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[Sashimi-commit] SF.net SVN: sashimi:[5124] trunk
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From: <sla...@us...> - 2010-08-25 22:04:42
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Revision: 5124
http://sashimi.svn.sourceforge.net/sashimi/?rev=5124&view=rev
Author: slagelwa
Date: 2010-08-25 22:04:31 +0000 (Wed, 25 Aug 2010)
Log Message:
-----------
[merge 4.4] Merging head of 4.4 branch back into trunk
Modified Paths:
--------------
trunk/trans_proteomic_pipeline/README
trunk/trans_proteomic_pipeline/installer_win32/CheckWebServer.nsh
trunk/trans_proteomic_pipeline/installer_win32/TPP_files.nsh
trunk/trans_proteomic_pipeline/installer_win32/tpp_installtest.bat
trunk/trans_proteomic_pipeline/installer_win32/tpp_perlVersionCheck.bat
trunk/trans_proteomic_pipeline/perl/ProphetModels.pl
trunk/trans_proteomic_pipeline/perl/ProtProphModels.pl
trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/RTCalculator.cxx
trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML/Out2XML.cxx
trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatioPeptideParser/ASAPRatioPeptideParser.cxx
trunk/trans_proteomic_pipeline/src/Quantitation/Option.h
trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx
trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.h
trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/DiscrimValMixtureDistr.cxx
trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/DiscrimValMixtureDistr.h
trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/Inspect/InspectDiscrimValMixtureDistr.cxx
trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/Mascot/MascotDiscrimValMixtureDistr.cxx
trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/Mascot/MascotDiscrimValMixtureDistr.h
trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/Myrimatch/MyrimatchDiscrimValMixtureDistr.cxx
trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/Myrimatch/MyrimatchDiscrimValMixtureDistr.h
trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/Tandem/TandemDiscrimValMixtureDistr.cxx
trunk/trans_proteomic_pipeline/src/Validation/DiscriminateFunction/Tandem/TandemDiscrimValMixtureDistr.h
trunk/trans_proteomic_pipeline/src/Validation/InterProphet/InterProphetParser/KDModel.cxx
trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/AccurateMassDiffDiscrMixtureDistr.cxx
trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/AccurateMassDiffDiscrMixtureDistr.h
trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/DiscreteMixtureDistr.cxx
trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/DiscreteMixtureDistr.h
trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/KernelDensityPIMixtureDistr.cxx
trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/KernelDensityRTMixtureDistr.cxx
trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/KernelDensityRTMixtureDistr.h
trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/MassDifferenceDiscrMixtureDistr.cxx
trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/MassDifferenceDiscrMixtureDistr.h
trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/MixtureDistr.cxx
trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/MixtureDistr.h
trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/MixtureDistrFactory.cxx
trunk/trans_proteomic_pipeline/src/Validation/MixtureModel/MixtureModel.cxx
trunk/trans_proteomic_pipeline/src/Validation/MixtureModel/MixtureModel.h
trunk/trans_proteomic_pipeline/src/Validation/PeptideProphet/PeptideProphetParser/PeptideProphetParser.cxx
trunk/trans_proteomic_pipeline/src/Visualization/xinteract/xinteract.cxx
trunk/trans_proteomic_pipeline/src/common/TPPVersion.h
trunk/trans_proteomic_pipeline/src/common/spectStrct.cpp
trunk/trans_proteomic_pipeline/src/common/spectStrct.h
Property Changed:
----------------
trunk/MaRiMba_Tutorial/
trunk/ProbID/
trunk/README
trunk/cprobid/
trunk/jrap/
trunk/msBID/
trunk/peptideSieve/
trunk/qualscore/
trunk/retired/
trunk/testdata/
trunk/trans_proteomic_pipeline/CGI/
trunk/trans_proteomic_pipeline/CGI/protxml2html.pl
trunk/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl
trunk/trans_proteomic_pipeline/COVERAGE/
trunk/trans_proteomic_pipeline/HELP_DIR/
trunk/trans_proteomic_pipeline/HTML/
trunk/trans_proteomic_pipeline/README
trunk/trans_proteomic_pipeline/README_LINUX
trunk/trans_proteomic_pipeline/README_OSX
trunk/trans_proteomic_pipeline/README_WIN.txt
trunk/trans_proteomic_pipeline/TESTING.txt
trunk/trans_proteomic_pipeline/XML_sample_files.tgz
trunk/trans_proteomic_pipeline/build-mingw-tpp.bat
trunk/trans_proteomic_pipeline/extern/
trunk/trans_proteomic_pipeline/extern/Makefile.boost
trunk/trans_proteomic_pipeline/extern/PerlSupport.tar.bz2
trunk/trans_proteomic_pipeline/extern/README.sashimi.ProteoWizard
trunk/trans_proteomic_pipeline/extern/UnxUtils.tar.bz2
trunk/trans_proteomic_pipeline/extern/apache-w32-2.2.8.tar.bz2
trunk/trans_proteomic_pipeline/extern/archive1.dll
trunk/trans_proteomic_pipeline/extern/bjam.zip
trunk/trans_proteomic_pipeline/extern/boost_vc8.vcproj
trunk/trans_proteomic_pipeline/extern/boost_vc9.vcproj
trunk/trans_proteomic_pipeline/extern/bsdtar-1.2.38-bin.tar.bz2
trunk/trans_proteomic_pipeline/extern/bsdtar-1_2_38.exe
trunk/trans_proteomic_pipeline/extern/build_boost_vc8.bat
trunk/trans_proteomic_pipeline/extern/build_boost_vc9.bat
trunk/trans_proteomic_pipeline/extern/bzip2.dll
trunk/trans_proteomic_pipeline/extern/common_win32/
trunk/trans_proteomic_pipeline/extern/do_swig.bat
trunk/trans_proteomic_pipeline/extern/do_swig.sh
trunk/trans_proteomic_pipeline/extern/gdwin32.tar.bz2
trunk/trans_proteomic_pipeline/extern/gnuplot.tar.bz2
trunk/trans_proteomic_pipeline/extern/hpctools/
trunk/trans_proteomic_pipeline/extern/libw32c.tar.bz2
trunk/trans_proteomic_pipeline/extern/setacl-cmdline.tar.bz2
trunk/trans_proteomic_pipeline/extern/swigwin-1.3.39.zip
trunk/trans_proteomic_pipeline/extern/uncompress_expat.bat
trunk/trans_proteomic_pipeline/extern/uncompress_win_lib.bat
trunk/trans_proteomic_pipeline/extern/xsltproc.tar.bz2
trunk/trans_proteomic_pipeline/extern/zlib1.dll
trunk/trans_proteomic_pipeline/extern/zlib123-dll.tar.bz2
trunk/trans_proteomic_pipeline/images/
trunk/trans_proteomic_pipeline/installer_linux/
trunk/trans_proteomic_pipeline/installer_linux/amazon_ec2_installer.sh
trunk/trans_proteomic_pipeline/installer_linux/amazon_ec2_notes
trunk/trans_proteomic_pipeline/installer_linux/install-prerequisites-ubuntu-8_04.sh
trunk/trans_proteomic_pipeline/installer_linux/install-ubuntu-9_04.sh
trunk/trans_proteomic_pipeline/installer_win32/
trunk/trans_proteomic_pipeline/perl/
trunk/trans_proteomic_pipeline/perl/ProphetModels.pl
trunk/trans_proteomic_pipeline/schema/
trunk/trans_proteomic_pipeline/src/
trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_numFns.cxx
trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_pepFns.cxx
trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_txtFns.cxx
trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideUpdateParser/mtables.cxx
trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideUpdateParser/xgd.cxx
trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideUpdateParser/xgdfonts.cxx
trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTMzXMLLibImporter.cpp
trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraST_base64.cpp
trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraST_kwset.cpp
trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraST_obstack.cpp
trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraST_util.cpp
trunk/trans_proteomic_pipeline/src/Visualization/Comet/comet-fastadb/calc_pI.cxx
trunk/trans_proteomic_pipeline/src/Visualization/Comet/cometresult1.cxx
trunk/trans_proteomic_pipeline/src/Visualization/Comet/plot-msms/plot-msms1.cxx
trunk/trans_proteomic_pipeline/src/Visualization/Comet/sequest-tgz-out/sequest-tgz-out1.cxx
trunk/trans_proteomic_pipeline/src/Visualization/Pep3D/Pep3D_functions.cxx
trunk/trans_proteomic_pipeline/src/Visualization/Pep3D/cgi_Pep3D_xml/cgi_Pep3D_xml.cxx
trunk/trans_proteomic_pipeline/src/Visualization/Pep3D/cgi_disCidData.cxx
trunk/trans_proteomic_pipeline/src/Visualization/Pep3D/cgi_getCidData.cxx
trunk/trans_proteomic_pipeline/src/Visualization/psm2pdf/
trunk/trans_proteomic_pipeline/src/Visualization/psm2pdf/psm2pdf.cxx
trunk/trans_proteomic_pipeline/src/common/crypt.cxx
trunk/trans_proteomic_pipeline/src/common/util.cxx
trunk/trans_proteomic_pipeline/src/common/win32_system.cxx
trunk/trans_proteomic_pipeline/src/mzXML/converters/ReAdW/
trunk/trans_proteomic_pipeline/src/mzXML/converters/mzWiff/
trunk/trans_proteomic_pipeline/src/mzXML/converters/trapper/
trunk/trans_proteomic_pipeline/src/mzXML/tools/mzXMLIndexer/indexmzXML.cpp
trunk/trans_proteomic_pipeline/src/mzXML/tools/mzXMLRecalibrator/calibrationRoutines.cpp
trunk/trans_proteomic_pipeline/src/mzXML/tools/mzXMLRecalibrator/guessCalibInterval.cpp
trunk/trans_proteomic_pipeline/src/mzXML/tools/mzXMLRecalibrator/mzXMLRecalibrator.cpp
trunk/trans_proteomic_pipeline/src/mzXML/tools/mzXMLRecalibrator/mzXMLRecalibratorBase64.cpp
trunk/trans_proteomic_pipeline/src/mzXML/tools/mzXMLRecalibrator/mzXMLRecalibratorOptions.cpp
trunk/trans_proteomic_pipeline/src/mzXML/tools/mzXMLRecalibrator/mzXMLRecalibratorRamp.cpp
trunk/trans_proteomic_pipeline/src/mzXML/tools/mzXMLRecalibrator/mzXMLUtils.cpp
trunk/trans_proteomic_pipeline/src/mzXML/tools/readmzXML/readmzXML.cpp
trunk/trans_proteomic_pipeline/src/refresh_interact/backup_obstack.cxx
trunk/trans_proteomic_pipeline/src/refresh_interact/kwset.cxx
trunk/trans_proteomic_pipeline/src/refresh_interact/obstack.cxx
trunk/trans_proteomic_pipeline/src/refresh_interact/obstack2.cxx
trunk/trans_proteomic_pipeline/src/refresh_interact/obstack3.cxx
trunk/trans_proteomic_pipeline/src/refresh_interact/obstack4.cxx
trunk/trans_proteomic_pipeline/src/refresh_interact/refresh_interact.cxx
trunk/trans_proteomic_pipeline/src/runperl_src/runperl.cxx
trunk/trans_proteomic_pipeline/src/util/calc_pI.cpp
trunk/trans_proteomic_pipeline/src/util/calculate_pi.cpp
trunk/trans_proteomic_pipeline/src/util/digestdb1.cpp
trunk/trans_proteomic_pipeline/src/util/dta-xml.cpp
trunk/trans_proteomic_pipeline/src/util/dtafilter1.cpp
trunk/trans_proteomic_pipeline/src/util/fdr_plot.cpp
trunk/trans_proteomic_pipeline/src/util/getdb.uniprot
trunk/trans_proteomic_pipeline/src/util/out2summary/out2summary.cpp
trunk/trans_proteomic_pipeline/src/util/plottic1.cpp
trunk/trans_proteomic_pipeline/src/util/runsearch1.cpp
trunk/trans_proteomic_pipeline/src/util/subsetdb1.cpp
trunk/trans_proteomic_pipeline/testing/
trunk/validateXML/
trunk/validateXML-java/
Property changes on: trunk/MaRiMba_Tutorial
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/4-2/trans_proteomic_pipeline/HELP_DIR/MaRiMba_Tutorial:4076-4242
/branches/win_lib-cleanup/trans_proteomic_pipeline/HELP_DIR/MaRiMba_Tutorial:4547-4556
+ /branches/4-2/trans_proteomic_pipeline/HELP_DIR/MaRiMba_Tutorial:4076-4242
/branches/4-4/MaRiMba_Tutorial:5092-5117
/branches/4-4/trans_proteomic_pipeline/HELP_DIR/MaRiMba_Tutorial:5054-5091
/branches/win_lib-cleanup/trans_proteomic_pipeline/HELP_DIR/MaRiMba_Tutorial:4547-4556
Property changes on: trunk/ProbID
___________________________________________________________________
Added: svn:mergeinfo
+ /branches/4-4/ProbID:5054-5117
Property changes on: trunk/README
___________________________________________________________________
Added: svn:mergeinfo
+ /branches/4-4/README:5054-5117
Property changes on: trunk/cprobid
___________________________________________________________________
Added: svn:mergeinfo
+ /branches/4-4/cprobid:5054-5117
Property changes on: trunk/jrap
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Added: svn:mergeinfo
+ /branches/4-4/jrap:5054-5117
Property changes on: trunk/msBID
___________________________________________________________________
Added: svn:mergeinfo
+ /branches/4-4/msBID:5054-5117
Property changes on: trunk/peptideSieve
___________________________________________________________________
Added: svn:mergeinfo
+ /branches/4-4/peptideSieve:5054-5117
Property changes on: trunk/qualscore
___________________________________________________________________
Added: svn:mergeinfo
+ /branches/4-4/qualscore:5054-5117
Property changes on: trunk/retired
___________________________________________________________________
Added: svn:mergeinfo
+ /branches/4-4/retired:5054-5117
Property changes on: trunk/testdata
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Added: svn:mergeinfo
+ /branches/4-4/testdata:5054-5117
Property changes on: trunk/trans_proteomic_pipeline/CGI
___________________________________________________________________
Added: svn:mergeinfo
+ /branches/4-2/trans_proteomic_pipeline/CGI:4076-4242
/branches/4-4/trans_proteomic_pipeline/CGI:5054-5117
/branches/win_lib-cleanup/trans_proteomic_pipeline/CGI:4547-4556
Property changes on: trunk/trans_proteomic_pipeline/CGI/protxml2html.pl
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/4-2/trans_proteomic_pipeline/CGI/protxml2html.pl:4076-4262
+ /branches/4-2/trans_proteomic_pipeline/CGI/protxml2html.pl:4076-4262
/branches/4-4/trans_proteomic_pipeline/CGI/protxml2html.pl:5054-5117
Property changes on: trunk/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/4-2/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl:4076-4242
/branches/course-apr09/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl:4132-4272
+ /branches/4-2/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl:4076-4242
/branches/4-4/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl:5054-5117
/branches/course-apr09/trans_proteomic_pipeline/CGI/tpp_gui/tpp_gui.pl:4132-4272
Property changes on: trunk/trans_proteomic_pipeline/COVERAGE
___________________________________________________________________
Added: svn:mergeinfo
+ /branches/4-2/trans_proteomic_pipeline/COVERAGE:4076-4242
/branches/4-4/trans_proteomic_pipeline/COVERAGE:5054-5117
/branches/win_lib-cleanup/trans_proteomic_pipeline/COVERAGE:4547-4556
Property changes on: trunk/trans_proteomic_pipeline/HELP_DIR
___________________________________________________________________
Added: svn:mergeinfo
+ /branches/4-2/trans_proteomic_pipeline/HELP_DIR:4076-4242
/branches/4-4/trans_proteomic_pipeline/HELP_DIR:5054-5117
/branches/win_lib-cleanup/trans_proteomic_pipeline/HELP_DIR:4547-4556
Property changes on: trunk/trans_proteomic_pipeline/HTML
___________________________________________________________________
Added: svn:mergeinfo
+ /branches/4-2/trans_proteomic_pipeline/HTML:4076-4242
/branches/4-4/trans_proteomic_pipeline/HTML:5054-5117
/branches/win_lib-cleanup/trans_proteomic_pipeline/HTML:4547-4556
Modified: trunk/trans_proteomic_pipeline/README
===================================================================
--- trunk/trans_proteomic_pipeline/README 2010-08-25 21:59:07 UTC (rev 5123)
+++ trunk/trans_proteomic_pipeline/README 2010-08-25 22:04:31 UTC (rev 5124)
@@ -857,5 +857,3 @@
....
-
-
Property changes on: trunk/trans_proteomic_pipeline/README
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/4-2/trans_proteomic_pipeline/README.txt:4076-4242
+ /branches/4-2/trans_proteomic_pipeline/README.txt:4076-4242
/branches/4-4/trans_proteomic_pipeline/README:5054-5117
Property changes on: trunk/trans_proteomic_pipeline/README_LINUX
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Added: svn:mergeinfo
+ /branches/4-2/trans_proteomic_pipeline/README_LINUX:4076-4242
/branches/4-4/trans_proteomic_pipeline/README_LINUX:5054-5117
/branches/win_lib-cleanup/trans_proteomic_pipeline/README_LINUX:4547-4556
Property changes on: trunk/trans_proteomic_pipeline/README_OSX
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Modified: svn:mergeinfo
- /branches/4-2/trans_proteomic_pipeline/README_OSX.txt:4076-4242
+ /branches/4-2/trans_proteomic_pipeline/README_OSX.txt:4076-4242
/branches/4-4/trans_proteomic_pipeline/README_OSX:5054-5117
Property changes on: trunk/trans_proteomic_pipeline/README_WIN.txt
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Added: svn:mergeinfo
+ /branches/4-2/trans_proteomic_pipeline/README_WIN.txt:4076-4242
/branches/4-4/trans_proteomic_pipeline/README_WIN.txt:5054-5117
/branches/win_lib-cleanup/trans_proteomic_pipeline/README_WIN.txt:4547-4556
Property changes on: trunk/trans_proteomic_pipeline/TESTING.txt
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Added: svn:mergeinfo
+ /branches/4-2/trans_proteomic_pipeline/TESTING.txt:4076-4242
/branches/4-4/trans_proteomic_pipeline/TESTING.txt:5054-5117
/branches/win_lib-cleanup/trans_proteomic_pipeline/TESTING.txt:4547-4556
Property changes on: trunk/trans_proteomic_pipeline/XML_sample_files.tgz
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Added: svn:mergeinfo
+ /branches/4-2/trans_proteomic_pipeline/XML_sample_files.tgz:4076-4242
/branches/4-4/trans_proteomic_pipeline/XML_sample_files.tgz:5054-5117
/branches/win_lib-cleanup/trans_proteomic_pipeline/XML_sample_files.tgz:4547-4556
Property changes on: trunk/trans_proteomic_pipeline/build-mingw-tpp.bat
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Added: svn:mergeinfo
+ /branches/4-2/trans_proteomic_pipeline/build-mingw-tpp.bat:4076-4242
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/branches/win_lib-cleanup/trans_proteomic_pipeline/build-mingw-tpp.bat:4547-4556
Property changes on: trunk/trans_proteomic_pipeline/extern
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Added: svn:mergeinfo
+ /branches/4-2/trans_proteomic_pipeline/extern:4076-4242
/branches/4-4/trans_proteomic_pipeline/extern:5054-5117
/branches/win_lib-cleanup/trans_proteomic_pipeline/extern:4547-4556
Property changes on: trunk/trans_proteomic_pipeline/extern/Makefile.boost
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Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/Makefile.boost:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/Makefile.boost:5054-5117
/branches/win_lib-cleanup/win_lib/Makefile.boost:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/PerlSupport.tar.bz2
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Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/PerlSupport.tar.bz2:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/PerlSupport.tar.bz2:5054-5117
/branches/win_lib-cleanup/win_lib/PerlSupport.tar.bz2:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/README.sashimi.ProteoWizard
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Modified: svn:mergeinfo
- /branches/4-2/trans_proteomic_pipeline/extern/ProteoWizard/README.sashimi.ProteoWizard:4076-4242
/branches/win_lib-cleanup/trans_proteomic_pipeline/extern/ProteoWizard/README.sashimi.ProteoWizard:4547-4556
+ /branches/4-2/trans_proteomic_pipeline/extern/ProteoWizard/README.sashimi.ProteoWizard:4076-4242
/branches/4-4/trans_proteomic_pipeline/extern/README.sashimi.ProteoWizard:5054-5117
/branches/win_lib-cleanup/trans_proteomic_pipeline/extern/ProteoWizard/README.sashimi.ProteoWizard:4547-4556
Property changes on: trunk/trans_proteomic_pipeline/extern/UnxUtils.tar.bz2
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Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/UnxUtils.tar.bz2:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/UnxUtils.tar.bz2:5054-5117
/branches/win_lib-cleanup/win_lib/UnxUtils.tar.bz2:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/apache-w32-2.2.8.tar.bz2
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Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/apache-w32-2.2.8.tar.bz2:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/apache-w32-2.2.8.tar.bz2:5054-5117
/branches/win_lib-cleanup/win_lib/apache-w32-2.2.8.tar.bz2:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/archive1.dll
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Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/archive1.dll:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/archive1.dll:5054-5117
/branches/win_lib-cleanup/win_lib/archive1.dll:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/bjam.zip
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Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/bjam.zip:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/bjam.zip:5054-5117
/branches/win_lib-cleanup/win_lib/bjam.zip:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/boost_vc8.vcproj
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Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/boost_vc8.vcproj:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/boost_vc8.vcproj:5054-5117
/branches/win_lib-cleanup/win_lib/boost_vc8.vcproj:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/boost_vc9.vcproj
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Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/boost_vc8.vcproj:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/boost_vc9.vcproj:5054-5117
/branches/win_lib-cleanup/win_lib/boost_vc8.vcproj:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/bsdtar-1.2.38-bin.tar.bz2
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/bsdtar-1.2.38-bin.tar.bz2:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/bsdtar-1.2.38-bin.tar.bz2:5054-5117
/branches/win_lib-cleanup/win_lib/bsdtar-1.2.38-bin.tar.bz2:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/bsdtar-1_2_38.exe
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/bsdtar-1_2_38.exe:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/bsdtar-1_2_38.exe:5054-5117
/branches/win_lib-cleanup/win_lib/bsdtar-1_2_38.exe:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/build_boost_vc8.bat
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/cpprename/trans_proteomic_pipeline/extern/build_boost_vc8.bat:4629-4655
/branches/win_lib-cleanup/win_lib/build_boost_vc8.bat:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/build_boost_vc8.bat:5054-5117
/branches/cpprename/trans_proteomic_pipeline/extern/build_boost_vc8.bat:4629-4655
/branches/win_lib-cleanup/win_lib/build_boost_vc8.bat:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/build_boost_vc9.bat
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/cpprename/trans_proteomic_pipeline/extern/build_boost_vc8.bat:4629-4655
/branches/win_lib-cleanup/win_lib/build_boost_vc8.bat:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/build_boost_vc9.bat:5054-5117
/branches/cpprename/trans_proteomic_pipeline/extern/build_boost_vc8.bat:4629-4655
/branches/win_lib-cleanup/win_lib/build_boost_vc8.bat:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/bzip2.dll
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/bzip2.dll:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/bzip2.dll:5054-5117
/branches/win_lib-cleanup/win_lib/bzip2.dll:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/common_win32
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/common_win32:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/common_win32:5054-5117
/branches/win_lib-cleanup/win_lib/common_win32:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/do_swig.bat
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/do_swig.bat:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/do_swig.bat:5054-5117
/branches/win_lib-cleanup/win_lib/do_swig.bat:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/do_swig.sh
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/do_swig.sh:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/do_swig.sh:5054-5117
/branches/win_lib-cleanup/win_lib/do_swig.sh:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/gdwin32.tar.bz2
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/gdwin32.tar.bz2:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/gdwin32.tar.bz2:5054-5117
/branches/win_lib-cleanup/win_lib/gdwin32.tar.bz2:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/gnuplot.tar.bz2
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/gnuplot.tar.bz2:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/gnuplot.tar.bz2:5054-5117
/branches/win_lib-cleanup/win_lib/gnuplot.tar.bz2:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/hpctools
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/4-2/trans_proteomic_pipeline/extern/TPPAWSSearch:4076-4242
/branches/win_lib-cleanup/trans_proteomic_pipeline/extern/TPPAWSSearch:4547-4556
+ /branches/4-2/trans_proteomic_pipeline/extern/TPPAWSSearch:4076-4242
/branches/4-4/trans_proteomic_pipeline/extern/hpctools:5054-5117
/branches/win_lib-cleanup/trans_proteomic_pipeline/extern/TPPAWSSearch:4547-4556
Property changes on: trunk/trans_proteomic_pipeline/extern/libw32c.tar.bz2
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/libw32c.tar.bz2:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/libw32c.tar.bz2:5054-5117
/branches/win_lib-cleanup/win_lib/libw32c.tar.bz2:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/setacl-cmdline.tar.bz2
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/setacl-cmdline.tar.bz2:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/setacl-cmdline.tar.bz2:5054-5117
/branches/win_lib-cleanup/win_lib/setacl-cmdline.tar.bz2:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/swigwin-1.3.39.zip
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/swigwin-1.3.39.zip:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/swigwin-1.3.39.zip:5054-5117
/branches/win_lib-cleanup/win_lib/swigwin-1.3.39.zip:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/uncompress_expat.bat
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/cpprename/trans_proteomic_pipeline/extern/uncompress_expat.bat:4629-4655
/branches/win_lib-cleanup/win_lib/uncompress_expat.bat:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/uncompress_expat.bat:5054-5117
/branches/cpprename/trans_proteomic_pipeline/extern/uncompress_expat.bat:4629-4655
/branches/win_lib-cleanup/win_lib/uncompress_expat.bat:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/uncompress_win_lib.bat
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/uncompress_win_lib.bat:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/uncompress_win_lib.bat:5054-5117
/branches/win_lib-cleanup/win_lib/uncompress_win_lib.bat:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/xsltproc.tar.bz2
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/xsltproc.tar.bz2:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/xsltproc.tar.bz2:5054-5117
/branches/win_lib-cleanup/win_lib/xsltproc.tar.bz2:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/zlib1.dll
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/zlib1.dll:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/zlib1.dll:5054-5117
/branches/win_lib-cleanup/win_lib/zlib1.dll:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/extern/zlib123-dll.tar.bz2
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/win_lib-cleanup/win_lib/zlib123-dll.tar.bz2:4547-4555
+ /branches/4-4/trans_proteomic_pipeline/extern/zlib123-dll.tar.bz2:5054-5117
/branches/win_lib-cleanup/win_lib/zlib123-dll.tar.bz2:4547-4555
Property changes on: trunk/trans_proteomic_pipeline/images
___________________________________________________________________
Added: svn:mergeinfo
+ /branches/4-2/trans_proteomic_pipeline/images:4076-4242
/branches/4-4/trans_proteomic_pipeline/images:5054-5117
/branches/win_lib-cleanup/trans_proteomic_pipeline/images:4547-4556
Property changes on: trunk/trans_proteomic_pipeline/installer_linux
___________________________________________________________________
Added: svn:mergeinfo
+ /branches/4-2/trans_proteomic_pipeline/installer_linux:4076-4242
/branches/4-4/trans_proteomic_pipeline/installer_linux:5054-5117
/branches/win_lib-cleanup/trans_proteomic_pipeline/installer_linux:4547-4556
Property changes on: trunk/trans_proteomic_pipeline/installer_linux/amazon_ec2_installer.sh
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/4-2/trans_proteomic_pipeline/amazon_ec2_ubuntu_notes.sh:4076-4242
+ /branches/4-2/trans_proteomic_pipeline/amazon_ec2_ubuntu_notes.sh:4076-4242
/branches/4-4/trans_proteomic_pipeline/installer_linux/amazon_ec2_installer.sh:5054-5117
Property changes on: trunk/trans_proteomic_pipeline/installer_linux/amazon_ec2_notes
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/4-2/trans_proteomic_pipeline/amazon_ec2_ubuntu_notes.txt:4076-4242
+ /branches/4-2/trans_proteomic_pipeline/amazon_ec2_ubuntu_notes.txt:4076-4242
/branches/4-4/trans_proteomic_pipeline/installer_linux/amazon_ec2_notes:5054-5117
Property changes on: trunk/trans_proteomic_pipeline/installer_linux/install-prerequisites-ubuntu-8_04.sh
___________________________________________________________________
Modified: svn:mergeinfo
-
+ /branches/4-4/trans_proteomic_pipeline/installer_linux/install-prerequisites-ubuntu-8_04.sh:5054-5117
Property changes on: trunk/trans_proteomic_pipeline/installer_linux/install-ubuntu-9_04.sh
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/4-2/trans_proteomic_pipeline/README_UBUNTU.txt:4076-4242
+ /branches/4-2/trans_proteomic_pipeline/README_UBUNTU.txt:4076-4242
/branches/4-4/trans_proteomic_pipeline/installer_linux/install-ubuntu-9_04.sh:5054-5117
Property changes on: trunk/trans_proteomic_pipeline/installer_win32
___________________________________________________________________
Added: svn:mergeinfo
+ /branches/4-2/trans_proteomic_pipeline/installer_win32:4076-4242
/branches/4-4/trans_proteomic_pipeline/installer_win32:5054-5117
/branches/win_lib-cleanup/trans_proteomic_pipeline/installer_win32:4547-4556
Modified: trunk/trans_proteomic_pipeline/installer_win32/CheckWebServer.nsh
===================================================================
--- trunk/trans_proteomic_pipeline/installer_win32/CheckWebServer.nsh 2010-08-25 21:59:07 UTC (rev 5123)
+++ trunk/trans_proteomic_pipeline/installer_win32/CheckWebServer.nsh 2010-08-25 22:04:31 UTC (rev 5124)
@@ -45,6 +45,7 @@
; no IIS found - do we have apache?
CheckApache:
+
; first thing is to check the registry - presence of config files proves nothing, could be old
ClearErrors
EnumRegKey $0 HKEY_LOCAL_MACHINE "SOFTWARE\Apache Software Foundation\Apache" 0
@@ -85,6 +86,27 @@
FindFirst $0 $1 $ApacheConfFile
IfErrors 0 doConfigApache
+ ; 32 bit Apache 2.0.x on 64 bit machines
+ ClearErrors
+ ExpandEnvStrings $ApacheConfFile "%ProgramFiles(x86)%\Apache Group\Apache2\conf\httpd.conf"
+ ExpandEnvStrings $ApacheExe '"%ProgramFiles(x86)%\Apache Group\Apache2\bin\Apache.exe"'
+ FindFirst $0 $1 $ApacheConfFile
+ IfErrors 0 doConfigApache
+
+ ; 32 bit Apache 2.2.x on 64 bit machines
+ ClearErrors
+ ExpandEnvStrings $ApacheConfFile "%ProgramFiles(x86)%\Apache Software Foundation\Apache2.2\conf\httpd.conf"
+ ExpandEnvStrings $ApacheExe '"%ProgramFiles(x86)%\Apache Software Foundation\Apache2.2\bin\httpd.exe" -n Apache2.2'
+ FindFirst $0 $1 $ApacheConfFile
+ IfErrors 0 doConfigApache
+
+ ; 32 bit Apache 2.3.x on 64 bit machines
+ ClearErrors
+ ExpandEnvStrings $ApacheConfFile "%ProgramFiles(x86)%\Apache Software Foundation\Apache2.3\conf\httpd.conf"
+ ExpandEnvStrings $ApacheExe '"%ProgramFiles(x86)%\Apache Software Foundation\Apache2.3\bin\httpd.exe" -n Apache2.3'
+ FindFirst $0 $1 $ApacheConfFile
+ IfErrors 0 doConfigApache
+
; no Apache found
Goto NoWebServer
@@ -104,7 +126,7 @@
If you are certain you have a webserver installed and have manually configured it as described in the links above, press No.$\r$\n$\r$\nInstall the Apache webserver now?" IDNO done IDCANCEL abort
!insertmacro LogDetail "Installing Apache: please use the default options."
MessageBox MB_OK|MB_ICONINFORMATION "Ready to begin installing Apache: please use the default options.$\r$\n$\r$\n\
-(Please note that a newer version of the Apache webserver may be available; you may want to check the Apache website after the ${PRODUCT_NAME} installtion completes.)"
+(Please note that a newer version of the Apache webserver may be available; you may want to check the Apache website after the ${PRODUCT_NAME} installation completes.)"
File "..\extern\apache-w32-2.2.8\apache.msi"
ExecWait 'MSIEXEC.EXE /I "$INSTDIR\apache.msi" ALLUSERS=1'
; Delete "apache.msi" ; don't delete - leave as cue (and tool) for uninstaller
Modified: trunk/trans_proteomic_pipeline/installer_win32/TPP_files.nsh
===================================================================
--- trunk/trans_proteomic_pipeline/installer_win32/TPP_files.nsh 2010-08-25 21:59:07 UTC (rev 5123)
+++ trunk/trans_proteomic_pipeline/installer_win32/TPP_files.nsh 2010-08-25 22:04:31 UTC (rev 5124)
@@ -194,6 +194,9 @@
!insertmacro ${addOrDelete} "." "residue_modifications.cfg" ""
SetOverwrite on
+!insertmacro ${addOrDelete} ${PRODUCT_BUILD_DIR} "RTCalc.exe" ""
+!insertmacro ${addOrDelete} ${PRODUCT_BUILD_DIR} "RTCalc.coeff" ""
+
; GUI - note that perlpaths.mak manupulates tpp_gui.pl
!insertmacro ${addOrDelete} "..\CGI\tpp_gui" "tpp_gui.css" ""
!insertmacro ${addOrDelete} "..\CGI\tpp_gui" "ASAPRatio.html" ""
@@ -243,7 +246,7 @@
!insertmacro ${addOrDelete} ${PRODUCT_BUILD_DIR} "tandem-style.xsl" "..\wwwroot\ISB\data\parameters"
; MaRiMba Tutorial Files
-!insertmacro ${addOrDelete} "..\HELP_DIR\MaRiMba_Tutorial" "*.*" "..\wwwroot\ISB\data\MaRiMba"
+!insertmacro ${addOrDelete} "..\HELP_DIR\MaRiMba_Tutorial" "README.txt" "..\wwwroot\ISB\data\MaRiMba"
; win32 versions of unix utilities from http://unxutils.sourceforge.net/
!insertmacro ${addOrDelete} "..\extern\UnxUtils\usr\local\wbin" "cp.exe" ""
@@ -272,10 +275,5 @@
!insertmacro ${addOrDelete} "..\extern\UnxUtils\usr\local\wbin" "xargs.exe" ""
; Mass-Spec to XML data converters
-; (TODO: could these build under MinGW?)
-!insertmacro ${addOrDelete} "..\src\release" "ReAdW.exe" ""
-!insertmacro ${addOrDelete} "..\src\release" "massWolf.exe" ""
-!insertmacro ${addOrDelete} "..\src\release" "mzWiff.exe" ""
!insertmacro ${addOrDelete} "..\src\release" "msconvert.exe" ""
-;!insertmacro ${addOrDelete} "..\src\release" "trapper_setup.exe" ""
-!macroend
\ No newline at end of file
+!macroend
Modified: trunk/trans_proteomic_pipeline/installer_win32/tpp_installtest.bat
===================================================================
--- trunk/trans_proteomic_pipeline/installer_win32/tpp_installtest.bat 2010-08-25 21:59:07 UTC (rev 5123)
+++ trunk/trans_proteomic_pipeline/installer_win32/tpp_installtest.bat 2010-08-25 22:04:31 UTC (rev 5124)
@@ -2,9 +2,9 @@
cls
ECHO a quick check to see if the TPP installation process went OK:
cd c:\inetpub\tpp-bin
-ECHO checking path... should include "c:\perl\bin;C:\Inetpub\tpp-bin;"
+ECHO checking path... should include "c:\perl(64)?\bin;C:\Inetpub\tpp-bin;"
path > test.txt
-grep -i perl\\bin < test.txt > test2.txt
+grep -iE "perl(64)?\\bin" < test.txt > test2.txt
IF %ERRORLEVEL% == 0 GOTO check1
path
ECHO ---
@@ -25,9 +25,9 @@
ECHO OK
:end1
ECHO ---
-ECHO checking perl... should say perl\bin\perl.exe
+ECHO checking perl... should say perl\bin\perl.exe or perl64\bin\perl.exe
which perl.exe > test.txt
-grep -i perl\\bin\\perl.exe test.txt
+grep -iE "perl(64)?\\bin\\perl.exe" test.txt
IF %ERRORLEVEL% == 0 GOTO OK2
ECHO ---
grep -i cygwin test.txt
Modified: trunk/trans_proteomic_pipeline/installer_win32/tpp_perlVersionCheck.bat
===================================================================
--- trunk/trans_proteomic_pipeline/installer_win32/tpp_perlVersionCheck.bat 2010-08-25 21:59:07 UTC (rev 5123)
+++ trunk/trans_proteomic_pipeline/installer_win32/tpp_perlVersionCheck.bat 2010-08-25 22:04:31 UTC (rev 5124)
@@ -8,7 +8,7 @@
REM pause
exit 1
:ANALYZEVERSION
-perl --version | perl -ne "my $foundActiveState=0;my $verMajor=-1;my $verMinor=-1; my $verRev=-1; while (<>) { if (/ActiveState/) { $foundActiveState=1;} if (/(\d+)\.(\d+)\.(\d+)/) {$verMajor=$1;$verMinor=$2;$verRev=$3;} } if($foundActiveState==1 && $verMajor==5 && $verMinor==8) {system('cp -f c:/inetpub/tpp-bin/tpplib_perl.58.dll c:/inetpub/tpp-bin/tpplib_perl.dll');} if($foundActiveState==1 && $verMajor==5 && $verMinor==10) {system('cp -f c:/inetpub/tpp-bin/tpplib_perl.510.dll c:/inetpub/tpp-bin/tpplib_perl.dll');} if ($foundActiveState==1 && ( ($verMajor==5 && $verMinor==8 && $verRev>=8) || ($verMajor==5 && $verMinor==10 && $verRev>=0) || ($verMajor >= 6) ) ) {exit 0;} else {exit -1;} "
+perl --version | perl -ne "my $foundActiveState=0;my $verMajor=-1;my $verMinor=-1; my $verRev=-1; while (<>) { if (/ActiveState/) { $foundActiveState=1;} if (/(\d+)\.(\d+)\.(\d+)/) {$verMajor=$1;$verMinor=$2;$verRev=$3;} } if ($foundActiveState==1 && ( ($verMajor==5 && $verMinor==8 && $verRev>=8) || ($verMajor==5 && $verMinor==10 && $verRev>=0) || ($verMajor==5 && $verMinor==12 && $verMinor>=0) ) ) {exit 0;} else {exit -1;} "
if %ERRORLEVEL% == 0 GOTO VERSIONOK
ECHO ActiveState Perl was not detected, or not of a recent-enough version.
REM pause
Property changes on: trunk/trans_proteomic_pipeline/perl
___________________________________________________________________
Added: svn:mergeinfo
+ /branches/4-2/trans_proteomic_pipeline/perl:4076-4242
/branches/4-4/trans_proteomic_pipeline/perl:5054-5117
/branches/win_lib-cleanup/trans_proteomic_pipeline/perl:4547-4556
Modified: trunk/trans_proteomic_pipeline/perl/ProphetModels.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/ProphetModels.pl 2010-08-25 21:59:07 UTC (rev 5123)
+++ trunk/trans_proteomic_pipeline/perl/ProphetModels.pl 2010-08-25 22:04:31 UTC (rev 5124)
@@ -561,7 +561,14 @@
$ip_decoy_ratio = $decoy_ratio;
if ($decoy_ratio < 0) {
- $pp_decoy_ratio = ($pp_prob_array_decoy[0] / $pp_prob_array[0]);
+ if ($pp_prob_array[0] > 0) {
+ $pp_decoy_ratio = ($pp_prob_array_decoy[0] / $pp_prob_array[0]);
+ print "Using decoy ratio of $pp_decoy_ratio for PeptideProphet.";
+ } else {
+ $pp_decoy_ratio = -1;
+ print "Cannot determine decoy ratio from PeptideProphet.";
+ }
+
print "Using decoy ratio of $pp_decoy_ratio for PeptideProphet.";
if ($has_iprophet == 1) {
if ($ip_prob_array[0] > 0) {
@@ -621,7 +628,7 @@
my $fdr_ip_decoy = 0.0;
my $num_corr_ip_decoy = $num_pos_ip;
- if ($has_iprophet == 1 and $num_pos_ip > 0) {
+ if ($has_iprophet == 1 and $num_pos_ip > 0 and $ip_decoy_ratio > 0) {
my $num_incorr_ip = ($num_ip_decoy - $ip_num_decoy_below_prob) / $ip_decoy_ratio;
$fdr_ip_decoy = $num_incorr_ip / $num_pos_ip;
$num_corr_ip_decoy = $num_pos_ip - $num_incorr_ip;
@@ -629,26 +636,26 @@
my $fdr_pp_decoy = 0.0;
my $num_corr_pp_decoy = $num_pos_pp;
- if ($num_hits - $pp_num_below_prob > 0) {
+ if ($num_hits - $pp_num_below_prob > 0 and $pp_decoy_ratio > 0 and $num_pos_pp > 0) {
my $num_incorr_pp = ($num_decoy - $pp_num_decoy_below_prob) / $pp_decoy_ratio;
$fdr_pp_decoy = $num_incorr_pp / $num_pos_pp;
$num_corr_pp_decoy = $num_pos_pp - $num_incorr_pp;
}
my $PP_uncert = 0;
- if ($fdr_pp*(1-$fdr_pp)/$num_pos_pp > 0){
- $PP_uncert = sqrt($fdr_pp*(1-$fdr_pp)/$num_pos_pp);
- }
+ if ($num_pos_pp > 0 && $fdr_pp*(1-$fdr_pp)/$num_pos_pp > 0){
+ $PP_uncert = sqrt($fdr_pp*(1-$fdr_pp)/$num_pos_pp);
+ }
my $PP_decoy_uncert = 0;
- if ($fdr_pp_decoy*(1-$fdr_pp_decoy)/$num_pos_pp > 0) {
+ if ($num_pos_pp > 0 && $fdr_pp_decoy*(1-$fdr_pp_decoy)/$num_pos_pp > 0) {
$PP_decoy_uncert = sqrt($fdr_pp_decoy*(1-$fdr_pp_decoy)/$num_pos_pp);
}
my $IP_uncert = 0;
- if ($has_iprophet == 1 && $fdr_ip*(1-$fdr_ip)/$num_pos_ip > 0){
+ if ($num_pos_ip > 0 && $has_iprophet == 1 && $fdr_ip*(1-$fdr_ip)/$num_pos_ip > 0){
$IP_uncert = sqrt($fdr_ip*(1-$fdr_ip)/$num_pos_ip);
}
my $IP_decoy_uncert = 0;
- if ($has_iprophet == 1 && $fdr_ip_decoy*(1-$fdr_ip_decoy)/$num_pos_ip > 0) {
+ if ($num_pos_ip > 0 && $has_iprophet == 1 && $fdr_ip_decoy*(1-$fdr_ip_decoy)/$num_pos_ip > 0) {
$IP_decoy_uncert = sqrt($fdr_ip_decoy*(1-$fdr_ip_decoy)/$num_pos_ip);
}
@@ -746,6 +753,7 @@
my $cnt = 0;
my $pp_pr = 0;
my $dec_count = 0;
+my $dec_prob = 0;
my @keys = sort {$pp_peps{$b} <=> $pp_peps{$a}} keys %pp_peps;
@@ -764,10 +772,13 @@
$dec_count -= $pp_dec{$keys[$cnt-$wdw]};
}
- my $dec_prob = ( $wdw - $dec_count / $pp_decoy_ratio ) / $wdw;
+ if ( $pp_decoy_ratio > 0 && $wdw > 0) {
+ $dec_prob = ( $wdw - $dec_count / $pp_decoy_ratio ) / $wdw;
+ }
- print PROUT $pp_pr/$wdw . "\t" . $dec_prob . "\n";
-
+ if ( $wdw > 0) {
+ print PROUT $pp_pr/$wdw . "\t" . $dec_prob . "\n";
+ }
}
close(PROUT);
Property changes on: trunk/trans_proteomic_pipeline/perl/ProphetModels.pl
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/4-2/trans_proteomic_pipeline/perl/ProphetModels.pl:4076-4271
/branches/course-apr09/trans_proteomic_pipeline/perl/ProphetModels.pl:4132-4270
+ /branches/4-2/trans_proteomic_pipeline/perl/ProphetModels.pl:4076-4271
/branches/4-4/trans_proteomic_pipeline/perl/ProphetModels.pl:5054-5117
/branches/course-apr09/trans_proteomic_pipeline/perl/ProphetModels.pl:4132-4270
Modified: trunk/trans_proteomic_pipeline/perl/ProtProphModels.pl
===================================================================
--- trunk/trans_proteomic_pipeline/perl/ProtProphModels.pl 2010-08-25 21:59:07 UTC (rev 5123)
+++ trunk/trans_proteomic_pipeline/perl/ProtProphModels.pl 2010-08-25 22:04:31 UTC (rev 5124)
@@ -129,7 +129,6 @@
my $num_hits_set = -1;
my $exclude = 0;
my $charge = 0;
-my $has_iprophet = 0;
my $has_fval = 0;
my $in_prot_group = 0;
my $pp_prob = 0;
@@ -228,12 +227,14 @@
my $ip_decoy_ratio = $decoy_ratio;
if ($decoy_ratio < 0) {
- $pp_decoy_ratio = ($pp_prob_array_decoy[0] / $pp_prob_array[0]);
- print "Using decoy ratio of $pp_decoy_ratio for ProteinProphet.";
- if ($has_iprophet == 1) {
- $ip_decoy_ratio = ($ip_prob_array_decoy[0] / $ip_prob_array[0]);
- print "Using decoy ratio of $ip_decoy_ratio for iProphet.";
+ if ($pp_prob_array[0] > 0) {
+ $pp_decoy_ratio = ($pp_prob_array_decoy[0] / $pp_prob_array[0]);
+ print "Using decoy ratio of $pp_decoy_ratio for ProteinProphet.";
}
+ else {
+ $pp_decoy_ratio = -1;
+ print "Cannot determine decoy ratio from ProteinProphet. ";
+ }
}
for (my $prob_cutoff = 0.0; $prob_cutoff <= 1.0; $prob_cutoff += 0.002) {
@@ -260,10 +261,6 @@
my $num_pos_ip = $num_hits - $ip_num_below_prob;
my $num_corr_ip = $num_pos_ip;
- if ($has_iprophet == 1 and $num_pos_ip > 0) {
- $fdr_ip = ($ip_total_neg - $ip_cum_neg_below_prob) / $num_pos_ip;
- $num_corr_ip = $num_pos_ip * (1 - $fdr_ip);
- }
my $fdr_pp = 0.0;
my $num_pos_pp = $num_hits - $pp_num_below_prob;
@@ -276,15 +273,10 @@
my $fdr_ip_decoy = 0.0;
my $num_corr_ip_decoy = $num_pos_ip;
- if ($has_iprophet == 1 and $num_pos_ip > 0) {
- my $num_incorr_ip = ($num_decoy - $ip_num_decoy_below_prob) / $ip_decoy_ratio;
- $fdr_ip_decoy = $num_incorr_ip / $num_pos_ip;
- $num_corr_ip_decoy = $num_pos_ip - $num_incorr_ip;
- }
my $fdr_pp_decoy = 0.0;
my $num_corr_pp_decoy = $num_pos_pp;
- if ($num_hits - $pp_num_below_prob > 0) {
+ if ($num_hits - $pp_num_below_prob > 0 and $pp_decoy_ratio > 0 and $num_pos_pp > 0) {
my $num_incorr_pp = ($num_decoy - $pp_num_decoy_below_prob) / $pp_decoy_ratio;
$fdr_pp_decoy = $num_incorr_pp / $num_pos_pp;
$num_corr_pp_decoy = $num_pos_pp - $num_incorr_pp;
@@ -327,26 +319,16 @@
# print GPOUT "plot [0.0 to 1.0] \"$infile_pfx" . "_FDR.tsv\" using 1:2 title \"iProphet_PRED\" with line lc $pos_color , \"$infile_pfx" . "_FDR.tsv\" using 1:3 title \"iProphet_DECOY\" with line lc $neg_color , \"$infile_pfx" . "_FDR.tsv\" using 1:4 title \"ProteinProphet_PRED\" with line lc 4 , \"$infile_pfx" . "_FDR.tsv\" using 1:5 title \"ProteinProphet_DECOY\" with line lc 5";
- if ($has_iprophet == 1) {
-
- print GPOUT "plot \"$infile_pfx" . "_FDR.tsv\" using 3:2 title \"iProphet\" with line lc $pos_color , \"$infile_pfx" . "_FDR.tsv\" using 5:4:11:10 title \"ProteinProphet\" with xyerrorbars lc $neg_color , x notitle with line lt 0 lc -1";
- print GPOUT "set output \"$infile_pfx" . "_FDR_5pc.png\"";
- print GPOUT "plot [0.0 to 0.05] \"$infile_pfx" . "_FDR.tsv\" using 3:2 title \"iProphet\" with line lc $pos_color , \"$infile_pfx" . "_FDR.tsv\" using 5:4:11:10 title \"ProteinProphet\" with xyerrorbars lc $neg_color , x notitle with line lt 0 lc -1";
- print GPOUT "set output \"$infile_pfx" . "_ROC.png\"";
- print GPOUT "set xlabel \"FDR\"";
- print GPOUT "set ylabel \"Number of Correct Hits\"";
- print GPOUT "plot [0.0 to 0.05] \"$infile_pfx" . "_FDR.tsv\" using 2:6 title \"iProphet(PREDICTED)\" with line lc $pos_color , \"$infile_pfx" . "_FDR.tsv\" using 3:7 title \"iProphet(DECOY)\" with line lc 4, \"$infile_pfx" . "_FDR.tsv\" using 4:8 title \"ProteinProphet(PREDICTED)\" with line lc $neg_color , \"$infile_pfx" . "_FDR.tsv\" using 5:9 title \"ProteinProphet(DECOY)\" with line lc 5";
- } else {
- print GPOUT "plot \"$infile_pfx" . "_FDR.tsv\" using 5:4:11:10 title \"ProteinProphet\" with xyerrorbars lc $neg_color , x notitle with line lt 0 lc -1";
- print GPOUT "set output \"$infile_pfx" . "_FDR_5pc.png\"";
- print GPOUT "plot [0.0 to 0.05] \"$infile_pfx" . "_FDR.tsv\" using 5:4:11:10 title \"ProteinProphet\" with xyerrorbars lc $neg_color , x notitle with line lt 0 lc -1";
- print GPOUT "set output \"$infile_pfx" . "_ROC.png\"";
- print GPOUT "set xlabel \"FDR\"";
- print GPOUT "set ylabel \"Number of Correct Hits\"";
- print GPOUT "plot [0.0 to 0.05] \"$infile_pfx" . "_FDR.tsv\" using (\$5-\$11):9 title \"ProteinProphet(DECOY) Low\" with lines lc 5, \"$infile_pfx" . "_FDR.tsv\" using (\$5+\$11):9 title \"ProteinProphet(DECOY) High\" with lines lc 5, \"$infile_pfx" . "_FDR.tsv\" using 4:8 title \"ProteinProphet(PREDICTED)\" with lines lc $neg_color ";
+ print GPOUT "plot \"$infile_pfx" . "_FDR.tsv\" using 5:4:11:10 title \"ProteinProphet\" with xyerrorbars lc $neg_color , x notitle with line lt 0 lc -1";
+ print GPOUT "set output \"$infile_pfx" . "_FDR_5pc.png\"";
+ print GPOUT "plot [0.0 to 0.05] \"$infile_pfx" . "_FDR.tsv\" using 5:4:11:10 title \"ProteinProphet\" with xyerrorbars lc $neg_color , x notitle with line lt 0 lc -1";
+ print GPOUT "set output \"$infile_pfx" . "_ROC.png\"";
+ print GPOUT "set xlabel \"FDR\"";
+ print GPOUT "set ylabel \"Number of Correct Hits\"";
+ print GPOUT "plot [0.0 to 0.05] \"$infile_pfx" . "_FDR.tsv\" using (\$5-\$11):9 title \"ProteinProphet(DECOY) Low\" with lines lc 5, \"$infile_pfx" . "_FDR.tsv\" using (\$5+\$11):9 title \"ProteinProphet(DECOY) High\" with lines lc 5, \"$infile_pfx" . "_FDR.tsv\" using 4:8 title \"ProteinProphet(PREDICTED)\" with lines lc $neg_color ";
+
- }
close(GPOUT);
Property changes on: trunk/trans_proteomic_pipeline/schema
___________________________________________________________________
Added: svn:mergeinfo
+ /branches/4-2/trans_proteomic_pipeline/schema:4076-4242
/branches/4-4/trans_proteomic_pipeline/schema:5054-5117
/branches/win_lib-cleanup/trans_proteomic_pipeline/schema:4547-4556
Property changes on: trunk/trans_proteomic_pipeline/src
___________________________________________________________________
Added: svn:mergeinfo
+ /branches/4-2/trans_proteomic_pipeline/src:4076-4242
/branches/4-4/trans_proteomic_pipeline/src:5054-5117
/branches/win_lib-cleanup/trans_proteomic_pipeline/src:4547-4556
Modified: trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/RTCalculator.cxx
===================================================================
--- trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/RTCalculator.cxx 2010-08-25 21:59:07 UTC (rev 5123)
+++ trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/RTCalculator.cxx 2010-08-25 22:04:31 UTC (rev 5124)
@@ -1135,7 +1135,7 @@
if (r_sq_ < 0.5) {
cerr << "WARNING: Not enough correlation in multifit linear RT model " << run_idx_ << ". RT Model has been disabled." << endl;
- // return False;
+ return False;
}
ready_ = true;
return True;
@@ -1148,7 +1148,7 @@
if (r_sq_ < 0.5) {
cerr << "WARNING: Not enough correlation in multifit linear RT model " << run_idx_ << ". RT Model has been disabled." << endl;
- // return False;
+ return False;
}
ready_ = true;
return True;
@@ -1173,7 +1173,7 @@
if (ready_) return True;
run_RT_used_count_ = 0;
- cout << "DDS: probsSize=" << probs->size() << " runRTNum=" << run_RT_count_<< endl;
+ // cout << "DDS: probsSize=" << probs->size() << " runRTNum=" << run_RT_count_<< endl;
assert(probs->size() == run_RT_count_);
int i;
for (i=0; i<run_RT_count_; i++) {
@@ -1252,10 +1252,10 @@
run_slope_ = SSxy / SSxx;
run_intercept_ = run_SCAN_mean_ - run_slope_ * run_RT_mean_;
r_sq_ = (SSxy*SSxy) / (SSxx*SSyy);
- // if (r_sq_ < 0.5) {
- // cerr << "WARNING: Not enough correlation r_sq=" << r_sq_ << " between theoretical RT values and scan numbers in run index " << run_idx_ << ". RT Model has been disabled." << endl;
- // return False;
- //}
+ if (r_sq_ < 0.5) {
+ cerr << "WARNING: Not enough correlation r_sq=" << r_sq_ << " between theoretical RT values and scan numbers in run index " << run_idx_ << ". RT Model has been disabled." << endl;
+ return False;
+ }
ready_ = true;
return True;
}
@@ -2945,7 +2945,7 @@
r_sq_ = (SSxy*SSxy) / (SSxx*SSyy);
if (r_sq_ < 0.5) {
cerr << "WARNING: Not enough correlation between theoretical RT values and scan numbers in run index " << run_idx_ << ". RT Model has been disabled." << endl;
- // return False;
+ return False;
}
ready_ = true;
return True;
@@ -4958,7 +4958,7 @@
r_sq_ = (SSxy*SSxy) / (SSxx*SSyy);
if (r_sq_ < 0.5) {
cerr << "WARNING: Not enough correlation between theoretical RT values and scan numbers in run index " << run_idx_ << ". RT Model has been disabled." << endl;
- // return False;
+ return False;
}
ready_ = true;
return True;
Modified: trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML/Out2XML.cxx
===================================================================
--- trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML/Out2XML.cxx 2010-08-25 21:59:07 UTC (rev 5123)
+++ trunk/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/Sequest2XML/Out2XML.cxx 2010-08-25 22:04:31 UTC (rev 5124)
@@ -206,14 +206,18 @@
fprintf(pepXmlFile_, "%c", outFiles_[i]->szBaseFileName[k]);
}
- char *chg = "1";
+ char *chg=(char*)malloc(10 * sizeof(char)); // assume a string of less than 9 characters will represent the charge state
+ strncpy(chg, "1", sizeof(chg)); // zero-fill the rest of the array
+
if (!maldi_) {
- chg = strrchr(outFiles_[i]->szBaseFileName, '.')+1;
+ char* newptr = strrchr(outFiles_[i]->szBaseFileName, '.')+1;
+ strncpy(chg, newptr, sizeof(chg));
}
fprintf(pepXmlFile_, "\" precursor_neutral_mass=\"%0.4f\" assumed_charge=\"%s\" index=\"%d\"",
outFiles_[i]->dAMass-dProtonMass, chg, i+1);
+ free(chg);
/* add RT from mzXML file */
if (pFI != NULL)
Modified: trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatioPeptideParser/ASAPRatioPeptideParser.cxx
===================================================================
--- trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatioPeptideParser/ASAPRatioPeptideParser.cxx 2010-08-25 21:59:07 UTC (rev 5123)
+++ trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatioPeptideParser/ASAPRatioPeptideParser.cxx 2010-08-25 22:04:31 UTC (rev 5124)
@@ -2460,9 +2460,10 @@
d[m][i]=0;
}
// (unreadable)
+ C4=(double *)calloc(size,sizeof(double));
+
for(m=loop-1;m>=0;m--)
{
- C4=(double *)calloc(size,sizeof(double));
for(i=0;i<size;i++)
C4[i]=0;
for(i=0; i<size; i++)
Property changes on: trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_numFns.cxx
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/4-2/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_numFns.c:4076-4242
/branches/cpprename/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_numFns.cxx:4629-4656
/branches/win_lib-cleanup/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_numFns.c:4547-4556
+ /branches/4-2/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_numFns.c:4076-4242
/branches/4-4/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_numFns.cxx:5054-5117
/branches/cpprename/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_numFns.cxx:4629-4656
/branches/win_lib-cleanup/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_numFns.c:4547-4556
Property changes on: trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_pepFns.cxx
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/4-2/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_pepFns.c:4076-4242
/branches/cpprename/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_pepFns.cxx:4629-4656
/branches/win_lib-cleanup/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_pepFns.c:4547-4556
+ /branches/4-2/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_pepFns.c:4076-4242
/branches/4-4/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_pepFns.cxx:5054-5117
/branches/cpprename/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_pepFns.cxx:4629-4656
/branches/win_lib-cleanup/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_pepFns.c:4547-4556
Property changes on: trunk/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_txtFns.cxx
___________________________________________________________________
Modified: svn:mergeinfo
- /branches/4-2/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_txtFns.c:4076-4242
/branches/cpprename/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_txtFns.cxx:4629-4656
/branches/win_lib-cleanup/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_txtFns.c:4547-4556
+ /branches/4-2/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_txtFns.c:4076-4242
/branches/4-4/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_txtFns.cxx:5054-5117
/branches/cpprename/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_txtFns.cxx:4629-4656
/branches/win_lib-cleanup/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_txtFns.c:4547-4556
Modified: trunk/trans_proteomic_pipeline/src/Quantitation/Option.h
===================================================================
--- trunk/trans_proteomic_pipeline/src/Quantitation/Option.h 2010-08-25 21:59:07 UTC (rev 5123)
+++ trunk/trans_proteomic_pipeline/src/Quantitation/Option.h 2010-08-25 22:04:31 UTC (rev 5124)
@@ -92,6 +92,8 @@
int min_RT_ntt_;
double min_RT_prob_;
Boolean accMass_;
+ Boolean ppm_;
+ float conservative_;
Boolean maldi_;
Boolean instrwarn_;
Boolean no_neg_init_;
Modified: trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx
===================================================================
--- trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx 2010-08-25 21:59:07 UTC (rev 5123)
+++ trunk/trans_proteomic_pipeline/src/Quantitation/XPress/XPressPeptideParser/XPressPeptideParser.cxx 2010-08-25 22:04:31 UTC (rev 5124)
@@ -225,58 +225,84 @@
pInput_.iAnalysisFirstScan = 1;
if (dTmpFilter_ != NULL)
- free(dTmpFilter_);
- if ( (dTmpFilter_ = (double *) malloc(sizeof(double) * (pInput_.iAnalysisLastScan+1)))==NULL)
+ delete dTmpFilter_;
+
+ //free(dTmpFilter_)
+
+ // if ( (dTmpFilter_ = (double *) malloc(sizeof(double) * (pInput_.iAnalysisLastScan+1)))==NULL)
+ //if ( (dTmpFilter_ = new double [pInput_.iAnalysisLastScan+1] )==NULL)
+ if ( (dTmpFilter_ = new Array<double> (pInput_.iAnalysisLastScan+1) )==NULL)
{
printf(" Error - cannot malloc dTmpFilter[%d]\n", (pInput_.iAnalysisLastScan+1));
exit(1);
}
if (dLightMS_ != NULL)
- free(dLightMS_);
- if ( (dLightMS_ = (double *) malloc(sizeof(double) * (pInput_.iAnalysisLastScan+1)))==NULL)
+ delete [] dLightMS_;
+
+ // free(dLightMS_);
+ //if ( (dLightMS_ = (double *) malloc(sizeof(double) *...
[truncated message content] |