added subsample, tiers and processors to tree.shared command. removed bootstrap.share...

[mothur.git] / matrixoutputcommand.cpp

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 73c38f7ca3b06cd5b38b45b070beb2c8fd2f0a8b..0bfb0098eba2de2600ab4939da8b3e3197b1b4fa 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);              
@@ -459,10 +457,7 @@ 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++) {