readphylip.cpp

   1 /*
   2  *  readphylip.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 4/21/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "readphylip.h"
  11 #include "progress.hpp"
  12
  13 /***********************************************************************/
  14
  15 ReadPhylipMatrix::ReadPhylipMatrix(string distFile){
  16
  17         successOpen = m->openInputFile(distFile, fileHandle);
  18                 sim=false;
  19
  20 }
  21 /***********************************************************************/
  22
  23 ReadPhylipMatrix::ReadPhylipMatrix(string distFile, bool s){
  24
  25         successOpen = m->openInputFile(distFile, fileHandle);
  26         sim=s;
  27 }
  28
  29
  30 /***********************************************************************/
  31
  32 int ReadPhylipMatrix::read(NameAssignment* nameMap){
  33         try {
  34
  35                         float distance;
  36                         int square, nseqs;
  37                         string name;
  38                         vector<string> matrixNames;
  39
  40                                                 string numTest;
  41                                                 fileHandle >> numTest >> name;
  42
  43                                                 if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
  44                                                 else { convert(numTest, nseqs); }
  45
  46                         matrixNames.push_back(name);
  47
  48                         if(nameMap == NULL){
  49                                 list = new ListVector(nseqs);
  50                                 list->set(0, name);
  51                         }
  52                         else{
  53                                 list = new ListVector(nameMap->getListVector());
  54                                 if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
  55                         }
  56
  57                         char d;
  58                         while((d=fileHandle.get()) != EOF){
  59
  60                                 if(isalnum(d)){
  61                                         square = 1;
  62                                         fileHandle.putback(d);
  63                                         for(int i=0;i<nseqs;i++){
  64                                                 fileHandle >> distance;
  65                                         }
  66                                         break;
  67                                 }
  68                                 if(d == '\n'){
  69                                         square = 0;
  70                                         break;
  71                                 }
  72                         }
  73
  74                         Progress* reading;
  75
  76                         if(square == 0){
  77
  78                                 reading = new Progress("Reading matrix:     ", nseqs * (nseqs - 1) / 2);
  79
  80                                 int        index = 0;
  81
  82                                 for(int i=1;i<nseqs;i++){
  83                                                                                 if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
  84
  85                                         fileHandle >> name;
  86                                         matrixNames.push_back(name);
  87
  88
  89                                         //there's A LOT of repeated code throughout this method...
  90                                         if(nameMap == NULL){
  91                                                 list->set(i, name);
  92
  93                                                 for(int j=0;j<i;j++){
  94
  95                                                                                                                 if (m->control_pressed) { delete reading; fileHandle.close(); return 0;  }
  96
  97                                                         fileHandle >> distance;
  98
  99
 100                                                         if (distance == -1) { distance = 1000000; }
 101                                                                                                                 else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
 102
 103                                                         if(distance < cutoff){
 104                                                                 PCell value(i, j, distance);
 105                                                                 D->addCell(value);
 106                                                         }
 107                                                         index++;
 108                                                         reading->update(index);
 109                                                 }
 110
 111                                         }
 112                                         else{
 113                                                 if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
 114
 115                                                 for(int j=0;j<i;j++){
 116                                                         fileHandle >> distance;
 117
 118                                                                                                                 if (m->control_pressed) { delete reading; fileHandle.close(); return 0;  }
 119
 120                                                         if (distance == -1) { distance = 1000000; }
 121                                                                                                                 else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
 122
 123                                                         if(distance < cutoff){
 124                                                                 PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
 125                                                                 D->addCell(value);
 126                                                         }
 127                                                         index++;
 128                                                         reading->update(index);
 129                                                 }
 130                                         }
 131                                 }
 132                         }
 133                         else{
 134
 135                                 reading = new Progress("Reading matrix:     ", nseqs * nseqs);
 136
 137                                 int index = nseqs;
 138
 139                                 for(int i=1;i<nseqs;i++){
 140                                         fileHandle >> name;
 141                                         matrixNames.push_back(name);
 142
 143
 144
 145                                         if(nameMap == NULL){
 146                                                 list->set(i, name);
 147                                                 for(int j=0;j<nseqs;j++){
 148                                                         fileHandle >> distance;
 149
 150                                                                                                                 if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
 151
 152                                                         if (distance == -1) { distance = 1000000; }
 153                                                                                                                 else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
 154
 155                                                         if(distance < cutoff && j < i){
 156                                                                 PCell value(i, j, distance);
 157                                                                 D->addCell(value);
 158                                                         }
 159                                                         index++;
 160                                                         reading->update(index);
 161                                                 }
 162
 163                                         }
 164                                         else{
 165                                                 if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
 166
 167                                                 for(int j=0;j<nseqs;j++){
 168                                                         fileHandle >> distance;
 169
 170                                                                                                                 if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
 171
 172                                                        if (distance == -1) { distance = 1000000; }
 173                                                                                                                 else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
 174
 175                                                                                                                 if(distance < cutoff && j < i){
 176                                                                 PCell value(nameMap->get(matrixNames[i]), nameMap->get(matrixNames[j]), distance);
 177                                                                 D->addCell(value);
 178                                                         }
 179                                                         index++;
 180                                                         reading->update(index);
 181                                                 }
 182                                         }
 183                                 }
 184                         }
 185
 186                                                 if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
 187
 188                         reading->finish();
 189                         delete reading;
 190
 191                         list->setLabel("0");
 192                         fileHandle.close();
 193
 194                      /*   if(nameMap != NULL){
 195                                 for(int i=0;i<matrixNames.size();i++){
 196                                         nameMap->erase(matrixNames[i]);
 197                                 }
 198                                 if(nameMap->size() > 0){
 199                                         //should probably tell them what is missing if we missed something
 200                                         m->mothurOut("missed something\t" + toString(nameMap->size())); m->mothurOutEndLine();
 201                                 }
 202                         } */
 203
 204                                                 return 1;
 205
 206                 }
 207         catch(exception& e) {
 208                m->errorOut(e, "ReadPhylipMatrix", "read");
 209                 exit(1);
 210         }
 211         }
 212
 213 /***********************************************************************/
 214
 215 ReadPhylipMatrix::~ReadPhylipMatrix(){
 216        // delete D;
 217        // delete list;
 218 }