fixed bug in sn handling

mkirchner · Jun 24, 2012 · e4864c6 · e4864c6
1 parent b6912cb
commit e4864c6
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Showing 3 changed files with 23 additions and 36 deletions.
diff --git a/examples/centroid.h b/examples/centroid.h
@@ -6,16 +6,16 @@
 struct Centroid 
 {
   double mz_;
-  unsigned int sn_;
+  int sn_;
   double rt_;
-  Centroid(const double& mz, const unsigned int  & sn, const double & rt) 
+  Centroid(const double& mz, const int  & sn, const double & rt) 
     : mz_(mz), sn_(sn), rt_(rt){}
 };
 
 namespace fbi {
 
   template<>
-  struct Traits<Centroid> : mpl::TraitsGenerator<float, float> {};
+  struct Traits<Centroid> : mpl::TraitsGenerator<float, int> {};
 
 } //end namespace fbi
 
@@ -30,18 +30,18 @@ struct CentroidBoxGenerator
   double mzWindowPpm_;
   double rtOffset_;
   double rtWindow_;
-  float snWindow_;
+  int snWindow_;
 
-  CentroidBoxGenerator(double mzWindowPpm, float snWindow)
+  CentroidBoxGenerator(double mzWindowPpm, int snWindow)
     : mzOffset_(0.0), mzWindowPpm_(mzWindowPpm), snWindow_(snWindow)
   {}
-  CentroidBoxGenerator(double mzWindowPpm, double rtWindow, unsigned int snWindow)
+  CentroidBoxGenerator(double mzWindowPpm, double rtWindow, int snWindow)
     : mzOffset_(0.0), mzWindowPpm_(mzWindowPpm),
     rtOffset_(0.0), rtWindow_(rtWindow), snWindow_(snWindow)
   {}
 
   CentroidBoxGenerator(double mzOffset, double mzWindowPpm, 
-      double rtOffset, double rtWindow, unsigned int snWindow)
+      double rtOffset, double rtWindow, int snWindow)
     : mzOffset_(mzOffset), mzWindowPpm_(mzWindowPpm),
     rtOffset_(rtOffset), rtWindow_(rtWindow), snWindow_(snWindow)
   {}
@@ -61,7 +61,7 @@ CentroidBoxGenerator::get<0>(const Centroid & centroid) const
 
 
 template <>
-std::pair<float, float>  
+std::pair<int, int>  
 CentroidBoxGenerator::get<1>(const Centroid & centroid) const 
 {
   return std::make_pair(

diff --git a/examples/example-bruker.cpp b/examples/example-bruker.cpp
@@ -39,7 +39,7 @@ int main(int argc, char * argv[]) {
 
   SNSplitter<SetType> splitter(options);
 
-  CentroidBoxGenerator gen(10,0.51);
+  CentroidBoxGenerator gen(10,1);
   //ResultType (*intersectFunctor)
   //(std::vector<Centroid>, CentroidBoxGenerator, CentroidBoxGenerator); 
 

diff --git a/examples/splitter.h b/examples/splitter.h
@@ -86,11 +86,10 @@ SNSplitter {
   typedef unsigned int LabelType;
     SNSplitter(const ProgramOptions& options) : options_(options) {
       overlap_ = options_.minClusterSize_ * options_.snWindowSize_ - 1;
-      std::cout << overlap_ << "overlap";
       adjListCounter_ = 0;
     }
      unsigned int 
-      parseString(const std::string & str, std::deque<Centroid> & centroids, unsigned int sn) {
+      parseString(const std::string & str, std::deque<Centroid> & centroids, int sn) {
         float mz=0, massrange_lo=0, massrange_hi=0, rt=0;
         char pol=0;
         char mode[101];
@@ -99,7 +98,6 @@ SNSplitter {
         int unknown=0, numentries=0, intensity=0;
         typedef boost::tokenizer<boost::char_separator<char> > Tokenizer;
         boost::char_separator<char> sep(",");
-        sn = 1;
 
         Tokenizer tokens(str, sep);
         Tokenizer::iterator it = tokens.begin();
@@ -117,52 +115,44 @@ SNSplitter {
       }
     ResultType
       filterAdjList(ResultType & adjList) {
-        ResultType filteredAdjList;
         std::vector<LabelType> labels;
         LabelType nComponents = findConnectedComponents(adjList, labels); 
         std::vector<unsigned int> counter(nComponents, 0);
         for (std::vector<LabelType>::size_type i = 0; i < labels.size(); ++i) {
           ++counter[labels[i] - 1];
         }
         //std::cout << "Counter" << counter;
-        filteredAdjList.resize(adjList.size());
+        typedef typename ResultType::value_type InnerType;
         for (std::vector<LabelType>::size_type i = 0; i < labels.size(); ++i) {
-          if (counter[labels[i]-1] >= options_.minClusterSize_) { 
-            adjList[i].swap(filteredAdjList[i]);
+          if (counter[labels[i]-1] < options_.minClusterSize_) { 
+            InnerType().swap(adjList[i]);
             //std::copy(adjList[i].begin(), adjList[i].end(), std::back_inserter(filteredAdjList[i]));
           }
         }
-        return filteredAdjList;
+        return adjList;
       }
       ResultType
-      joinAdjLists(const ResultType & filteredAdjList, ResultType & fullAdjList, typename ResultType::size_type offset) {
+      joinAdjLists(ResultType & filteredAdjList, ResultType & fullAdjList, typename ResultType::size_type offset) {
         fullAdjList.resize(filteredAdjList.size() + offset);
-        std::cout << "OFFSET" << offset << std::endl;
         typename ResultType::size_type index;
+        typedef typename ResultType::value_type InnerType;
         typename ResultType::value_type::const_iterator it1;
         for (index = 0; index < filteredAdjList.size(); ++index) {
           for (it1 = filteredAdjList[index].begin(); it1 != filteredAdjList[index].end(); ++it1) {
             fullAdjList[index + offset].insert(fullAdjList[index + offset].end(), typename ResultType::value_type::value_type(*it1 + offset));
+
           }
+          InnerType().swap(filteredAdjList[index]);
         }
-        //std::cout << adjListCounter_ << "adjCounter" << std::endl;
         return fullAdjList;
       }
     ResultType
       createShortAdjList(boost::function<ResultType(std::deque<Centroid>)> & intersectFunctor, const std::deque<Centroid> & centroids) {
-        //ResultType shortAdjList = intersectFunctor(centroids);
-        ResultType shortAdjList = SetType::intersect(centroids, CentroidBoxGenerator(10,0.51),CentroidBoxGenerator(10,0.51));
+        ResultType shortAdjList = intersectFunctor(centroids);
 
-        ResultType filteredAdjList = filterAdjList(shortAdjList);
-        for (int i = 0; i < 10; ++i) {
-        //std::cout << shortAdjList[i] << std::endl;
-        }
-        //std::cout << "FUBLA" << std::endl;
-        for (int i = 0; i < 10; ++i) {
-        //std::cout << filteredAdjList[i] << std::endl;
-        }
+        filterAdjList(shortAdjList);
 
-        return filteredAdjList;
+        return shortAdjList;
       }
 
     ResultType & makeUnique(ResultType & resultVector) {
@@ -192,7 +182,6 @@ SNSplitter {
           unsigned int numEntries = parseString(str, centroids, segmentCounter);
           segmentCounter++;
           centroidCounter += numEntries;
-
           if (segmentCounter % options_.segmentSize_ == 0) {
             nextCentroidCounter = centroidCounter;
           }
@@ -212,16 +201,14 @@ SNSplitter {
             centroids.erase(centroids.begin(), centroids.begin() + numNewCentroids);
 
 
-            std::cout << "pong" << std::endl;
           }
-
         }
-        std::cout << "beep" << std::endl; 
+        ifs.close();
         ResultType filteredAdjList = createShortAdjList(intersectFunctor, centroids);
-        std::cout << "boop" << std::endl;
         joinAdjLists(filteredAdjList, fullAdjList, oldCentroidCounter);
 
         fullAdjList = makeUnique(fullAdjList);
+
         return fullAdjList;
       }