[Sashimi-commit] SF.net SVN: sashimi:[5126] trunk/trans_proteomic_pipeline/src/Validation/ MixtureDistribution

[<ds...@us...>]

Revision: 5126
          http://sashimi.svn.sourceforge.net/sashimi/?rev=5126&view=rev
Author:   dshteyn
Date:     2010-08-25 22:29:41 +0000 (Wed, 25 Aug 2010)

Log Message:
-----------
Support for Crux

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/MixtureDistrFactory.cxx
    trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/MixtureDistrFactory.h

Modified: trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/MixtureDistrFactory.cxx
===================================================================
--- trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/MixtureDistrFactory.cxx	2010-08-25 22:26:49 UTC (rev 5125)
+++ trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/MixtureDistrFactory.cxx	2010-08-25 22:29:41 UTC (rev 5126)
@@ -38,7 +38,7 @@
   scoreOpts_ = options;
   modelOpts_ = modelopts;
   // HENRY: add SpectraST
-  const char* engines[] = {"SEQUEST", "MASCOT", "COMET", "PROBID", "X! TANDEM", "SPECTRAST", "PHENYX", "OMSSA", "MYRIMATCH", "INSPECT", "YABSE"};
+  const char* engines[] = {"SEQUEST", "MASCOT", "COMET", "PROBID", "X! TANDEM", "SPECTRAST", "PHENYX", "OMSSA", "MYRIMATCH", "INSPECT", "YABSE", "CRUX"};
   int num_engines = sizeof(engines)/sizeof(char*);
   Boolean found = False;
 
@@ -145,6 +145,9 @@
   else if(! strcasecmp(modelOpts_.engine_, "INSPECT")) {
     return new InspectResult(tags);
   }
+ else if(! strcasecmp(modelOpts_.engine_, "CRUX")) {
+    return new CruxResult(tags);
+  }
   else {
     // error
     //    cout << "NULL" << endl;
@@ -255,7 +258,7 @@
 DiscrimValMixtureDistr* MixtureDistrFactory::getDiscrimValMixtureDistr(int charge, Boolean gamma, Boolean nonparam) {
   return getDiscrimValMixtureDistr(charge, gamma, nonparam, False) ;
 }
-DiscrimValMixtureDistr* MixtureDistrFactory::getDiscrimValMixtureDistr(int charge, Boolean gamma, Boolean nonparam, Boolean use_expect) {
+DiscrimValMixtureDistr* MixtureDistrFactory::getDiscrimValMixtureDistr(int charge, Boolean gamma, Boolean nonparam, Boolean use) {
 
   DiscrimValMixtureDistr* distr = NULL;
   //Boolean gamma = True;
@@ -268,6 +271,13 @@
     distr = new DiscrimValMixtureDistr(charge, getDiscrMixtureDistrName(), "fval", True, maldi, qtof, nonparam);
 
   }
+  else if(! strcasecmp(search_engine_.c_str(), "CRUX")) {
+    //cout << "making SQ f distr" << endl;
+    //distr = new DiscrimValMixtureDistr(charge, getDiscrMixtureDistrName(), "fval", gamma, maldi, qtof);
+    distr = new CruxDiscrimValMixtureDistr(charge, search_engine_.c_str(), getDiscrMixtureDistrName(), "fval", modelOpts_.maldi_, qtof, gamma, nonparam, use);
+    //    distr = new CruxDiscrimValMixtureDistr(charge, getDiscrMixtureDistrName(), "fval", True, maldi, qtof, nonparam);
+
+  }
   else if(! strcasecmp(search_engine_.c_str(), "MASCOT")) {
     //cout << "making mascot f distr" << endl;
     //distr = new MascotDiscrimValMixtureDistr(charge, getDiscrMixtureDistrName(), "fval", maldi, qtof, scoreOpts_.inputfile_, nonparam);
@@ -286,7 +296,7 @@
   }
   else if(! strncmp(search_engine_.c_str(), "X! Tandem", 9)) {
     //cout << "making mascot f distr" << endl;
-    distr = new TandemDiscrimValMixtureDistr(charge, search_engine_.c_str(), getDiscrMixtureDistrName(), "fval", modelOpts_.maldi_, qtof, gamma, nonparam, use_expect);
+    distr = new TandemDiscrimValMixtureDistr(charge, search_engine_.c_str(), getDiscrMixtureDistrName(), "fval", modelOpts_.maldi_, qtof, gamma, nonparam, use);
 
   }
   // HENRY: add SpectraST

Modified: trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/MixtureDistrFactory.h
===================================================================
--- trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/MixtureDistrFactory.h	2010-08-25 22:26:49 UTC (rev 5125)
+++ trunk/trans_proteomic_pipeline/src/Validation/MixtureDistribution/MixtureDistrFactory.h	2010-08-25 22:29:41 UTC (rev 5126)
@@ -3,6 +3,7 @@
 
 #include "Parsers/Algorithm2XML/SearchResult/SearchResult.h"
 #include "Parsers/Algorithm2XML/SearchResult/SequestResult.h"
+#include "Parsers/Algorithm2XML/SearchResult/CruxResult.h"
 #include "Parsers/Algorithm2XML/SearchResult/MascotResult.h"
 #include "Parsers/Algorithm2XML/SearchResult/ProbIDResult.h"
 #include "Parsers/Algorithm2XML/SearchResult/TandemResult.h"
@@ -25,6 +26,7 @@
 #include "Validation/DiscriminateFunction/Inspect/InspectDiscrimValMixtureDistr.h"
 // HENRY: add SpectraST
 #include "Validation/DiscriminateFunction/SpectraST/SpectraSTDiscrimValMixtureDistr.h"
+#include "Validation/DiscriminateFunction/Crux/CruxDiscrimValMixtureDistr.h"
 #include "NTTMixtureDistr.h"
 #include "NMCMixtureDistr.h"
 /*
@@ -90,7 +92,7 @@
   DiscrimValMixtureDistr* getDiscrimValMixtureDistr(int charge);
   DiscrimValMixtureDistr* getDiscrimValMixtureDistr(int charge, Boolean gamma);
   DiscrimValMixtureDistr* getDiscrimValMixtureDistr(int charge, Boolean gamma, Boolean nonparam);
-  DiscrimValMixtureDistr* getDiscrimValMixtureDistr(int charge, Boolean gamma, Boolean nonparam, Boolean use_expect);
+  DiscrimValMixtureDistr* getDiscrimValMixtureDistr(int charge, Boolean gamma, Boolean nonparam, Boolean use);
   IsoMassDiffDiscrMixtureDistr* getIsoMassDiffDiscrMixtureDistr(int charge);
   NTTMixtureDistr* getNTTMixtureDistr(int charge);
   NMCMixtureDistr* getNMCMixtureDistr(int charge);


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