fullmatrix.cpp

   1 /*
   2  *  fullmatrix.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 3/6/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "fullmatrix.h"
  11
  12 /**************************************************************************/
  13 //This constructor reads a distance matrix file and stores the data in the matrix.
  14 FullMatrix::FullMatrix(ifstream& filehandle) {
  15         try{
  16                 globaldata = GlobalData::getInstance();
  17                 groupmap = globaldata->gGroupmap;
  18
  19                 string name, group;
  20                 filehandle >> numSeqs >> name;
  21
  22                 //make the matrix filled with zeros
  23                 matrix.resize(numSeqs);
  24                 for(int i = 0; i < numSeqs; i++) {
  25                         matrix[i].resize(numSeqs, 0);
  26                 }
  27
  28                 group = groupmap->getGroup(name);
  29                 if(group == "not found") {      cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); }
  30                 index[0].groupname = group;
  31                 index[0].seqName = name;
  32
  33                 //determine if matrix is square or lower triangle
  34                 //if it is square read the distances for the first sequence
  35                 char d;
  36                 while((d=filehandle.get()) != EOF){
  37
  38                         //is d a number meaning its square
  39                         if(isalnum(d)){
  40                                 square = true;
  41                                 filehandle.putback(d);
  42                                 for(int i=0;i<numSeqs;i++){
  43                                         filehandle >> matrix[0][i];
  44                                 }
  45                                 break;
  46                         }
  47
  48                         //is d a line return meaning its lower triangle
  49                         if(d == '\n'){
  50                                 square = false;
  51                                 break;
  52                         }
  53                 }
  54
  55                 //read rest of matrix
  56                 if (square == true) { readSquareMatrix(filehandle); }
  57                 else { readLTMatrix(filehandle); }
  58
  59                 //sort sequences so they are gathered in groups for processing
  60                 sortGroups(0, numSeqs-1);
  61
  62         }
  63         catch(exception& e) {
  64                 cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function FullMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  65                 exit(1);
  66         }
  67         catch(...) {
  68                 cout << "An unknown error has occurred in the FullMatrix class function FullMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  69                 exit(1);
  70         }
  71 }
  72 /**************************************************************************/
  73 void FullMatrix::readSquareMatrix(ifstream& filehandle) {
  74         try {
  75
  76                 Progress* reading;
  77                 reading = new Progress("Reading matrix:    ", numSeqs * numSeqs);
  78
  79                 int count = 0;
  80                 float distance;
  81                 string group, name;
  82
  83                 for(int i=1;i<numSeqs;i++){
  84                         filehandle >> name;
  85
  86                         group = groupmap->getGroup(name);
  87                         index[i].groupname = group;
  88                         index[i].seqName = name;
  89
  90                         if(group == "not found") {      cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); }
  91
  92                         for(int j=0;j<numSeqs;j++){
  93                                 filehandle >> distance;
  94
  95                                 matrix[i][j] = distance;
  96                                 count++;
  97                                 reading->update(count);
  98                         }
  99                 }
 100                 reading->finish();
 101                 delete reading;
 102         }
 103         catch(exception& e) {
 104                 cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function readSquareMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 105                 exit(1);
 106         }
 107         catch(...) {
 108                 cout << "An unknown error has occurred in the FullMatrix class function readSquareMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 109                 exit(1);
 110         }
 111
 112 }
 113 /**************************************************************************/
 114 void FullMatrix::readLTMatrix(ifstream& filehandle) {
 115         try {
 116                 Progress* reading;
 117                 reading = new Progress("Reading matrix:    ", numSeqs * (numSeqs - 1) / 2);
 118
 119                 int count = 0;
 120                 float distance;
 121                 string group, name;
 122
 123                 for(int i=1;i<numSeqs;i++){
 124                         filehandle >> name;
 125
 126                         group = groupmap->getGroup(name);
 127                         index[i].groupname = group;
 128                         index[i].seqName = name;
 129
 130                         if(group == "not found") {      cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl;  exit(1); }
 131
 132                         for(int j=0;j<i;j++){
 133                                 filehandle >> distance;
 134
 135                                 matrix[i][j] = distance;  matrix[j][i] = distance;
 136                                 count++;
 137                                 reading->update(count);
 138                         }
 139                 }
 140                 reading->finish();
 141                 delete reading;
 142         }
 143         catch(exception& e) {
 144                 cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function readLTMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 145                 exit(1);
 146         }
 147         catch(...) {
 148                 cout << "An unknown error has occurred in the FullMatrix class function readLTMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 149                 exit(1);
 150         }
 151
 152 }
 153
 154 /**************************************************************************/
 155 void FullMatrix::sortGroups(int low, int high){
 156         try{
 157
 158                 int i = low;
 159                 int j = high;
 160                 int y = 0;
 161                 string name;
 162
 163                 /* compare value */
 164                 //what group does this row belong to
 165                 string z = index[(low + high) / 2].groupname;
 166
 167                 /* partition */
 168                 do {
 169                         /* find member above ... */
 170                         while(index[i].groupname < z) i++;
 171
 172                         /* find element below ... */
 173                         while(index[j].groupname > z) j--;
 174
 175                         if(i <= j) {
 176                                 /* swap rows*/
 177                                 for (int h = 0; h < numSeqs; h++) {
 178                                         y = matrix[i][h];
 179                                         matrix[i][h] = matrix[j][h];
 180                                         matrix[j][h] = y;
 181                                 }
 182
 183                                 /* swap columns*/
 184                                 for (int b = 0; b < numSeqs; b++) {
 185                                         y = matrix[b][i];
 186                                         matrix[b][i] = matrix[b][j];
 187                                         matrix[b][j] = y;
 188                                 }
 189
 190                                 //swap map elements
 191                                 z = index[i].groupname;
 192                                 index[i].groupname = index[j].groupname;
 193                                 index[j].groupname = z;
 194
 195                                 name = index[i].seqName;
 196                                 index[i].seqName = index[j].seqName;
 197                                 index[j].seqName = name;
 198
 199
 200                                 i++;
 201                                 j--;
 202                         }
 203                 } while(i <= j);
 204
 205                 /* recurse */
 206                 if(low < j)
 207                 sortGroups(low, j);
 208
 209                 if(i < high)
 210                 sortGroups(i, high);
 211
 212
 213         }
 214         catch(exception& e) {
 215                 cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function sortGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 216                 exit(1);
 217         }
 218         catch(...) {
 219                 cout << "An unknown error has occurred in the FullMatrix class function sortGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 220                 exit(1);
 221         }
 222
 223 }
 224
 225 /**************************************************************************/
 226 int FullMatrix::getNumSeqs(){ return numSeqs; }
 227 /**************************************************************************/
 228 //print out matrix
 229 void FullMatrix::printMatrix(ostream& out) {
 230         try{
 231                 for (int i = 0; i < numSeqs; i++) {
 232                         out << "row " << i << " group = " << index[i].groupname << " name = " << index[i].seqName << endl;
 233                         for (int j = 0; j < numSeqs; j++) {
 234                                 out << matrix[i][j] << " ";
 235                         }
 236                         out << endl;
 237                 }
 238         }
 239         catch(exception& e) {
 240                 cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function printMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 241                 exit(1);
 242         }
 243         catch(...) {
 244                 cout << "An unknown error has occurred in the FullMatrix class function printMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 245                 exit(1);
 246         }
 247
 248 }
 249 /**************************************************************************/
 250