[Sashimi-commit] trans_proteomic_pipeline/src Makefile,1.69,1.70

[Henry L. <hen...@us...>]

Update of /cvsroot/sashimi/trans_proteomic_pipeline/src
In directory sc8-pr-cvs8.sourceforge.net:/tmp/cvs-serv19916

Modified Files:
	Makefile 
Log Message:
Major SpectraST update (v2.0)

Index: Makefile
===================================================================
RCS file: /cvsroot/sashimi/trans_proteomic_pipeline/src/Makefile,v
retrieving revision 1.69
retrieving revision 1.70
diff -C2 -d -r1.69 -r1.70
*** Makefile	17 Nov 2006 20:14:25 -0000	1.69
--- Makefile	18 Nov 2006 00:25:09 -0000	1.70
***************
*** 441,445 ****
  #
  
! EXE_XML = regenerate_VersionInfo/regenerate_VersionInfo PeptideProphetParser EnzymeDigestionParser XPressPeptideParser ASAPRatioPeptideParser ASAPRatioProteinRatioParser InteractParser DatabaseParser RefreshParser MzXML2Search XPressProteinRatioParser Q3ProteinRatioParser ASAPRatioPvalueParser CompactParser xinteract runprophet runperl Sequest2XML Mascot2XML Comet2XML Tandem2XML LibraPeptideParser LibraProteinRatioParser spectrast Out2XML CombineOut
  
  EXE_HTML = ASAPRatioPeptideCGIDisplayParser.cgi ASAPCGIDisplay.cgi ModelParser.cgi XPressPeptideUpdateParser.cgi XPressCGIProteinDisplayParser.cgi Pep3D_xml.cgi disCidData_xml.cgi getCidData_xml.cgi AnalysisSummaryParser.cgi comet-fastadb.cgi plot-msms.cgi sequest-tgz-out.cgi xpress-prophet-update.cgi cometresult.cgi PepXMLViewer.cgi plotspectrast.cgi
--- 441,445 ----
  #
  
! EXE_XML = regenerate_VersionInfo/regenerate_VersionInfo PeptideProphetParser EnzymeDigestionParser XPressPeptideParser ASAPRatioPeptideParser ASAPRatioProteinRatioParser InteractParser DatabaseParser RefreshParser MzXML2Search XPressProteinRatioParser Q3ProteinRatioParser ASAPRatioPvalueParser CompactParser xinteract runprophet runperl Sequest2XML Mascot2XML Comet2XML Tandem2XML LibraPeptideParser LibraProteinRatioParser spectrast Out2XML CombineOut plotspectrast
  
  EXE_HTML = ASAPRatioPeptideCGIDisplayParser.cgi ASAPCGIDisplay.cgi ModelParser.cgi XPressPeptideUpdateParser.cgi XPressCGIProteinDisplayParser.cgi Pep3D_xml.cgi disCidData_xml.cgi getCidData_xml.cgi AnalysisSummaryParser.cgi comet-fastadb.cgi plot-msms.cgi sequest-tgz-out.cgi xpress-prophet-update.cgi cometresult.cgi PepXMLViewer.cgi plotspectrast.cgi
***************
*** 610,618 ****
  	$(LD) $(DEBUG)   -O2 -o cometresult.cgi cometresult1.o util.o TPPVersionInfo.o win32_system.o  $(LDFLAGS)
  
! plotspectrast.cgi : plotspectrast.o FileUtils.o Peptide.o cramp.o ramp.o base64.o TPPVersionInfo.o win32_system.o
! 	$(LD) $(DEBUG)   -O2 -o plotspectrast.cgi plotspectrast.o FileUtils.o Peptide.o cramp.o ramp.o base64.o TPPVersionInfo.o win32_system.o -lz $(LDFLAGS)
  
! spectrast : SpectraSTLib.o SpectraSTLibIndex.o SpectraSTLibEntry.o SpectraSTPeakList.o SpectraSTLibImporter.o SpectraSTMspLibImporter.o SpectraSTSearchTask.o SpectraSTMspSearchTask.o SpectraSTMzXMLSearchTask.o SpectraSTCandidate.o SpectraSTSearch.o SpectraSTSearchOutput.o SpectraSTTxtSearchOutput.o SpectraSTXlsSearchOutput.o SpectraSTPepXMLSearchOutput.o SpectraSTMzLibIndex.o SpectraSTPeptideLibIndex.o SpectraSTSimScores.o SpectraSTSearchParams.o SpectraSTMain.o base64.o ramp.o cramp.o FileUtils.o Peptide.o TPPVersionInfo.o win32_system.o util.o
! 	$(LD) $(DEBUG)   -O2 -o spectrast SpectraSTLib.o SpectraSTLibIndex.o SpectraSTLibEntry.o SpectraSTPeakList.o SpectraSTLibImporter.o SpectraSTMspLibImporter.o SpectraSTSearchTask.o SpectraSTMspSearchTask.o SpectraSTMzXMLSearchTask.o SpectraSTCandidate.o SpectraSTSearch.o SpectraSTSearchOutput.o SpectraSTTxtSearchOutput.o SpectraSTXlsSearchOutput.o SpectraSTPepXMLSearchOutput.o SpectraSTMzLibIndex.o SpectraSTPeptideLibIndex.o SpectraSTSimScores.o SpectraSTSearchParams.o SpectraSTMain.o base64.o ramp.o cramp.o FileUtils.o Peptide.o TPPVersionInfo.o win32_system.o util.o $(LDFLAGS) -lz
  
  xinteract :  xinteract.o TPPVersionInfo.o win32_system.o util.o
--- 610,621 ----
  	$(LD) $(DEBUG)   -O2 -o cometresult.cgi cometresult1.o util.o TPPVersionInfo.o win32_system.o  $(LDFLAGS)
  
! plotspectrast : plotspectrast.o FileUtils.o Peptide.o SpectraSTLibEntry.o SpectraSTQuery.o SpectraSTPeakList.o cramp.o ramp.o base64.o TPPVersionInfo.o win32_system.o
! 	$(LD) $(DEBUG)   -O2 -o plotspectrast plotspectrast.o FileUtils.o Peptide.o SpectraSTLibEntry.o SpectraSTQuery.o SpectraSTPeakList.o cramp.o ramp.o base64.o TPPVersionInfo.o win32_system.o -lz $(LDFLAGS)
  
! plotspectrast.cgi : plotspectrast_cgi.o FileUtils.o Peptide.o SpectraSTLibEntry.o SpectraSTQuery.o SpectraSTPeakList.o cramp.o ramp.o base64.o TPPVersionInfo.o win32_system.o
! 	$(LD) $(DEBUG)   -O2 -o plotspectrast.cgi plotspectrast_cgi.o FileUtils.o Peptide.o SpectraSTLibEntry.o SpectraSTQuery.o SpectraSTPeakList.o cramp.o ramp.o base64.o TPPVersionInfo.o win32_system.o -lz $(LDFLAGS)
! 
! spectrast : SpectraSTLib.o SpectraSTLibIndex.o SpectraSTLibEntry.o SpectraSTPeakList.o SpectraSTLibImporter.o SpectraSTMspLibImporter.o SpectraSTXHunterLibImporter.o SpectraSTSearchTask.o SpectraSTMspSearchTask.o SpectraSTMzXMLSearchTask.o SpectraSTDtaSearchTask.o SpectraSTCandidate.o SpectraSTQuery.o SpectraSTSearch.o SpectraSTSearchOutput.o SpectraSTTxtSearchOutput.o SpectraSTXlsSearchOutput.o SpectraSTPepXMLSearchOutput.o SpectraSTMzLibIndex.o SpectraSTPeptideLibIndex.o SpectraSTSimScores.o SpectraSTSearchParams.o SpectraSTCreateParams.o SpectraSTMain.o base64.o ramp.o cramp.o FileUtils.o Peptide.o ProgressCount.o TPPVersionInfo.o win32_system.o util.o
! 	$(LD) $(DEBUG)   -O2 -o spectrast SpectraSTLib.o SpectraSTLibIndex.o SpectraSTLibEntry.o SpectraSTPeakList.o SpectraSTLibImporter.o SpectraSTMspLibImporter.o SpectraSTXHunterLibImporter.o SpectraSTSearchTask.o SpectraSTMspSearchTask.o SpectraSTMzXMLSearchTask.o SpectraSTDtaSearchTask.o SpectraSTCandidate.o SpectraSTQuery.o SpectraSTSearch.o SpectraSTSearchOutput.o SpectraSTTxtSearchOutput.o SpectraSTXlsSearchOutput.o SpectraSTPepXMLSearchOutput.o SpectraSTMzLibIndex.o SpectraSTPeptideLibIndex.o SpectraSTSimScores.o SpectraSTSearchParams.o SpectraSTCreateParams.o SpectraSTMain.o base64.o ramp.o cramp.o FileUtils.o Peptide.o ProgressCount.o TPPVersionInfo.o win32_system.o util.o $(LDFLAGS) -lz
  
  xinteract :  xinteract.o TPPVersionInfo.o win32_system.o util.o
***************
*** 1061,1064 ****
--- 1064,1069 ----
  Peptide.o : Peptide.cpp Peptide.hpp
  
+ ProgressCount.o : ProgressCount.cpp ProgressCount.hpp
+ 
  SpectraSTLib.o : SpectraSTLib.cpp  SpectraSTLib.hpp  SpectraSTLibIndex.hpp  SpectraSTPeptideLibIndex.hpp  SpectraSTLibImporter.hpp  FileUtils.hpp Peptide.hpp
  
***************
*** 1073,1085 ****
  SpectraSTMspLibImporter.o : SpectraSTMspLibImporter.cpp SpectraSTMspLibImporter.hpp  SpectraSTLibImporter.hpp FileUtils.hpp Peptide.hpp
  
  SpectraSTSearchTask.o : SpectraSTSearchTask.cpp  SpectraSTSearchTask.hpp  SpectraSTLib.hpp SpectraSTSearchOutput.hpp  SpectraSTMspSearchTask.hpp  SpectraSTMzXMLSearchTask.hpp FileUtils.hpp
  
! SpectraSTMspSearchTask.o : SpectraSTMspSearchTask.cpp SpectraSTMspSearchTask.hpp SpectraSTSearch.hpp SpectraSTPeakList.hpp FileUtils.hpp
  
! SpectraSTMzXMLSearchTask.o : SpectraSTMzXMLSearchTask.cpp SpectraSTMzXMLSearchTask.hpp SpectraSTSearch.hpp SpectraSTPeakList.hpp FileUtils.hpp cramp.hpp ramp.h
  
  SpectraSTCandidate.o : SpectraSTCandidate.cpp  SpectraSTCandidate.hpp  SpectraSTLibEntry.hpp  FileUtils.hpp
  
! SpectraSTSearch.o : SpectraSTSearch.cpp  SpectraSTSearch.hpp  SpectraSTLib.hpp SpectraSTCandidate.hpp  SpectraSTSearchOutput.hpp  SpectraSTLibEntry.hpp  FileUtils.hpp
  
  SpectraSTSearchOutput.o : SpectraSTSearchOutput.cpp SpectraSTSearchOutput.hpp  SpectraSTSearchParams.hpp  SpectraSTSimScores.hpp  SpectraSTTxtSearchOutput.hpp  SpectraSTXlsSearchOutput.hpp  SpectraSTPepXMLSearchOutput.hpp  FileUtils.hpp
--- 1078,1096 ----
  SpectraSTMspLibImporter.o : SpectraSTMspLibImporter.cpp SpectraSTMspLibImporter.hpp  SpectraSTLibImporter.hpp FileUtils.hpp Peptide.hpp
  
+ SpectraSTXHunterLibImporter.o : SpectraSTXHunterLibImporter.cpp SpectraSTXHunterLibImporter.hpp  SpectraSTLibImporter.hpp FileUtils.hpp Peptide.hpp
+ 
  SpectraSTSearchTask.o : SpectraSTSearchTask.cpp  SpectraSTSearchTask.hpp  SpectraSTLib.hpp SpectraSTSearchOutput.hpp  SpectraSTMspSearchTask.hpp  SpectraSTMzXMLSearchTask.hpp FileUtils.hpp
  
! SpectraSTMspSearchTask.o : SpectraSTMspSearchTask.cpp SpectraSTMspSearchTask.hpp SpectraSTSearchTask.hpp SpectraSTSearch.hpp SpectraSTQuery.hpp SpectraSTPeakList.hpp FileUtils.hpp SpectraSTConstants.hpp
  
! SpectraSTMzXMLSearchTask.o : SpectraSTMzXMLSearchTask.cpp SpectraSTMzXMLSearchTask.hpp SpectraSTSearchTask.hpp SpectraSTSearch.hpp SpectraSTQuery.hpp SpectraSTPeakList.hpp FileUtils.hpp cramp.hpp ramp.h SpectraSTConstants.hpp
! 
! SpectraSTDtaSearchTask.o : SpectraSTDtaSearchTask.cpp SpectraSTDtaSearchTask.hpp SpectraSTSearchTask.hpp SpectraSTSearch.hpp SpectraSTQuery.hpp SpectraSTPeakList.hpp FileUtils.hpp SpectraSTConstants.hpp
  
  SpectraSTCandidate.o : SpectraSTCandidate.cpp  SpectraSTCandidate.hpp  SpectraSTLibEntry.hpp  FileUtils.hpp
  
! SpectraSTQuery.o : SpectraSTQuery.cpp SpectraSTQuery.hpp SpectraSTPeakList.hpp FileUtils.hpp
! 
! SpectraSTSearch.o : SpectraSTSearch.cpp  SpectraSTSearch.hpp  SpectraSTLib.hpp SpectraSTCandidate.hpp  SpectraSTSearchOutput.hpp  SpectraSTQuery.hpp SpectraSTLibEntry.hpp  FileUtils.hpp
  
  SpectraSTSearchOutput.o : SpectraSTSearchOutput.cpp SpectraSTSearchOutput.hpp  SpectraSTSearchParams.hpp  SpectraSTSimScores.hpp  SpectraSTTxtSearchOutput.hpp  SpectraSTXlsSearchOutput.hpp  SpectraSTPepXMLSearchOutput.hpp  FileUtils.hpp
***************
*** 1097,1103 ****
  SpectraSTSimScores.o : SpectraSTSimScores.cpp SpectraSTSimScores.hpp
  
! SpectraSTSearchParams.o : SpectraSTSearchParams.cpp  SpectraSTSearchParams.hpp  FileUtils.hpp
  
! SpectraSTMain.o : SpectraSTMain.cpp SpectraSTLib.hpp  SpectraSTLibEntry.hpp  SpectraSTLibIndex.hpp  SpectraSTSearchTask.hpp  SpectraSTSearchParams.hpp  SpectraSTConstants.hpp
  
  ifeq (${XML_ONLY},1)
--- 1108,1120 ----
  SpectraSTSimScores.o : SpectraSTSimScores.cpp SpectraSTSimScores.hpp
  
! SpectraSTSearchParams.o : SpectraSTSearchParams.cpp SpectraSTSearchParams.hpp FileUtils.hpp SpectraSTConstants.hpp
  
! SpectraSTCreateParams.o : SpectraSTCreateParams.cpp SpectraSTCreateParams.hpp FileUtils.hpp SpectraSTConstants.hpp
! 
! SpectraSTMain.o : SpectraSTMain.cpp SpectraSTLib.hpp  SpectraSTLibEntry.hpp  SpectraSTLibIndex.hpp  SpectraSTSearchTask.hpp  SpectraSTSearchParams.hpp  SpectraSTCreateParams.hpp SpectraSTConstants.hpp
! 
! plotspectrast.o : plotspectrast.cpp SpectraSTLibEntry.hpp SpectraSTQuery.hpp SpectraSTPeakList.hpp cramp.hpp SpectraSTConstants.hpp
! 
! plotspectrast_cgi.o : plotspectrast_cgi.cpp SpectraSTLibEntry.hpp SpectraSTQuery.hpp SpectraSTPeakList.hpp cramp.hpp SpectraSTConstants.hpp
  
  ifeq (${XML_ONLY},1)
***************
*** 1228,1231 ****
--- 1245,1249 ----
  	cp -f Q3ProteinRatioParser ${BIN_DIR}
  	cp -f spectrast ${BIN_DIR}
+ 	cp -f plotspectrast ${BIN_DIR}
  	cp -f ../schema/msms_analysis3.dtd ${SCHEMA_DIR}
  	cp -f ../schema/pepXML_std.xsl ${SCHEMA_DIR}