added cutoff change to hcluster

[mothur.git] / hcluster.cpp

diff --git a/hcluster.cpp b/hcluster.cpp
index 8a596f3163c06dd55129cdc8de0f5779a5d6cb4d..e6e97fa9144f4ab4b79c35480e1c57b0235d733f 100644 (file)
--- a/hcluster.cpp
+++ b/hcluster.cpp
@@ -259,7 +259,7 @@ void HCluster::updateArrayandLinkTable() {
        }
 }
 /***********************************************************************/
-bool HCluster::update(int row, int col, float distance){
+double HCluster::update(int row, int col, float distance){
        try {
                bool cluster = false;
                smallRow = row;
@@ -296,7 +296,7 @@ bool HCluster::update(int row, int col, float distance){
                        }
                }
                
-               return cluster;
+               return cutoff;
                //printInfo();
        }
        catch(exception& e) {
@@ -430,7 +430,6 @@ vector<seqDist> HCluster::getSeqsFNNN(){
        }
 }
 //**********************************************************************************************************************
-//don't need cutoff since processFile removes all distance above cutoff and changes names to indexes
 vector<seqDist> HCluster::getSeqsAN(){
        try {
                int firstName, secondName;
@@ -572,7 +571,9 @@ int HCluster::combineFile() {
                                                        smallRowColValues[0][mergedMin[count].seq1] = mergedMin[count].dist;
                                                }else { //if no, write to temp file
                                                        //outputString += toString(mergedMin[count].seq1) + '\t' + toString(mergedMin[count].seq2) + '\t' + toString(mergedMin[count].dist) + '\n';
-                                                       out << mergedMin[count].seq1 << '\t' << mergedMin[count].seq2 << '\t' << mergedMin[count].dist << endl;
+                                                       //if (mergedMin[count].dist < cutoff) { 
+                                                               out << mergedMin[count].seq1 << '\t' << mergedMin[count].seq2 << '\t' << mergedMin[count].dist << endl;
+                                                       //}
                                                }
                                                count++;
                                        }else{   break; }
@@ -592,7 +593,9 @@ int HCluster::combineFile() {
                           
                           }else { //if no, write to temp file
                                        //outputString += toString(first) + '\t' + toString(second) + '\t' + toString(dist) + '\n';
-                                       out << first << '\t' << second << '\t' << dist << endl;
+                                  //if (dist < cutoff) {
+                                          out << first << '\t' << second << '\t' << dist << endl;
+                                  //}
                           }
                        }
                        
@@ -617,7 +620,9 @@ int HCluster::combineFile() {
                                smallRowColValues[0][mergedMin[count].seq1] = mergedMin[count].dist;
                                
                        }else { //if no, write to temp file
-                               out << mergedMin[count].seq1 << '\t' << mergedMin[count].seq2 << '\t' << mergedMin[count].dist << endl;
+                               //if (mergedMin[count].dist < cutoff) {
+                                       out << mergedMin[count].seq1 << '\t' << mergedMin[count].seq2 << '\t' << mergedMin[count].dist << endl;
+                               //}
                        }
                        count++;
                }
@@ -650,9 +655,17 @@ int HCluster::combineFile() {
                                
                                seqDist temp(clusterArray[smallRow].parent, itMerge->first, average);
                                mergedMin.push_back(temp);
+                       }else {  
+                               //can't find value so update cutoff
+                               if (cutoff > itMerge->second) { cutoff = itMerge->second; }
                        }
                }
-
+               
+               //update cutoff
+               for(itMerge = smallRowColValues[1].begin(); itMerge != smallRowColValues[1].end(); itMerge++) { 
+                       if (cutoff > itMerge->second) { cutoff = itMerge->second; }
+               }
+               
                //sort merged values
                sort(mergedMin.begin(), mergedMin.end(), compareSequenceDistance);