added warning about merging with something above cutoff to cluster. working on chimeras

[mothur.git] / matrixoutputcommand.cpp

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index fb74875159a0aabe98e8ea79a540802d25ca2f21..87e6489a5e4c79010b8d57df7511117e028cc312 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -36,7 +36,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"label","calc","groups","outputdir","inputdir"};
+                       string Array[] =  {"label","calc","groups","outputdir","inputdir", "output"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -70,6 +70,9 @@ MatrixOutputCommand::MatrixOutputCommand(string option){
                                else { allLines = 1;  }
                        }
                        
+                       output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "lt"; }
+                       if ((output != "lt") && (output != "square")) { mothurOut(output + " is not a valid output form. Options are lt and square. I will use lt."); mothurOutEndLine(); output = "lt"; }
+                       
                        //if the user has not specified any labels use the ones from read.otu
                        if (label == "") {  
                                allLines = globaldata->allLines; 
@@ -136,10 +139,11 @@ MatrixOutputCommand::MatrixOutputCommand(string option){
 void MatrixOutputCommand::help(){
        try {
                mothurOut("The dist.shared command can only be executed after a successful read.otu command.\n");
-               mothurOut("The dist.shared command parameters are groups, calc and label.  No parameters are required.\n");
+               mothurOut("The dist.shared command parameters are groups, calc, output and label.  No parameters are required.\n");
                mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included used.\n");
                mothurOut("The group names are separated by dashes. The label parameter allows you to select what distance levels you would like distance matrices created for, and is also separated by dashes.\n");
                mothurOut("The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n");
+               mothurOut("The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n");
                mothurOut("Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n");
                mothurOut("The default value for groups is all the groups in your groupfile.\n");
                mothurOut("The default value for calc is jclass and thetayc.\n");
@@ -262,17 +266,28 @@ int MatrixOutputCommand::execute(){
 void MatrixOutputCommand::printSims(ostream& out) {
        try {
                
-               //output column headers
+               out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+               
+               //output num seqs
                out << simMatrix.size() << endl;
                
-               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'; 
+               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'; 
+                               }
+                               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'; 
+                               }
+                               out << endl;
                        }
-                       out << endl;
                }
-
        }
        catch(exception& e) {
                errorOut(e, "MatrixOutputCommand", "printSims");
@@ -315,7 +330,7 @@ void MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
                                                }
                                        }
                                        
-                                       exportFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + ".dist";
+                                       exportFileName = outputDir + getRootName(getSimpleName(globaldata->inputFileName)) + matrixCalculators[i]->getName() + "." + thisLookup[0]->getLabel() + "." + output + ".dist";
                                        openOutputFile(exportFileName, out);
                                        printSims(out);
                                        out.close();