created mothurOut class to handle logfiles

[mothur.git] / cluster.cpp

diff --git a/cluster.cpp b/cluster.cpp
index c6a9ca4059b0fafb4dc2529ccf12bf3f134eb69e..bd5986e7d7a2d0bdfe759088c8306e206a4ee9ad 100644 (file)
--- a/cluster.cpp
+++ b/cluster.cpp
@@ -14,8 +14,8 @@
 
 /***********************************************************************/
 
-Cluster::Cluster(RAbundVector* rav, ListVector* lv, SparseMatrix* dm, float c, string m) :
-rabund(rav), list(lv), dMatrix(dm), method(m)
+Cluster::Cluster(RAbundVector* rav, ListVector* lv, SparseMatrix* dm, float c, string f) :
+rabund(rav), list(lv), dMatrix(dm), method(f)
 {
 /*
        cout << "sizeof(MatData): " << sizeof(MatData) << endl;
@@ -59,6 +59,7 @@ rabund(rav), list(lv), dMatrix(dm), method(m)
        
        //save so you can modify as it changes in average neighbor
        cutoff = c;
+       m = MothurOut::getInstance();
 }
 
 /***********************************************************************/
@@ -77,7 +78,7 @@ void Cluster::getRowColCells() {
                nColCells = colCells.size();
        }
        catch(exception& e) {
-               errorOut(e, "Cluster", "getRowColCells");
+               m->errorOut(e, "Cluster", "getRowColCells");
                exit(1);
        }
 
@@ -142,7 +143,7 @@ void Cluster::clusterBins(){
        //      cout << '\t' << rabund->get(smallRow) << '\t' << rabund->get(smallCol) << endl;
        }
        catch(exception& e) {
-               errorOut(e, "Cluster", "clusterBins");
+               m->errorOut(e, "Cluster", "clusterBins");
                exit(1);
        }
 
@@ -163,7 +164,7 @@ void Cluster::clusterNames(){
        //      cout << '\t' << list->get(smallRow) << '\t' << list->get(smallCol) << endl;
     }
        catch(exception& e) {
-               errorOut(e, "Cluster", "clusterNames");
+               m->errorOut(e, "Cluster", "clusterNames");
                exit(1);
        }
 
@@ -213,10 +214,10 @@ 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(); 
+                                       //m->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."); m->mothurOutEndLine(); 
                                        if (cutOFF > rowCells[i]->dist) {  
                                                cutOFF = rowCells[i]->dist;  
-                                               //mothurOut("changing cutoff to " + toString(cutOFF));  mothurOutEndLine(); 
+                                               //m->mothurOut("changing cutoff to " + toString(cutOFF));  m->mothurOutEndLine(); 
                                        }
 
                                }
@@ -233,10 +234,10 @@ 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();
+                                               //m->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."); m->mothurOutEndLine();
                                                if (cutOFF > colCells[i]->dist) {  
                                                        cutOFF = colCells[i]->dist;  
-                                                       //mothurOut("changing cutoff to " + toString(cutOFF));  mothurOutEndLine(); 
+                                                       //m->mothurOut("changing cutoff to " + toString(cutOFF));  m->mothurOutEndLine(); 
                                                }
                                        }
                                }
@@ -245,14 +246,14 @@ void Cluster::update(double& cutOFF){
                }
        }
        catch(exception& e) {
-               errorOut(e, "Cluster", "update");
+               m->errorOut(e, "Cluster", "update");
                exit(1);
        }
 }
 /***********************************************************************/
-void Cluster::setMapWanted(bool m)  {  
+void Cluster::setMapWanted(bool f)  {  
        try {
-               mapWanted = m;
+               mapWanted = f;
                
                //initialize map
                for (int i = 0; i < list->getNumBins(); i++) {
@@ -273,7 +274,7 @@ void Cluster::setMapWanted(bool m)  {
                
        }
        catch(exception& e) {
-               errorOut(e, "Cluster", "setMapWanted");
+               m->errorOut(e, "Cluster", "setMapWanted");
                exit(1);
        }
 }
@@ -295,7 +296,7 @@ try {
                
        }
        catch(exception& e) {
-               errorOut(e, "Cluster", "updateMap");
+               m->errorOut(e, "Cluster", "updateMap");
                exit(1);
        }
 }