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
  60
  61         printMatrix(cout);
  62                 //sort sequences so they are gathered in groups for processing
  63                 sortGroups(0, numSeqs-1);
  64                 cout << "after sort" << endl;
  65         printMatrix(cout);
  66
  67         }
  68         catch(exception& e) {
  69                 cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function FullMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  70                 exit(1);
  71         }
  72         catch(...) {
  73                 cout << "An unknown error has occurred in the FullMatrix class function FullMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  74                 exit(1);
  75         }
  76 }
  77 /**************************************************************************/
  78 void FullMatrix::readSquareMatrix(ifstream& filehandle) {
  79         try {
  80
  81                 Progress* reading;
  82                 reading = new Progress("Reading matrix:    ", numSeqs * numSeqs);
  83
  84                 int count = 0;
  85                 float distance;
  86                 string group, name;
  87
  88                 for(int i=1;i<numSeqs;i++){
  89                         filehandle >> name;
  90
  91                         group = groupmap->getGroup(name);
  92                         index[i].groupname = group;
  93                         index[i].seqName = name;
  94
  95                         if(group == "not found") {      cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); }
  96
  97                         for(int j=0;j<numSeqs;j++){
  98                                 filehandle >> distance;
  99
 100                                 matrix[i][j] = distance;
 101                                 count++;
 102                                 reading->update(count);
 103                         }
 104                 }
 105                 reading->finish();
 106                 delete reading;
 107         }
 108         catch(exception& e) {
 109                 cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function readSquareMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 110                 exit(1);
 111         }
 112         catch(...) {
 113                 cout << "An unknown error has occurred in the FullMatrix class function readSquareMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 114                 exit(1);
 115         }
 116
 117 }
 118 /**************************************************************************/
 119 void FullMatrix::readLTMatrix(ifstream& filehandle) {
 120         try {
 121                 Progress* reading;
 122                 reading = new Progress("Reading matrix:    ", numSeqs * (numSeqs - 1) / 2);
 123
 124                 int count = 0;
 125                 float distance;
 126                 string group, name;
 127
 128                 for(int i=1;i<numSeqs;i++){
 129                         filehandle >> name;
 130
 131                         group = groupmap->getGroup(name);
 132                         index[i].groupname = group;
 133                         index[i].seqName = name;
 134
 135                         if(group == "not found") {      cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl;  exit(1); }
 136
 137                         for(int j=0;j<i;j++){
 138                                 filehandle >> distance;
 139
 140                                 matrix[i][j] = distance;  matrix[j][i] = distance;
 141                                 count++;
 142                                 reading->update(count);
 143                         }
 144                 }
 145                 reading->finish();
 146                 delete reading;
 147         }
 148         catch(exception& e) {
 149                 cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function readLTMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 150                 exit(1);
 151         }
 152         catch(...) {
 153                 cout << "An unknown error has occurred in the FullMatrix class function readLTMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 154                 exit(1);
 155         }
 156
 157 }
 158
 159 /**************************************************************************/
 160 void FullMatrix::sortGroups(int low, int high){
 161         try{
 162
 163                 int i = low;
 164                 int j = high;
 165                 int y = 0;
 166                 string name;
 167
 168                 /* compare value */
 169                 //what group does this row belong to
 170                 string z = index[(low + high) / 2].groupname;
 171
 172                 /* partition */
 173                 do {
 174                         /* find member above ... */
 175                         while(index[i].groupname < z) i++;
 176
 177                         /* find element below ... */
 178                         while(index[j].groupname > z) j--;
 179
 180                         if(i <= j) {
 181                                 /* swap rows*/
 182                                 for (int h = 0; h < numSeqs; h++) {
 183                                         y = matrix[i][h];
 184                                         matrix[i][h] = matrix[j][h];
 185                                         matrix[j][h] = y;
 186                                 }
 187
 188                                 /* swap columns*/
 189                                 for (int b = 0; b < numSeqs; b++) {
 190                                         y = matrix[b][i];
 191                                         matrix[b][i] = matrix[b][j];
 192                                         matrix[b][j] = y;
 193                                 }
 194
 195                                 //swap map elements
 196                                 z = index[i].groupname;
 197                                 index[i].groupname = index[j].groupname;
 198                                 index[j].groupname = z;
 199
 200                                 name = index[i].seqName;
 201                                 index[i].seqName = index[j].seqName;
 202                                 index[j].seqName = name;
 203
 204
 205                                 i++;
 206                                 j--;
 207 cout << "swapping rows " << i << " " << j << endl;
 208 printMatrix(cout); cout << endl;
 209                         }
 210                 } while(i <= j);
 211
 212                 /* recurse */
 213                 if(low < j)
 214                 sortGroups(low, j);
 215
 216                 if(i < high)
 217                 sortGroups(i, high);
 218
 219
 220         }
 221         catch(exception& e) {
 222                 cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function sortGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 223                 exit(1);
 224         }
 225         catch(...) {
 226                 cout << "An unknown error has occurred in the FullMatrix class function sortGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 227                 exit(1);
 228         }
 229
 230 }
 231
 232 /**************************************************************************/
 233 int FullMatrix::getNumSeqs(){ return numSeqs; }
 234 /**************************************************************************/
 235 //print out matrix
 236 void FullMatrix::printMatrix(ostream& out) {
 237         try{
 238                 for (int i = 0; i < numSeqs; i++) {
 239                         out << "row " << i << " group = " << index[i].groupname << " name = " << index[i].seqName << endl;
 240                         for (int j = 0; j < numSeqs; j++) {
 241                                 out << matrix[i][j] << " ";
 242                         }
 243                         out << endl;
 244                 }
 245         }
 246         catch(exception& e) {
 247                 cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function printMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 248                 exit(1);
 249         }
 250         catch(...) {
 251                 cout << "An unknown error has occurred in the FullMatrix class function printMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 252                 exit(1);
 253         }
 254
 255 }
 256 /**************************************************************************/
 257