fixed metastats, added resize to cluster.classic, added code to kill children if...

[mothur.git] / clusterclassic.cpp

diff --git a/clusterclassic.cpp b/clusterclassic.cpp
index 41c1647bccf6196efb54b31333a7d5298feaaeed..0e48690dc57059bb2ab1af1df3da5df0ea71efa4 100644 (file)
--- a/clusterclassic.cpp
+++ b/clusterclassic.cpp
@@ -226,7 +226,7 @@ int ClusterClassic::readPhylipFile(string filename, NameAssignment* nameMap) {
 //sets smallCol and smallRow, returns distance
 double ClusterClassic::getSmallCell() {
        try {
-               
+                       
                smallDist = aboveCutoff;
                smallRow = 1;
                smallCol = 0;
@@ -279,6 +279,10 @@ void ClusterClassic::clusterBins(){
 
                rabund->set(smallRow, rabund->get(smallRow)+rabund->get(smallCol));     
                rabund->set(smallCol, 0);       
+               for (int i = smallCol+1; i < rabund->size(); i++) {
+                       rabund->set((i-1), rabund->get(i));
+               }
+               rabund->resize((rabund->size()-1));
                rabund->setLabel(toString(smallDist));
 
        //      cout << '\t' << rabund->get(smallRow) << '\t' << rabund->get(smallCol) << endl;
@@ -296,6 +300,10 @@ void ClusterClassic::clusterNames(){
                
                list->set(smallRow, list->get(smallRow)+','+list->get(smallCol));
                list->set(smallCol, "");        
+               for (int i = smallCol+1; i < list->size(); i++) {
+                       list->set((i-1), list->get(i));
+               }
+               list->resize((list->size()-1));
                list->setLabel(toString(smallDist));
        
        //      cout << '\t' << list->get(smallRow) << '\t' << list->get(smallCol) << endl;
@@ -308,36 +316,21 @@ void ClusterClassic::clusterNames(){
 /***********************************************************************/
 void ClusterClassic::update(double& cutOFF){
        try {
-//cout << "before update " << endl;
 //print();             
                getSmallCell();
                
                int r, c;
                r = smallRow; c = smallCol;
-               //because we only store lt, we need to make sure we grab the right location
-               //if (smallRow < smallCol) { c = smallRow; r = smallCol; } //smallRow is really our column value
-               //else { r = smallRow; c = smallCol; } //smallRow is the row value
-               
-               //reset rows smallest distance
-               //rowSmallDists[r].dist = aboveCutoff; rowSmallDists[r].row = 0; rowSmallDists[r].col = 0;
-               //rowSmallDists[c].dist = aboveCutoff; rowSmallDists[c].row = 0; rowSmallDists[c].col = 0;
-               
-               //if your rows smallest distance is from smallRow or smallCol, reset
-               //for(int i=0;i<nseqs;i++){
-                       //if ((rowSmallDists[i].row == r) || (rowSmallDists[i].row == c) || (rowSmallDists[i].col == r) || (rowSmallDists[i].col == c)) {
-                       //      rowSmallDists[i].dist = aboveCutoff; rowSmallDists[i].row = 0; rowSmallDists[i].col = 0;
-                       //}
-               //}
-               
+                               
                for(int i=0;i<nseqs;i++){
                        if(i != r && i != c){
                                double distRow, distCol, newDist;
                                if (i > r) { distRow = dMatrix[i][r]; }
                                else { distRow =  dMatrix[r][i]; }
-                               
+
                                if (i > c) { distCol = dMatrix[i][c]; dMatrix[i][c] = aboveCutoff; } //like removeCell
                                else { distCol =  dMatrix[c][i]; dMatrix[c][i] = aboveCutoff; }
-                                       
+                               
                                if(method == "furthest"){
                                        newDist = max(distRow, distCol);
                                }
@@ -352,39 +345,33 @@ void ClusterClassic::update(double& cutOFF){
                                else if (method == "nearest"){
                                        newDist = min(distRow, distCol);
                                }
-                               
+                               //cout << "newDist = " << newDist << endl;      
                                if (i > r) { dMatrix[i][r] = newDist; }
                                else { dMatrix[r][i] = newDist; }
                                
-                               //if (newDist < rowSmallDists[i].dist) {  rowSmallDists[i].dist = newDist; rowSmallDists[i].col = r; rowSmallDists[i].row = i;  }
                        }
-                       //cout << "rowsmall = " << i << '\t' << rowSmallDists[i].dist << endl;  
                }
                        
                clusterBins();
                clusterNames();
-       
-               //find new small for 2 rows we just merged
-               //colDist temp(0,0,100.0);
-               //rowSmallDists[r] = temp;
-
-               //for (int i = 0; i < dMatrix[r].size(); i++) {
-               //      if (dMatrix[r][i] < rowSmallDists[r].dist) { rowSmallDists[r].dist = dMatrix[r][i]; rowSmallDists[r].col = r; rowSmallDists[r].row = i; }
-               //}
-               //for (int i = dMatrix[r].size()+1; i < dMatrix.size(); i++) {
-               //      if (dMatrix[i][dMatrix[r].size()] < rowSmallDists[r].dist) { rowSmallDists[r].dist = dMatrix[i][dMatrix[r].size()]; rowSmallDists[r].col = r; rowSmallDists[r].row = i; }
-               //}
                
-               //rowSmallDists[c] = temp;
-               //for (int i = 0; i < dMatrix[c].size(); i++) {
-               //      if (dMatrix[c][i] < rowSmallDists[c].dist) { rowSmallDists[c].dist = dMatrix[c][i]; rowSmallDists[c].col = c; rowSmallDists[c].row = i; }
-               //}
-               //for (int i = dMatrix[c].size()+1; i < dMatrix.size(); i++) {
-               //      if (dMatrix[i][dMatrix[c].size()] < rowSmallDists[c].dist) { rowSmallDists[c].dist = dMatrix[i][dMatrix[c].size()]; rowSmallDists[c].col = c; rowSmallDists[c].row = i; }
-               //}
+               //resize each row
+               for(int i=0;i<nseqs;i++){
+                       for(int j=c+1;j<dMatrix[i].size();j++){
+                               dMatrix[i][j-1]=dMatrix[i][j];
+                       }
+               }                       
+               
+               //resize each col
+               for(int i=c+1;i<nseqs;i++){
+                       for(int j=0;j < dMatrix[i-1].size();j++){
+                               dMatrix[i-1][j]=dMatrix[i][j];
+                       }
+               }       
                
-               //cout << "after update " << endl;
-               //print();
+               nseqs--;
+               dMatrix.pop_back();
+
        }
        catch(exception& e) {
                m->errorOut(e, "ClusterClassic", "update");