fixed bug with dist.shared subsampling. added mode parameter to dist.shared so...

[mothur.git] / pcoacommand.cpp

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index 6ebf6536e70042941fe4d4ec401f7035949da66c..02e165e978dc071ba19808139060866d7e41388c 100644 (file)
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -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) {
@@ -69,6 +69,7 @@ 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 +111,7 @@ 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 +158,7 @@ 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 +172,7 @@ 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 +180,13 @@ 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; }
                        }
                }