added parse.list command

[mothur.git] / cluster.cpp

diff --git a/cluster.cpp b/cluster.cpp
index e360624dbfc599f94901fe12c1518fe8c11e877d..c6a9ca4059b0fafb4dc2529ccf12bf3f134eb69e 100644 (file)
--- a/cluster.cpp
+++ b/cluster.cpp
@@ -213,8 +213,11 @@ void Cluster::update(double& cutOFF){
                                }
                                //if not merged it you need it for warning 
                                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(); }
+                                       //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);  
@@ -230,8 +233,11 @@ void Cluster::update(double& cutOFF){
                        if (foundCol[i] == 0) {
                                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(); }
+                                               //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);