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 73c38f7ca3b06cd5b38b45b070beb2c8fd2f0a8b..87929a4d9f8d8c91998e6e9d9760a22c67c60df0 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -65,7 +65,6 @@ MatrixOutputCommand::MatrixOutputCommand(){
                setParameters();
                vector<string> tempOutNames;
                outputTypes["phylip"] = tempOutNames;
-        outputTypes["subsample"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "MatrixOutputCommand", "MatrixOutputCommand");
@@ -100,7 +99,6 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
                        //initialize outputTypes
                        vector<string> tempOutNames;
                        outputTypes["phylip"] = tempOutNames;
-            outputTypes["subsample"] = tempOutNames;
                        
                        //if the user changes the input directory command factory will send this info to us in the output parameter 
                        string inputDir = validParameter.validFile(parameters, "inputdir", false);              
@@ -300,13 +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
@@ -332,8 +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
@@ -434,18 +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;
                        }
@@ -459,10 +459,7 @@ void MatrixOutputCommand::printSims(ostream& out, vector< vector<double> >& simM
 /***********************************************************/
 int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
        try {
-               EstOutput data;
-               vector<SharedRAbundVector*> subset;
                vector< vector< vector<seqDist> > > calcDistsTotals;  //each iter, one for each calc, then each groupCombos dists. this will be used to make .dist files
-
         vector< vector<seqDist>  > calcDists; calcDists.resize(matrixCalculators.size());              
 
         for (int thisIter = 0; thisIter < iters; thisIter++) {