TPP:4.4.0 Release Notes

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Trans-Proteomic Pipeline (TPP) "Vuvuzela" 4.4.0 release notes

(Changes since the last official release, 4.3.1)

We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP) software, release 4.4.0 (4.4 revision). The software is available for Windows as well as linux (and unofficially) through OSX source from all the usual locations (please see the section below, "Getting the software"). Most users are recommended to use the Windows installer, which installs and configures the TPP and other required software (such as a webserver). For advanced users who need to customize the TPP, or for those who run high-throughput experiments, you can download the source code. Again, most users don't need build from source, and should use the Windows installer.

-''To developers:
+Trans-Proteomic Pipeline (TPP) "Vuvuzela" 4.4.0 release notes
-I put this page in place to help manage the 4.4.0 "Vuvuzela" release. The punch list is a list of tasks/issues that need to be
-resolved for the list. I'll incorporate the known issues and the release notes into the final release bulletin.  To facilitate the generation of the release notes I've captured all of the subversion change logs and sorted them by user.  Please review your set of changes condense them into what you want to say about the changes for the release.
-''
-== Punch List ==
+(Changes since the last official release, 4.3.1)
-* rebuild ReadW.exe, trapper, and mzWiff to include a message about their deprecation and also to update the version string
+We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP) software, release 4.4.0 (4.4 revision).  The software is available for Windows as well as linux (and unofficially) through OSX source from all the usual locations (please see the section below, "Getting the software").  Most users are recommended to use the Windows installer, which installs and configures the TPP and other required software (such as a webserver).  For advanced users who need to customize the TPP, or for those who run high-throughput experiments, you can download the source code.  Again, most users don't need build from source, and should use the Windows installer.
-== Known issues ==
-* none so far...
+== New Features/Changes ==
-== Release Notes ==
+=== Deprecation of Conversion Tools ===
-'' Trunk changes since revision 4498 (creation of 4.3 branch by spacepod)''
+* The mzXML conversion tools ReAdW, massWolf, trapper, and mzWiff and been deprecated and are no longer included in TPP.  All users are encouraged to use the converter tool <i>msconvert</i> produced as part of the ProeoWizard project.  This tool supports all the same native formats as the previous tools, is better supported, and implements the new HUPO-PSI mzML standard. For convenience a version of this tool has been included with this TPP release.
-=== cpaulse ===
+=== pepXML schema ===
-------------------------------------------------------------------------
+* New pepXML 1.15: Adds more search engines (ProteinPilot, ProteinLynx, Spectrum Mill, greylag, Phenyx, Proteios, Crux, Tide) and activation methods (ETD/CID, HCD).
-r4974 | cpaulse | 2010-05-13 12:13:21 -0700 (Thu, 13 May 2010) | 1 line
-fix tpp.sln for vc9
+=== MzXML2Search ===
-------------------------------------------------------------------------
+* Added "mzML" to usage statement
-r4918 | cpaulse | 2010-03-29 14:33:30 -0700 (Mon, 29 Mar 2010) | 5 lines
-Branch visual studio 8 tpp.sln file (and dependent vcproj files) to tppvc8.sln.
+=== Petunia ===
+* Moved mzXML utils to new tab
+* Changed wording on home page to state using mzML as the standard
+* Added indexmzXML page
+* Optionally authenticate against an .htpasswd entry (from J.Slagel)
+* Fix tabs (from 4.3 branch)
-tpp.sln and dependent vcproj files converted to visual studio 2008 express, with atl/mfc dependent projects (mzwiff, trapper, masswolf, readw), msconvert,  and pwiz_swig projects removed from tpp.sln (last two don't compile in 2008 express and have no internal dependencies).  extern/build_boost_vc8.bat renamed.
+New options
+* PeptideProphet:
+** Use Phospho model
-minor bug fix to release configuration of readmzXML.vcproj.
+* XPRESS:
-------------------------------------------------------------------------
+** Allow passing of negative mass offsets
-r4917 | cpaulse | 2010-03-29 11:08:10 -0700 (Mon, 29 Mar 2010) | 2 lines
+** Min Points needed
+** Sum N isotopic peaks)
+* MzXML2Search:
+** Output N Top Peaks
+** Max Charge State
+** Output Precision
+** Removed ion mass option
-Fix reading of search engine specific input data where multiple search results are present for a single spectrum.
+Technical changes:
-Compile warning in Visual C++ (PhosphoMixtureDistr.cxx).
+* Minor corrections to session handling
-------------------------------------------------------------------------
+* Add trailing slash to tppbin definition
-r4901 | cpaulse | 2010-03-12 08:51:32 -0800 (Fri, 12 Mar 2010) | 1 line
+* Added a variable to hold location of tpp-bin
+* Refer to tpp_hostname by full path
+* Silence perl warning (more to go...)
+* Provide path to plotspectrast.cgi when calling Lib2HTML
+* Minor form closing changes to avoid mis-formatting in IE
-fix destructor semantics for iProphet
-------------------------------------------------------------------------
-r4899 | cpaulse | 2010-03-10 12:04:17 -0800 (Wed, 10 Mar 2010) | 1 line
-don't delete RT and PI mixtureDistr's twice.
+=== xinteract ===
-------------------------------------------------------------------------
+* Adding isotopic peaks XPRESS option to usage statement
-r4898 | cpaulse | 2010-03-10 09:13:32 -0800 (Wed, 10 Mar 2010) | 1 line
-fix memory leaks in PeptideProphetParser, and type cast warnings generated by visual studio in spectrast
-------------------------------------------------------------------------
-r4890 | cpaulse | 2010-02-28 14:32:24 -0800 (Sun, 28 Feb 2010) | 1 line
-undo my destruction of Peptide::mods semantics.
+=== readmzXML ===
-------------------------------------------------------------------------
+* Add -r option to output spectrum data only; no title or extra CR's.  (Replicates functionality of Jimmy's getSpectrum)
-r4889 | cpaulse | 2010-02-26 11:35:58 -0800 (Fri, 26 Feb 2010) | 1 line
-more missed files intended for changeset 4885
-------------------------------------------------------------------------
-r4887 | cpaulse | 2010-02-26 11:19:01 -0800 (Fri, 26 Feb 2010) | 1 line
-missed from changeset 4885
+=== Pep3D ===
-------------------------------------------------------------------------
+* Enable viewing of MS2-only data (no elution, but at least you can see the distribution of sequencing events)
-r4885 | cpaulse | 2010-02-25 15:21:11 -0800 (Thu, 25 Feb 2010) | 1 line
+* Larger input field for filename
+* Use dhtml to print/display messages (also simplify error messages so they display correctly).
-modernize integer definitions enough to stop visual studio 9 from issuing warnings at level 3.
-------------------------------------------------------------------------
-=== real_procopio ===
-------------------------------------------------------------------------
+=== plot-msms (spectrum viewer) ===
-r5050 | real_procopio | 2010-07-08 19:52:33 -0700 (Thu, 08 Jul 2010) | 1 line
+* Added Image Size option
+* Update to unified look and feel
-Adding pepXML 1.15: more search engines and activation methods
-------------------------------------------------------------------------
-r5049 | real_procopio | 2010-07-08 19:48:18 -0700 (Thu, 08 Jul 2010) | 1 line
-Adding pepXML 1.15: more search engines and activation methods
+=== protxml2html (ProteinProphet viewer) ===
-------------------------------------------------------------------------
+* Add command-line usage statement
-r5048 | real_procopio | 2010-07-08 14:55:56 -0700 (Thu, 08 Jul 2010) | 1 line
+* Took out a bunch of commented-out code.
+* Performance improvements:
+** Define several 'global' variables in xsl to avoid costly lookups
+** Add option not to generate Gaggle files
+Limited testing gives speeds up to 5x faster than previous version.
-Add mzML to usage statement
-------------------------------------------------------------------------
-r4962 | real_procopio | 2010-04-23 17:36:19 -0700 (Fri, 23 Apr 2010) | 6 lines
-Added indexmzXML page;
+=== build system ===
-Moved mzXML utils to new tab;
-Changed wording on home page to state using mzML as the standard;
-Minor form closing changes to avoid mis-formatting in IE.
+TPP project fully converted to be built under C++ rules (vs mix of C and C++).
-------------------------------------------------------------------------
+OS X (not an officially supported system)
-r4960 | real_procopio | 2010-04-23 14:17:13 -0700 (Fri, 23 Apr 2010) | 1 line
+* use macports vs fink search paths for extra libraries;
+* add dectection for 64-bit OS X systems
-[petunia] Allow passing of negative mass offsets to XPRESS
+"win_lib" directory retired; relevant components moved into tpp/extern directory; components stored as compressed files when possible.
-------------------------------------------------------------------------
-r4959 | real_procopio | 2010-04-23 13:24:09 -0700 (Fri, 23 Apr 2010) | 1 line
-[petunia] Fix session logic mangled in commit 4952
+=== ASAPRatio ===
-------------------------------------------------------------------------
+* added experimental wavelet smoothing.  Test using new ASAPRatioPeptideParser -w command line option.  From WaveletQuant implmentation, http://www.biomedcentral.com/1471-2105/11/219
-r4958 | real_procopio | 2010-04-21 16:59:24 -0700 (Wed, 21 Apr 2010) | 1 line
-[petunia] Adding options to PeptideProphet (use Phospho model); XPRESS (Min Points needed, Sum N isotopic peaks); MzXML2Search (Output N Top Peaks, Max Charge State, Output Precision; removed ion mass option)
-------------------------------------------------------------------------
-r4957 | real_procopio | 2010-04-21 16:10:30 -0700 (Wed, 21 Apr 2010) | 1 line
-[xinteract] Adding isotopic peaks XPRESS option to usage statement
-------------------------------------------------------------------------
-r4952 | real_procopio | 2010-04-19 15:46:33 -0700 (Mon, 19 Apr 2010) | 1 line
-Minor corrections to session handling
-------------------------------------------------------------------------
-r4902 | real_procopio | 2010-03-12 15:51:22 -0800 (Fri, 12 Mar 2010) | 1 line
-Add -r option to output spectrum data only; no title or extra CR's.  (Replicates functionality of Jimmy's getSpectrum)
-------------------------------------------------------------------------
-r4883 | real_procopio | 2010-02-24 13:57:56 -0800 (Wed, 24 Feb 2010) | 1 line
-Enable viewing of MS2-only data (no elution, but at least you can see the distribution of sequencing events)
-------------------------------------------------------------------------
-r4880 | real_procopio | 2010-02-23 16:31:31 -0800 (Tue, 23 Feb 2010) | 1 line
-Larger input field for filename; use dhtml to print/display messages (also simplify error messages so they display correctly).
-------------------------------------------------------------------------
-r4812 | real_procopio | 2010-01-08 11:18:06 -0800 (Fri, 08 Jan 2010) | 1 line
-[Petunia] Add trailing slash to tppbin definition
-------------------------------------------------------------------------
-r4806 | real_procopio | 2009-12-22 17:28:35 -0800 (Tue, 22 Dec 2009) | 5 lines
-Optionally authenticate against an .htpasswd entry (from J.Slagel);
-Fix tabs (from 4.3 branch);
-Added a variable to hold location of tpp-bin;
-Refer to tpp_hostname by full path.
-------------------------------------------------------------------------
-r4799 | real_procopio | 2009-12-16 16:12:37 -0800 (Wed, 16 Dec 2009) | 1 line
-[plot-msms] Update to unified look and feel; add Image Size option
-------------------------------------------------------------------------
-r4797 | real_procopio | 2009-12-14 15:53:42 -0800 (Mon, 14 Dec 2009) | 9 lines
-Performance improvements:
-- Define several 'global' variables in xsl to avoid costly lookups;
-- Add option not to generate Gaggle files;
-Add command-line usage statement;
-Took out a bunch of commented-out code.
-Limited testing gives speeds up to 5x faster than previous version.
-------------------------------------------------------------------------
-r4796 | real_procopio | 2009-12-14 14:13:59 -0800 (Mon, 14 Dec 2009) | 1 line
-[Petunia] Silence perl warning (more to go...)
-------------------------------------------------------------------------
-r4516 | real_procopio | 2009-08-04 12:58:17 -0700 (Tue, 04 Aug 2009) | 1 line
-[Petunia] Provide path to plotspectrast.cgi when calling Lib2HTML
-------------------------------------------------------------------------
 === dctrud ===
 [win32 installer] temp rename of README to README.txt while building installer allows windows to know how to display the readme doc at install time.  Already did this for the MSVC installer build process, forgot about mingw.
 ------------------------------------------------------------------------
-=== ppatrick ===
+===PeptideProphetParser===
-------------------------------------------------------------------------
+* Replace SSRCalc with RTCalc for retention time modelling.
-r4850 | ppatrick | 2010-01-15 09:30:24 -0800 (Fri, 15 Jan 2010) | 1 line
-Fixed basePeak m/z and intensity bug for centroided data.
+* Using ppm in the accurate mass model
-------------------------------------------------------------------------
-=== dshteyn ===
-------------------------------------------------------------------------
+* Report error and don't model spectra with assumed_charge not equal to encoded charge in the name. Fix bug reported by Ludovic.
-r5035 | dshteyn | 2010-06-11 16:23:04 -0700 (Fri, 11 Jun 2010) | 1 line
-Removing debugging output
+* Adding InspectFvalue, PHOSPHO model, TOPCAT model.
-------------------------------------------------------------------------
-r5032 | dshteyn | 2010-06-10 10:26:29 -0700 (Thu, 10 Jun 2010) | 1 line
-Make sure there are enough bits.
+* tuning params on Tandem's semi-parametric model
-------------------------------------------------------------------------
-r5028 | dshteyn | 2010-06-09 11:13:33 -0700 (Wed, 09 Jun 2010) | 1 line
-RTCalc: copy coefficients file to staging area.
+* Inspect f-value model.
-------------------------------------------------------------------------
-r5027 | dshteyn | 2010-06-08 10:22:06 -0700 (Tue, 08 Jun 2010) | 1 line
-Adding RTCalc to list of executables to build
+* adjusting Myrimatch f-value params.
-------------------------------------------------------------------------
-r5026 | dshteyn | 2010-06-07 14:18:24 -0700 (Mon, 07 Jun 2010) | 1 line
-RTCalc: fix memory leak.
+* tweaking the discriminant function params for OMSSA analysis
-------------------------------------------------------------------------
-r5025 | dshteyn | 2010-06-07 11:33:34 -0700 (Mon, 07 Jun 2010) | 1 line
-Fix install of RTCalc under linux.
+* Caching variable bandwidth for quicker runtime.  New function varBWdensityFit now can also take an additional parameter of a pointer to a Fit object.
-------------------------------------------------------------------------
-r5024 | dshteyn | 2010-06-04 11:54:40 -0700 (Fri, 04 Jun 2010) | 1 line
-Remove source control directories after the PepcView copy.
+* PeptideProphetParser now stores all proteins matched by a search result.
-------------------------------------------------------------------------
-r5023 | dshteyn | 2010-06-04 11:27:02 -0700 (Fri, 04 Jun 2010) | 1 line
-Out2XML: Use all of the last part of the encoded spectrum name for the charge not just one character, for multi character charge states
+* Make tool more robust by auto trimming whitespace from spectrum names.  Tandem searches submitted by Scott Stansfield (Aug 2009) where generated with method mzXML->mgf->tandem->pepXML was adding an extra space to the end of spectrum name.  This commit addresses the issue with Scott's data.
-------------------------------------------------------------------------
-r5022 | dshteyn | 2010-06-04 11:05:43 -0700 (Fri, 04 Jun 2010) | 1 line
-Changes to get Pepc to install
+* Fixing seg fault appearing in MALDI mode on PROBID results.
-------------------------------------------------------------------------
-r5021 | dshteyn | 2010-06-04 10:40:48 -0700 (Fri, 04 Jun 2010) | 1 line
-RTCalc switch from size_t to int since value is initialized to -1
+* Fix memory leaks
-------------------------------------------------------------------------
-r5020 | dshteyn | 2010-06-03 12:05:33 -0700 (Thu, 03 Jun 2010) | 1 line
-Installing RTCalc and coefficients.
+=== David Shteynberg ===
-------------------------------------------------------------------------
-r5019 | dshteyn | 2010-06-03 12:04:59 -0700 (Thu, 03 Jun 2010) | 1 line
-Default coefficients.
+RTCalc new tool for RT prediction
-------------------------------------------------------------------------
-r5018 | dshteyn | 2010-06-03 12:03:45 -0700 (Thu, 03 Jun 2010) | 1 line
-Replace hard paths.
+Out2XML: Use all of the last part of the encoded spectrum name for the charge not just one character, for multi character charge states
-------------------------------------------------------------------------
-r5017 | dshteyn | 2010-06-02 12:57:19 -0700 (Wed, 02 Jun 2010) | 1 line
 PepXMLViewer: Display only top ranked search_hit.  Populate fields with search scores from any of the engines used in the analysis (useful for iProphet viewing).
-------------------------------------------------------------------------
-r5016 | dshteyn | 2010-06-02 12:52:13 -0700 (Wed, 02 Jun 2010) | 1 line
 ASAPRatio: changes to display ratios of secondary proteins from protein groups. TODO: Next and Prev Protein buttons will take you to the next protein group not the next protein in the group, should be corrected or disabled.
-------------------------------------------------------------------------
-r5015 | dshteyn | 2010-06-02 12:46:59 -0700 (Wed, 02 Jun 2010) | 1 line
-PeptideProphetParser: Replace SSRCalc with RTCalc for retention time modelling.
-------------------------------------------------------------------------
-r5014 | dshteyn | 2010-06-02 12:45:51 -0700 (Wed, 02 Jun 2010) | 1 line
-PeptideProphetParser: Replace SSRCalc with RTCalc for retention time modelling.
-------------------------------------------------------------------------
-r5013 | dshteyn | 2010-06-02 12:44:37 -0700 (Wed, 02 Jun 2010) | 1 line
-PeptideProphetParser: Add writing of .RTcoeff file for RT modeling
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-r5012 | dshteyn | 2010-06-02 12:40:18 -0700 (Wed, 02 Jun 2010) | 1 line
 RefreshParser: Only map unrejected peptides.
-------------------------------------------------------------------------
-r5011 | dshteyn | 2010-06-02 12:38:25 -0700 (Wed, 02 Jun 2010) | 1 line
-Store modified_peptide separately for RT calculation
-------------------------------------------------------------------------
-r5010 | dshteyn | 2010-06-02 12:36:45 -0700 (Wed, 02 Jun 2010) | 1 line
-RTCalc: New tool for replacing of SSRCalc in the TPP.
-------------------------------------------------------------------------
-r5009 | dshteyn | 2010-06-02 12:35:27 -0700 (Wed, 02 Jun 2010) | 1 line
-Add consts to unchanged input strings
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-r5008 | dshteyn | 2010-06-02 12:33:55 -0700 (Wed, 02 Jun 2010) | 1 line
-Add consts to unchanged input strings
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-r5007 | dshteyn | 2010-06-02 12:32:44 -0700 (Wed, 02 Jun 2010) | 1 line
-FANN and GSL build targets
-------------------------------------------------------------------------
-r5006 | dshteyn | 2010-06-02 12:31:55 -0700 (Wed, 02 Jun 2010) | 1 line
-FANN and GSL build targets
-------------------------------------------------------------------------
-r5005 | dshteyn | 2010-06-02 12:28:54 -0700 (Wed, 02 Jun 2010) | 1 line
-New libraries for RTCalc. Fast Artificial Neural Network (FANN).  GNU Scientific Lib (GSL)
-------------------------------------------------------------------------
-r5004 | dshteyn | 2010-06-02 12:24:03 -0700 (Wed, 02 Jun 2010) | 1 line
 ASAPRatio: changes to display ratios of secondary proteins from protein groups.
-------------------------------------------------------------------------
-r5002 | dshteyn | 2010-06-01 16:17:00 -0700 (Tue, 01 Jun 2010) | 1 line
-Using ppm in the accurate mass model
-------------------------------------------------------------------------
-r5001 | dshteyn | 2010-06-01 16:10:14 -0700 (Tue, 01 Jun 2010) | 1 line
-PeptideProphetParser:  New RT model.
-------------------------------------------------------------------------
-r5000 | dshteyn | 2010-06-01 16:06:39 -0700 (Tue, 01 Jun 2010) | 1 line
-PeptideProphetParser: Report error and don't model spectra with assumed_charge not equal to encoded charge in the name. Fix bug reported by Ludovic.
-------------------------------------------------------------------------
-r4956 | dshteyn | 2010-04-21 11:15:56 -0700 (Wed, 21 Apr 2010) | 1 line
 InteractParser: Make sure to not strip out the enzyme info when not specified on commandline.
-------------------------------------------------------------------------
-r4934 | dshteyn | 2010-04-07 17:05:46 -0700 (Wed, 07 Apr 2010) | 1 line
 InteractParser: BUGFIX prevent double delete of tag pointer.
-------------------------------------------------------------------------
-r4927 | dshteyn | 2010-04-01 11:17:31 -0700 (Thu, 01 Apr 2010) | 1 line
 InteractParser: Fix crash when -E option is not specified.
-------------------------------------------------------------------------
-r4915 | dshteyn | 2010-03-24 16:51:31 -0700 (Wed, 24 Mar 2010) | 1 line
 Tandem2XML: Handle multiple variable mods on same AA
-------------------------------------------------------------------------
-r4882 | dshteyn | 2010-02-24 11:45:34 -0800 (Wed, 24 Feb 2010) | 1 line
-InteractParser: fix my compilation bug.
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-r4881 | dshteyn | 2010-02-23 18:50:35 -0800 (Tue, 23 Feb 2010) | 1 line
-Correct MINPROB option problem.
-------------------------------------------------------------------------
-r4879 | dshteyn | 2010-02-23 16:18:00 -0800 (Tue, 23 Feb 2010) | 1 line
 RefreshParser: report the prev_aa and next_aa for top NTT match in the protein, not just the first entry. Test that db defn line actually has a '|' before testing if it comes before a ' '.
-------------------------------------------------------------------------
-r4878 | dshteyn | 2010-02-23 14:29:53 -0800 (Tue, 23 Feb 2010) | 1 line
 InteractParser: When an enzyme is given on the commandline overwrite the current sample_enzyme tag with the enzyme specified, old behaviour introduced competing sample_enzyme tags creating an inconsistency under certain conditions of use.
-------------------------------------------------------------------------
-r4875 | dshteyn | 2010-02-17 11:49:26 -0800 (Wed, 17 Feb 2010) | 1 line
 InterProphetParser - better usage statement, new option to output only peptides above a certain probability value.
-------------------------------------------------------------------------
-r4874 | dshteyn | 2010-02-17 11:46:22 -0800 (Wed, 17 Feb 2010) | 1 line
 InterProphetParser - adding computation of observed fits among initially low and high probability results, using variable bandwidths from the modeled fits.
-------------------------------------------------------------------------
-r4871 | dshteyn | 2010-02-10 15:48:48 -0800 (Wed, 10 Feb 2010) | 1 line
-Undo last checkin.
-------------------------------------------------------------------------
-r4870 | dshteyn | 2010-02-10 15:39:55 -0800 (Wed, 10 Feb 2010) | 1 line
-Xpress refered to this value.
-------------------------------------------------------------------------
-r4853 | dshteyn | 2010-01-15 14:03:41 -0800 (Fri, 15 Jan 2010) | 1 line
 ProteinProphet Store a separate value with peptide's total weight in the protein group.
-------------------------------------------------------------------------
-r4849 | dshteyn | 2010-01-14 14:36:03 -0800 (Thu, 14 Jan 2010) | 1 line
-Switch to a more robust split statement.
-------------------------------------------------------------------------
-r4848 | dshteyn | 2010-01-14 12:00:53 -0800 (Thu, 14 Jan 2010) | 1 line
-Adding InspectFvalue, PHOSPHO model, TOPCAT model.
-------------------------------------------------------------------------
-r4847 | dshteyn | 2010-01-14 11:55:41 -0800 (Thu, 14 Jan 2010) | 1 line
 xinteract PHOSPHO model and enable option InteractParser -P for correcting protein names in omssa output.
-------------------------------------------------------------------------
-r4846 | dshteyn | 2010-01-14 11:46:01 -0800 (Thu, 14 Jan 2010) | 1 line
 PeptideProphetParser new PHOSPHO model. Check all matching proteins for a peptide and count it as decoy only if all are decoys.  Tuning max reward parameters for ACCMASS model.  Print warning if not decoys are found. Count decoys and forward PSMs found.
-------------------------------------------------------------------------
-r4845 | dshteyn | 2010-01-14 11:45:21 -0800 (Thu, 14 Jan 2010) | 1 line
-PeptideProphetParser new PHOSPHO model. Check all matching proteins for a peptide and count it as decoy only if all are decoys.  Tuning max reward parameters for ACCMASS model.  Print warning if not decoys are found.
-------------------------------------------------------------------------
-r4844 | dshteyn | 2010-01-14 11:42:42 -0800 (Thu, 14 Jan 2010) | 1 line
-PeptideProphetParser new PHOSPHO model.
-------------------------------------------------------------------------
-r4843 | dshteyn | 2010-01-14 11:42:23 -0800 (Thu, 14 Jan 2010) | 1 line
-PeptideProphetParser new PHOSPHO model.
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-r4842 | dshteyn | 2010-01-14 11:24:48 -0800 (Thu, 14 Jan 2010) | 1 line
-PeptideProphetParser new PHOSPHO model.
-------------------------------------------------------------------------
-r4841 | dshteyn | 2010-01-14 11:23:48 -0800 (Thu, 14 Jan 2010) | 1 line
 PeptideProphetParser new PHOSPHO model.  Also fix the output when there are multiple top_hits so the probability is reported with the top most hit.
-------------------------------------------------------------------------
-r4840 | dshteyn | 2010-01-14 11:05:58 -0800 (Thu, 14 Jan 2010) | 1 line
-InterProphetParser TOPCAT model.
-------------------------------------------------------------------------
-r4839 | dshteyn | 2010-01-14 11:05:18 -0800 (Thu, 14 Jan 2010) | 1 line
 InterProphetParser Compute and report observed distributions in addition to the modeled distributions already reported.
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-r4838 | dshteyn | 2010-01-14 11:04:38 -0800 (Thu, 14 Jan 2010) | 1 line
-InterProphetParser TOPCAT model. Filter out any old iProphet results from the final output file.
-------------------------------------------------------------------------
-r4837 | dshteyn | 2010-01-14 11:03:47 -0800 (Thu, 14 Jan 2010) | 1 line
-InterProphetParser TOPCAT model.
+InterProphetParser Filter out any old iProphet results from the final output file.
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-r4836 | dshteyn | 2010-01-14 11:03:10 -0800 (Thu, 14 Jan 2010) | 1 line
-InterProphetParser TOPCAT model.
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-r4835 | dshteyn | 2010-01-14 11:02:39 -0800 (Thu, 14 Jan 2010) | 1 line
-InterProphetParser TOPCAT model.
-------------------------------------------------------------------------
-r4834 | dshteyn | 2010-01-14 11:01:38 -0800 (Thu, 14 Jan 2010) | 1 line
 InterProphetParser Compute and report observed distributions in addition to the modeled distributions already reported.
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-r4833 | dshteyn | 2010-01-14 10:48:56 -0800 (Thu, 14 Jan 2010) | 1 line
-InterProphetParser TOPCAT model.
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-r4832 | dshteyn | 2010-01-14 10:46:27 -0800 (Thu, 14 Jan 2010) | 1 line
 ProteinProphet store peptide group weight (sum of peptide's weight in the protein group) separatelly from peptide's weight in the protein.
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-r4831 | dshteyn | 2010-01-14 10:27:49 -0800 (Thu, 14 Jan 2010) | 1 line
-PeptideProphetParser tuning params on Tandem's semi-parametric model
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-r4830 | dshteyn | 2010-01-14 10:23:10 -0800 (Thu, 14 Jan 2010) | 1 line
-PeptideProphetParser Inspect f-value model.
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-r4829 | dshteyn | 2010-01-14 10:22:35 -0800 (Thu, 14 Jan 2010) | 1 line
-PeptideProphetParser Inspect f-value model.
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-r4828 | dshteyn | 2010-01-14 10:22:08 -0800 (Thu, 14 Jan 2010) | 1 line
-PeptideProphetParser Inspect f-value model.
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-r4827 | dshteyn | 2010-01-14 10:18:07 -0800 (Thu, 14 Jan 2010) | 1 line
-PeptideProphetParser Inspect f-value model.
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-r4826 | dshteyn | 2010-01-14 10:02:25 -0800 (Thu, 14 Jan 2010) | 1 line
-PeptideProphetParser adjusting Myrimatch f-value params.
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-r4825 | dshteyn | 2010-01-13 14:53:47 -0800 (Wed, 13 Jan 2010) | 1 line
-PeptideProphetParser tweaking the discriminant function params for OMSSA analysis
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-r4824 | dshteyn | 2010-01-13 14:48:27 -0800 (Wed, 13 Jan 2010) | 1 line
-PeptideProphetParser tweaking the discriminant function params for OMSSA analysis
-------------------------------------------------------------------------
-r4823 | dshteyn | 2010-01-13 14:36:25 -0800 (Wed, 13 Jan 2010) | 1 line
-Caching variable bandwidth for quicker runtime.  New function varBWdensityFit now can also take an additional parameter of a pointer to a Fit object.
-------------------------------------------------------------------------
-r4822 | dshteyn | 2010-01-13 14:35:13 -0800 (Wed, 13 Jan 2010) | 1 line
-Caching variable bandwidth for quicker runtime.  New function varBWdensityFit now can also take an additional parameter of a pointer to a Fit object.
-------------------------------------------------------------------------
-r4821 | dshteyn | 2010-01-13 14:28:57 -0800 (Wed, 13 Jan 2010) | 1 line
-Safer way to clean up
-------------------------------------------------------------------------
-r4820 | dshteyn | 2010-01-13 12:06:44 -0800 (Wed, 13 Jan 2010) | 1 line
-New option for enabling the PHOSPHO PeptideProphet model.
-------------------------------------------------------------------------
-r4819 | dshteyn | 2010-01-13 11:59:37 -0800 (Wed, 13 Jan 2010) | 1 line
-PeptideProphetParser now stores all proteins matched by a search result.
-------------------------------------------------------------------------
-r4818 | dshteyn | 2010-01-13 11:27:39 -0800 (Wed, 13 Jan 2010) | 1 line
-PeptideProphetParser now stores all proteins matched by a search result.
-------------------------------------------------------------------------
-r4817 | dshteyn | 2010-01-13 11:24:10 -0800 (Wed, 13 Jan 2010) | 1 line
-MascotResult parsing memory bug fix
-------------------------------------------------------------------------
-r4791 | dshteyn | 2009-12-10 16:01:30 -0800 (Thu, 10 Dec 2009) | 1 line
 ASAPRATIO: Bug Fix, wrong masses were being computed for charge 5+, now corrected.
-------------------------------------------------------------------------
-r4775 | dshteyn | 2009-11-17 11:25:44 -0800 (Tue, 17 Nov 2009) | 1 line
 ASAPCGIDisplay.cgi: BUG FIX Normalized Ratio was not getting displayed.
-------------------------------------------------------------------------
-r4627 | dshteyn | 2009-09-21 16:39:51 -0700 (Mon, 21 Sep 2009) | 1 line
-PeptideProphet: Fixing seg fault appearing in MALDI mode on PROBID results.
-------------------------------------------------------------------------
-r4598 | dshteyn | 2009-09-01 10:18:32 -0700 (Tue, 01 Sep 2009) | 1 line
 RefreshParser: Bug fix with UNMAPPED peptides not showing up UNMAPPED under some conditions.  Use minimum number of enzymatic termini from the search_hit num_tol_term attribute.
-------------------------------------------------------------------------
-r4528 | dshteyn | 2009-08-05 15:04:15 -0700 (Wed, 05 Aug 2009) | 1 line
 [ProteinProphet] Fix bug of indistinguishable_peptides being reported wrong with bad charge and first 2 chars stripped off.
-------------------------------------------------------------------------
-r4519 | dshteyn | 2009-08-04 16:15:31 -0700 (Tue, 04 Aug 2009) | 1 line
-[PeptideProphetParser] Make tool more robust by auto trimming whitespace from spectrum names.  Tandem searches submitted by Scott Stansfield (Aug 2009) where generated with method mzXML->mgf->tandem->pepXML was adding an extra space to the end of spectrum name.  This commit addresses the issue with Scott's data.
-------------------------------------------------------------------------
-r4509 | dshteyn | 2009-08-03 12:26:22 -0700 (Mon, 03 Aug 2009) | 1 line
 [InteractParser] Fix seg fault bug when dbtype option is set -T
-------------------------------------------------------------------------
-=== henrylam ===
-------------------------------------------------------------------------
+=== SpectraST ===
-r5047 | henrylam | 2010-07-06 19:34:51 -0700 (Tue, 06 Jul 2010) | 1 line
-[SpectraST] Add APPEND combineAction. Unhide several create options available in version 4.0
+* New features (SpectraST v.4.0)
-------------------------------------------------------------------------
+** ETD support
-r5046 | henrylam | 2010-07-06 19:05:32 -0700 (Tue, 06 Jul 2010) | 1 line
+** iProphet support
+** Artificial decoy spectrum generation (-cAD, -cc, -cy options. Ref. Lam et al., J. Proteome Res. 9, 605-610 (2010))
+** MRM transition list generation (-cM option. Ref. Sherwood et al., J. Proteome Res. 8, 4396-4405 (2009))
+** User-defined modifications (-M option)
+** Semi-empirical spectrum generation based on user-specified modifications (-cAM, -cx options)
+** Searching MGF (Mascot Generic Format) files
+** Clickable (HTML) search output format
+** Gzipped (.gz) file support
+** Non-peptide and unidentified entries
+** Combining libraries by appending (-cJA option)
+** Searching all charges (ignore specified query charge state) (-sz option)
+** Lib2HTML option to display by sorted precursor m/z
+** "Butterfly" plot for two library spectra using plotspectrast
+** Several other advanced options
-[SpectraST] Change treatment of warnings. PepXMLImport will raise warning when pepXML file has no probabilities.
+* Other changes and bug fixes
-------------------------------------------------------------------------
+** Modernized library statistics reporting to stdout and in .pepidx file
-r5045 | henrylam | 2010-07-06 18:52:02 -0700 (Tue, 06 Jul 2010) | 1 line
+** Better book-keeping: fragmentation method, precursor intensity, and collision energy stored with library spectra
+** Improved annotation algorithm
+** Various bug fixes
-[SpectraST] Compute NTT even if prev_aa or next_aa is X (treated as non-K,R,P)
+=== calctppstats.pl ===
-------------------------------------------------------------------------
-r5042 | henrylam | 2010-06-20 02:37:35 -0700 (Sun, 20 Jun 2010) | 1 line
-[SpectraST] Modernize library statistics reporting in pepidx: higher charges, more modifications, etc
+* Option to specify probability or FDR threshold
-------------------------------------------------------------------------
+* Option to count number of unique proteins mapped to by PSMs
-r5041 | henrylam | 2010-06-19 09:18:57 -0700 (Sat, 19 Jun 2010) | 1 line
-[SpectraST] Add two new search options: -sz (search all charge) and -s_FDL (specify fraction of delta in f-value)
+=== xinteract ===
-------------------------------------------------------------------------
-r5040 | henrylam | 2010-06-19 08:49:53 -0700 (Sat, 19 Jun 2010) | 1 line
-[SpectraST] Print sample info when protein is not available for xls and txt search output, good for non-peptide entries
+* Allow specification of protein database for RefreshParser (and hence for ProteinProphet) by -D option (in case that information is not in the pepXML file).
-------------------------------------------------------------------------
+* Skip RefreshParser, rather than crashing, if the database is not specified or not found.
-r5039 | henrylam | 2010-06-19 08:29:53 -0700 (Sat, 19 Jun 2010) | 1 line
-[SpectraST] -c_DTA option: Print first line without leading space to satisfy dta2mzxml
+=== XPRESS ===
-------------------------------------------------------------------------
-r5038 | henrylam | 2010-06-18 20:06:51 -0700 (Fri, 18 Jun 2010) | 1 line
-[RTCalc] Catch return value of tpplib_system() to fix compiling warning/error on g++ 4.4.1 (Ubuntu 8.04)
+* Added support for intensity ratios (versus area based ratios) and specifying negative mass offsets.  XPRESS includes better support for highres data by optionally summing individual isotope peaks for chromatogram reconstruction.
-------------------------------------------------------------------------
-r5037 | henrylam | 2010-06-18 20:00:50 -0700 (Fri, 18 Jun 2010) | 1 line
-[SpectraST] Add Lib2HTML option to display entries sorted by precursor m/z
+* Added minimum chromatrogram ion count parameter -c<num>.  This parameter filters out entries from being quantified unless the reconstruction chromatogram meets the minimum number of peaks specified.
-------------------------------------------------------------------------
-r4953 | henrylam | 2010-04-20 02:51:16 -0700 (Tue, 20 Apr 2010) | 1 line
-[SpectraST] Parse and store collision energy information with library spectrum; Add code to keep or delete both of conflicting IDs for same spectrum (commented out for now)
+* Added -l label free option.  This option will calculate stats on precursor ions only.  Resulting analysis is labeled as 'xpresslabelfree' in pep.xml.
-------------------------------------------------------------------------
-r4951 | henrylam | 2010-04-16 00:38:37 -0700 (Fri, 16 Apr 2010) | 1 line
-[ProphetModels.pl] Fix regex error when parsing newer iProphet pepXML files with neg_obs_dens and pos_obs_dens fields
+=== MzXML2Search ===
-------------------------------------------------------------------------
-r4950 | henrylam | 2010-04-16 00:31:26 -0700 (Fri, 16 Apr 2010) | 1 line
-[calctppstat.pl] Options to specify probability or FDR threshold, to count number of unique proteins mapped to by PSMs
+* Added -N option to print out top N most intense peaks in a spectrum.  Needed for large peaklists from new instrument as Mascot will complain if input peak list exceeds 10,000 count.
-------------------------------------------------------------------------
-r4949 | henrylam | 2010-04-16 00:23:03 -0700 (Fri, 16 Apr 2010) | 1 line
-[PeptideProphet] Printing error_point elements for lower (<1%) FDR thresholds
-------------------------------------------------------------------------
-r4948 | henrylam | 2010-04-16 00:22:14 -0700 (Fri, 16 Apr 2010) | 1 line
-[iProphet] Printing error_point elements for lower (<1%) FDR thresholds
-------------------------------------------------------------------------
-r4947 | henrylam | 2010-04-16 00:08:36 -0700 (Fri, 16 Apr 2010) | 1 line
-[xinteract] Allow specification of protein database for RefreshParser(and indirectly for ProteinProphet) by -D option (in case that information is not in the pepXML file). Skip RefreshParser, rather than quitting, if the database is not specified or not found.
+=== Full Integration of MaRiMba  ===
-------------------------------------------------------------------------
-r4946 | henrylam | 2010-04-15 23:52:57 -0700 (Thu, 15 Apr 2010) | 1 line
-[ProteinProphet] Add NOPROTLEN option (now that PROTLEN is true by default); Continue execution even if protein database file is not specified or not present at the specified path.
+*  Completion of the full integration of MaRiMba into the TPP.
-------------------------------------------------------------------------
-r4892 | henrylam | 2010-03-02 03:06:21 -0800 (Tue, 02 Mar 2010) | 1 line
-[SpectraST] Replace size_t with abstract types - undoing changes in r4885 - and add explicit casts (hopefully enabling smooth compilation on MSVS)
-------------------------------------------------------------------------
-r4891 | henrylam | 2010-03-02 02:59:13 -0800 (Tue, 02 Mar 2010) | 1 line
-[SpectraST] Fix msp import bug for M(O) containing peptides (bug introduced in r4815 on Jan12, 2010)
+=== New "High Performance Computing" Tools ===
-------------------------------------------------------------------------
-r4868 | henrylam | 2010-02-09 17:23:14 -0800 (Tue, 09 Feb 2010) | 1 line
-[SpectraST] Change meaning of C[177] from Propionamide:2H(3) to Propionamide:13C(3)
+Two new tool sets for high performance computing have been added to the extern/ directory of TPP. Both of these
-------------------------------------------------------------------------
+sets can be downloaded and installed to provide greater functionality to TPP.
-r4867 | henrylam | 2010-02-09 01:56:10 -0800 (Tue, 09 Feb 2010) | 1 line
-[SpectraST] Improved annotation algorithm
+* Grid (../extern/hpctools/grid)
-------------------------------------------------------------------------
-r4866 | henrylam | 2010-02-04 00:51:58 -0800 (Thu, 04 Feb 2010) | 1 line
-[SpectraST] Fix naming errors when searching .gz files
+The intend of this project was to share to the community the set of bash scripts used by ISB to submit various  TPP jobs to a compute cluster.  These scripts where designed to work for either the open source version of the portable batch system (PBS) or the Sun Grid Engine.  The scripts where written in bash for portability between
-------------------------------------------------------------------------
+cluster platforms are are intended to be modified to suite you site's particular needs.
-r4865 | henrylam | 2010-02-01 18:15:41 -0800 (Mon, 01 Feb 2010) | 1 line
-[SpectraST] PepXML import can now use all RAMP-supported types, including .gz
+* AWS Search Tool (..extern/hpctools/aws)
-------------------------------------------------------------------------
-r4863 | henrylam | 2010-01-26 18:13:16 -0800 (Tue, 26 Jan 2010) | 1 line
-[SpectraST] Minor fix of precursor neutral mass calculation in pepXML search output -- use mono or ave proton mass as appropriate
+Set of programs and services which can be used to run MS/MS peptide spectra searches on Amazon Web Services. Currently supports X!Tandem, OMSSA, and Inspect.  For each search algorithm a single control program is
-------------------------------------------------------------------------
+provided which manages all aspects of connecting to Amazon Web Services, starting and stopping EC2 compute nodes
-r4859 | henrylam | 2010-01-18 22:22:36 -0800 (Mon, 18 Jan 2010) | 1 line
-[SpectraST] Change version number to 4.0
+===tpp.sln (Windows only)===
-------------------------------------------------------------------------
-r4858 | henrylam | 2010-01-18 21:14:08 -0800 (Mon, 18 Jan 2010) | 1 line
-[SpectraST] Semi-empirical spectra generation based on suer-specified modifications (beta). Evaluate phosphosite assignment (alpha - hidden option for now).
+ported solution and vcproj files to Visual Studio 2008 express (necessitates the exclusion of ATL/MFC dependent projects, in this case the raw data file converters -- to be succeeded by proteowizard msconvert).
-------------------------------------------------------------------------
-r4857 | henrylam | 2010-01-17 22:40:53 -0800 (Sun, 17 Jan 2010) | 1 line
-[xinteract] Pass user-specified decoy tag to ProphetModels.pl call too
+== Other bug fixes and improvements ==
-------------------------------------------------------------------------
-r4815 | henrylam | 2010-01-11 19:39:43 -0800 (Mon, 11 Jan 2010) | 1 line
-[SpectraST] Allow user to define modifications in a file. Instructions will be in wiki shortly.
+* Fixed basePeak m/z and intensity bug for centroided data in ReAdW for Thermo Interface.
-------------------------------------------------------------------------
-r4813 | henrylam | 2010-01-09 01:09:52 -0800 (Sat, 09 Jan 2010) | 1 line
-[SpectraST] Minor inconsequential changes
+== Known Issues ==
-------------------------------------------------------------------------
-r4811 | henrylam | 2010-01-06 00:07:22 -0800 (Wed, 06 Jan 2010) | 1 line
-[SpectraST] Add a few modifications: oxidation/nitro/dimethylation/trimethylation
+* None to report
-------------------------------------------------------------------------
-r4810 | henrylam | 2009-12-28 18:17:49 -0800 (Mon, 28 Dec 2009) | 1 line
-[SpectraST] Simple fix to allow .sptxt files (after renaming to .msp) to be imported like .msp files
+== Getting the TPP Software ==
-------------------------------------------------------------------------
-r4809 | henrylam | 2009-12-23 01:15:59 -0800 (Wed, 23 Dec 2009) | 1 line
-[SpectraST] Filter by prob table (-cT option) allows any-charge matches if charge is not specified in prob table
+* Download the TPP version 4.4.0 native windows installer (TPP_Setup_v4_4.exe) from the Sashimi SourceForge project file release page:
-------------------------------------------------------------------------
-r4808 | henrylam | 2009-12-23 00:49:18 -0800 (Wed, 23 Dec 2009) | 1 line
-[SpectraST] Add \#include of C libraries to fix stand-alone compilation (which stops working in Ubuntu 9.10 (64-bit) for some reason.
+  "http://sourceforge.net/projects/sashimi/files/"
-------------------------------------------------------------------------
-r4807 | henrylam | 2009-12-22 17:50:34 -0800 (Tue, 22 Dec 2009) | 1 line
-[SpectraST] Fix hidden bug in SpectraSTPeakList::operator=; make peakMap a class member (rather than passed around); implement findPeak (based on m/z)
+* Everyone is encouraged to read and contribute to our wiki, at
-------------------------------------------------------------------------
+  "http://tools.proteomecenter.org/wiki/"
-r4805 | henrylam | 2009-12-22 17:18:19 -0800 (Tue, 22 Dec 2009) | 1 line
-[SpectraST] Add -c_MGF option to print library in MGF format
+* For guides to installing and using our software, please see our wiki:
-------------------------------------------------------------------------
+  "http://tools.proteomecenter.org/wiki/index.php?title=Software:TPP"
-r4804 | henrylam | 2009-12-22 17:12:11 -0800 (Tue, 22 Dec 2009) | 1 line
-[SpectraST] Put DECOY or REV proteins at the back of the list in the Protein comment field
+* For downloading the source code, please go to the following link:
-------------------------------------------------------------------------
+  "http://sourceforge.net/projects/sashimi/files/" and find the 4.4.0 source code .zip package;
-r4801 | henrylam | 2009-12-17 18:21:09 -0800 (Thu, 17 Dec 2009) | 1 line
+or, check out the code directly from svn:
+  "svn co http://sashimi.svn.sourceforge.net/svnroot/sashimi/tags/release_4-4-0"
-[ProphetModels.pl] Check alternative_protein for non-decoys
+  For building from source, please refer to the readme file in TPP/src as well as the wiki.
-------------------------------------------------------------------------
-r4800 | henrylam | 2009-12-17 18:19:17 -0800 (Thu, 17 Dec 2009) | 1 line
-[calctppstat.pl] Initialize num_missed_cleavage; Allow 10+ charge; Check alternative_protein for non-decoys
+The TPP Team: Luis, David, Brian, Natalie, and Joe plus all other developers who contributed to this release from the ISB.  Thanks to developers and users from the TPP's user community who provided feedback and code contributions.
-------------------------------------------------------------------------
-r4798 | henrylam | 2009-12-15 00:50:21 -0800 (Tue, 15 Dec 2009) | 1 line
-[RefreshParser] Fix seg fault when num_tol_term is not present, e.g. in OMSSA files
-------------------------------------------------------------------------
-r4749 | henrylam | 2009-11-10 17:14:27 -0800 (Tue, 10 Nov 2009) | 1 line
-[SpectraST] Fix bug of missing first peak when searching MGF files
-------------------------------------------------------------------------
-r4729 | henrylam | 2009-10-28 19:09:47 -0700 (Wed, 28 Oct 2009) | 1 line
-[SpectraST] Allow uppercase file extensions MGF, DTA, MSP for search mode
-------------------------------------------------------------------------
-r4699 | henrylam | 2009-10-13 23:06:46 -0700 (Tue, 13 Oct 2009) | 1 line
-[SpectraST] Fix bug where consensus spectra are not annotated -- introduced in r4610, Sept 8, 2009
-------------------------------------------------------------------------
-r4674 | henrylam | 2009-10-04 23:14:53 -0700 (Sun, 04 Oct 2009) | 1 line
-[SpectraST] Clean up fragmentation type handling
-------------------------------------------------------------------------
-r4612 | henrylam | 2009-09-07 22:52:18 -0700 (Mon, 07 Sep 2009) | 1 line
-[SpectraST] Improve book-keeping for mzXML file import.
-------------------------------------------------------------------------
-r4611 | henrylam | 2009-09-07 21:10:24 -0700 (Mon, 07 Sep 2009) | 1 line
-[SpectraST] PepXML import supports merged scans (when startScan and endScan are different, say ABCD.1234.1240.3): will fetch multiple scans from mzXML files and merge them by consensus algorithm before including in library.
-------------------------------------------------------------------------
-r4610 | henrylam | 2009-09-07 21:05:58 -0700 (Mon, 07 Sep 2009) | 1 line
-[SpectraST] Import unidentified spectra from mzXML files directly. Minor changes to SpectraSTReplicates's consensus code to facilitate clustering without identifications
-------------------------------------------------------------------------
-r4609 | henrylam | 2009-09-07 00:49:46 -0700 (Mon, 07 Sep 2009) | 1 line
-[SpectraST] For logging purpose, also count Remark=DECOY as decoys
-------------------------------------------------------------------------
-r4537 | henrylam | 2009-08-06 21:43:15 -0700 (Thu, 06 Aug 2009) | 1 line
-[SpectraST] Fix minor bug when Peptide objects are copied
-------------------------------------------------------------------------
-r4527 | henrylam | 2009-08-04 20:21:53 -0700 (Tue, 04 Aug 2009) | 1 line
-[XTandem] Fix wrong recommended params for NATIVE Tandem
-------------------------------------------------------------------------
-r4526 | henrylam | 2009-08-04 19:21:26 -0700 (Tue, 04 Aug 2009) | 1 line
-[SpectraST] Entry filter will treat value as double only when it's strictly all numbers
-------------------------------------------------------------------------
-r4525 | henrylam | 2009-08-04 19:13:18 -0700 (Tue, 04 Aug 2009) | 1 line
-[SpectraST] Enable plotspectrast to plot two library spectra head-to-tail
-------------------------------------------------------------------------
-r4524 | henrylam | 2009-08-04 19:07:48 -0700 (Tue, 04 Aug 2009) | 1 line
-[SpectraST] Non-peptide entries now use preceeding underscore as flag instead of angle brackets
-------------------------------------------------------------------------
-r4523 | henrylam | 2009-08-04 19:01:58 -0700 (Tue, 04 Aug 2009) | 1 line
-[SpectraST] New ubiquitin-like mods
-------------------------------------------------------------------------
-r4522 | henrylam | 2009-08-04 18:59:28 -0700 (Tue, 04 Aug 2009) | 1 line
-[SpectraST] Decoy peak reposition considers first annotation only
-------------------------------------------------------------------------
-r4521 | henrylam | 2009-08-04 18:42:59 -0700 (Tue, 04 Aug 2009) | 1 line
-[SpectraST] Lib2HTML includes column of precursor m/z
-------------------------------------------------------------------------
-r4507 | henrylam | 2009-07-31 19:36:47 -0700 (Fri, 31 Jul 2009) | 1 line
-[SpectraST] Fix minor bug with option qualityImmuneProbThreshold when used in spectrast_create.params
-------------------------------------------------------------------------
-=== eng_jk ===
-------------------------------------------------------------------------
-r5031 | eng_jk | 2010-06-10 10:22:48 -0700 (Thu, 10 Jun 2010) | 1 line
-------------------------------------------------------------------------
-r5030 | eng_jk | 2010-06-10 10:12:50 -0700 (Thu, 10 Jun 2010) | 2 lines
-change default last scan to big value
-------------------------------------------------------------------------
-r5029 | eng_jk | 2010-06-10 09:12:26 -0700 (Thu, 10 Jun 2010) | 2 lines
-add option to remove N-term methionine
-------------------------------------------------------------------------
-r5003 | eng_jk | 2010-06-02 12:16:48 -0700 (Wed, 02 Jun 2010) | 2 lines
-add support to zooming into TMT reporter region
-------------------------------------------------------------------------
-r4999 | eng_jk | 2010-05-31 20:08:39 -0700 (Mon, 31 May 2010) | 2 lines
-add RTINSECONDS to mgf output
-------------------------------------------------------------------------
-r4997 | eng_jk | 2010-05-28 13:35:43 -0700 (Fri, 28 May 2010) | 2 lines
-also pulled out the accession in the deflines in the contaminant files that get appended to each database
-------------------------------------------------------------------------
-r4996 | eng_jk | 2010-05-28 13:20:29 -0700 (Fri, 28 May 2010) | 2 lines
-just pull accession as first word in defline
-------------------------------------------------------------------------
-r4976 | eng_jk | 2010-05-14 08:52:28 -0700 (Fri, 14 May 2010) | 2 lines
-update script to grab uniprot (sprot and trembl) and create subsets with contaminants
-------------------------------------------------------------------------
-r4973 | eng_jk | 2010-05-11 16:28:56 -0700 (Tue, 11 May 2010) | 2 lines
-update phosphate loss peaks highlighting; highlighting happens when 'Phos=1' present on URL
-------------------------------------------------------------------------
-r4970 | eng_jk | 2010-05-07 17:01:08 -0700 (Fri, 07 May 2010) | 2 lines
-fix -M metabolic heavy function; chromatograms endpoints were being based on the light chromatograms and not the heavy chromatograms
-------------------------------------------------------------------------
-r4968 | eng_jk | 2010-05-06 07:53:18 -0700 (Thu, 06 May 2010) | 2 lines
-add in -nodta option to create archive of .out only and not include the spectra
-------------------------------------------------------------------------
-r4966 | eng_jk | 2010-04-28 15:12:10 -0700 (Wed, 28 Apr 2010) | 2 lines
-update new command line options for xpress; forgot to include this in prev checkin
-------------------------------------------------------------------------
-r4965 | eng_jk | 2010-04-28 15:11:13 -0700 (Wed, 28 Apr 2010) | 17 lines
-[xpress] Add -l label free option.
-This option will calculate stats on precursor ions only.
-Resulting analysis is labeled as 'xpresslabelfree' in pep.xml.
-When using this option, every precursor that passes filters such as minimum peaks will get
-an xpresslabelfree_result element that contains
-- first_scan                  scan # of chromatographic peak start
-- last_scan                   scan # of chromatographic peak end
-- first_scan_RT_seconds       retention time of chromatographic peak start
-- last_scan_RT_seconds        retention time of chromatographic peak end
-- precursor_mz                precursor m/z
-- peak_area                   sum peak area
-- peak_intensity              maximum intensity (presumably at peak apex)
-- peak_intensity_RT_seconds   retention time of maximum intensity
-- peak_intensity_scan         scan number of maximum intensity
-------------------------------------------------------------------------
-r4964 | eng_jk | 2010-04-28 14:58:23 -0700 (Wed, 28 Apr 2010) | 1 line
-------------------------------------------------------------------------
-r4963 | eng_jk | 2010-04-27 17:05:15 -0700 (Tue, 27 Apr 2010) | 2 lines
-correct 'chymotryptic' to 'chymotrypsin'
-------------------------------------------------------------------------
-r4961 | eng_jk | 2010-04-23 15:38:48 -0700 (Fri, 23 Apr 2010) | 2 lines
-add -P option to print out normalized intensity values for neutral loss masses associated with phosphate loss
-------------------------------------------------------------------------
-r4945 | eng_jk | 2010-04-15 13:02:28 -0700 (Thu, 15 Apr 2010) | 2 lines
-parsing update for entry with protein n-term modification which doesn't seem to be handled by current code
-------------------------------------------------------------------------
-r4942 | eng_jk | 2010-04-14 10:37:16 -0700 (Wed, 14 Apr 2010) | 2 lines
-remove tilde hack; i'll deal with the issue (dashes for negative numbers not being argument delimiters when all args are concatenated together in xinteract) upstream of xpress when needed
-------------------------------------------------------------------------
-r4941 | eng_jk | 2010-04-14 10:13:25 -0700 (Wed, 14 Apr 2010) | 2 lines
-this should've gone with commit 4940 to support intensity based ratios
-------------------------------------------------------------------------
-r4940 | eng_jk | 2010-04-13 17:33:35 -0700 (Tue, 13 Apr 2010) | 2 lines
-add support for intensity ratios and specifying negative mass offsets
-------------------------------------------------------------------------
-r4923 | eng_jk | 2010-03-31 21:18:50 -0700 (Wed, 31 Mar 2010) | 3 lines
-[mzxml2search] Add -N option to print out top N most intense peaks in a spectrum; needed for large peaklists from new instruments.
-Also add logic to semi-properly handle application of both minimum intensity filter and minimum peak count.
-------------------------------------------------------------------------
-r4904 | eng_jk | 2010-03-15 16:58:28 -0700 (Mon, 15 Mar 2010) | 2 lines
-make the peaklist mass and intensity precisions a user defined option with -pm<num> -pi<num>
-------------------------------------------------------------------------
-r4903 | eng_jk | 2010-03-15 16:26:32 -0700 (Mon, 15 Mar 2010) | 2 lines
-update help text to add/clarify description of output columns
-------------------------------------------------------------------------
-r4900 | eng_jk | 2010-03-11 09:58:18 -0800 (Thu, 11 Mar 2010) | 2 lines
-dynamically allocate large arrays to address memory issues
-------------------------------------------------------------------------
-r4873 | eng_jk | 2010-02-10 18:28:37 -0800 (Wed, 10 Feb 2010) | 2 lines
-add missing mass filter to ms2 and odta output; change default max mass to 5K
-------------------------------------------------------------------------
-r4869 | eng_jk | 2010-02-09 22:15:08 -0800 (Tue, 09 Feb 2010) | 2 lines
-fix wrong mass used for 3rd modification mass
-------------------------------------------------------------------------
-r4864 | eng_jk | 2010-01-28 01:13:14 -0800 (Thu, 28 Jan 2010) | 2 lines
-found .out file where incomplete header date killed parsing; simple workaround
-------------------------------------------------------------------------
-r4862 | eng_jk | 2010-01-21 16:04:32 -0800 (Thu, 21 Jan 2010) | 2 lines
-change triangle polygons to vertical lines in chromatogram display
-------------------------------------------------------------------------
-r4861 | eng_jk | 2010-01-21 15:34:53 -0800 (Thu, 21 Jan 2010) | 2 lines
-tweak filter params
-------------------------------------------------------------------------
-r4860 | eng_jk | 2010-01-21 14:33:35 -0800 (Thu, 21 Jan 2010) | 2 lines
-[xpress] modify butterworth filter to not give as tight of fit to smoothed (low-pass) curve; modify chromatogram display to show larger scan range
-------------------------------------------------------------------------
-r4803 | eng_jk | 2009-12-21 11:52:02 -0800 (Mon, 21 Dec 2009) | 2 lines
-extra period being appended to generated pep.shtml link
-------------------------------------------------------------------------
-r4802 | eng_jk | 2009-12-18 10:42:33 -0800 (Fri, 18 Dec 2009) | 4 lines
-also scale precursor for large image
-make y-ions red and b-ions blue to conform to pseudo standard
-fix ugly errors in output when chosen but nothing to plot for E-value chart
-------------------------------------------------------------------------
-r4794 | eng_jk | 2009-12-10 18:12:33 -0800 (Thu, 10 Dec 2009) | 2 lines
-[readw] add LTQ Velos and TSQ Vantage to instrument types; sadly both LTQ Velos and LTQ Orbitrap Velos report as "LTQ Velos" using GetInstModel()
-------------------------------------------------------------------------
-r4783 | eng_jk | 2009-11-25 11:08:32 -0800 (Wed, 25 Nov 2009) | 2 lines
-[xpress] correctly calculate m/z with more precision in update CGI
-------------------------------------------------------------------------
-r4782 | eng_jk | 2009-11-24 10:18:32 -0800 (Tue, 24 Nov 2009) | 2 lines
-[xpress] additional mods for quantification using individual isotope peak chromatograms
-------------------------------------------------------------------------
-r4778 | eng_jk | 2009-11-18 13:40:19 -0800 (Wed, 18 Nov 2009) | 2 lines
-[sqt2xml] use get_pepxml_dot_ext() to derive output pep.xml extension
-------------------------------------------------------------------------
-r4777 | eng_jk | 2009-11-18 11:43:54 -0800 (Wed, 18 Nov 2009) | 8 lines
-[sqt2xml] updates contributed by Mike Coleman including
-- define proton mass using double-precision constant
-- trim whitespace from SEQUEST output to give correct peptide
-- trim locus, defensively
-- default DeltaCn is 0 (not 1)
-- require only one argument
-- change created file extension from .pepXML to .pep.xml [JKE]
-------------------------------------------------------------------------
-r4766 | eng_jk | 2009-11-13 10:40:56 -0800 (Fri, 13 Nov 2009) | 2 lines
-[out2xml] add support for another variant of n- and c-term variable mods
-------------------------------------------------------------------------
-r4765 | eng_jk | 2009-11-13 10:31:50 -0800 (Fri, 13 Nov 2009) | 2 lines
-[xpress] revert changes made in revision 1177.  Set minimum peptide probabilities for contributing to protein ratio.  Without this change, ratios for incorrect peptide assignments contribute to the protein ratio.
-------------------------------------------------------------------------
-r4764 | eng_jk | 2009-11-13 10:15:06 -0800 (Fri, 13 Nov 2009) | 2 lines
-add support for tracking individual isotope peaks for chromatogram reconstruction of highres data
-------------------------------------------------------------------------
-r4758 | eng_jk | 2009-11-12 10:54:38 -0800 (Thu, 12 Nov 2009) | 2 lines
-get rid of unnecessary backslashes in the sed command
-------------------------------------------------------------------------
-r4757 | eng_jk | 2009-11-12 10:27:38 -0800 (Thu, 12 Nov 2009) | 2 lines
-escape ', ", & and replace <, > with [, ] respectively in the def lines
-------------------------------------------------------------------------
-r4730 | eng_jk | 2009-10-30 11:03:06 -0700 (Fri, 30 Oct 2009) | 2 lines
-add maximum charge output option; get rid of incorrect hydrogen mass option for charge calculation
-------------------------------------------------------------------------
-r4623 | eng_jk | 2009-09-16 09:13:05 -0700 (Wed, 16 Sep 2009) | 2 lines
-[subsetdb] add -D option for user specified reverse description prefix
-------------------------------------------------------------------------
-r4619 | eng_jk | 2009-09-14 11:55:15 -0700 (Mon, 14 Sep 2009) | 2 lines
-add 2 more digits of precision for expect score output
-------------------------------------------------------------------------
-r4617 | eng_jk | 2009-09-09 15:03:24 -0700 (Wed, 09 Sep 2009) | 2 lines
-[Out2XML] modify parsing of .out files with duplicate references
-------------------------------------------------------------------------
-r4595 | eng_jk | 2009-08-27 14:06:37 -0700 (Thu, 27 Aug 2009) | 2 lines
-[comet-fastadb.cgi] update URLs
-------------------------------------------------------------------------
-r4594 | eng_jk | 2009-08-27 13:06:11 -0700 (Thu, 27 Aug 2009) | 2 lines
-[ProteinProphet] deal with missing description lines for IPI database searches
-------------------------------------------------------------------------
-r4593 | eng_jk | 2009-08-26 14:48:55 -0700 (Wed, 26 Aug 2009) | 2 lines
-[XPRESS] add chromatogram minimum ion count for a peptide to be quantified; -c<num> option with default value of 5.  The goal is to avoid calculating areas/ratios for spurious peaks (those with fewer than 5 MS1 scan signals contributing to elution area calculation).
-------------------------------------------------------------------------
-r4592 | eng_jk | 2009-08-26 14:26:50 -0700 (Wed, 26 Aug 2009) | 2 lines
-[readmzXML] add precursorCharge to -H output
-------------------------------------------------------------------------
-r4591 | eng_jk | 2009-08-26 13:16:33 -0700 (Wed, 26 Aug 2009) | 2 lines
-[XPressCGIProteinDisplayParser.cgi] a counter/index variable was re-used in an inner loop causing outer loop to exit prematurely resulting in the CGI not displaying peptide ratios from all input files; problem appears to be present in initial commit
-------------------------------------------------------------------------
-r4589 | eng_jk | 2009-08-26 11:42:00 -0700 (Wed, 26 Aug 2009) | 2 lines
-[XPRESS] fix bug that causes N15 metabolic labeling option to run incorrectly (introduced when C13 option added)
-------------------------------------------------------------------------
-r4585 | eng_jk | 2009-08-20 11:48:05 -0700 (Thu, 20 Aug 2009) | 2 lines
-[psm2pdf] add e-value score cutoff option (versus PP probability) and clean up
-------------------------------------------------------------------------
-r4576 | eng_jk | 2009-08-18 11:20:12 -0700 (Tue, 18 Aug 2009) | 2 lines
-[psm2pdf] Initial add of program that generates a pdf of annotated spectra from input interact.pep.xml files.  Requires htmldoc and ghostscript.
-------------------------------------------------------------------------
-r4575 | eng_jk | 2009-08-18 11:15:11 -0700 (Tue, 18 Aug 2009) | 2 lines
-[psm2pdf] create source directory
-------------------------------------------------------------------------
-r4574 | eng_jk | 2009-08-14 10:23:19 -0700 (Fri, 14 Aug 2009) | 2 lines
-[plot-msms] modifications to support bulk image generation for publication
-------------------------------------------------------------------------
-r4536 | eng_jk | 2009-08-06 16:56:19 -0700 (Thu, 06 Aug 2009) | 2 lines
-[Out2XML] address negative deltacnstar values that were being reported.
-------------------------------------------------------------------------
-r4534 | eng_jk | 2009-08-06 16:35:15 -0700 (Thu, 06 Aug 2009) | 2 lines
-[Out2XML] Set deltacnstar to 0.001 when xcorr of top 2 homologous peptides are exactly the same; fixes current behavior (since rev 3913) which would have this attribute value be set to 0.0 under this scenario. Retention time is retrieved from start_scan whereas code before would grab from end_scan; those scan numbers are the same in our pipeline.  Print more precision for spscore for UW version of Sequest that replaces spsore with e-value.
-------------------------------------------------------------------------
-=== zhisun ===
-------------------------------------------------------------------------
-r4784 | zhisun | 2009-11-30 13:02:05 -0800 (Mon, 30 Nov 2009) | 1 line
-Chris Paulse modified the script and made it more permissive regarding the precursorCharge target string (doesn’t expect space immediately after the close quote.)
-------------------------------------------------------------------------
-r4545 | zhisun | 2009-08-07 15:02:14 -0700 (Fri, 07 Aug 2009) | 1 line
-solve memory problem
-------------------------------------------------------------------------
-=== csherwood ===
-------------------------------------------------------------------------
-r4816 | csherwood | 2010-01-12 10:52:52 -0800 (Tue, 12 Jan 2010) | 1 line
-[MaRiMba Merge] Adding/updating all MaRiMba-related files for the full integration of MaRiMba into the TPP.
-------------------------------------------------------------------------
-=== spacepod ===
-------------------------------------------------------------------------
-r4972 | spacepod | 2010-05-10 12:24:18 -0700 (Mon, 10 May 2010) | 2 lines
-[build process] 1) add dectection for 64-bit OS X systems; 2) use macports vs fink search paths for extra libraries (can add detection, if requested)
-------------------------------------------------------------------------
-r4971 | spacepod | 2010-05-10 12:21:03 -0700 (Mon, 10 May 2010) | 2 lines
-[PepXMLViewer] adding casts to work under boost 1.43.0
-------------------------------------------------------------------------
-r4967 | spacepod | 2010-05-04 17:20:10 -0700 (Tue, 04 May 2010) | 2 lines
-[ASAPRatioPeptideParser] adding experimental wavelet smoothing.  Test using new ASAPRatioPeptideParser -w option.  From WaveletQuant implmentation, http://www.biomedcentral.com/1471-2105/11/219
-------------------------------------------------------------------------
-r4922 | spacepod | 2010-03-31 16:21:57 -0700 (Wed, 31 Mar 2010) | 2 lines
-[Makefile] removing extra tab character
-------------------------------------------------------------------------
-r4921 | spacepod | 2010-03-31 11:53:14 -0700 (Wed, 31 Mar 2010) | 2 lines
-[linux install] generalizing ubuntu 9.04 install to 9.10 as well (tested)
-------------------------------------------------------------------------
-r4872 | spacepod | 2010-02-10 16:19:05 -0800 (Wed, 10 Feb 2010) | 1 line
-[OS requirements] updating ubuntu 8.10 install
-------------------------------------------------------------------------
-r4785 | spacepod | 2009-11-30 17:46:38 -0800 (Mon, 30 Nov 2009) | 1 line
-[mingw build] updates for mingw build
-------------------------------------------------------------------------
-r4660 | spacepod | 2009-09-28 14:17:22 -0700 (Mon, 28 Sep 2009) | 3 lines
-[c to c++ cleanup] catching a few files that svn got confused on the first time.
-------------------------------------------------------------------------
-r4659 | spacepod | 2009-09-28 14:07:53 -0700 (Mon, 28 Sep 2009) | 3 lines
-[c to c++ cleanup] catching a few files that svn got confused on the first time.
-------------------------------------------------------------------------
-r4658 | spacepod | 2009-09-28 14:02:07 -0700 (Mon, 28 Sep 2009) | 3 lines
-[c to c++ cleanup] catching a few files that svn got confused on the first time.
-------------------------------------------------------------------------
-r4657 | spacepod | 2009-09-28 13:44:33 -0700 (Mon, 28 Sep 2009) | 4 lines
-[c to c++ rename] merging changes to convert file extensions and build process from c to c++, from cpprename.  fully
-tested in 'cpprename' branch.
-------------------------------------------------------------------------
-r4656 | spacepod | 2009-09-28 13:19:44 -0700 (Mon, 28 Sep 2009) | 1 line
-[windows builds] updating paths for boost, expat dependencies; from cpprename branch
-------------------------------------------------------------------------
-r4655 | spacepod | 2009-09-28 12:25:19 -0700 (Mon, 28 Sep 2009) | 1 line
-[restoring trunk/tpp to cleaner history, before c->c++ thrashing
-------------------------------------------------------------------------
-r4587 | spacepod | 2009-08-24 12:13:54 -0700 (Mon, 24 Aug 2009) | 1 line
-[mingw build] adding script for building TPP under mingw, so that it's easier to get this going from outside the mingw/msys environment.
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-r4573 | spacepod | 2009-08-13 17:48:57 -0700 (Thu, 13 Aug 2009) | 1 line
-[pwiz] attempting re-adding local copies in stages
-------------------------------------------------------------------------
-r4572 | spacepod | 2009-08-13 17:47:42 -0700 (Thu, 13 Aug 2009) | 1 line
-[pwiz] attempting re-adding local copies in stages
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-r4571 | spacepod | 2009-08-13 17:46:34 -0700 (Thu, 13 Aug 2009) | 1 line
-[pwiz] attempting re-adding local copies in stages
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-r4570 | spacepod | 2009-08-13 17:45:39 -0700 (Thu, 13 Aug 2009) | 1 line
-[pwiz] attempting re-adding local copies in stages
-------------------------------------------------------------------------
-r4569 | spacepod | 2009-08-13 17:45:09 -0700 (Thu, 13 Aug 2009) | 1 line
-[pwiz] attempting re-adding local copies in stages
-------------------------------------------------------------------------
-r4568 | spacepod | 2009-08-13 17:43:43 -0700 (Thu, 13 Aug 2009) | 1 line
-[pwiz] attempting re-adding local copies in stages
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-r4567 | spacepod | 2009-08-13 17:39:50 -0700 (Thu, 13 Aug 2009) | 2 lines
-[pwiz] grr, trying again
-------------------------------------------------------------------------
-r4566 | spacepod | 2009-08-13 16:56:51 -0700 (Thu, 13 Aug 2009) | 1 line
-[pwiz] adding local copy, staging as sourceforge keeps rejecting large checkins
-------------------------------------------------------------------------
-r4565 | spacepod | 2009-08-13 16:56:05 -0700 (Thu, 13 Aug 2009) | 1 line
-[pwiz] adding local copy
-------------------------------------------------------------------------
-r4564 | spacepod | 2009-08-13 15:59:03 -0700 (Thu, 13 Aug 2009) | 3 lines
-[pwiz] zapping pwiz method using svn extern; will be replaced with sashimi's own copy
-------------------------------------------------------------------------
-r4563 | spacepod | 2009-08-13 11:44:15 -0700 (Thu, 13 Aug 2009) | 2 lines
-[pwiz] moving and updating pwiz notes to tpp/extern in prep for compressing pwiz
-------------------------------------------------------------------------
-r4560 | spacepod | 2009-08-12 17:23:22 -0700 (Wed, 12 Aug 2009) | 3 lines
-[moving win_lib into tpp/extern] moving files and making changes to reflect new locations.  Followups likely.
-------------------------------------------------------------------------
-r4557 | spacepod | 2009-08-12 14:23:21 -0700 (Wed, 12 Aug 2009) | 3 lines
-[win_lib cleanup] part 1 of 2: merging changes from "win_lib-cleanup" branch to deal with compressed win_lib directories
-------------------------------------------------------------------------
-=== slagelwa ===
-------------------------------------------------------------------------
-r5044 | slagelwa | 2010-06-29 15:45:15 -0700 (Tue, 29 Jun 2010) | 2 lines
-Numerous bug fixes, addtion of params directory
-------------------------------------------------------------------------
-r4998 | slagelwa | 2010-05-28 14:49:00 -0700 (Fri, 28 May 2010) | 5 lines
-Fixed issue with polling quitting too early
-Fixed issue with output files being written to the wrong place if the
-   input file was a link
-Now handles mzXML.gz files
-------------------------------------------------------------------------
-r4981 | slagelwa | 2010-05-18 15:18:07 -0700 (Tue, 18 May 2010) | 2 lines
-Added qspectrast
-------------------------------------------------------------------------
-r4980 | slagelwa | 2010-05-18 15:14:41 -0700 (Tue, 18 May 2010) | 2 lines
-ignore propset again
-------------------------------------------------------------------------
-r4979 | slagelwa | 2010-05-18 15:10:17 -0700 (Tue, 18 May 2010) | 2 lines
-Setting some ignore properties
-------------------------------------------------------------------------
-r4969 | slagelwa | 2010-05-07 10:02:16 -0700 (Fri, 07 May 2010) | 2 lines
-Changed interface, lots of little fixes and changes
-------------------------------------------------------------------------
-r4955 | slagelwa | 2010-04-20 16:20:36 -0700 (Tue, 20 Apr 2010) | 2 lines
-Added README, quoted some paths, added back email functionality and fixed PBS not exporting users PATH
-------------------------------------------------------------------------
-r4944 | slagelwa | 2010-04-14 17:35:00 -0700 (Wed, 14 Apr 2010) | 2 lines
-Added inspect search engine and reworked the services architecture
-------------------------------------------------------------------------
-r4943 | slagelwa | 2010-04-14 17:32:53 -0700 (Wed, 14 Apr 2010) | 3 lines
-Now looks for both .mzXML and .mzML files (although all search engines might
-not be able to handel .mzML files...)
-------------------------------------------------------------------------
-r4939 | slagelwa | 2010-04-12 15:41:45 -0700 (Mon, 12 Apr 2010) | 2 lines
-Updated EC2 image, adding omssa support
-------------------------------------------------------------------------
-r4933 | slagelwa | 2010-04-07 15:16:03 -0700 (Wed, 07 Apr 2010) | 2 lines
-More errors in checkin
-------------------------------------------------------------------------
-r4932 | slagelwa | 2010-04-07 14:33:03 -0700 (Wed, 07 Apr 2010) | 2 lines
-Renaming extern directory to reflect more what the contents are, being high performance computing tools or "hpctools"
-------------------------------------------------------------------------
-r4931 | slagelwa | 2010-04-07 14:29:10 -0700 (Wed, 07 Apr 2010) | 2 lines
-Including some stuff left out of previous commit due to svn errors
-------------------------------------------------------------------------
-r4930 | slagelwa | 2010-04-07 14:23:37 -0700 (Wed, 07 Apr 2010) | 2 lines
-Added set of "qcmds" wrapper scripts which can be used to submit searches to a sun grid engine or PBS cluster.  Restructured directory hierarchy so that new qcmds are in their own directory as is the aws stuff.  Revamped the aws even more, many bug fixes.
-------------------------------------------------------------------------
-r4916 | slagelwa | 2010-03-25 14:36:19 -0700 (Thu, 25 Mar 2010) | 2 lines
-Cleaned up reporting, code in prepartion for supporing more search programs and more clusters
-------------------------------------------------------------------------
-r4910 | slagelwa | 2010-03-19 16:28:55 -0700 (Fri, 19 Mar 2010) | 2 lines
-Cleaned up parameters and documentation to prepare for a name change and addition of more search programs
-------------------------------------------------------------------------
-r4909 | slagelwa | 2010-03-19 13:44:15 -0700 (Fri, 19 Mar 2010) | 5 lines
-Changed file key format to postfix the filepath with the checksum instead of prefixing it.  This way tools such as s3fm which treat keys containing a "/" as a file hierarchy can display and navigate better.
-(Checksum in key is still a problem as the '/' character frequently occurs.
-Like to remove the checksum and rely on AWS checksum only).
-------------------------------------------------------------------------
-r4908 | slagelwa | 2010-03-18 12:17:09 -0700 (Thu, 18 Mar 2010) | 13 lines
-* Spel institute correctly :)
-* No longer shuts down the client downloader after being idle for 30 minutes (searches can take longer than that...)
-* For each search request it now starts up a new EC2 instance, up to <MAX> instances instead of starting them all at once.  Since the boot time is slightly
-longer then the upload time this means that the new instance should be available shortly after the request gets submitted.  This should solve the timeout
-problem with EC2 instances not getting work in time, and be a little less expensive as you are not starting all instances at once but as needed.
-* Added coded to report message errors and keep going.  i noticed at least one situation were you could create a message error and the program would stop.  this might address the "lost" message issue I saw as I suspect one of the nodes might have exited upon getting an message error.
-* Log files are now kept on each ec2 instance, and are copied back to the client when each are shutdown.  should make it easier for any future debugging or reporting
-~
-------------------------------------------------------------------------
-r4907 | slagelwa | 2010-03-18 10:10:15 -0700 (Thu, 18 Mar 2010) | 2 lines
-Included for testing/development
-------------------------------------------------------------------------
-r4906 | slagelwa | 2010-03-18 10:09:39 -0700 (Thu, 18 Mar 2010) | 5 lines
-Added a make target that uses the program aws to upload this program's
-distribution to a public S3 bucket.  Each EC2 instance has a bootstartup
-script which will download this file and install it -- providing a nice
-automatic upgrade capability to the cloud.
-------------------------------------------------------------------------
-r4905 | slagelwa | 2010-03-18 10:07:23 -0700 (Thu, 18 Mar 2010) | 4 lines
-Updated/corrected end block to leave test files in tmp directory if(when) the
-tests fail.  Fixed filename error bug in test itself that only became
-apparent after the code it was testing was changed.
-------------------------------------------------------------------------
-r4897 | slagelwa | 2010-03-09 16:41:19 -0800 (Tue, 09 Mar 2010) | 3 lines
-Updated documentation.  Added a automatic "shutdown" feature of the search daemon to
-shutdown the EC2 node if no search requests have been received in over 15 minutes.
-------------------------------------------------------------------------
-r4896 | slagelwa | 2010-03-09 15:44:17 -0800 (Tue, 09 Mar 2010) | 3 lines
-Added threads parameter
-hack to fix timestamp issue in EC2 api
-------------------------------------------------------------------------
-r4895 | slagelwa | 2010-03-09 15:18:18 -0800 (Tue, 09 Mar 2010) | 2 lines
-Added target to upload new versions of the  distro to S3 to be automatically deployed on the EC2 instances
-------------------------------------------------------------------------
-r4876 | slagelwa | 2010-02-18 14:08:56 -0800 (Thu, 18 Feb 2010) | 2 lines
-Skip xml elements that don't have attributes
-------------------------------------------------------------------------
-r4711 | slagelwa | 2009-10-19 13:18:08 -0700 (Mon, 19 Oct 2009) | 2 lines
-Use XML parser to parse params file.  Strip leading/trailing blanks from taxon name
-------------------------------------------------------------------------
-r4710 | slagelwa | 2009-10-19 13:13:34 -0700 (Mon, 19 Oct 2009) | 2 lines
-Adding grep of threads parameter
-------------------------------------------------------------------------
-r4667 | slagelwa | 2009-09-29 12:23:08 -0700 (Tue, 29 Sep 2009) | 4 lines
-* Fixed various related path bugs
-* Reorganized tandem objects
-* --start 0 works
-------------------------------------------------------------------------
-r4624 | slagelwa | 2009-09-16 11:40:21 -0700 (Wed, 16 Sep 2009) | 2 lines
-Set keyword properties
-------------------------------------------------------------------------
-r4622 | slagelwa | 2009-09-15 16:11:02 -0700 (Tue, 15 Sep 2009) | 2 lines
-One last file to move to fix import
-------------------------------------------------------------------------
-r4621 | slagelwa | 2009-09-15 16:08:07 -0700 (Tue, 15 Sep 2009) | 2 lines
-Fixing import as it when into the topdir instead of the subdir
-------------------------------------------------------------------------
-r4620 | slagelwa | 2009-09-15 15:50:44 -0700 (Tue, 15 Sep 2009) | 1 line
-Importing TPP AWS Search Tool
-------------------------------------------------------------------------

TPP:4.4.0 Release Notes

From SPCTools

Current revision

Contents

New Features/Changes

Deprecation of Conversion Tools

pepXML schema

MzXML2Search

Petunia

xinteract

readmzXML

Pep3D

plot-msms (spectrum viewer)

protxml2html (ProteinProphet viewer)

build system

ASAPRatio

dctrud

pcbrefugee

PeptideProphetParser

David Shteynberg

SpectraST

calctppstats.pl

xinteract

XPRESS

MzXML2Search

Full Integration of MaRiMba

New "High Performance Computing" Tools

tpp.sln (Windows only)

Other bug fixes and improvements

Known Issues

Getting the TPP Software

Views

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