]> git.donarmstrong.com Git - mothur.git/blobdiff - pcoacommand.cpp
added oligos, pdiffs, bdiffs, ldiffs, sdiffs, tiffs parameters to sffinfo to allow...
[mothur.git] / pcoacommand.cpp
index 6ebf6536e70042941fe4d4ec401f7035949da66c..354826f8c0b27a359b1eb1530e6a0d7a9fbaf32f 100644 (file)
@@ -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) {
@@ -46,6 +46,27 @@ string PCOACommand::getHelpString(){
        }
 }
 
+//**********************************************************************************************************************
+string PCOACommand::getOutputFileNameTag(string type, string inputName=""){    
+       try {
+        string outputFileName = "";
+               map<string, vector<string> >::iterator it;
+        
+        //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 == "pcoa") {  outputFileName =  "pcoa.axes"; }
+            else if (type == "loadings") {  outputFileName =  "pcoa.loadings"; }
+            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, "PCOACommand", "getOutputFileNameTag");
+               exit(1);
+       }
+}
 
 //**********************************************************************************************************************
 PCOACommand::PCOACommand(){    
@@ -69,6 +90,7 @@ 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 +132,7 @@ 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 +179,7 @@ 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 +193,7 @@ 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 +201,13 @@ 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 +250,21 @@ void PCOACommand::output(string fnameRoot, vector<string> name_list, vector<vect
                        }
                }
                
-               ofstream pcaData((fnameRoot+"pcoa.axes").c_str(), ios::trunc);
+               ofstream pcaData;
+        string pcoaDataFile = fnameRoot+getOutputFileNameTag("pcoa");
+        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 = fnameRoot+getOutputFileNameTag("loadings");
+        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++){