you can now use a distance matrix as input for the heatmap.sim command.

[mothur.git] / pcacommand.cpp

diff --git a/pcacommand.cpp b/pcacommand.cpp
index ef89ae50cd43ad16101b4288931881027d03dcd6..09324c9d3eaf3dd5a525a44cf233abe7df6e7285 100644 (file)
--- a/pcacommand.cpp
+++ b/pcacommand.cpp
@@ -21,7 +21,7 @@ PCACommand::PCACommand(string option){
                
                else {
                        //valid paramters for this command
-                       string Array[] =  {"phylip","lt"};
+                       string Array[] =  {"phylip"};
                        vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
                        
                        OptionParser parser(option);
@@ -59,11 +59,11 @@ PCACommand::PCACommand(string option){
                        //      if (namefile == "") {  mothurOut("You need to provide a namefile if you are going to use the column format."); mothurOutEndLine(); abort = true; }
                        //}
                        
-                       string temp = validParameter.validFile(parameters, "lt", false);                                if (temp == "not found") { temp = "false"; }
-                       bool lt = isTrue(temp);
+                       //string temp = validParameter.validFile(parameters, "lt", false);                              if (temp == "not found") { temp = "false"; }
+                       //bool lt = isTrue(temp);
                        
-                       if (lt)         {  matrix = 2;  }
-                       else            {  matrix = 1;  }
+                       //if (lt)               {  matrix = 2;  }
+                       //else          {  matrix = 1;  }
 
 
                }
@@ -108,14 +108,14 @@ int PCACommand::execute(){
                else{
                        fbase += ".";
                }
-               read(filename, matrix, names, D);
+               read(filename, names, D);
        
                double offset = 0.0000;
                vector<double> d;
                vector<double> e;
                vector<vector<double> > G = D;
                vector<vector<double> > copy_G;
-               int rank = D.size();
+               //int rank = D.size();
                
                cout << "\nProcessing...\n";
                
@@ -160,7 +160,7 @@ void PCACommand::get_comment(istream& f, char begin, char end){
 
 /*********************************************************************************************************************************/
 
-void PCACommand::read_mega(istream& f, int square_m, vector<string>& name_list, vector<vector<double> >& d){
+void PCACommand::read_mega(istream& f, vector<string>& name_list, vector<vector<double> >& d){
        try {
                get_comment(f, '#', '\n');
                
@@ -262,23 +262,47 @@ void PCACommand::read_phylip(istream& f, int square_m, vector<string>& name_list
 
 /*********************************************************************************************************************************/
 
-void PCACommand::read(string fname, int m, vector<string>& names, vector<vector<double> >& D){
+void PCACommand::read(string fname, vector<string>& names, vector<vector<double> >& D){
        try {
-               ifstream f(fname.c_str());
-               if(!f) {
-                       cerr << "Error: Could not open " << fname << endl;
-                       exit(1);
-               }
+               ifstream f;
+               openInputFile(fname, f);
+               
                char test = f.peek();
                
                if(test == '#'){
-                       read_mega(f, m, names, D);
+                       read_mega(f, names, D);
                }
                else{
+                       //check whether matrix is square
+                       char d;
+                       int m = 1;
+                       int numSeqs;
+                       string name;
+                       
+                       f >> numSeqs >> name; 
+                       
+                       while((d=f.get()) != EOF){
+                               
+                               //is d a number meaning its square
+                               if(isalnum(d)){ 
+                                       m = 1; 
+                                       break; 
+                               }
+                               
+                               //is d a line return meaning its lower triangle
+                               if(d == '\n'){
+                                       m = 2;
+                                       break;
+                               }
+                       }
+                       f.close();
+                       
+                       //reopen to get back to beginning
+                       openInputFile(fname, f);                        
                        read_phylip(f, m, names, D);
                }
                
-               int rank = D.size();
+               //int rank = D.size();
        }
        catch(exception& e) {
                errorOut(e, "PCACommand", "read");