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 4009ed075e63c78e4fb661352c675cff3209e030..e360624dbfc599f94901fe12c1518fe8c11e877d 100644 (file)
--- a/cluster.cpp
+++ b/cluster.cpp
@@ -14,8 +14,8 @@
 
 /***********************************************************************/
 
-Cluster::Cluster(RAbundVector* rav, ListVector* lv, SparseMatrix* dm, float c) :
-rabund(rav), list(lv), dMatrix(dm)
+Cluster::Cluster(RAbundVector* rav, ListVector* lv, SparseMatrix* dm, float c, string m) :
+rabund(rav), list(lv), dMatrix(dm), method(m)
 {
 /*
        cout << "sizeof(MatData): " << sizeof(MatData) << endl;
@@ -212,7 +212,7 @@ void Cluster::update(double& cutOFF){
                                        }               
                                }
                                //if not merged it you need it for warning 
-                               if (!merged) {  
+                               if ((!merged) && (method == "average")) {  
                                        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(); }
 
@@ -228,9 +228,11 @@ void Cluster::update(double& cutOFF){
                // could be avoided
                for (int i=nColCells-1;i>=0;i--) {
                        if (foundCol[i] == 0) {
-                               if (!((colCells[i]->row == smallRow) && (colCells[i]->column == smallCol))) {
-                                       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(); }
+                               if (method == "average") {
+                                       if (!((colCells[i]->row == smallRow) && (colCells[i]->column == smallCol))) {
+                                               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);
                        }