TPP:4.6.3 SVN Log
From SPCTools
(Difference between revisions)
Revision as of 23:01, 7 June 2013
[edit]
Changes since 4.6.2 release
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r6204 | eng_jk | 2013-06-07 10:54:03 -0700 (Fri, 07 Jun 2013) | 2 lines
get rid of Comet2XML
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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)
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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.
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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.
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r6200 | slagelwa | 2013-06-04 10:53:39 -0700 (Tue, 04 Jun 2013) | 2 lines
Development snapshot
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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.
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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
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r6197 | dshteyn | 2013-05-31 12:39:38 -0700 (Fri, 31 May 2013) | 1 line
InteractParser: large memory issue bug.
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r6196 | dshteyn | 2013-05-31 12:34:36 -0700 (Fri, 31 May 2013) | 1 line
RTCatalog: use XICs to compute RT stats.
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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.
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r6194 | mhoopmann | 2013-05-29 13:13:54 -0700 (Wed, 29 May 2013) | 1 line
Added filter line to scan header output.
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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.
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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
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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.
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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.
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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
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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.
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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.
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r6186 | dshteyn | 2013-05-15 10:47:38 -0700 (Wed, 15 May 2013) | 1 line
SpectraST: BUG not reading usernmods correctly FIXED
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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.
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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)
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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
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r6182 | dshteyn | 2013-04-30 11:02:43 -0700 (Tue, 30 Apr 2013) | 1 line
PTMProphet: fixing bug with handling of unusual mods.
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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.
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r6180 | dshteyn | 2013-04-09 14:20:26 -0700 (Tue, 09 Apr 2013) | 1 line
SpectraST change for PTMProphet: recongnize Lys4 mod.
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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.
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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.
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r6177 | eng_jk | 2013-04-02 13:35:01 -0700 (Tue, 02 Apr 2013) | 2 lines
update getdb scripts
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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
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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.
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r6174 | eng_jk | 2013-03-29 12:37:31 -0700 (Fri, 29 Mar 2013) | 2 lines
forgot to delete these lines before 6173 checkin
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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.
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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)
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r6171 | dshteyn | 2013-03-28 14:24:49 -0700 (Thu, 28 Mar 2013) | 1 line
RTCalc: bugfix in memory with artificial neural network usage.
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r6170 | dshteyn | 2013-03-27 16:27:08 -0700 (Wed, 27 Mar 2013) | 1 line
iProphet: NSP model was broken.
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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.
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r6168 | slagelwa | 2013-03-27 14:04:29 -0700 (Wed, 27 Mar 2013) | 2 lines
Include the actual binaries
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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.
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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.
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r6165 | slagelwa | 2013-03-25 15:09:54 -0700 (Mon, 25 Mar 2013) | 1 line
Fixed what looked to be a typo.
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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).
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r6163 | slagelwa | 2013-03-25 10:40:08 -0700 (Mon, 25 Mar 2013) | 2 lines
Sloppy cut&paster.
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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.
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r6161 | ppatrick | 2013-03-25 06:40:09 -0700 (Mon, 25 Mar 2013) | 2 lines
Added support for ppm tolerance (-a) to XPRESS.
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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.
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r6159 | slagelwa | 2013-03-18 14:42:37 -0700 (Mon, 18 Mar 2013) | 2 lines
Removing said file from r6158
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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'.
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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.
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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.
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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
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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.
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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.
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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!
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r6151 | slagelwa | 2013-03-08 15:12:37 -0800 (Fri, 08 Mar 2013) | 3 lines
Now validates interprophet pep.xml
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r6150 | dshteyn | 2013-03-08 15:07:41 -0800 (Fri, 08 Mar 2013) | 1 line
Sequest model: expect score not implemented...disable by default.
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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.
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r6148 | dshteyn | 2013-03-08 15:06:04 -0800 (Fri, 08 Mar 2013) | 1 line
xinteract: options to run PTMProphet.
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r6147 | dshteyn | 2013-03-08 14:22:52 -0800 (Fri, 08 Mar 2013) | 1 line
iProphet: auto-disable models without data
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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...
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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.
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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
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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.
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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.
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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
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r6140 | real_procopio | 2013-03-05 18:31:39 -0800 (Tue, 05 Mar 2013) | 1 line
[MzXML2Search] Update usage statement
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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.
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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
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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.
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r6136 | dshteyn | 2013-03-05 15:17:56 -0800 (Tue, 05 Mar 2013) | 1 line
iProphet: fix bug introduced with NSP value caching.
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r6135 | dshteyn | 2013-03-05 13:47:51 -0800 (Tue, 05 Mar 2013) | 1 line
iProphet: passing wrong hashtable fixed.
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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.
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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.
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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.
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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
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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).
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r6129 | dshteyn | 2013-03-04 14:52:20 -0800 (Mon, 04 Mar 2013) | 1 line
follow-up commit
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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.
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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.
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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.
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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)
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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
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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.
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r6122 | dshteyn | 2013-02-27 12:24:17 -0800 (Wed, 27 Feb 2013) | 1 line
PepXMLViewer.cgi: correct valgrind issues.
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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 ;)
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r6120 | eng_jk | 2013-02-27 09:36:39 -0800 (Wed, 27 Feb 2013) | 2 lines
fix parsing mass types, misc cleanup
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r6119 | eng_jk | 2013-02-26 17:33:32 -0800 (Tue, 26 Feb 2013) | 2 lines
bit of file parsing optimization
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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
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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
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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
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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
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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
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r6113 | dshteyn | 2013-02-26 11:13:27 -0800 (Tue, 26 Feb 2013) | 1 line
iProphet: more meaningful error
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r6112 | dshteyn | 2013-02-26 09:33:40 -0800 (Tue, 26 Feb 2013) | 1 line
Thiophospho modification
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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.
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r6110 | dshteyn | 2013-02-22 15:38:26 -0800 (Fri, 22 Feb 2013) | 2 lines
exit header
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r6109 | dshteyn | 2013-02-22 12:49:05 -0800 (Fri, 22 Feb 2013) | 1 line
PTMProphet: additional output.
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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.
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r6107 | dshteyn | 2013-02-22 11:17:11 -0800 (Fri, 22 Feb 2013) | 1 line
PTMProphet: fix datafile error checking issue.
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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.
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r6105 | dshteyn | 2013-02-22 10:03:03 -0800 (Fri, 22 Feb 2013) | 1 line
extra character
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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()
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r6103 | dshteyn | 2013-02-21 23:28:21 -0800 (Thu, 21 Feb 2013) | 1 line
remove extra character
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r6102 | dshteyn | 2013-02-21 23:26:51 -0800 (Thu, 21 Feb 2013) | 1 line
MSGF+ support
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r6101 | dshteyn | 2013-02-21 22:49:21 -0800 (Thu, 21 Feb 2013) | 1 line
MSGF+ support
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r6100 | dshteyn | 2013-02-21 22:47:02 -0800 (Thu, 21 Feb 2013) | 1 line
MSGF+ support
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r6099 | dshteyn | 2013-02-21 22:45:28 -0800 (Thu, 21 Feb 2013) | 1 line
MSGF+ support
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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.
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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
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r6096 | slagelwa | 2013-02-20 10:19:07 -0800 (Wed, 20 Feb 2013) | 2 lines
Doesn't like x's :(
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r6095 | slagelwa | 2013-02-19 17:32:15 -0800 (Tue, 19 Feb 2013) | 2 lines
Let everyone know who we are
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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.
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