readphylipvector.cpp

   1 /*
   2  *  readphylipvector.cpp
   3  *  mothur
   4  *
   5  *  Created by westcott on 1/11/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "readphylipvector.h"
  11
  12 /***********************************************************************/
  13 ReadPhylipVector::ReadPhylipVector(string d) {
  14         try {
  15                 m = MothurOut::getInstance();
  16                 distFile = d;
  17         }
  18         catch(exception& e) {
  19                 m->errorOut(e, "ReadPhylipVector", "ReadPhylipVector");
  20                 exit(1);
  21         }
  22 }
  23 /***********************************************************************/
  24 vector<string> ReadPhylipVector::read(vector< vector<double> >& matrix) {
  25         try {
  26                 vector<string> names;
  27
  28                 ifstream in;
  29                 m->openInputFile(distFile, in);
  30
  31                 //check whether matrix is square
  32                 char d;
  33                 int square = 1;
  34                 int numSeqs;
  35                 string name;
  36
  37                 string numTest;
  38                 in >> numTest >> name;
  39
  40                 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); }
  41                 else { convert(numTest, numSeqs); }
  42
  43                 while((d=in.get()) != EOF){
  44
  45                         //is d a number meaning its square
  46                         if(isalnum(d)){
  47                                 square = 1;
  48                                 break;
  49                         }
  50
  51                         //is d a line return meaning its lower triangle
  52                         if(d == '\n'){
  53                                 square = 2;
  54                                 break;
  55                         }
  56                 }
  57                 in.close();
  58
  59
  60                 //reopen and read now that you know whether you are square
  61                 ifstream f;
  62                 m->openInputFile(distFile, f);
  63
  64                 int rank;
  65                 f >> rank;
  66
  67                 names.resize(rank);
  68                 matrix.resize(rank);
  69                 if(square == 1){
  70                         for(int i=0;i<rank;i++)
  71                                 matrix[i].resize(rank);
  72                         for(int i=0;i<rank;i++) {
  73                                 f >> names[i];
  74                                 for(int j=0;j<rank;j++) {
  75                                         if (m->control_pressed) { return names; }
  76
  77                                         f >> matrix[i][j];
  78                                         if (matrix[i][j] == -0.0000)
  79                                                 matrix[i][j] = 0.0000;
  80                                 }
  81                         }
  82                 }
  83                 else if(square == 2){
  84                         for(int i=0;i<rank;i++){
  85                                 matrix[i].resize(rank);
  86                         }
  87                         matrix[0][0] = 0.0000;
  88                         f >> names[0];
  89                         for(int i=1;i<rank;i++){
  90                                 f >> names[i];
  91                                 matrix[i][i]=0.0000;
  92                                 for(int j=0;j<i;j++){
  93                                         if (m->control_pressed) { return names; }
  94                                         f >> matrix[i][j];
  95                                         if (matrix[i][j] == -0.0000)
  96                                                 matrix[i][j] = 0.0000;
  97                                         matrix[j][i]=matrix[i][j];
  98                                 }
  99                         }
 100                 }
 101                 f.close();
 102
 103                 return names;
 104         }
 105         catch(exception& e) {
 106                 m->errorOut(e, "ReadPhylipVector", "read");
 107                 exit(1);
 108         }
 109 }
 110 /***********************************************************************/
 111 vector<string> ReadPhylipVector::read(vector<seqDist>& matrix) {
 112         try {
 113                 vector<string> names;
 114
 115                 ifstream in;
 116                 m->openInputFile(distFile, in);
 117
 118                 //check whether matrix is square
 119                 char d;
 120                 int square = 1;
 121                 int numSeqs;
 122                 string name;
 123
 124                 in >> numSeqs >> name;
 125
 126                 while((d=in.get()) != EOF){
 127
 128                         //is d a number meaning its square
 129                         if(isalnum(d)){
 130                                 square = 1;
 131                                 break;
 132                         }
 133
 134                         //is d a line return meaning its lower triangle
 135                         if(d == '\n'){
 136                                 square = 2;
 137                                 break;
 138                         }
 139                 }
 140                 in.close();
 141
 142
 143                 //reopen and read now that you know whether you are square
 144                 ifstream f;
 145                 m->openInputFile(distFile, f);
 146
 147                 int rank;
 148                 float temp;
 149                 f >> rank;
 150
 151                 names.resize(rank);
 152                 if(square == 1){
 153                         for(int i=0;i<rank;i++) {
 154                                 f >> names[i];
 155                                 for(int j=0;j<rank;j++) {
 156                                         if (m->control_pressed) { return names; }
 157
 158                                         f >> temp;
 159
 160                                         if (j < i) { //only save lt
 161                                                 seqDist dist(i, j, temp);
 162                                                 matrix.push_back(dist);
 163                                         }
 164                                 }
 165                         }
 166                 }
 167                 else if(square == 2){
 168                         f >> names[0];
 169                         for(int i=1;i<rank;i++){
 170                                 f >> names[i];
 171                                 for(int j=0;j<i;j++){
 172                                         if (m->control_pressed) { return names; }
 173                                         f >> temp;
 174                                         seqDist dist(i, j, temp);
 175                                         matrix.push_back(dist);
 176                                 }
 177                         }
 178                 }
 179                 f.close();
 180
 181                 return names;
 182         }
 183         catch(exception& e) {
 184                 m->errorOut(e, "ReadPhylipVector", "read");
 185                 exit(1);
 186         }
 187 }
 188 /***********************************************************************/
 189
 190