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[Sashimi-commit] SF.net SVN: sashimi:[7096] branches/TPP5-Refactor/trans_proteomic_pipeline
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From: <ds...@us...> - 2015-10-28 17:20:09
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Revision: 7096
http://sourceforge.net/p/sashimi/code/7096
Author: dshteyn
Date: 2015-10-28 17:20:05 +0000 (Wed, 28 Oct 2015)
Log Message:
-----------
msys64/mingw64 build tweaks for TPP-5...also adding dependencies for new DISCO features
Modified Paths:
--------------
branches/TPP5-Refactor/trans_proteomic_pipeline/Makefile
branches/TPP5-Refactor/trans_proteomic_pipeline/common.mk
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Makefile
branches/TPP5-Refactor/trans_proteomic_pipeline/installer_win32/tpp.iss
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Common/win32_system.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Parsers/Algorithm2XML/RTCalculator.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Parsers/Makefile
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/ASAPRatio_Fns/ASAPRatio_pepFns.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Quantitation/ASAPRatio/PvalueModel/PvalueModel.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Search/XTandem/src_tpp/mscore.h
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Search/XTandem/src_tpp/tandem.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Validation/Disco/DiscoFilter.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Validation/Disco/DiscoFilter.h
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Validation/Disco/DiscoMain.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Validation/Makefile
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Validation/ModelParser/ModelParser.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Validation/Respect/RespectFilter.h
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Validation/iModelParser/IModelParser.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Visualization/Makefile
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PMap.h
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXField.h
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PepXNode.h
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/PipelineAnalysis.h
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/XMLNode.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/XMLNode.h
branches/TPP5-Refactor/trans_proteomic_pipeline/src/Visualization/PepXMLViewer/XMLTree.h
branches/TPP5-Refactor/trans_proteomic_pipeline/src/mzXML/tools/mzXMLIndexer/indexmzXMLSHA1.hpp
Added Paths:
-----------
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Averagine.dat
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CAveragine.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CAveragine.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CHardklor.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CHardklor.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CHardklor2.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CHardklor2.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CHardklorFileReader.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CHardklorFileReader.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CHardklorParser.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CHardklorParser.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CHardklorProtein.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CHardklorProtein.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CHardklorSetting.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CHardklorSetting.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CHardklorVariant.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CHardklorVariant.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CMercury8.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CMercury8.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CModelLibrary.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CModelLibrary.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CNoiseReduction.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CNoiseReduction.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CPeriodicTable.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CPeriodicTable.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CSettings.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CSettings.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CSpecAnalyze.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CSpecAnalyze.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CSplitSpectrum.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CSplitSpectrum.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/FFT-HK.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/FFT-HK.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/FFT.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/FFT.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Hardklor.conf
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Hardklor.dat
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Hardklor2008.aps
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Hardklor2008.rc
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Hardklor2008.vcproj
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Hardklor2008Lib/
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Hardklor2008Lib/Hardklor2008Lib.vcproj
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/HardklorApp.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/HardklorTypes.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/ISOTOPE.DAT
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/ISOTOPE.ORIG
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Images/
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Images/Hardklor5.ico
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Images/hardklor.ico
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Images/hardklor128.ico
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Images/hardklor128.png
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Images/hardklor2.ico
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Images/hardklor256.ico
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Images/hardklor256.png
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Images/hardklor3.ico
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Images/hardklor32.ico
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Images/hardklor32.png
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Images/hardklor4.ico
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Images/hardklor64.ico
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Images/hardklor64.png
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Kronik2/
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Kronik2/CKronik2.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Kronik2/CKronik2.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Kronik2/Kronik2
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Kronik2/Kronik2.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Kronik2/Kronik2.sln
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Kronik2/Kronik2.vcproj
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Makefile
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/README.txt
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/S2N.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/S2N.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Smooth.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Smooth.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/SpecAnalyzeSupport.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/SpecAnalyzeSupport.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/mercury.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/resource.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/resource1.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/MSSingleScan/
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/MSSingleScan/MSSingleScan.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/MSSingleScan/MSSingleScan.vcproj
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/MSToolkit.sln
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/MSToolkit.vcproj
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/MSToolkitCLR.vcproj
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/MSToolkitLite.vcproj
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/MSToolkitLiteCLR.vcproj
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/Makefile
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/MSNumpress.hpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/MSObject.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/MSReader.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/MSToolkitTypes.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/RAWReader.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/Spectrum.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/ascii.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/asciitab.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/crc32.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/deflate.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/expat.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/expat_config.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/expat_external.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/gzguts.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/iasciitab.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/inffast.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/inffixed.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/inflate.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/inftrees.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/internal.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/latin1tab.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/make.out
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/mzParser.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/nametab.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/sqlite3.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/trees.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/utf8tab.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/winconfig.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/xmlrole.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/xmltok.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/xmltok_impl.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/zconf.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/zlib.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/include/zutil.h
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/MSToolkit/
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/MSToolkit/MSObject.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/MSToolkit/MSReader.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/MSToolkit/RAWReader.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/MSToolkit/Spectrum.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/expat-2.0.1/
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/expat-2.0.1/xmlparse.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/expat-2.0.1/xmlparse.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/expat-2.0.1/xmlrole.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/expat-2.0.1/xmlrole.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/expat-2.0.1/xmltok.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/expat-2.0.1/xmltok.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/expat-2.0.1/xmltok_impl.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/expat-2.0.1/xmltok_impl.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/expat-2.0.1/xmltok_ns.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/expat-2.0.1/xmltok_ns.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/mzParser/
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/mzParser/BasicChromatogram.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/mzParser/BasicSpectrum.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/mzParser/Czran.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/mzParser/MSNumpress.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/mzParser/PWIZface.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/mzParser/RAMPface.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/mzParser/mz5handler.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/mzParser/mzMLReader.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/mzParser/mzParser.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/mzParser/mzpMz5Config.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/mzParser/mzpMz5Structs.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/mzParser/mzp_base64.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/mzParser/saxhandler.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/mzParser/saxmzmlhandler.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/mzParser/saxmzxmlhandler.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/sqlite-3.7.7.1/
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/sqlite-3.7.7.1/sqlite3.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/sqlite-3.7.7.1/sqlite3.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/adler32.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/adler32.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/compress.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/compress.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/crc32.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/crc32.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/deflate.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/deflate.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/gzclose.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/gzclose.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/gzlib.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/gzlib.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/gzread.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/gzread.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/gzwrite.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/gzwrite.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/infback.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/infback.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/inffast.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/inffast.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/inflate.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/inflate.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/inftrees.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/inftrees.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/trees.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/trees.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/uncompr.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/uncompr.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/zutil.c
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/src/zLib-1.2.5/zutil.cpp
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/MSToolkit/test.mzML
branches/TPP5-Refactor/trans_proteomic_pipeline/extern/libgd-2.1.0.mingwpatch
Modified: branches/TPP5-Refactor/trans_proteomic_pipeline/Makefile
===================================================================
--- branches/TPP5-Refactor/trans_proteomic_pipeline/Makefile 2015-10-28 17:12:52 UTC (rev 7095)
+++ branches/TPP5-Refactor/trans_proteomic_pipeline/Makefile 2015-10-28 17:20:05 UTC (rev 7096)
@@ -245,7 +245,7 @@
# Empty directory(s)
$(INSTALL_LOG) : $(INNO)
- mkdir -p -m 444 $(INSTALL_LOG)
+ mkdir -p -m 755 $(INSTALL_LOG)
install :: $(INSTALL_LOG)
Modified: branches/TPP5-Refactor/trans_proteomic_pipeline/common.mk
===================================================================
--- branches/TPP5-Refactor/trans_proteomic_pipeline/common.mk 2015-10-28 17:12:52 UTC (rev 7095)
+++ branches/TPP5-Refactor/trans_proteomic_pipeline/common.mk 2015-10-28 17:20:05 UTC (rev 7096)
@@ -163,6 +163,8 @@
OS := Darwin
else ifneq (,$(findstring mingw, $(TARGET)))
OS := $(OS)
+else ifneq (,$(findstring msys, $(TARGET)))
+ OS := $(OS)
else
$(error Unable to determine target platform using $$(CXX) -dumpmachine)
endif
@@ -205,7 +207,7 @@
# option -Wno-errors=deprecated.
#
# TODO: remove the deprecated calls
-CXXFLAGS += -Werror -Wno-deprecated
+CXXFLAGS += -Wno-deprecated
# Always include large file support
CXXFLAGS += -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
@@ -307,6 +309,19 @@
MZPARSER_CXXFLAGS := -I$(TPP_SRC)/Parsers/mzParser $(HDF_CXXFLAGS) $(EXPAT_CXXFLAGS)
MZPARSER_LDFLAGS := $(LIBMZPARSER) $(HDF5_LDFLAGS) $(EXPAT_LDFLAGS) -lz
+MSTOOLKIT_CXXFLAGS := -I$(TPP_EXT)/MSToolkit/include
+MSTOOLKIT_LDFLAGS := -lmstoolkitlite
+
+MSTK_PATH = $(TPP_EXT)/MSToolkit
+MSTK_OBJDIR := $(BUILD_OBJ)/MSToolkit
+
+HARDKLOR_CXXFLAGS := -I$(TPP_EXT)/Hardklor
+HARDKLOR_LDFLAGS := -lhardklor
+
+HKLR_PATH = $(TPP_EXT)/Hardklor
+HKLR_OBJDIR := $(BUILD_OBJ)/Hardklor
+
+
PNG_CXXFLAGS :=
PNG_LDFLAGS := -lpng
Added: branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Averagine.dat
===================================================================
--- branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Averagine.dat (rev 0)
+++ branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/Averagine.dat 2015-10-28 17:20:05 UTC (rev 7096)
@@ -0,0 +1,104 @@
+0 X 0 0 0 0
+1 H 1.0078246 0.999855 2.0141021 0.000145
+2 He 3.01603 0.00000138 4.00260 0.99999862
+3 Li 6.015121 0.075 7.016003 0.925
+4 Be 0 0 0 0
+5 B 10.012937 0.199 1.009305 0.801
+6 C 12.0000000 0.98916 13.0033554 0.01084
+7 N 14.0030732 0.99633 15.0001088 0.00366
+8 O 15.9949141 0.997576009706 16.9991322 0.000378998479
+9 X 0 0 0 0
+10 X 0 0 0 0
+11 X 0 0 0 0
+12 X 0 0 0 0
+13 X 0 0 0 0
+14 X 0 0 0 0
+15 X 0 0 0 0
+16 S 31.972070 0.95021 32.971456 0.00745
+17 X 0 0 0 0
+18 X 0 0 0 0
+19 X 0 0 0 0
+20 X 0 0 0 0
+21 X 0 0 0 0
+22 X 0 0 0 0
+23 X 0 0 0 0
+24 X 0 0 0 0
+25 X 0 0 0 0
+26 X 0 0 0 0
+27 X 0 0 0 0
+28 X 0 0 0 0
+29 X 0 0 0 0
+30 X 0 0 0 0
+31 X 0 0 0 0
+32 X 0 0 0 0
+33 X 0 0 0 0
+34 X 0 0 0 0
+35 X 0 0 0 0
+36 X 0 0 0 0
+37 X 0 0 0 0
+38 X 0 0 0 0
+39 X 0 0 0 0
+40 X 0 0 0 0
+41 X 0 0 0 0
+42 X 0 0 0 0
+43 X 0 0 0 0
+44 X 0 0 0 0
+45 X 0 0 0 0
+46 X 0 0 0 0
+47 X 0 0 0 0
+48 X 0 0 0 0
+49 X 0 0 0 0
+50 X 0 0 0 0
+51 X 0 0 0 0
+52 X 0 0 0 0
+53 X 0 0 0 0
+54 X 0 0 0 0
+55 X 0 0 0 0
+56 X 0 0 0 0
+57 X 0 0 0 0
+58 X 0 0 0 0
+59 X 0 0 0 0
+60 X 0 0 0 0
+61 X 0 0 0 0
+62 X 0 0 0 0
+63 X 0 0 0 0
+64 X 0 0 0 0
+65 X 0 0 0 0
+66 X 0 0 0 0
+67 X 0 0 0 0
+68 X 0 0 0 0
+69 X 0 0 0 0
+70 X 0 0 0 0
+71 X 0 0 0 0
+72 X 0 0 0 0
+73 X 0 0 0 0
+74 X 0 0 0 0
+75 X 0 0 0 0
+76 X 0 0 0 0
+77 X 0 0 0 0
+78 X 0 0 0 0
+79 X 0 0 0 0
+80 X 0 0 0 0
+81 X 0 0 0 0
+82 X 0 0 0 0
+83 X 0 0 0 0
+84 X 0 0 0 0
+85 X 0 0 0 0
+86 X 0 0 0 0
+87 X 0 0 0 0
+88 X 0 0 0 0
+89 X 0 0 0 0
+90 X 0 0 0 0
+91 X 0 0 0 0
+92 X 0 0 0 0
+93 X 0 0 0 0
+94 X 0 0 0 0
+95 X 0 0 0 0
+96 X 0 0 0 0
+97 X 0 0 0 0
+98 X 0 0 0 0
+99 X 0 0 0 0
+100 X 0 0 0 0
+101 X 0 0 0 0
+102 X 0 0 0 0
+103 X 0 0 0 0
Added: branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CAveragine.cpp
===================================================================
--- branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CAveragine.cpp (rev 0)
+++ branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CAveragine.cpp 2015-10-28 17:20:05 UTC (rev 7096)
@@ -0,0 +1,306 @@
+#include <iomanip>
+#include <iostream>
+#include "CAveragine.h"
+using namespace std;
+
+CAveragine::CAveragine(char* fn, char* fn2){
+ PT = new CPeriodicTable(fn2);
+ atoms = new int[PT->size()];
+ for(int i=0;i<PT->size();i++) atoms[i]=0;
+ enrich = new vector<atomInfo>;
+ loadTable(fn);
+}
+
+CAveragine::~CAveragine(){
+ delete [] atoms;
+ delete enrich;
+}
+
+void CAveragine::calcAveragine(double dMass, CHardklorVariant hv) {
+ int i,j;
+ int iso;
+ int atom;
+ double fixedD = dMass;
+ double units;
+ double *enr;
+ double *abun;
+ double maxAbun;
+ double totAbun;
+ enr = new double[PT->size()];
+ for(i=0;i<PT->size();i++) enr[i]=0;
+
+ for(i=0;i<hv.sizeEnrich();i++){
+
+ atom = hv.atEnrich(i).atomNum;
+ iso = enrich->at(atom).numIsotopes;
+ abun = new double[iso];
+
+ //Set our abundance array and find maximum
+ maxAbun=0;
+ for(j=0;j<iso;j++){
+ abun[j]=enrich->at(atom).abundance->at(j);
+ if(abun[j]>maxAbun) maxAbun=abun[j];
+ }
+
+ //Normalize to 1
+ for(j=0;j<iso;j++) abun[j]/=maxAbun;
+
+ //Normalize, then Calculate enrichment
+ totAbun=0;
+ enr[atom]=0;
+ for(j=0;j<iso;j++){
+ abun[j]/=maxAbun;
+ if(j==hv.atEnrich(i).isotope) abun[j]=(1-hv.atEnrich(i).ape)*abun[j]+hv.atEnrich(i).ape;
+ else abun[j]=(1-hv.atEnrich(i).ape)*abun[j];
+ totAbun+=abun[j];
+ enr[atom]+=abun[j]*enrich->at(atom).mass->at(j);
+ }
+
+ //Calculate average mass
+ enr[atom] /= totAbun;
+ enr[atom] -= PT->at(atom).mass;
+
+ delete [] abun;
+ }
+
+ for(i=0;i<hv.sizeAtom();i++) {
+
+ atoms[hv.atAtom(i).iLower]+=hv.atAtom(i).iUpper;
+ fixedD -= hv.atAtom(i).iUpper*(PT->at(hv.atAtom(i).iLower).mass + enr[hv.atAtom(i).iLower]);
+ }
+
+ units = (fixedD)/(AVE_MASS + enr[1]*AVE_H + enr[6]*AVE_C + enr[7]*AVE_N + enr[8]*AVE_O + enr[16]*AVE_S);
+
+ //Quick fix; assumes complete periodic table
+ atoms[6] += (int)(AVE_C*units+0.5);
+ atoms[8] += (int)(AVE_O*units+0.5);
+ atoms[7] += (int)(AVE_N*units+0.5);
+ atoms[16] += (int)(AVE_S*units+0.5);
+
+ atoms[1] += (int)(fixedD-( ((int)(AVE_C*units+0.5)) * (PT->at(6).mass + enr[6]) +
+ ((int)(AVE_N*units+0.5)) * (PT->at(7).mass + enr[7]) +
+ ((int)(AVE_O*units+0.5)) * (PT->at(8).mass + enr[8]) +
+ ((int)(AVE_S*units+0.5)) * (PT->at(16).mass + enr[16]) )+0.5);
+
+ delete [] enr;
+
+}
+
+void CAveragine::defaultValues(){
+
+ string el[109] = {"X","H","He","Li","Be","B","C","N","O","F","Ne","Na","Mg","Al","Si","P","S","Cl","Ar",
+ "K","Ca","Sc","Ti","V","Cr","Mn","Fe","Co","Ni","Cu","Zn","Ga","Ge","As","Se","Br","Kr","Rb","Sr","Y","Zr",
+ "Nb","Mo","Tc","Ru","Rh","Pd","Ag","Cd","In","Sn","Sb","Te","I","Xe","Cs","Ba","La","Ce","Pr","Nd","Pm","Sm",
+ "Eu","Gd","Tb","Dy","Ho","Er","Tm","Yb","Lu","Hf","Ta","W","Re","Os","Ir","Pt","Au","Hg","Tl","Pb","Bi","Po",
+ "At","Rn","Fr","Ra","Ac","Th","Pa","U","Np","Pu","Am","Cm","Bk","Cf","Es","Fm","Md","No","Lr","Hx","Cx","Nx",
+ "Ox","Sx"};
+ int sz[109] = {2,2,2,2,1,2,2,2,3,1,3,1,3,1,3,1,4,2,3,3,6,1,5,2,4,1,4,1,5,2,5,2,5,1,6,2,6,2,4,1,5,1,7,1,7,
+ 1,6,2,8,2,10,2,8,1,9,1,7,2,4,1,7,1,7,2,7,1,7,1,6,1,7,2,6,2,5,2,7,2,6,1,7,2,4,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,1,
+ 1,1,1,1,1,2,2,2,3,4};
+ double m[322] = {1.000000000000,2.000000000000,1.007824600000,2.014102100000,3.016030000000,4.002600000000,
+ 6.015121000000,7.016003000000,9.012182000000,10.012937000000,11.009305000000,12.000000000000,13.003355400000,
+ 14.003073200000,15.000108800000,15.994914100000,16.999132200000,17.999161600000,18.998403200000,
+ 19.992435000000,20.993843000000,21.991383000000,22.989767000000,23.985042000000,24.985837000000,
+ 25.982593000000,26.981539000000,27.976927000000,28.976495000000,29.973770000000,30.973762000000,
+ 31.972070000000,32.971456000000,33.967866000000,35.967080000000,34.968853100000,36.965903400000,
+ 35.967545000000,37.962732000000,39.962384000000,38.963707000000,39.963999000000,40.961825000000,
+ 39.962591000000,41.958618000000,42.958766000000,43.955480000000,45.953689000000,47.952533000000,
+ 44.955910000000,45.952629000000,46.951764000000,47.947947000000,48.947871000000,49.944792000000,
+ 49.947161000000,50.943962000000,49.946046000000,51.940509000000,52.940651000000,53.938882000000,
+ 54.938047000000,53.939612000000,55.934939000000,56.935396000000,57.933277000000,58.933198000000,
+ 57.935346000000,59.930788000000,60.931058000000,61.928346000000,63.927968000000,62.939598000000,
+ 64.927793000000,63.929145000000,65.926034000000,66.927129000000,67.924846000000,69.925325000000,
+ 68.925580000000,70.924700000000,69.924250000000,71.922079000000,72.923463000000,73.921177000000,
+ 75.921401000000,74.921594000000,73.922475000000,75.919212000000,76.919912000000,77.919000000000,
+ 79.916520000000,81.916698000000,78.918336000000,80.916289000000,77.914000000000,79.916380000000,
+ 81.913482000000,82.914135000000,83.911507000000,85.910616000000,84.911794000000,86.909187000000,
+ 83.913430000000,85.909267000000,86.908884000000,87.905619000000,88.905849000000,89.904703000000,
+ 90.905644000000,91.905039000000,93.906314000000,95.908275000000,92.906377000000,91.906808000000,
+ 93.905085000000,94.905840000000,95.904678000000,96.906020000000,97.905406000000,99.907477000000,
+ 98.000000000000,95.907599000000,97.905287000000,98.905939000000,99.904219000000,100.905582000000,
+ 101.904348000000,103.905424000000,102.905500000000,101.905634000000,103.904029000000,104.905079000000,
+ 105.903478000000,107.903895000000,109.905167000000,106.905092000000,108.904757000000,105.906461000000,
+ 107.904176000000,109.903005000000,110.904182000000,111.902758000000,112.904400000000,113.903357000000,
+ 115.904754000000,112.904061000000,114.903880000000,111.904826000000,113.902784000000,114.903348000000,
+ 115.901747000000,116.902956000000,117.901609000000,118.903310000000,119.902200000000,121.903440000000,
+ 123.905274000000,120.903821000000,122.904216000000,119.904048000000,121.903054000000,122.904271000000,
+ 123.902823000000,124.904433000000,125.903314000000,127.904463000000,129.906229000000,126.904473000000,
+ 123.905894000000,125.904281000000,127.903531000000,128.904780000000,129.903509000000,130.905072000000,
+ 131.904144000000,133.905395000000,135.907214000000,132.905429000000,129.906282000000,131.905042000000,
+ 133.904486000000,134.905665000000,135.904553000000,136.905812000000,137.905232000000,137.907110000000,
+ 138.906347000000,135.907140000000,137.905985000000,139.905433000000,141.909241000000,140.907647000000,
+ 141.907719000000,142.909810000000,143.910083000000,144.912570000000,145.913113000000,147.916889000000,
+ 149.920887000000,145.000000000000,143.911998000000,146.914895000000,147.914820000000,148.917181000000,
+ 149.917273000000,151.919729000000,153.922206000000,150.919847000000,152.921225000000,151.919786000000,
+ 153.920861000000,154.922618000000,155.922118000000,156.923956000000,157.924099000000,159.927049000000,
+ 158.925342000000,155.925277000000,157.924403000000,159.925193000000,160.926930000000,161.926795000000,
+ 162.928728000000,163.929171000000,164.930319000000,161.928775000000,163.929198000000,165.930290000000,
+ 166.932046000000,167.932368000000,169.935461000000,168.934212000000,167.933894000000,169.934759000000,
+ 170.936323000000,171.936378000000,172.938208000000,173.938859000000,175.942564000000,174.940770000000,
+ 175.942679000000,173.940044000000,175.941406000000,176.943217000000,177.943696000000,178.945812000000,
+ 179.946545000000,179.947462000000,180.947992000000,179.946701000000,181.948202000000,182.950220000000,
+ 183.950928000000,185.954357000000,184.952951000000,186.955744000000,183.952488000000,185.953830000000,
+ 186.955741000000,187.955860000000,188.958137000000,189.958436000000,191.961467000000,190.960584000000,
+ 192.962917000000,189.959917000000,191.961019000000,193.962655000000,194.964766000000,195.964926000000,
+ 197.967869000000,196.966543000000,195.965807000000,197.966743000000,198.968254000000,199.968300000000,
+ 200.970277000000,201.970617000000,203.973467000000,202.972320000000,204.974401000000,203.973020000000,
+ 205.974440000000,206.975872000000,207.976627000000,208.980374000000,209.000000000000,210.000000000000,
+ 222.000000000000,223.000000000000,226.025000000000,227.028000000000,232.038054000000,231.035900000000,
+ 234.040946000000,235.043924000000,238.050784000000,237.048000000000,244.000000000000,243.000000000000,
+ 247.000000000000,247.000000000000,251.000000000000,252.000000000000,257.000000000000,258.000000000000,
+ 259.000000000000,260.000000000000,1.007824600000,2.014102100000,12.000000000000,13.003355400000,
+ 14.003073200000,15.000108800000,15.994914100000,16.999132200000,17.999161600000,31.972070000000,
+ 32.971456000000,33.967866000000,35.967080000000};
+ double r[322] = {0.900000000000,0.100000000000,0.999855000000,0.000145000000,0.000001380000,0.999998620000,
+ 0.075000000000,0.925000000000,1.000000000000,0.199000000000,0.801000000000,0.989160000000,0.010840000000,
+ 0.996330000000,0.003660000000,0.997576009706,0.000378998479,0.002044991815,1.000000000000,0.904800000000,
+ 0.002700000000,0.092500000000,1.000000000000,0.789900000000,0.100000000000,0.110100000000,1.000000000000,
+ 0.922300000000,0.046700000000,0.031000000000,1.000000000000,0.950210000000,0.007450000000,0.042210000000,
+ 0.000130000000,0.755290000000,0.244710000000,0.003370000000,0.000630000000,0.996000000000,0.932581000000,
+ 0.000117000000,0.067302000000,0.969410000000,0.006470000000,0.001350000000,0.020860000000,0.000040000000,
+ 0.001870000000,1.000000000000,0.080000000000,0.073000000000,0.738000000000,0.055000000000,0.054000000000,
+ 0.002500000000,0.997500000000,0.043450000000,0.837900000000,0.095000000000,0.023650000000,1.000000000000,
+ 0.059000000000,0.917200000000,0.021000000000,0.002800000000,1.000000000000,0.682700000000,0.261000000000,
+ 0.011300000000,0.035900000000,0.009100000000,0.691700000000,0.308300000000,0.486000000000,0.279000000000,
+ 0.041000000000,0.188000000000,0.006000000000,0.601080000000,0.398920000000,0.205000000000,0.274000000000,
+ 0.078000000000,0.365000000000,0.078000000000,1.000000000000,0.009000000000,0.091000000000,0.076000000000,
+ 0.236000000000,0.499000000000,0.089000000000,0.506900000000,0.493100000000,0.003500000000,0.022500000000,
+ 0.116000000000,0.115000000000,0.570000000000,0.173000000000,0.721700000000,0.278300000000,0.005600000000,
+ 0.098600000000,0.070000000000,0.825800000000,1.000000000000,0.514500000000,0.112200000000,0.171500000000,
+ 0.173800000000,0.028000000000,1.000000000000,0.148400000000,0.092500000000,0.159200000000,0.166800000000,
+ 0.095500000000,0.241300000000,0.096300000000,1.000000000000,0.055400000000,0.018600000000,0.127000000000,
+ 0.126000000000,0.171000000000,0.316000000000,0.186000000000,1.000000000000,0.010200000000,0.111400000000,
+ 0.223300000000,0.273300000000,0.264600000000,0.117200000000,0.518390000000,0.481610000000,0.012500000000,
+ 0.008900000000,0.124900000000,0.128000000000,0.241300000000,0.122200000000,0.287300000000,0.074900000000,
+ 0.043000000000,0.957000000000,0.009700000000,0.006500000000,0.003600000000,0.145300000000,0.076800000000,
+ 0.242200000000,0.085800000000,0.325900000000,0.046300000000,0.057900000000,0.574000000000,0.426000000000,
+ 0.000950000000,0.025900000000,0.009050000000,0.047900000000,0.071200000000,0.189300000000,0.317000000000,
+ 0.338700000000,1.000000000000,0.001000000000,0.000900000000,0.019100000000,0.264000000000,0.041000000000,
+ 0.212000000000,0.269000000000,0.104000000000,0.089000000000,1.000000000000,0.001060000000,0.001010000000,
+ 0.024200000000,0.065930000000,0.078500000000,0.112300000000,0.717000000000,0.000900000000,0.999100000000,
+ 0.001900000000,0.002500000000,0.884300000000,0.111300000000,1.000000000000,0.271300000000,0.121800000000,
+ 0.238000000000,0.083000000000,0.171900000000,0.057600000000,0.056400000000,1.000000000000,0.031000000000,
+ 0.150000000000,0.113000000000,0.138000000000,0.074000000000,0.267000000000,0.227000000000,0.478000000000,
+ 0.522000000000,0.002000000000,0.021800000000,0.148000000000,0.204700000000,0.156500000000,0.248400000000,
+ 0.218600000000,1.000000000000,0.000600000000,0.001000000000,0.023400000000,0.189000000000,0.255000000000,
+ 0.249000000000,0.282000000000,1.000000000000,0.001400000000,0.016100000000,0.336000000000,0.229500000000,
+ 0.268000000000,0.149000000000,1.000000000000,0.001300000000,0.030500000000,0.143000000000,0.219000000000,
+ 0.161200000000,0.318000000000,0.127000000000,0.974100000000,0.025900000000,0.001620000000,0.052060000000,
+ 0.186060000000,0.272970000000,0.136290000000,0.351000000000,0.000120000000,0.999880000000,0.001200000000,
+ 0.263000000000,0.142800000000,0.307000000000,0.286000000000,0.374000000000,0.626000000000,0.000200000000,
+ 0.015800000000,0.016000000000,0.133000000000,0.161000000000,0.264000000000,0.410000000000,0.373000000000,
+ 0.627000000000,0.000100000000,0.007900000000,0.329000000000,0.338000000000,0.253000000000,0.072000000000,
+ 1.000000000000,0.001500000000,0.100000000000,0.169000000000,0.231000000000,0.132000000000,0.298000000000,
+ 0.068500000000,0.295240000000,0.704760000000,0.014000000000,0.241000000000,0.221000000000,0.524000000000,
+ 1.000000000000,1.000000000000,1.000000000000,1.000000000000,1.000000000000,1.000000000000,1.000000000000,
+ 1.000000000000,1.000000000000,0.000055000000,0.007200000000,0.992745000000,1.000000000000,1.000000000000,
+ 1.000000000000,1.000000000000,1.000000000000,1.000000000000,1.000000000000,1.000000000000,1.000000000000,
+ 1.000000000000,1.000000000000,0.999855000000,0.000145000000,0.989160000000,0.010840000000,0.996330000000,
+ 0.003660000000,0.997576009706,0.000378998479,0.002044991815,0.950210000000,0.007450000000,0.042210000000,
+ 0.000130000000};
+
+ int i=0;
+ int j=0;
+ int k;
+ atomInfo a;
+
+ for(k=0;k<109;k++){
+ strcpy(a.symbol,&el[k][0]);
+ a.numIsotopes=sz[k];
+ a.mass->clear();
+ a.abundance->clear();
+ for(j=0;j<a.numIsotopes;j++){
+ a.mass->push_back(m[i]);
+ a.abundance->push_back(r[i]);
+ i++;
+ }
+ enrich->push_back(a);
+ }
+
+}
+
+void CAveragine::clear(){
+ delete [] atoms;
+ atoms = new int[PT->size()];
+ for(int i=0;i<PT->size();i++) atoms[i]=0;
+}
+
+int CAveragine::getElement(int i){
+ return atoms[i];
+}
+
+void CAveragine::getAveragine(char *str){
+ char tstr[10];
+ int i;
+ str[0]=0;
+
+ //Create formula string
+ for(i=0;i<PT->size();i++){
+ if(atoms[i]>0){
+ sprintf(tstr,"%s%i",PT->at(i).symbol,atoms[i]);
+ strcat(str,tstr);
+ }
+ }
+
+}
+
+double CAveragine::getMonoMass(){
+ double d=0;
+ int i;
+
+ for(i=0;i<PT->size();i++) d+=atoms[i]*PT->at(i).mass;
+ return d;
+
+}
+
+CPeriodicTable* CAveragine::getPT(){
+ return PT;
+}
+
+void CAveragine::loadTable(char* c){
+
+ FILE *f;
+ int j;
+ atomInfo a;
+ double d1,d2;
+
+ if(c==NULL || strlen(c)==0){
+ defaultValues();
+ return;
+ }
+
+ f = fopen(c,"rt");
+ if(f==NULL) {
+ cout << "Cannot read " << c << endl;
+ exit(-1);
+ }
+
+ while(!feof(f)){
+
+ fscanf(f,"%2s\t%d\n",&a.symbol,&a.numIsotopes);
+ a.mass->clear();
+ a.abundance->clear();
+
+ for(j=0;j<a.numIsotopes;j++){
+ fscanf(f,"%lf\t%lf\n",&d1,&d2);
+ a.mass->push_back(d1);
+ a.abundance->push_back(d2);
+ }
+
+ enrich->push_back(a);
+ fscanf(f," \n");
+
+ }
+
+ fclose(f);
+
+}
+
+//This is not to be used normally - just here to make my life easier.
+void CAveragine::setAveragine(int C, int H, int N, int O, int S){
+ atoms[1]=H;
+ atoms[6]=C;
+ atoms[7]=N;
+ atoms[8]=O;
+ atoms[16]=S;
+}
Added: branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CAveragine.h
===================================================================
--- branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CAveragine.h (rev 0)
+++ branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CAveragine.h 2015-10-28 17:20:05 UTC (rev 7096)
@@ -0,0 +1,101 @@
+#ifndef _CAVERAGINE_H
+#define _CAVERAGINE_H
+
+#include "CHardklorVariant.h"
+#include "CPeriodicTable.h"
+
+#include <cstdlib>
+#include <fstream>
+#include <vector>
+#include <cstring>
+
+using namespace std;
+
+/*
+const double AVE_MASS = 111.1254;
+const double AVE_C = 4.9384;
+const double AVE_H = 7.7583;
+const double AVE_N = 1.3577;
+const double AVE_O = 1.4773;
+const double AVE_S = 0.0417;
+*/
+
+const double AVE_MASS = 111.2137;
+const double AVE_C = 4.9558;
+const double AVE_H = 7.8241;
+const double AVE_N = 1.3571;
+const double AVE_O = 1.4716;
+const double AVE_S = 0.0390;
+
+typedef struct atomInfo {
+ char symbol[3];
+ int numIsotopes;
+ vector<double> *mass;
+ vector<double> *abundance;
+ atomInfo(){
+ strcpy(symbol,"X");
+ numIsotopes=0;
+ mass = new vector<double>;
+ abundance = new vector<double>;
+ }
+ atomInfo(const atomInfo& a){
+ strcpy(symbol,a.symbol);
+ numIsotopes=a.numIsotopes;
+ mass = new vector<double>;
+ abundance = new vector<double>;
+ unsigned int i;
+ for(i=0;i<a.mass->size();i++) mass->push_back(a.mass->at(i));
+ for(i=0;i<a.abundance->size();i++) abundance->push_back(a.abundance->at(i));
+ }
+ ~atomInfo(){
+ delete mass;
+ delete abundance;
+ }
+ atomInfo& operator=(const atomInfo& a){
+ if(&a!=this){
+ strcpy(symbol,a.symbol);
+ numIsotopes=a.numIsotopes;
+ delete mass;
+ delete abundance;
+ mass = new vector<double>;
+ abundance = new vector<double>;
+ unsigned int i;
+ for(i=0;i<a.mass->size();i++) mass->push_back(a.mass->at(i));
+ for(i=0;i<a.abundance->size();i++) abundance->push_back(a.abundance->at(i));
+ }
+ return *this;
+ }
+
+} atomInfo;
+
+class CAveragine {
+
+ public:
+ //Constructors & Destructors
+ //CAveragine();
+ CAveragine(char* fn="ISOTOPE.DAT", char* fn2="Hardklor.dat");
+ ~CAveragine();
+
+ //Methods:
+ void calcAveragine(double,CHardklorVariant);
+ void clear();
+ void defaultValues();
+ void getAveragine(char*);
+ void setAveragine(int,int,int,int,int);
+ int getElement(int);
+ double getMonoMass();
+ CPeriodicTable* getPT();
+ void loadTable(char*);
+
+ protected:
+
+ private:
+ //Data Members:
+ //double monoMass;
+ int *atoms;
+ CPeriodicTable *PT;
+ vector<atomInfo> *enrich;
+
+};
+
+#endif
Added: branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CHardklor.cpp
===================================================================
--- branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CHardklor.cpp (rev 0)
+++ branches/TPP5-Refactor/trans_proteomic_pipeline/extern/Hardklor/CHardklor.cpp 2015-10-28 17:20:05 UTC (rev 7096)
@@ -0,0 +1,2280 @@
+
+/*
+ Hardkl\xF6r - Thanks to Aaron Klammer (Klezmer) and
+ Greg Finney for the name suggestions.
+
+ This program scans through high resolution mass spectra,
+ predicts the monoisotopic mass and charge state of any potential
+ peptides (or proteins), generates predicted isotope distributions
+ of averagine and modified averagine molecules matching the mass
+ of each distribution, then correlates the various combinations of each
+ distribution with the spectrum data to find a best match.
+
+ This application was first designed to identify chlorinated peptides,
+ hence the name Hardkl\xF6r. Due to the distinguishing characteristics of
+ a chlorinated distribution, this application makes it possible to predict
+ if the observed distribution is in fact chlorinated. The application
+ has since been extended to differentiate any measurable atomic or
+ enrichment modification.
+
+ The application utilizes an object model, so components may
+ be used in other applications. Furthermore, the design was made
+ to be extended, or possibly embedded in other software.
+
+ Version 1.0 is the first public release.
+*/
+
+#include "CHardklor.h"
+#include "CAveragine.h"
+#include "CMercury8.h"
+#include "CSpecAnalyze.h"
+#include "Smooth.h"
+#include <iomanip>
+using namespace std;
+
+
+SSObject::SSObject(){
+ pepVar = new vector<sInt>;
+ corr=0;
+}
+
+SSObject::SSObject(const SSObject& c){
+ corr = c.corr;
+ pepVar = new vector<sInt>;
+ for(unsigned int i=0;i<c.pepVar->size();i++) pepVar->push_back(c.pepVar->at(i));
+}
+
+SSObject::~SSObject(){
+ delete pepVar;
+}
+
+SSObject& SSObject::operator=(const SSObject& c){
+ if (this != &c) {
+ corr = c.corr;
+ delete pepVar;
+ pepVar = new vector<sInt>;
+ for(unsigned int i=0;i<c.pepVar->size();i++) pepVar->push_back(c.pepVar->at(i));
+ }
+ return *this;
+}
+
+void SSObject::addVar(int a, int b){
+ sInt s;
+ s.iLower = a;
+ s.iUpper = b;
+ pepVar->push_back(s);
+}
+
+void SSObject::clear(){
+ delete pepVar;
+ pepVar = new vector<sInt>;
+ corr = 0;
+}
+
+CHardklor::CHardklor(){
+ averagine=NULL;
+ mercury=NULL;
+ bEcho=true;
+ bMem=false;
+}
+
+CHardklor::CHardklor(CAveragine *a, CMercury8 *m){
+ averagine=a;
+ mercury=m;
+ sa.setAveragine(averagine);
+ sa.setMercury(mercury);
+ bEcho=true;
+ bMem=false;
+}
+
+CHardklor::~CHardklor(){
+ averagine=NULL;
+ mercury=NULL;
+}
+
+void CHardklor::Echo(bool b){
+ bEcho=b;
+}
+
+void CHardklor::SetAveragine(CAveragine *a){
+ averagine=a;
+ sa.setAveragine(averagine);
+}
+
+void CHardklor::SetMercury(CMercury8 *m){
+ mercury=m;
+ sa.setMercury(mercury);
+}
+
+int CHardklor::GoHardklor(CHardklorSetting sett, Spectrum* s){
+ cs = sett;
+ Analyze(s);
+ return 0;
+}
+
+//sorts vector of Results from high to low
+int CHardklor::compareData(const void *p1, const void *p2){
+ const Result d1 = *(Result *)p1;
+ const Result d2 = *(Result *)p2;
+ if(d1.data<d2.data) return 1;
+ else if(d1.data>d2.data) return -1;
+ else return 0;
+}
+
+void CHardklor::Analyze(Spectrum* s) {
+
+ //Objects
+ MSReader r;
+ CNoiseReduction nr(&r,cs);
+ PT=averagine->getPT();
+
+ //iterators
+ unsigned int k; //counters for loops
+
+ int TotalIterations=0;
+ int TotalScans=0;
+ int i;
+
+ //Variables for file and clock management
+ int minutes, seconds;
+ loadTime=0;
+ analysisTime=0;
+ splitTime=0;
+
+ //placeholders for data output to file
+ //int pepID;
+ //int varID;
+
+ //Variables for some basic information output.
+ int iPercent;
+ int zeroPep=0; //Stores the number of spectra from which no potential peptides could be identified
+ int manyPep=0; //Stores the number of spectra from which the number of potential peptides
+ //exceeds the user-defined threshold.
+ int lowSigPep=0; //Stores the number of spectra whose max intensity was below the user defined threshold.
+
+
+ //Build variants (modifications) used in the analysis
+ pepVariants.clear();
+ if(!cs.noBase) {
+ CHardklorVariant hkv;
+ pepVariants.push_back(hkv);
+ }
+ for(k=0;k<cs.variant->size();k++) pepVariants.push_back(cs.variant->at(k));
+
+ //Our temporary spectrum
+ Spectrum curSpec;
+ Spectrum cutSpec;
+
+ //These are for splitting large spectra
+ bool bCutMe=false;
+ bool ReadScan=false;
+ bool bFirst=true;
+ CSplitSpectrum* cSS;
+ int winCount=0;
+
+ vResults.clear();
+
+ //Ouput file info to user
+ if(bEcho){
+ if(s==NULL) cout << "Reading from file: " << cs.inFile << endl;
+ if(!bMem) cout << "Writing to file: " << cs.outFile << endl;
+ }
+
+ if(cs.fileFormat==dunno) {
+ cout << "Unknown file format or bad extension." << endl;
+ return;
+ }
+
+ //Start of algorithm here.
+ getTimerFrequency(timerFrequency);
+ getExactTime(startTime);
+
+ //Read in the initial spectrum
+ r.setFilter(cs.mzXMLFilter);
+ r.setRawFilter(cs.rawFilter);
+ if(s!=NULL){
+ curSpec=*s;
+ } else {
+ if(cs.boxcar==0){
+ if((cs.scan.iLower>0) && (cs.scan.iLower==cs.scan.iUpper)) r.readFile(&cs.inFile[0],curSpec,cs.scan.iLower);
+ else if(cs.scan.iLower>0) r.readFile(&cs.inFile[0],curSpec,cs.scan.iLower);
+ else r.readFile(&cs.inFile[0],curSpec);
+
+ //this is the command to filter by persistence without boxcar averaging
+ // if(!nr.DeNoise(curSpec)) curSpec.setScanNumber(0);
+
+ } else {
+ if(cs.boxcarFilter>0){
+ if(!nr.DeNoiseC(curSpec)) curSpec.setScanNumber(0);
+ } else {
+ if(!nr.DeNoiseD(curSpec)) curSpec.setScanNumber(0);
+ }
+ }
+ }
+
+ TotalScans++;
+
+ getExactTime(stopTime);
+ tmpTime1=toMicroSec(stopTime);
+ tmpTime2=toMicroSec(startTime);
+ loadTime=tmpTime1-tmpTime2;
+
+ //Check that file was read
+ if(curSpec.getScanNumber()==0) {
+ if(s!=NULL) {
+ cout << "Spectrum is invalid." << endl;
+ return;
+ }
+ if(cs.scan.iLower>0) cout << cs.inFile << " is invalid, or requested scan number is of incorrect format." << endl;
+ else cout << cs.inFile << " is invalid, or contains no spectrum." << endl;
+ return;
+ }
+ currentScanNumber = curSpec.getScanNumber();
+
+ //Open a file for output. Results will be written on the fly as they come out of the algorithm.
+ if(!bMem){
+ fptr.open(&cs.outFile[0],ios::out|ios::app);
+ if(!fptr.good()) cout << "Output file error" << endl;
+ fptr << setiosflags(ios::fixed) << setprecision(4);
+ }
+
+ if(!bMem && cs.xml){
+ fptr << "<Hardklor>" << endl;
+ fptr << "<File InputFilename=\"" << cs.inFile << "\" OutputFilename=\"" << cs.outFile << "\">" << endl;
+ WriteParams(fptr,1);
+ }
+
+ //Reset some basic stat counters
+ manyPep=0;
+ zeroPep=0;
+ lowSigPep=0;
+
+ //Set and display on screen percentage counter
+ iPercent=0;
+ if(bEcho) cout << iPercent;
+
+ //While there is still data to read in the file.
+ while(true){
+
+ //Load next spectrum to analyze
+ if(!bFirst){
+
+ //close out xml tag for previous spectrum
+ if(!bMem && cs.xml) fptr << "</Spectrum>" << endl;
+
+ if(s!=NULL) break;
+
+ //track load time
+ getExactTime(startTime);
+ if(cs.boxcar==0){
+ r.readFile(NULL,curSpec);
+ //case 1: nr.DeNoise(curSpec); break;
+ } else {
+ if(cs.boxcarFilter>0) nr.DeNoiseC(curSpec);
+ else nr.DeNoiseD(curSpec);
+ }
+ getExactTime(stopTime);
+ tmpTime1=toMicroSec(stopTime);
+ tmpTime2=toMicroSec(startTime);
+ loadTime+=tmpTime1-tmpTime2;
+
+ } else {
+
+ bFirst=false; //mark that the first scan has been processed
+
+ }
+
+ //Write scan information to output file.
+ if(curSpec.getScanNumber()!=0){
+ if(!bMem){
+ if(cs.scan.iUpper>0 && curSpec.getScanNumber()>cs.scan.iUpper) break;
+ if(cs.reducedOutput) WriteScanLine(curSpec,fptr,2);
+ else if(cs.xml) WriteScanLine(curSpec,fptr,1);
+ else WriteScanLine(curSpec,fptr,0);
+ } else {
+ currentScanNumber = curSpec.getScanNumber();
+ }
+ } else {
+ break; //exit if there is no spectrum left to analyze
+ }
+ TotalScans++;
+
+ //Preprocess spectrum
+ //If we have an empty spectrum, go on to the next one
+ if(curSpec.size()==0) continue;
+
+ getExactTime(startTime);
+ if(cs.smooth>0) SG_Smooth(curSpec,cs.smooth,4);
+ //if(curSpec.getScanNumber()==1999){
+ // for(int xx=0;xx<curSpec.size();xx++) cout << curSpec[xx].mz << "\t" << curSpec[xx].intensity << endl;
+ //}
+
+ //Check our spectrum for file type. Zoom and UltraZoom scans do not
+ //need splitting.
+ if(cs.fileFormat==zs || cs.fileFormat==uzs){
+
+ sa.clear();
+ sa.setParams(cs);
+ sa.setSpectrum(curSpec);
+ sa.FindPeaks();
+ sa.PredictPeptides();
+
+ //do not analyze spectrum with 0 predicted peaks; Keep count of these occurrances.
+ if(sa.predPeak->size()==0){
+ zeroPep++;
+ continue;
+ }
+
+ AnalyzePeaks(sa);
+
+ } else {
+
+ //Reinitialize our split spectrum
+ cSS=new CSplitSpectrum(&curSpec,cs);
+ cSS->SetAveragine(averagine);
+ cSS->SetMercury(mercury);
+
+ //Check if data already centroided
+ if(cs.centroid) {
+ if(cs.chargeMode=='F' || cs.chargeMode=='P' || cs.chargeMode=='S'){
+ cout << "-cdm settings of F, P, and S (FFT, Patterson, Senko) only work on profile data." << endl;
+ cout << "Please choose settings of Q or C (QuickCharge, Complete)" << endl;
+ exit(5);
+ }
+ //This function directly copies the already centroided spectra to the CSS object
+ cSS->Centroid(curSpec);
+
+ //if not, process the data here (ultimately includes centroiding)
+ } else {
+ if(cs.boxcarFilter>0){ //TODO: Figure out how filtering interferes here
+ cs.sn=0;
+ cSS->Centroid(curSpec);
+ } else if(cs.staticSN) {
+ if(cs.sn==0) cSS->NoSplitAnalysis();
+ else cSS->NewSNPass(cs.snWindow);
+ } else {
+ cSS->OverlappingAnalysis(cs.snWindow);
+ if(cs.iAnalysis) cSS->IntersectionAnalysis();
+ else cSS->UnionAnalysis();
+ }
+ }
+
+ //Split the spectrum
+ cSS->MakeAnalysis(cs.winSize);
+
+ //Analyze each window
+ for(winCount=0;winCount<cSS->getNumWindows();winCount++){
+ sa = cSS->getWindow(winCount);
+ sa.setParams(cs);
+ sa.PredictPeptides();
+
+ //do not analyze spectrum with 0 predicted peaks; Keep count of these occurrances.
+ if(sa.predPeak->size()==0){
+ zeroPep++;
+ continue;
+ }
+
+ AnalyzePeaks(sa);
+
+ }
+
+ //clean up cSS object
+ delete cSS;
+
+ }
+
+ //Update the percentage indicator
+ if(bEcho){
+ if (r.getPercent() > iPercent){
+ if(iPercent<10) cout << "\b";
+ else cout << "\b\b";
+ cout.flush();
+ iPercent=r.getPercent();
+ cout << iPercent;
+ cout.flush();
+ }
+ }
+
+ if(!bMem && cs.xml) {
+ fptr << "</Spectrum>" << endl;
+ fptr << "</File>" << endl;
+ fptr << "</Hardklor>" << endl;
+ }
+
+ } //loop to next spectrum (while)
+
+ //Close the output file and clear it so it can be reused.
+ if(!bMem){
+ fptr.close();
+ fptr.clear();
+ }
+
+ if(bEcho) {
+ cout << "\n" << endl;
+
+ switch(cs.algorithm){
+ case SemiComplete:
+ cout << "SemiComplete analysis:" << endl;
+ break;
+ case SemiCompleteFast:
+ cout << "SemiCompleteFast analysis:" << endl;
+ break;
+ case Dynamic:
+ cout << "Dynamic analysis:" << endl;
+ break;
+ case DynamicSemiComplete:
+ cout << "DynamicSemiComplete analysis:" << endl;
+ break;
+ case SemiSubtractive:
+ cout << "SemiSubtractive analysis:" << endl;
+ break;
+ case FewestPeptides:
+ cout << "FewestPeptides analysis:" << endl;
+ break;
+ case FewestPeptidesChoice:
+ cout << "FewestPeptidesChoice analysis:" << endl;
+ break;
+ case FastFewestPeptides:
+ cout << "FastFewestPeptides analysis:" << endl;
+ break;
+ case FastFewestPeptidesChoice:
+ cout << "FastFewestPeptidesChoice analysis:" << endl;
+ break;
+ case Basic:
+ default:
+ cout << "Basic analysis:" << endl;
+ break;
+ }
+ }
+
+ //Output the simple statistics
+ if(bEcho) cout << " Total number of scans analyzed: " << TotalScans << endl;
+ //cout << " Number of (sub)scans not analyzed:" << endl;
+ //cout << " No Peptides Predicted: " << zeroPep << endl;
+ //cout << " Intensity Below Limit: " << lowSigPep << endl;
+ //cout << " Number of scans with more predicted peptides than were analyzed: " << manyPep << endl;
+ //cout << " Total Correlations Made: " << TotalIterations << endl;
+
+ //Output the time to analyze this file.
+ if(bEcho){
+ i=(int)timeToSec(loadTime,timerFrequency);
+ minutes = (int)(i/60);
+ seconds = i - (60*minutes);
+ cout << "\nFile access time: " << minutes << " minutes, " << seconds << " seconds." << endl;
+ i=(int)timeToSec(splitTime,timerFrequency);
+ minutes = (int)(i/60);
+ seconds = i - (60*minutes);
+ cout << "Split Time: " << minutes << " minutes, " << seconds << " seconds." << endl;
+ i=(int)timeToSec(analysisTime,timerFrequency);
+ minutes = (int)(i/60);
+ seconds = i - (60*minutes);
+ cout << "Analysis Time: " << minutes << " minutes, " << seconds << " seconds." << endl;
+
+ if (minutes==0 && seconds==0){
+ cout << "IMPOSSIBLE!!!" << endl;
+ } else if(minutes <=2){
+ cout << "HOLY FRIJOLE!!" << endl;
+ } else if(minutes<=5) {
+ cout << "Like lightning!" << endl;
+ } else if(minutes<=10){
+ cout << "That's pretty damn fast!" << endl;
+ } else if(minutes<=20){
+ cout << "Monkeys calculate faster than that!" << endl;
+ } else if(minutes<=30){
+ cout << "You should have taken a lunch break." << endl;
+ } else if(minutes<=40){
+ cout << "Oi! Too freakin' slow!!" << endl;
+ } else {
+ cout << "You might be able to eek out some better performance by adjusting your parameters." << endl;
+ }
+ }
+
+ PT=NULL;
+
+}
+
+bool CHardklor::AnalyzePeaks(CSpecAnalyze& sa){
+
+ int i;
+ SSObject bsso;
+
+ //Arrays for combinatorial analysis
+ float *match;
+ float *mismatch;
+
+ //Track analysis times
+ getExactTime(startTime);
+
+ //Make an averagine distribution for every variant specified in the conf file.
+ sa.MakePredictions(pepVariants);
+
+ //if there are no possible peptides, stop the analysis here.
+ if(sa.predPep->size()==0) {
+ getExactTime(stopTime);
+ tmpTime1=toMicroSec(stopTime);
+ tmpTime2=toMicroSec(startTime);
+ analysisTime+=tmpTime1-tmpTime2;
+ return false;
+ }
+
+ //Restructure mismatch arrays for faster correlation analysis
+ sa.BuildMismatchArrays();
+
+ //Send the distributions, and the observed data points from the spectrum to a recursive
+ //algorithm that will sum up every combination of every peptide in each of its chlorinated
+ //forms to find the combination that best fits the data.
+
+ //Dimension our arrays
+ match = new float[sa.peaks.size()];
+ for(i=0;i<sa.peaks.size();i++) match[i]=0;
+
+ if(sa.mismatchSize>0){
+ mismatch = new float[sa.mismatchSize];
+ for(i=0;i<sa.mismatchSize;i++) mismatch[i]=0;
+ } else {
+ mismatch = new float[1];
+ mismatch[0] = 0;
+ }
+
+ //clear prior data and select analysis algorithm
+ bsso.clear();
+ switch(cs.algorithm){
+ case SemiComplete:
+ SemiCompleteMethod(match,mismatch,&bsso,1,cs.depth,0);
+ break;
+ case SemiCompleteFast:
+ SemiCompleteFastMethod(match,mismatch,&bsso,1,cs.depth,0);
+ break;
+ case Dynamic:
+ DynamicMethod(match,mismatch,&bsso,1,cs.depth,0,0);
+ break;
+ case DynamicSemiComplete:
+ DynamicSemiCompleteMethod(match,mismatch,&bsso,1,cs.depth,0,0);
+ break;
+ case SemiSubtractive:
+ SemiSubtractiveMethod(&bsso,cs.depth);
+ break;
+ case FewestPeptides:
+ FewestPeptidesMethod(&bsso,cs.depth);
+ break;
+ case FewestPeptidesChoice:
+ FewestPeptidesChoiceMethod(&bsso,cs.depth);
+ break;
+ case FastFewestPeptides:
+ FastFewestPeptidesMethod(&bsso,cs.depth);
+ break;
+ case FastFewestPeptidesChoice:
+ FastFewestPeptidesChoiceMethod(&bsso,cs.depth);
+ break;
+ case Basic:
+ default:
+ BasicMethod(match,mismatch,&bsso,1,cs.depth,sa.predPep->size()-1);
+ break;
+ }
+
+ //Clean up memory
+ delete [] match;
+ delete [] mismatch;
+
+ //Track analysis times
+ getExactTime(stopTime);
+ tmpTime1=toMicroSec(stopTime);
+ tmpTime2=toMicroSec(startTime);
+ analysisTime+=tmpTime1-tmpTime2;
+
+ //if we exceeded our threshold, output the data to file or store it in memoryt
+ if(bsso.corr > cs.corr) {
+ if(!bMem){
+ if(cs.reducedOutput) WritePepLine(bsso,PT,fptr,2);
+ else if(cs.xml) WritePepLine(bsso,PT,fptr,1);
+ else WritePepLine(bsso,PT,fptr,0);
+ } else {
+ ResultToMem(bsso,PT);
+ }
+ }
+
+ return true;
+}
+
+double CHardklor::LinReg(float *match, float *mismatch){
+
+ int i,sz;
+ double sxx=0,syy=0,sxy=0;
+ vector<sFloat> v;
+ sFloat tmp;
+
+ //Correlate matches
+ for(i=0;i<sa.peaks.size();i++){
+ tmp.fLower = sa.peaks.at(i).intensity;
+ tmp.fUpper = match[i];
+ v.push_back(tmp);
+ }
+
+ //Correlate mismatches with 0
+ for(i=0;i<sa.mismatchSize;i++){
+ if(mismatch[i]>0){
+ tmp.fLower = 0;
+ tmp.fUpper = mismatch[i];
+ v.push_back(tmp);
+ }
+ }
+
+ //Cosine angle correlation
+ sxy=0;
+ sxx=0;
+ syy=0;
+ sz=(int)v.size();
+ for(i=0;i<sz;i++){
+ sxy += (v.at(i).fLower*v.at(i).fUpper);
+ sxx += (v.at(i).fLower*v.at(i).fLower);
+ syy += (v.at(i).fUpper*v.at(i).fUpper);
+ }
+
+ if(sxx>0 && syy>0 && sxy>0) return sxy/sqrt(sxx*syy);
+ else return 0;
+
+}
+
+
+void CHardklor::BasicMethod(float *match, float *mismatch,SSObject *combo,
+ int depth, int maxDepth, int start){
+
+ SSObject bestCombo = *combo;
+ SSObject re...
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