fixed some bugs and added mgcluster command

[mothur.git] / hcluster.cpp

diff --git a/hcluster.cpp b/hcluster.cpp
index 7613ecbf43e245713880a26444b3e68baaad808c..2d88533757a1495d54423ad87354532a96d3e053 100644 (file)
--- a/hcluster.cpp
+++ b/hcluster.cpp
@@ -16,7 +16,7 @@
 
 HCluster::HCluster(RAbundVector* rav, ListVector* lv) :  rabund(rav), list(lv){
        try {
-       
+               mapWanted = false;
                numSeqs = list->getNumSeqs();
                
                //initialize cluster array
@@ -56,7 +56,8 @@ void HCluster::clusterBins(){
 void HCluster::clusterNames(){
        try {
                ///cout << smallCol << '\t' << smallRow << '\t' << smallDist << '\t' << list->get(clusterArray[smallRow].smallChild) << '\t' << list->get(clusterArray[smallCol].smallChild);
-
+               if (mapWanted) {  updateMap();  }
+               
                list->set(clusterArray[smallCol].smallChild, list->get(clusterArray[smallRow].smallChild)+','+list->get(clusterArray[smallCol].smallChild));
                list->set(clusterArray[smallRow].smallChild, "");       
                list->setLabel(toString(smallDist));
@@ -256,7 +257,7 @@ void HCluster::updateArrayandLinkTable() {
        }
 }
 /***********************************************************************/
-bool HCluster::update(int row, int col, float distance){
+void HCluster::update(int row, int col, float distance){
        try {
                
                smallRow = row;
@@ -284,15 +285,62 @@ bool HCluster::update(int row, int col, float distance){
                }
                
                //printInfo();
-               return clustered;
        }
        catch(exception& e) {
                errorOut(e, "HCluster", "update");
                exit(1);
        }
 }
-
-
 /***********************************************************************/
+void HCluster::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, "HCluster", "setMapWanted");
+               exit(1);
+       }
+}
+/***********************************************************************/
+void HCluster::updateMap() {
+try {
+               //update location of seqs in smallRow since they move to smallCol now
+               string names = list->get(clusterArray[smallRow].smallChild);
+               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] = clusterArray[smallCol].smallChild;
+                       names = names.substr(names.find_first_of(',')+1, names.length());
+               }
+                       
+               //get last name
+               seq2Bin[names] = clusterArray[smallCol].smallChild;
+       }
+       catch(exception& e) {
+               errorOut(e, "HCluster", "updateMap");
+               exit(1);
+       }
+}
+/***********************************************************************/
+