fixed trim.seqs bug with qtrim parameter and added num=1 special case to database...

[mothur.git] / pcoacommand.cpp

diff --git a/pcoacommand.cpp b/pcoacommand.cpp
index d1d919c93d5f43086658a86cf79f11a09de8ae9f..6777b5a56cb1182654c66bf6d065f9f973a10525 100644 (file)
--- a/pcoacommand.cpp
+++ b/pcoacommand.cpp
@@ -9,6 +9,7 @@
  */
 
 #include "pcoacommand.h"
+#include "readphylipvector.h"
 
 //**********************************************************************************************************************
 vector<string> PCOACommand::getValidParameters(){      
@@ -160,7 +161,8 @@ int PCOACommand::execute(){
        
                fbase = outputDir + m->getRootName(m->getSimpleName(filename));
                
-               read(filename, names, D);
+               ReadPhylipVector readFile(filename);
+               names = readFile.read(D);
                
                if (m->control_pressed) { return 0; }
        
@@ -227,103 +229,6 @@ void PCOACommand::get_comment(istream& f, char begin, char end){
                exit(1);
        }
 }      
-
-/*********************************************************************************************************************************/
-
-int PCOACommand::read_phylip(istream& f, int square_m, vector<string>& name_list, vector<vector<double> >& d){
-       try {
-               //     int count1=0;
-               //     int count2=0;
-               
-               int rank;
-               f >> rank;
-               
-               name_list.resize(rank);
-               d.resize(rank);
-               if(square_m == 1){
-                       for(int i=0;i<rank;i++)
-                               d[i].resize(rank);
-                       for(int i=0;i<rank;i++) {
-                               f >> name_list[i];
-                               //                      cout << i << "\t" << name_list[i] << endl;
-                               for(int j=0;j<rank;j++) {
-                                       if (m->control_pressed) { return 0; }
-                                       
-                                       f >> d[i][j];
-                                       if (d[i][j] == -0.0000)
-                                               d[i][j] = 0.0000;
-                               }
-                       }
-               }
-               else if(square_m == 2){
-                       for(int i=0;i<rank;i++){
-                               d[i].resize(rank);
-                       }
-                       d[0][0] = 0.0000;
-                       f >> name_list[0];
-                       for(int i=1;i<rank;i++){
-                               f >> name_list[i];
-                               d[i][i]=0.0000;
-                               for(int j=0;j<i;j++){
-                                       if (m->control_pressed) { return 0; }
-                                       f >> d[i][j];
-                                       if (d[i][j] == -0.0000)
-                                               d[i][j] = 0.0000;
-                                       d[j][i]=d[i][j];
-                               }
-                       }
-               }
-               
-               return 0;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "PCOACommand", "read_phylip");
-               exit(1);
-       }
-
-}
-
-/*********************************************************************************************************************************/
-
-void PCOACommand::read(string fname, vector<string>& names, vector<vector<double> >& D){
-       try {
-               ifstream f;
-               m->openInputFile(fname, f);
-                       
-               //check whether matrix is square
-               char d;
-               int q = 1;
-               int numSeqs;
-               string name;
-               
-               f >> numSeqs >> name; 
-               
-               while((d=f.get()) != EOF){
-                       
-                       //is d a number meaning its square
-                       if(isalnum(d)){ 
-                               q = 1; 
-                               break; 
-                       }
-                       
-                       //is d a line return meaning its lower triangle
-                       if(d == '\n'){
-                               q = 2;
-                               break;
-                       }
-               }
-               f.close();
-               
-               //reopen to get back to beginning
-               m->openInputFile(fname, f);                     
-               read_phylip(f, q, names, D);
-       }
-               catch(exception& e) {
-               m->errorOut(e, "PCOACommand", "read");
-               exit(1);
-       }
-}
-
 /*********************************************************************************************************************************/
 
 void PCOACommand::recenter(double offset, vector<vector<double> > D, vector<vector<double> >& G){