fixes while testing 1.33.0

[mothur.git] / corraxescommand.cpp

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index c27eb4b9ac335112f19244c708cee9bb8630feda..72fa03b75edc196aafcaaa4b6ade6f95d1106d48 100644 (file)
--- a/corraxescommand.cpp
+++ b/corraxescommand.cpp
@@ -14,16 +14,16 @@
 //**********************************************************************************************************************
 vector<string> CorrAxesCommand::setParameters(){       
        try {
-               CommandParameter paxes("axes", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(paxes);
-               CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pshared);
-               CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(prelabund);
-               CommandParameter pmetadata("metadata", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none",false,false); parameters.push_back(pmetadata);
-               CommandParameter pnumaxes("numaxes", "Number", "", "3", "", "", "",false,false); parameters.push_back(pnumaxes);
-               CommandParameter plabel("label", "String", "", "", "", "", "",false,false); parameters.push_back(plabel);
-               CommandParameter pgroups("groups", "String", "", "", "", "", "",false,false); parameters.push_back(pgroups);
-               CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "",false,false); parameters.push_back(pmethod);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter paxes("axes", "InputTypes", "", "", "none", "none", "none","corraxes",false,true,true); parameters.push_back(paxes);
+               CommandParameter pshared("shared", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","",false,false,true); parameters.push_back(pshared);
+               CommandParameter prelabund("relabund", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","",false,false,true); parameters.push_back(prelabund);
+               CommandParameter pmetadata("metadata", "InputTypes", "", "", "SharedRelMeta", "SharedRelMeta", "none","",false,false); parameters.push_back(pmetadata);
+               CommandParameter pnumaxes("numaxes", "Number", "", "3", "", "", "","",false,false); parameters.push_back(pnumaxes);
+               CommandParameter plabel("label", "String", "", "", "", "", "","",false,false); parameters.push_back(plabel);
+               CommandParameter pgroups("groups", "String", "", "", "", "", "","",false,false); parameters.push_back(pgroups);
+               CommandParameter pmethod("method", "Multiple", "pearson-spearman-kendall", "pearson", "", "", "","",false,false); parameters.push_back(pmethod);
+               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
+               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
                
                vector<string> myArray;
                for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
@@ -55,13 +55,29 @@ string CorrAxesCommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string CorrAxesCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "corraxes") {  pattern = "[filename],[tag],corr.axes"; }
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "CorrAxesCommand", "getOutputPattern");
+        exit(1);
+    }
+}
+
 //**********************************************************************************************************************
 CorrAxesCommand::CorrAxesCommand(){    
        try {
                abort = true; calledHelp = true; 
                setParameters();
                vector<string> tempOutNames;
-               outputTypes["corr.axes"] = tempOutNames;
+               outputTypes["corraxes"] = tempOutNames;
        }
        catch(exception& e) {
                m->errorOut(e, "CorrAxesCommand", "CorrAxesCommand");
@@ -92,7 +108,7 @@ CorrAxesCommand::CorrAxesCommand(string option)  {
                        }
                        
                        vector<string> tempOutNames;
-                       outputTypes["corr.axes"] = tempOutNames;
+                       outputTypes["corraxes"] = 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);              
@@ -265,9 +281,11 @@ int CorrAxesCommand::execute(){
                /*************************************************************************************/
                // calc the r values                                                                                                                            //
                /************************************************************************************/
-               
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + method + ".corr.axes";
-               outputNames.push_back(outputFileName); outputTypes["corr.axes"].push_back(outputFileName);      
+        map<string, string> variables; 
+        variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(inputFileName));
+        variables["[tag]"] = method;
+               string outputFileName = getOutputFileName("corraxes", variables);
+               outputNames.push_back(outputFileName); outputTypes["corraxes"].push_back(outputFileName);       
                ofstream out;
                m->openOutputFile(outputFileName, out);
                out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
@@ -321,7 +339,7 @@ int CorrAxesCommand::calcPearson(map<string, vector<float> >& axes, ofstream& ou
           //for each otu
           for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) {
                   
-                  if (metadatafile == "") {  out << m->currentBinLabels[i];    }
+                  if (metadatafile == "") {  out << m->currentSharedBinLabels[i];      }
                   else {  out << metadataLabels[i];            }
                                   
                   //find the averages this otu - Y
@@ -456,7 +474,7 @@ int CorrAxesCommand::calcSpearman(map<string, vector<float> >& axes, ofstream& o
                //for each otu
                for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) {
                        
-                       if (metadatafile == "") {  out << m->currentBinLabels[i];       }
+                       if (metadatafile == "") {  out << m->currentSharedBinLabels[i]; }
                        else {  out << metadataLabels[i];               }
                        
                        //find the ranks of this otu - Y
@@ -609,7 +627,7 @@ int CorrAxesCommand::calcKendall(map<string, vector<float> >& axes, ofstream& ou
                //for each otu
                for (int i = 0; i < lookupFloat[0]->getNumBins(); i++) {
                
-                       if (metadatafile == "") {  out << m->currentBinLabels[i];       }
+                       if (metadatafile == "") {  out << m->currentSharedBinLabels[i]; }
                        else {  out << metadataLabels[i];               }
                        
                        //find the ranks of this otu - Y
@@ -816,7 +834,7 @@ int CorrAxesCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thisloo
                                        for (int h = 0; h < diff; h++) { binLabel += "0"; }
                                }
                                binLabel += sbinNumber; 
-                               if (i < m->currentBinLabels.size()) {  binLabel = m->currentBinLabels[i]; }
+                               if (i < m->currentSharedBinLabels.size()) {  binLabel = m->currentSharedBinLabels[i]; }
                                
                                newBinLabels.push_back(binLabel);
                        }
@@ -825,7 +843,7 @@ int CorrAxesCommand::eliminateZeroOTUS(vector<SharedRAbundFloatVector*>& thisloo
                for (int j = 0; j < thislookup.size(); j++) {  delete thislookup[j];  }
                
                thislookup = newLookup;
-               m->currentBinLabels = newBinLabels;
+               m->currentSharedBinLabels = newBinLabels;
                
                return 0;
                
@@ -905,16 +923,11 @@ int CorrAxesCommand::getMetadata(){
                m->openInputFile(metadatafile, in);
                
                string headerLine = m->getline(in); m->gobble(in);
-               istringstream iss (headerLine,istringstream::in);
-               
-               //read the first label, because it refers to the groups
-               string columnLabel;
-               iss >> columnLabel; m->gobble(iss); 
+               vector<string> pieces = m->splitWhiteSpace(headerLine);
                
                //save names of columns you are reading
-               while (!iss.eof()) {
-                       iss >> columnLabel; m->gobble(iss);
-                       metadataLabels.push_back(columnLabel);
+               for (int i = 1; i < pieces.size(); i++) {
+                       metadataLabels.push_back(pieces[i]);
                }
                int count = metadataLabels.size();