added warning about merging with something above cutoff to cluster. working on chimeras

[mothur.git] / cluster.cpp

diff --git a/cluster.cpp b/cluster.cpp
index 931b44d70288c120cf151487f88580e07207cc68..4009ed075e63c78e4fb661352c675cff3209e030 100644 (file)
--- a/cluster.cpp
+++ b/cluster.cpp
@@ -15,7 +15,7 @@
 /***********************************************************************/
 
 Cluster::Cluster(RAbundVector* rav, ListVector* lv, SparseMatrix* dm, float c) :
-rabund(rav), list(lv), dMatrix(dm), cutoff(c)
+rabund(rav), list(lv), dMatrix(dm)
 {
 /*
        cout << "sizeof(MatData): " << sizeof(MatData) << endl;
@@ -56,6 +56,9 @@ rabund(rav), list(lv), dMatrix(dm), cutoff(c)
                seqVec[currentCell->column].push_back(currentCell);
        }
        mapWanted = false;  //set to true by mgcluster to speed up overlap merge
+       
+       //save so you can modify as it changes in average neighbor
+       cutoff = c;
 }
 
 /***********************************************************************/
@@ -170,11 +173,12 @@ void Cluster::clusterNames(){
 //This function clusters based on the method of the derived class
 //At the moment only average and complete linkage are covered, because
 //single linkage uses a different approach.
-void Cluster::update(){
+void Cluster::update(double& cutOFF){
        try {
                getRowColCells();       
        
-               vector<int> found(nColCells, 0);
+               vector<int> foundCol(nColCells, 0);
+
                int search;
                bool changed;
 
@@ -187,11 +191,13 @@ void Cluster::update(){
                                } else {
                                        search = rowCells[i]->row;
                                }
-               
+                               
+                               bool merged = false;
                                for (int j=0;j<nColCells;j++) {
-                                       if (!((colCells[j]->row == smallRow) && (colCells[j]->column == smallCol))) {
+                                       if (!((colCells[j]->row == smallRow) && (colCells[j]->column == smallCol))) { //if you are not hte smallest distance
                                                if (colCells[j]->row == search || colCells[j]->column == search) {
-                                                       found[j] = 1;
+                                                       foundCol[j] = 1;
+                                                       merged = true;
                                                        changed = updateDistance(colCells[j], rowCells[i]);
                                                        // If the cell's distance changed and it had the same distance as 
                                                        // the smallest distance, invalidate the mins vector in SparseMatrix
@@ -203,9 +209,16 @@ void Cluster::update(){
                                                        }
                                                        break;
                                                }
-                                       }
+                                       }               
                                }
-                               removeCell(rowCells[i], i , -1);
+                               //if not merged it you need it for warning 
+                               if (!merged) {  
+                                       mothurOut("Warning: trying to merge cell " + toString(rowCells[i]->row+1) + " " + toString(rowCells[i]->column+1) + " distance " + toString(rowCells[i]->dist) + " with value above cutoff. Results may vary from using cutoff at cluster command instead of read.dist."); mothurOutEndLine(); 
+                                       if (cutOFF > rowCells[i]->dist) {  cutOFF = rowCells[i]->dist;  mothurOut("changing cutoff to " + toString(cutOFF));  mothurOutEndLine(); }
+
+                               }
+                               removeCell(rowCells[i], i , -1);  
+                               
                        }
                }
                clusterBins();
@@ -214,12 +227,12 @@ void Cluster::update(){
                // Special handling for singlelinkage case, not sure whether this
                // could be avoided
                for (int i=nColCells-1;i>=0;i--) {
-                       if (found[i] == 0) {
-                               removeCell(colCells[i], -1, i);
-cout << "smallRow = " << smallRow+1 << " smallCol = " << smallCol+1 << endl;
+                       if (foundCol[i] == 0) {
                                if (!((colCells[i]->row == smallRow) && (colCells[i]->column == smallCol))) {
-                                       mothurOut("Warning: merging " + toString(colCells[i]->row+1)  + " " + toString(colCells[i]->column+1) + " distance " + toString(colCells[i]->dist) + " value above cutoff. Results will differ from those if cutoff was used in the read.dist command."); mothurOutEndLine();
+                                       mothurOut("Warning: merging cell " + toString(colCells[i]->row+1) + " " + toString(colCells[i]->column+1) + " distance " + toString(colCells[i]->dist) + " value above cutoff. Results may vary from using cutoff at cluster command instead of read.dist."); mothurOutEndLine();
+                                       if (cutOFF > colCells[i]->dist) {  cutOFF = colCells[i]->dist;  mothurOut("changing cutoff to " + toString(cutOFF));  mothurOutEndLine(); }
                                }
+                               removeCell(colCells[i], -1, i);
                        }
                }
        }