X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=matrixoutputcommand.cpp;h=87929a4d9f8d8c91998e6e9d9760a22c67c60df0;hb=2009a1a1f47e7467094d844e7c07ab8ddf7bb447;hp=73c38f7ca3b06cd5b38b45b070beb2c8fd2f0a8b;hpb=91a27e0483827c06c21c4fe89558923bbfe86573;p=mothur.git

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 73c38f7..87929a4 100644
--- 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++) {