current mechanisms in TPP.
* Updated myrimatch parameters in test to match new version
* Added even more input directory/output directory/input
  file name/output filename handling of the searches
* Now runs InteractParser on the output files of myrimatch,
  OMSSA to correct pep.xml issues.

------------------------------------------------------------------------
r6122 | dshteyn | 2013-02-27 12:24:17 -0800 (Wed, 27 Feb 2013) | 1 line

PepXMLViewer.cgi: correct valgrind issues.
------------------------------------------------------------------------
r6121 | dshteyn | 2013-02-27 11:43:49 -0800 (Wed, 27 Feb 2013) | 1 line

PepXMLViewer: was crashing inside std::sort, changed to std::stable_sort which seems more stable ;)
------------------------------------------------------------------------
r6120 | eng_jk | 2013-02-27 09:36:39 -0800 (Wed, 27 Feb 2013) | 2 lines

fix parsing mass types, misc cleanup

------------------------------------------------------------------------
r6119 | eng_jk | 2013-02-26 17:33:32 -0800 (Tue, 26 Feb 2013) | 2 lines

bit of file parsing optimization

------------------------------------------------------------------------
r6118 | eng_jk | 2013-02-26 17:11:53 -0800 (Tue, 26 Feb 2013) | 2 lines

add two css entries to support comet-pepxml.cgi

------------------------------------------------------------------------
r6117 | eng_jk | 2013-02-26 17:02:55 -0800 (Tue, 26 Feb 2013) | 2 lines

add link to comet-pepxml.cgi for Comet search hits

------------------------------------------------------------------------
r6116 | eng_jk | 2013-02-26 16:53:27 -0800 (Tue, 26 Feb 2013) | 2 lines

add Makefile support for comet-pepxml.cgi to view top N hits from a Comet pep.xml file

------------------------------------------------------------------------
r6115 | eng_jk | 2013-02-26 16:32:13 -0800 (Tue, 26 Feb 2013) | 2 lines

add cgi to display top N peptide hits from comet pep.xml file

------------------------------------------------------------------------
r6114 | real_procopio | 2013-02-26 15:15:51 -0800 (Tue, 26 Feb 2013) | 1 line

[plot-msms-js] Move web path to a global variable so it's easier to override
------------------------------------------------------------------------
r6113 | dshteyn | 2013-02-26 11:13:27 -0800 (Tue, 26 Feb 2013) | 1 line

iProphet: more meaningful error
------------------------------------------------------------------------
r6112 | dshteyn | 2013-02-26 09:33:40 -0800 (Tue, 26 Feb 2013) | 1 line

Thiophospho modification
------------------------------------------------------------------------
r6111 | dshteyn | 2013-02-22 16:28:39 -0800 (Fri, 22 Feb 2013) | 1 line

PTMProphet: more error tolerant to various pepXML flavors of referencing the data.
------------------------------------------------------------------------
r6110 | dshteyn | 2013-02-22 15:38:26 -0800 (Fri, 22 Feb 2013) | 2 lines

exit header

------------------------------------------------------------------------
r6109 | dshteyn | 2013-02-22 12:49:05 -0800 (Fri, 22 Feb 2013) | 1 line

PTMProphet: additional output.
------------------------------------------------------------------------
r6108 | dshteyn | 2013-02-22 12:13:19 -0800 (Fri, 22 Feb 2013) | 1 line

SpectraST:  BUGFIX crashed on simplify since the rankByIntensity function can remove some peaks, numPeaks needs to be reset.
------------------------------------------------------------------------
r6107 | dshteyn | 2013-02-22 11:17:11 -0800 (Fri, 22 Feb 2013) | 1 line

PTMProphet: fix datafile error checking issue.
------------------------------------------------------------------------
r6106 | dshteyn | 2013-02-22 11:07:43 -0800 (Fri, 22 Feb 2013) | 1 line

PTMProphet: remove unused SpectraST call that was breaking with seg fault, also more error checking to specify a data file that couldn't be opened.
------------------------------------------------------------------------
r6105 | dshteyn | 2013-02-22 10:03:03 -0800 (Fri, 22 Feb 2013) | 1 line

extra character
------------------------------------------------------------------------
r6104 | henryhlam | 2013-02-22 03:38:45 -0800 (Fri, 22 Feb 2013) | 1 line

[SpectraST] Fix potential crash when building consensus library in SpectraSTPeakList::simplify()
------------------------------------------------------------------------
r6103 | dshteyn | 2013-02-21 23:28:21 -0800 (Thu, 21 Feb 2013) | 1 line

remove extra character
------------------------------------------------------------------------
r6102 | dshteyn | 2013-02-21 23:26:51 -0800 (Thu, 21 Feb 2013) | 1 line

MSGF+ support
------------------------------------------------------------------------
r6101 | dshteyn | 2013-02-21 22:49:21 -0800 (Thu, 21 Feb 2013) | 1 line

MSGF+ support
------------------------------------------------------------------------
r6100 | dshteyn | 2013-02-21 22:47:02 -0800 (Thu, 21 Feb 2013) | 1 line

MSGF+ support
------------------------------------------------------------------------
r6099 | dshteyn | 2013-02-21 22:45:28 -0800 (Thu, 21 Feb 2013) | 1 line

MSGF+ support
------------------------------------------------------------------------
r6098 | dshteyn | 2013-02-21 15:10:35 -0800 (Thu, 21 Feb 2013) | 1 line

gzstream: if file cannot be opened capture the error, print and exit.
------------------------------------------------------------------------
r6097 | real_procopio | 2013-02-20 17:18:00 -0800 (Wed, 20 Feb 2013) | 1 line

[Petunia] Add HCD and no activation options to MzXML2Search; clean up mzML/mzXML text throughout
------------------------------------------------------------------------
r6096 | slagelwa | 2013-02-20 10:19:07 -0800 (Wed, 20 Feb 2013) | 2 lines

Doesn't like x's :(

------------------------------------------------------------------------
r6095 | slagelwa | 2013-02-19 17:32:15 -0800 (Tue, 19 Feb 2013) | 2 lines

Let everyone know who we are

------------------------------------------------------------------------
r6094 | slagelwa | 2013-02-19 16:04:47 -0800 (Tue, 19 Feb 2013) | 4 lines

Merged the 4.6 branch (release 4.6.2) into the trunk.  This was a manual merge
starting with revision 6013 on the branch to the HEAD of the branch.


------------------------------------------------------------------------


 
Personal tools