Pre-empt div0 error in PepXML import
Apply div0 bugfix to ProtXML import
Add 'spectator' spectrum viewer. To use, change peptide view url to 'hit_spectrum_2'. Some functionality missing + needs UI polish.
Use http address for OMSSA download in Makefile.PL, so works without hassle via UTSW proxy
Update TITLE parse regex to account for new versions of msconvert appending additional data to title field by default.
Various ModLS Fixes / Improvements. Remove the variable peak depth experimental stuff. Remove incorrect inclusion of mass-error match filtering even on vdepth. Correct the scoring losses. In the ModLS summary annotate spectra to show only the ions that ModLS considers for scoring.
Merge branch 'utsw' of /srv/git/cpfp into utsw
Remove pasted in junk from dodgy mouse wheel button
Don't add a VDEPTH_SCORE param for MODLS tasks. This experimental stuff was removed
Fix fragment calculation and plotting so MH peaks are computed and annotated correctly
Pass name of local downloaded unimod.xml file as arg to import_unimod.pl to allow update behind proxy that needs sign-in etc.
Restore access to main results viewers for searches.
Write neutral loss information for modifications into the OMSSA usermods.xml file
Update Makefile.PL - Download MyriMatch, Download pwiz for MS-GF+ mzid->pepxml conversion, update COMET download.
MyriMatch Searches : Disable 13C MonoisotopeAdjustmentSet if precuror tol >=0.2Da or search will not run. Also add unimplemented mod code
Add HTTP_PROXY config var for Mascot http requests
COMET: Write out a much more full comet.params file that works with 2013.02 r2. Add additional modification handling
Remove experimental and modification notes for new search engines on search submission form
Mascot - Allow submission to a server using Mascot security with login via username and password specified in cpfp.conf
TPP - ProphetModels decoy ratio parameter is total/decoy not target/decoy. See https://groups.google.com/forum/#\!topic/spctools-discuss/mLAMdJUP8AQ