[Sashimi-commit] SF.net SVN: sashimi:[4366] trunk/trans_proteomic_pipeline/src/Search/ SpectraST

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

Revision: 4366
          http://sashimi.svn.sourceforge.net/sashimi/?rev=4366&view=rev
Author:   henrylam
Date:     2009-05-29 06:19:46 +0000 (Fri, 29 May 2009)

Log Message:
-----------
[SpectraST] Add MRM table format SHOWINFO which prints additional info about each transition (including the score)

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibEntry.cpp
    trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.cpp
    trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.hpp

Modified: trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibEntry.cpp
===================================================================
--- trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibEntry.cpp	2009-05-28 19:25:19 UTC (rev 4365)
+++ trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTLibEntry.cpp	2009-05-29 06:19:46 UTC (rev 4366)
@@ -619,7 +619,7 @@
   cess.precision(2);
   cess << fixed << showpoint << collisionEnergy;
   
-  if (format == "DEFAULT") {
+  if (format == "DEFAULT" || format == "SHOWINFO") {
     stringstream press;
     press << bestSamp << '\t' << maxNumUsed << '/' << totNumUsed << '\t';
     press.precision(2);

Modified: trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.cpp
===================================================================
--- trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.cpp	2009-05-28 19:25:19 UTC (rev 4365)
+++ trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.cpp	2009-05-29 06:19:46 UTC (rev 4366)
@@ -674,7 +674,13 @@
     for (vector<Peak*>::iterator i = m_intensityRanked->begin(); i != m_intensityRanked->end(); i++) {
       fout << pre << '\t' << (*i)->mz << '\t' << (*i)->intensity << '\t' << (*i)->annotation << '\t' << post << endl;
     }
-  }  
+  } else if (format == "SHOWINFO") {
+     rankByIntensity();
+     for (vector<Peak*>::iterator i = m_intensityRanked->begin(); i != m_intensityRanked->end(); i++) {
+       fout << pre << '\t' << (*i)->mz << '\t' << (*i)->intensity << '\t' << (*i)->annotation << '\t' << post << '\t' << (*i)->info << endl;
+     }
+  }
+     
 }
 
 
@@ -1035,7 +1041,7 @@
     // consider all 'a' ions rare
   if (annotation[0] != 'y' && annotation[0] != 'b') return (false);	
     
-  string::size_type minusPos = annotation.find('-');
+  string::size_type minusPos = annotation.find_first_of("+-");
   if (minusPos != string::npos) {
     return (false);
   }
@@ -2927,3 +2933,20 @@
   }
 
 }
+
+void SpectraSTPeakList::flattenAllPeaks() {
+
+  for (vector<Peak>::iterator j = m_peaks.begin(); j != m_peaks.end(); j++) {
+    j->intensity = 10000.0;
+  }
+
+}
+
+void SpectraSTPeakList::removeNoncanonicalPeaks() {
+
+  for (vector<Peak>::iterator j = m_peaks.begin(); j != m_peaks.end(); j++) {
+    if (!(isBorY(j->annotation))) {
+      j->intensity = 0.0;
+    }
+  }
+}

Modified: trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.hpp
===================================================================
--- trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.hpp	2009-05-28 19:25:19 UTC (rev 4365)
+++ trunk/trans_proteomic_pipeline/src/Search/SpectraST/SpectraSTPeakList.hpp	2009-05-29 06:19:46 UTC (rev 4366)
@@ -146,6 +146,10 @@
   void repositionPeaks();
 
   void shiftAllPeaks(double mzShift);
+
+  void removeNoncanonicalPeaks();
+  void flattenAllPeaks();
+
   
 private:
 	


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