changes while testing

[mothur.git] / pcoacommand.cpp

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index 6ebf6536e70042941fe4d4ec401f7035949da66c..2043a128bd94bc755cb7ef10f5a8b8d9bdb5a6be 100644 (file)
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -15,10 +15,10 @@
 //**********************************************************************************************************************
 vector<string> PCOACommand::setParameters(){   
        try {
-               CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none",false,true); parameters.push_back(pphylip);
-               CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "",false,false); parameters.push_back(pmetric);
-               CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
-               CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
+               CommandParameter pphylip("phylip", "InputTypes", "", "", "none", "none", "none","pcoa-loadings",false,true,true); parameters.push_back(pphylip);
+               CommandParameter pmetric("metric", "Boolean", "", "T", "", "", "","",false,false); parameters.push_back(pmetric);
+               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);          }
@@ -37,7 +37,7 @@ string PCOACommand::getHelpString(){
                helpString += "The phylip parameter allows you to enter your distance file.";
                helpString += "The metric parameter allows indicate you if would like the pearson correlation coefficient calculated. Default=True"; 
                helpString += "Example pcoa(phylip=yourDistanceFile).\n";
-               helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n\n";
+               helpString += "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourDistanceFile).\n";
                return helpString;
        }
        catch(exception& e) {
@@ -45,6 +45,22 @@ string PCOACommand::getHelpString(){
                exit(1);
        }
 }
+//**********************************************************************************************************************
+string PCOACommand::getOutputPattern(string type) {
+    try {
+        string pattern = "";
+        
+        if (type == "pcoa") {  pattern = "[filename],pcoa.axes"; } 
+        else if (type == "loadings") {  pattern = "[filename],pcoa.loadings"; } 
+        else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
+        
+        return pattern;
+    }
+    catch(exception& e) {
+        m->errorOut(e, "PCOACommand", "getOutputPattern");
+        exit(1);
+    }
+}
 
 
 //**********************************************************************************************************************
@@ -69,6 +85,7 @@ PCOACommand::PCOACommand(string option)  {
                
                //allow user to run help
                if(option == "help") { help(); abort = true; calledHelp = true; }
+               else if(option == "citation") { citation(); abort = true; calledHelp = true;}
                
                else {
                        vector<string> myArray = setParameters();
@@ -110,7 +127,7 @@ PCOACommand::PCOACommand(string option)  {
                                phylipfile = m->getPhylipFile(); 
                                if (phylipfile != "") { m->mothurOut("Using " + phylipfile + " as input file for the phylip parameter."); m->mothurOutEndLine(); }
                                else {  m->mothurOut("You have no current phylip file and the phylip parameter is required."); m->mothurOutEndLine(); abort = true; }
-                       }       
+                       }else { m->setPhylipFile(phylipfile); } 
                        
                        filename = phylipfile;  
                        
@@ -157,7 +174,7 @@ int PCOACommand::execute(){
                vector<vector<double> > G = D;
                //vector<vector<double> > copy_G;
                                
-               m->mothurOut("\nProcessing...\n\n");
+               m->mothurOut("\nProcessing...\n");
                
                for(int count=0;count<2;count++){
                        linearCalc.recenter(offset, D, G);              if (m->control_pressed) { return 0; }
@@ -171,7 +188,7 @@ int PCOACommand::execute(){
                
                output(fbase, names, G, d);
                
-               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
+               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
                
                if (metric) {   
                        
@@ -179,13 +196,13 @@ int PCOACommand::execute(){
                                                        
                                vector< vector<double> > EuclidDists = linearCalc.calculateEuclidianDistance(G, i); //G is the pcoa file
                                
-                               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
+                               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
                                
                                double corr = linearCalc.calcPearson(EuclidDists, D); //G is the pcoa file, D is the users distance matrix
                                
                                m->mothurOut("Rsq " + toString(i) + " axis: " + toString(corr * corr)); m->mothurOutEndLine();
                                
-                               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        remove(outputNames[i].c_str());  } return 0; }
+                               if (m->control_pressed) { for (int i = 0; i < outputNames.size(); i++) {        m->mothurRemove(outputNames[i]);  } return 0; }
                        }
                }
                
@@ -228,17 +245,23 @@ void PCOACommand::output(string fnameRoot, vector<string> name_list, vector<vect
                        }
                }
                
-               ofstream pcaData((fnameRoot+"pcoa.axes").c_str(), ios::trunc);
+               ofstream pcaData;
+        map<string, string> variables; 
+        variables["[filename]"] = fnameRoot;
+        string pcoaDataFile = getOutputFileName("pcoa",variables);
+        m->openOutputFile(pcoaDataFile, pcaData);
                pcaData.setf(ios::fixed, ios::floatfield);
                pcaData.setf(ios::showpoint);   
-               outputNames.push_back(fnameRoot+"pcoa.axes");
-               outputTypes["pcoa"].push_back(fnameRoot+"pcoa.axes");
+               outputNames.push_back(pcoaDataFile);
+               outputTypes["pcoa"].push_back(pcoaDataFile);
                
-               ofstream pcaLoadings((fnameRoot+"pcoa.loadings").c_str(), ios::trunc);
+               ofstream pcaLoadings;
+        string loadingsFile = getOutputFileName("loadings",variables);
+        m->openOutputFile(loadingsFile, pcaLoadings);
                pcaLoadings.setf(ios::fixed, ios::floatfield);
                pcaLoadings.setf(ios::showpoint);
-               outputNames.push_back(fnameRoot+"pcoa.loadings");
-               outputTypes["loadings"].push_back(fnameRoot+"pcoa.loadings");   
+               outputNames.push_back(loadingsFile);
+               outputTypes["loadings"].push_back(loadingsFile);        
                
                pcaLoadings << "axis\tloading\n";
                for(int i=0;i<rank;i++){