[proteowizard-commit] SF.net SVN: proteowizard:[788] trunk/pwiz/pwiz/analysis/peakdetect/ FeatureDetectorSimple.cpp

[<kh...@us...>]

Revision: 788
          http://proteowizard.svn.sourceforge.net/proteowizard/?rev=788&view=rev
Author:   khoff
Date:     2009-04-28 19:00:25 +0000 (Tue, 28 Apr 2009)

Log Message:
-----------
Changed feature aggregation to allow peakels to go undetected for one scan and still be eligible for update.  Added control flow to skip non-FT scans. 

Modified Paths:
--------------
    trunk/pwiz/pwiz/analysis/peakdetect/FeatureDetectorSimple.cpp

Modified: trunk/pwiz/pwiz/analysis/peakdetect/FeatureDetectorSimple.cpp
===================================================================
--- trunk/pwiz/pwiz/analysis/peakdetect/FeatureDetectorSimple.cpp	2009-04-28 17:57:31 UTC (rev 787)
+++ trunk/pwiz/pwiz/analysis/peakdetect/FeatureDetectorSimple.cpp	2009-04-28 19:00:25 UTC (rev 788)
@@ -179,9 +179,11 @@
 
 void FeatureDetectorSimple::Impl::detect(const MSData& msd, vector<Feature>& detected) const 
 {   
-    // initialize buffer map    
+    // initialize buffer maps    
    
-    map<FeatureKey, FeatureID> bufferMap;
+    map<FeatureKey, FeatureID> grandparentBuffer;
+    map<FeatureKey, FeatureID> parentBuffer;
+
     map<FeatureID, Feature> featureMap;
     size_t featureCount = 0;
 
@@ -191,7 +193,7 @@
     for(size_t spectrum_index = 0; spectrum_index < cache.size(); spectrum_index ++) 
     {
         
-        map<FeatureKey, FeatureID> updatedBufferMap;
+        map<FeatureKey, FeatureID> buffer;
         const SpectrumInfo info = cache.spectrumInfo(spectrum_index, true); //getBinaryData ? 
        
         // call peak family detector on each scan
@@ -199,6 +201,14 @@
         vector<MZIntensityPair> mzIntensityPairs = info.data;       
 
         vector<PeakFamily> result;
+		
+		if (info.massAnalyzerType != MS_FT_ICR && info.massAnalyzerType != MS_orbitrap)
+		  {
+			cerr << "Skipping non-FT scan number " << info.scanNumber << endl;
+			continue;
+
+		  }
+
         _pfd.detect(mzIntensityPairs,result);
   
         // iterate thru peak families
@@ -213,10 +223,11 @@
               
                 // make keys for search
                 FeatureKey featureKey(floor(result_it->mzMonoisotopic*100)/100, result_it->charge, result_it->peaks.size()); // no digits past 10e-3
-                map<FeatureKey,FeatureID>::iterator location = bufferMap.find(featureKey);
+                map<FeatureKey,FeatureID>::iterator grandparentLocation = grandparentBuffer.find(featureKey);
+		map<FeatureKey,FeatureID>::iterator parentLocation = parentBuffer.find(featureKey);
                 
 
-                if (location == bufferMap.end())
+                if ( parentLocation == parentBuffer.end() && grandparentLocation == grandparentBuffer.end())
                     {   
 
                         // feature doesn't exist, make new feature
@@ -225,24 +236,33 @@
                         Feature feature = makeFeature(*result_it,featureID);
 
                         featureMap.insert(pair<FeatureID, Feature>(featureID, feature));
-                        updatedBufferMap.insert(pair<FeatureKey, FeatureID>(featureKey, featureID));
+                        buffer.insert(pair<FeatureKey, FeatureID>(featureKey, featureID));
                                         
 
                     }
 
                 else
                     {
-                        // update existing feature
-                        FeatureID foundID = location->second;
+   		      // if parent location update from parent
+		        FeatureID foundID;
+
+		        if ( parentLocation != parentBuffer.end() ) foundID = parentLocation->second;
+		        else foundID = grandparentLocation->second;
+			
+			// update existing feature
                         updateFeature(*result_it, featureMap[foundID]);
-                        updatedBufferMap.insert(pair<FeatureKey, FeatureID>(featureKey,foundID));
-                        
+                        buffer.insert(pair<FeatureKey, FeatureID>(featureKey,foundID));
+
                     }
                    
             }
 
         // old buffer map := new buffer map
-        bufferMap.swap(updatedBufferMap);
+	//  bufferMap.swap(updatedBufferMap);
+
+	grandparentBuffer.swap(parentBuffer);
+	parentBuffer.swap(buffer);
+
     }
  
     


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