fixes while testing 1.33.0

[mothur.git] / matrixoutputcommand.cpp

diff --git a/matrixoutputcommand.cpp b/matrixoutputcommand.cpp
index 95b881190d085135539601c17836ce7d123592da..2e6943f0eb7aed1c0b881b5dd5a5d079cdd4fb87 100644 (file)
--- a/matrixoutputcommand.cpp
+++ b/matrixoutputcommand.cpp
@@ -17,8 +17,8 @@ vector<string> MatrixOutputCommand::setParameters(){
                CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
         CommandParameter psubsample("subsample", "String", "", "", "", "", "","",false,false); parameters.push_back(psubsample);
                CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
-               CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc);
-               CommandParameter poutput("output", "Multiple", "lt-square", "lt", "", "", "","",false,false); parameters.push_back(poutput);
+               CommandParameter pcalc("calc", "Multiple", "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan-kstest-sharednseqs-ochiai-anderberg-kulczynski-kulczynskicody-lennon-morisitahorn-braycurtis-whittaker-odum-canberra-structeuclidean-structchord-hellinger-manhattan-structpearson-soergel-spearman-structkulczynski-speciesprofile-hamming-structchi2-gower-memchi2-memchord-memeuclidean-mempearson-jsd-rjsd", "jclass-thetayc", "", "", "","",true,false,true); parameters.push_back(pcalc);
+               CommandParameter poutput("output", "Multiple", "lt-square-column", "lt", "", "", "","",false,false); parameters.push_back(poutput);
         CommandParameter pmode("mode", "Multiple", "average-median", "average", "", "", "","",false,false); parameters.push_back(pmode);
                CommandParameter pprocessors("processors", "Number", "", "1", "", "", "","",false,false,true); parameters.push_back(pprocessors);
         CommandParameter piters("iters", "Number", "", "1000", "", "", "","",false,false); parameters.push_back(piters);
@@ -45,7 +45,7 @@ string MatrixOutputCommand::getHelpString(){
         helpString += "The iters parameter allows you to choose the number of times you would like to run the subsample.\n";
         helpString += "The subsample parameter allows you to enter the size pergroup of the sample or you can set subsample=T and mothur will use the size of your smallest group.\n";
                helpString += "The dist.shared command should be in the following format: dist.shared(groups=yourGroups, calc=yourCalcs, label=yourLabels).\n";
-               helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, and square. The default is lt.\n";
+               helpString += "The output parameter allows you to specify format of your distance matrix. Options are lt, column and square. The default is lt.\n";
         helpString += "The mode parameter allows you to specify if you want the average or the median values reported when subsampling. Options are average, and median. The default is average.\n";
                helpString += "Example dist.shared(groups=A-B-C, calc=jabund-sorabund).\n";
                helpString += "The default value for groups is all the groups in your groupfile.\n";
@@ -156,7 +156,7 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
                        }
                        
                        output = validParameter.validFile(parameters, "output", false);         if(output == "not found"){      output = "lt"; }
-                       if ((output != "lt") && (output != "square")) { m->mothurOut(output + " is not a valid output form. Options are lt and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
+                       if ((output != "lt") && (output != "square") && (output != "column")) { m->mothurOut(output + " is not a valid output form. Options are lt, column and square. I will use lt."); m->mothurOutEndLine(); output = "lt"; }
             
             mode = validParameter.validFile(parameters, "mode", false);                if(mode == "not found"){        mode = "average"; }
                        if ((mode != "average") && (mode != "median")) { m->mothurOut(mode + " is not a valid mode. Options are average and medina. I will use average."); m->mothurOutEndLine(); output = "average"; }
@@ -281,6 +281,10 @@ MatrixOutputCommand::MatrixOutputCommand(string option)  {
                                                        matrixCalculators.push_back(new MemEuclidean());
                                                }else if (Estimators[i] == "mempearson") { 
                                                        matrixCalculators.push_back(new MemPearson());
+                        }else if (Estimators[i] == "jsd") {
+                                matrixCalculators.push_back(new JSD());
+                        }else if (Estimators[i] == "rjsd") {
+                            matrixCalculators.push_back(new RJSD());
                                                }
                                        }
                                }
@@ -449,11 +453,9 @@ void MatrixOutputCommand::printSims(ostream& out, vector< vector<double> >& simM
        try {
                
                out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
-               
-               //output num seqs
-               out << simMatrix.size() << endl;
-               
+                               
                if (output == "lt") {
+            out << simMatrix.size() << endl;
                        for (int b = 0; b < simMatrix.size(); b++)      {
                                out << lookup[b]->getGroup() << '\t';
                                for (int n = 0; n < b; n++)     {
@@ -461,7 +463,14 @@ void MatrixOutputCommand::printSims(ostream& out, vector< vector<double> >& simM
                                }
                                out << endl;
                        }
+        }else if (output == "column") {
+            for (int b = 0; b < simMatrix.size(); b++) {
+                for (int n = 0; n < b; n++)    {
+                    out << lookup[b]->getGroup() << '\t' << lookup[n]->getGroup() << '\t' << simMatrix[b][n] << endl;
+                }
+            }
                }else{
+            out << simMatrix.size() << endl;
                        for (int b = 0; b < simMatrix.size(); b++)      {
                                out << lookup[b]->getGroup() << '\t';
                                for (int n = 0; n < simMatrix[b].size(); n++)   {
@@ -647,7 +656,7 @@ int MatrixOutputCommand::process(vector<SharedRAbundVector*> thisLookup){
             }
             
             if (subsample && (thisIter != 0)) {  
-                if((thisIter) % 100 == 0){     m->mothurOut(toString(thisIter)); m->mothurOutEndLine();                }
+                if((thisIter) % 100 == 0){     m->mothurOutJustToScreen(toString(thisIter)+"\n");              }
                 calcDistsTotals.push_back(calcDists);
                 for (int i = 0; i < calcDists.size(); i++) {
                     for (int j = 0; j < calcDists[i].size(); j++) {
@@ -786,7 +795,7 @@ int MatrixOutputCommand::driver(vector<SharedRAbundVector*> thisLookup, int star
                                                vector<double> tempdata = matrixCalculators[i]->getValues(subset); //saves the calculator outputs
                                                
                                                if (m->control_pressed) { return 1; }
-                                               
+        
                                                seqDist temp(l, k, tempdata[0]);
                                                calcDists[i].push_back(temp);
                                        }