forced rarefaction.single to output ending line for all groups. added subsample...

[mothur.git] / matrixoutputcommand.cpp

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 0bfb0098eba2de2600ab4939da8b3e3197b1b4fa..87929a4d9f8d8c91998e6e9d9760a22c67c60df0 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -298,13 +298,6 @@ int MatrixOutputCommand::execute(){
                set<string> userLabels = labels;
                                        
                if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } return 0;}
-               
-               numGroups = lookup.size();
-               lines.resize(processors);
-               for (int i = 0; i < processors; i++) {
-                       lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
-                       lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
-               }       
         
         if (subsample) { 
             if (subsampleSize == -1) { //user has not set size, set size = smallest samples size
@@ -330,8 +323,17 @@ int MatrixOutputCommand::execute(){
                 lookup = temp;
                 m->setGroups(Groups);
             }
+            
+            if (lookup.size() < 2) { m->mothurOut("You have not provided enough valid groups.  I cannot run the command."); m->mothurOutEndLine(); m->control_pressed = true; delete input; return 0; }
         }
-               
+        
+               numGroups = lookup.size();
+        lines.resize(processors);
+               for (int i = 0; i < processors; i++) {
+                       lines[i].start = int (sqrt(float(i)/float(processors)) * numGroups);
+                       lines[i].end = int (sqrt(float(i+1)/float(processors)) * numGroups);
+               }       
+        
                if (m->control_pressed) { delete input; for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  } m->clearGroups(); return 0;  }
                                
                //as long as you are not at the end of the file or done wih the lines you want
@@ -432,18 +434,18 @@ void MatrixOutputCommand::printSims(ostream& out, vector< vector<double> >& simM
                out << simMatrix.size() << endl;
                
                if (output == "lt") {
-                       for (int m = 0; m < simMatrix.size(); m++)      {
-                               out << lookup[m]->getGroup() << '\t';
-                               for (int n = 0; n < m; n++)     {
-                                       out << simMatrix[m][n] << '\t'; 
+                       for (int b = 0; b < simMatrix.size(); b++)      {
+                               out << lookup[b]->getGroup() << '\t';
+                               for (int n = 0; n < b; n++)     {
+                                       out << simMatrix[b][n] << '\t'; 
                                }
                                out << endl;
                        }
                }else{
-                       for (int m = 0; m < simMatrix.size(); m++)      {
-                               out << lookup[m]->getGroup() << '\t';
-                               for (int n = 0; n < simMatrix[m].size(); n++)   {
-                                       out << simMatrix[m][n] << '\t'; 
+                       for (int b = 0; b < simMatrix.size(); m++)      {
+                               out << lookup[b]->getGroup() << '\t';
+                               for (int n = 0; n < simMatrix[b].size(); n++)   {
+                                       out << simMatrix[b][n] << '\t'; 
                                }
                                out << endl;
                        }