[Sashimi-commit] SF.net SVN: sashimi:[5279] trunk/trans_proteomic_pipeline/extern/ ProteoWizard/pwiz/pwiz/data/msdata

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

Revision: 5279
          http://sashimi.svn.sourceforge.net/sashimi/?rev=5279&view=rev
Author:   dshteyn
Date:     2011-01-04 00:11:00 +0000 (Tue, 04 Jan 2011)

Log Message:
-----------
Allow InteractParser (or RAMP in general) to read FAIMS Compensation Voltage from mzML filter line. TODO: need to make sure this makes it into the real PWIZ.

Modified Paths:
--------------
    trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/RAMPAdapter.cpp
    trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/ramp/ramp.h

Modified: trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/RAMPAdapter.cpp
===================================================================
--- trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/RAMPAdapter.cpp	2011-01-03 19:07:30 UTC (rev 5278)
+++ trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/RAMPAdapter.cpp	2011-01-04 00:11:00 UTC (rev 5279)
@@ -165,7 +165,24 @@
     result.precursorMZ = 0;
     result.precursorCharge = 0;
     result.precursorIntensity = 0;
+    result.compensationVoltage = 0;
+    
 
+    std::string filterLine = scan.cvParam(MS_filter_string).value;
+    
+    size_t found = filterLine.find("cv=");
+    
+    if (found!=string::npos) {
+      filterLine = filterLine.substr(found+3);
+      found = filterLine.find_first_of(" ");
+      if (found!=string::npos) {
+	filterLine = filterLine.substr(0, found);
+	result.compensationVoltage = atof(filterLine.c_str());
+      }
+    }
+
+
+
     if (!spectrum->precursors.empty())
     {
         const Precursor& precursor = spectrum->precursors[0];

Modified: trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/ramp/ramp.h
===================================================================
--- trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/ramp/ramp.h	2011-01-03 19:07:30 UTC (rev 5278)
+++ trunk/trans_proteomic_pipeline/extern/ProteoWizard/pwiz/pwiz/data/msdata/ramp/ramp.h	2011-01-04 00:11:00 UTC (rev 5279)
@@ -155,6 +155,7 @@
    double basePeakMZ;
    double basePeakIntensity;
    double collisionEnergy;
+   double compensationVoltage;
    double ionisationEnergy;
    double lowMZ;
    double highMZ;


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