fixed some bugs and added mgcluster command

[mothur.git] / cluster.cpp

diff --git a/cluster.cpp b/cluster.cpp
index 6fd463116e65becc0ef2a969c08d5bfaf6dfea15..429e19aaeacce39b1a85943b31cd32da70739239 100644 (file)
--- a/cluster.cpp
+++ b/cluster.cpp
@@ -55,6 +55,7 @@ rabund(rav), list(lv), dMatrix(dm)
                seqVec[currentCell->row].push_back(currentCell);
                seqVec[currentCell->column].push_back(currentCell);
        }
+       mapWanted = false;  //set to true by mgcluster to speed up overlap merge
 }
 
 /***********************************************************************/
@@ -78,7 +79,7 @@ void Cluster::getRowColCells() {
        }
 
 }
-
+/***********************************************************************/
 // Remove the specified cell from the seqVec and from the sparse
 // matrix
 void Cluster::removeCell(const MatData& cell, int vrow, int vcol, bool rmMatrix)
@@ -150,7 +151,8 @@ void Cluster::clusterBins(){
 void Cluster::clusterNames(){
        try {
        //      cout << smallCol << '\t' << smallRow << '\t' << smallDist << '\t' << list->get(smallRow) << '\t' << list->get(smallCol);
-
+               if (mapWanted) {  updateMap();  }
+               
                list->set(smallCol, list->get(smallRow)+','+list->get(smallCol));
                list->set(smallRow, "");        
                list->setLabel(toString(smallDist));
@@ -222,7 +224,57 @@ void Cluster::update(){
                exit(1);
        }
 }
+/***********************************************************************/
+void Cluster::setMapWanted(bool m)  {  
+       try {
+               mapWanted = m;
+               
+               //initialize map
+               for (int i = 0; i < list->getNumBins(); i++) {
+                       
+                       //parse bin 
+                       string names = list->get(i);
+                       while (names.find_first_of(',') != -1) { 
+                               //get name from bin
+                               string name = names.substr(0,names.find_first_of(','));
+                               //save name and bin number
+                               seq2Bin[name] = i;
+                               names = names.substr(names.find_first_of(',')+1, names.length());
+                       }
+                       
+                       //get last name
+                       seq2Bin[names] = i;
+               }
+               
+       }
+       catch(exception& e) {
+               errorOut(e, "Cluster", "setMapWanted");
+               exit(1);
+       }
+}
+/***********************************************************************/
+void Cluster::updateMap() {
+try {
+               //update location of seqs in smallRow since they move to smallCol now
+               string names = list->get(smallRow);
+               while (names.find_first_of(',') != -1) { 
+                       //get name from bin
+                       string name = names.substr(0,names.find_first_of(','));
+                       //save name and bin number
+                       seq2Bin[name] = smallCol;
+                       names = names.substr(names.find_first_of(',')+1, names.length());
+               }
+                       
+               //get last name
+               seq2Bin[names] = smallCol;
+               
+       }
+       catch(exception& e) {
+               errorOut(e, "Cluster", "updateMap");
+               exit(1);
+       }
+}
+/***********************************************************************/
 
 
-/***********************************************************************/