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