moved mothur's source into a folder to make grabbing just the source easier on github

[mothur.git] / readphylipvector.cpp

diff --git a/readphylipvector.cpp b/readphylipvector.cpp
deleted file mode 100644 (file)
index 85f4777..0000000
--- a/readphylipvector.cpp
+++ /dev/null
@@ -1,190 +0,0 @@
-/*
- *  readphylipvector.cpp
- *  mothur
- *
- *  Created by westcott on 1/11/11.
- *  Copyright 2011 Schloss Lab. All rights reserved.
- *
- */
-
-#include "readphylipvector.h"
-
-/***********************************************************************/
-ReadPhylipVector::ReadPhylipVector(string d) {
-       try {
-               m = MothurOut::getInstance();
-               distFile = d;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ReadPhylipVector", "ReadPhylipVector");
-               exit(1);
-       }
-}
-/***********************************************************************/
-vector<string> ReadPhylipVector::read(vector< vector<double> >& matrix) {
-       try {
-               vector<string> names;
-               
-               ifstream in;
-               m->openInputFile(distFile, in);
-               
-               //check whether matrix is square
-               char d;
-               int square = 1;
-               int numSeqs;
-               string name;
-               
-               string numTest;
-               in >> numTest >> name;
-               
-               if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ". I suspect you entered a column formatted file as a phylip file, quitting."); m->mothurOutEndLine(); exit(1); }
-               else { convert(numTest, numSeqs); }
-               
-               while((d=in.get()) != EOF){
-                       
-                       //is d a number meaning its square
-                       if(isalnum(d)){ 
-                               square = 1; 
-                               break; 
-                       }
-                       
-                       //is d a line return meaning its lower triangle
-                       if(d == '\n'){
-                               square = 2;
-                               break;
-                       }
-               }
-               in.close();
-               
-               
-               //reopen and read now that you know whether you are square
-               ifstream f;
-               m->openInputFile(distFile, f);
-               
-               int rank;
-               f >> rank;
-               
-               names.resize(rank);
-               matrix.resize(rank);
-               if(square == 1){
-                       for(int i=0;i<rank;i++)
-                               matrix[i].resize(rank);
-                       for(int i=0;i<rank;i++) {
-                               f >> names[i];
-                               for(int j=0;j<rank;j++) {
-                                       if (m->control_pressed) { return names; }
-                                       
-                                       f >> matrix[i][j];
-                                       if (matrix[i][j] == -0.0000)
-                                               matrix[i][j] = 0.0000;
-                               }
-                       }
-               }
-               else if(square == 2){
-                       for(int i=0;i<rank;i++){
-                               matrix[i].resize(rank);
-                       }
-                       matrix[0][0] = 0.0000;
-                       f >> names[0];
-                       for(int i=1;i<rank;i++){
-                               f >> names[i];
-                               matrix[i][i]=0.0000;
-                               for(int j=0;j<i;j++){
-                                       if (m->control_pressed) { return names; }
-                                       f >> matrix[i][j];
-                                       if (matrix[i][j] == -0.0000)
-                                               matrix[i][j] = 0.0000;
-                                       matrix[j][i]=matrix[i][j];
-                               }
-                       }
-               }
-               f.close();
-               
-               return names;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ReadPhylipVector", "read");
-               exit(1);
-       }
-}
-/***********************************************************************/
-vector<string> ReadPhylipVector::read(vector<seqDist>& matrix) {
-       try {
-               vector<string> names;
-               
-               ifstream in;
-               m->openInputFile(distFile, in);
-               
-               //check whether matrix is square
-               char d;
-               int square = 1;
-               int numSeqs;
-               string name;
-               
-               in >> numSeqs >> name; 
-               
-               while((d=in.get()) != EOF){
-                       
-                       //is d a number meaning its square
-                       if(isalnum(d)){ 
-                               square = 1; 
-                               break; 
-                       }
-                       
-                       //is d a line return meaning its lower triangle
-                       if(d == '\n'){
-                               square = 2;
-                               break;
-                       }
-               }
-               in.close();
-               
-               
-               //reopen and read now that you know whether you are square
-               ifstream f;
-               m->openInputFile(distFile, f);
-               
-               int rank;
-               float temp;
-               f >> rank;
-               
-               names.resize(rank);
-               if(square == 1){
-                       for(int i=0;i<rank;i++) {
-                               f >> names[i];
-                               for(int j=0;j<rank;j++) {
-                                       if (m->control_pressed) { return names; }
-                                       
-                                       f >> temp;
-                                       
-                                       if (j < i) { //only save lt
-                                               seqDist dist(i, j, temp);
-                                               matrix.push_back(dist);
-                                       }
-                               }
-                       }
-               }
-               else if(square == 2){
-                       f >> names[0];
-                       for(int i=1;i<rank;i++){
-                               f >> names[i];
-                               for(int j=0;j<i;j++){
-                                       if (m->control_pressed) { return names; }
-                                       f >> temp;
-                                       seqDist dist(i, j, temp);
-                                       matrix.push_back(dist);
-                               }
-                       }
-               }
-               f.close();
-               
-               return names;
-       }
-       catch(exception& e) {
-               m->errorOut(e, "ReadPhylipVector", "read");
-               exit(1);
-       }
-}
-/***********************************************************************/
-
-