changes while testing

[mothur.git] / corraxescommand.cpp

diff --git a/corraxescommand.cpp b/corraxescommand.cpp
index f8083cc01c10a23b4626c6ea2ccd285a15f59c87..853c174ac63012c2ebf8d21800c4886138f8ab16 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);          }
@@ -56,25 +56,21 @@ string CorrAxesCommand::getHelpString(){
        }
 }
 //**********************************************************************************************************************
-string CorrAxesCommand::getOutputFileNameTag(string type, string inputName=""){        
-       try {
-        string outputFileName = "";
-               map<string, vector<string> >::iterator it;
+string CorrAxesCommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
         
-        //is this a type this command creates
-        it = outputTypes.find(type);
-        if (it == outputTypes.end()) {  m->mothurOut("[ERROR]: this command doesn't create a " + type + " output file.\n"); }
-        else {
-            if (type == "corraxes") {  outputFileName =  "corr.axes"; }
-            else { m->mothurOut("[ERROR]: No definition for type " + type + " output file tag.\n"); m->control_pressed = true;  }
-        }
-        return outputFileName;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "CorrAxesCommand", "getOutputFileNameTag");
-               exit(1);
-       }
+        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 {
@@ -285,8 +281,10 @@ int CorrAxesCommand::execute(){
                /*************************************************************************************/
                // calc the r values                                                                                                                            //
                /************************************************************************************/
-               
-               string outputFileName = outputDir + m->getRootName(m->getSimpleName(inputFileName)) + method + "." + getOutputFileNameTag("corraxes");
+        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);
@@ -925,16 +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();