moved utilities out of mothur.h and into mothurOut class.

[mothur.git] / pcacommand.cpp

diff --git a/pcacommand.cpp b/pcacommand.cpp
index c9fecd58ca08d9103770dd5f0e3afd7f2274c89d..c982d7563c8f26066924eeab070f5fd16a5b30e5 100644 (file)
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -42,7 +42,7 @@ PCACommand::PCACommand(string option)  {
                                it = parameters.find("phylip");
                                //user has given a template file
                                if(it != parameters.end()){ 
-                                       path = hasPath(it->second);
+                                       path = m->hasPath(it->second);
                                        //if the user has not given a path then, add inputdir. else leave path alone.
                                        if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
                                }
@@ -57,7 +57,7 @@ PCACommand::PCACommand(string option)  {
                        //if the user changes the output directory command factory will send this info to us in the output parameter 
                        outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  
                                outputDir = ""; 
-                               outputDir += hasPath(phylipfile); //if user entered a file with a path then preserve it 
+                               outputDir += m->hasPath(phylipfile); //if user entered a file with a path then preserve it      
                        }
                        
                        //error checking on files       
@@ -97,7 +97,7 @@ int PCACommand::execute(){
                vector<string> names;
                vector<vector<double> > D;
        
-               fbase = outputDir + getRootName(getSimpleName(filename));
+               fbase = outputDir + m->getRootName(m->getSimpleName(filename));
                
                read(filename, names, D);
                
@@ -219,11 +219,11 @@ int PCACommand::read_phylip(istream& f, int square_m, vector<string>& name_list,
 void PCACommand::read(string fname, vector<string>& names, vector<vector<double> >& D){
        try {
                ifstream f;
-               openInputFile(fname, f);
+               m->openInputFile(fname, f);
                        
                //check whether matrix is square
                char d;
-               int m = 1;
+               int q = 1;
                int numSeqs;
                string name;
                
@@ -233,21 +233,21 @@ void PCACommand::read(string fname, vector<string>& names, vector<vector<double>
                        
                        //is d a number meaning its square
                        if(isalnum(d)){ 
-                               m = 1; 
+                               q = 1; 
                                break; 
                        }
                        
                        //is d a line return meaning its lower triangle
                        if(d == '\n'){
-                               m = 2;
+                               q = 2;
                                break;
                        }
                }
                f.close();
                
                //reopen to get back to beginning
-               openInputFile(fname, f);                        
-               read_phylip(f, m, names, D);
+               m->openInputFile(fname, f);                     
+               read_phylip(f, q, names, D);
        }
                catch(exception& e) {
                m->errorOut(e, "PCACommand", "read");