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] = group;
  31
  32                 //determine if matrix is square or lower triangle
  33                 //if it is square read the distances for the first sequence
  34                 char d;
  35                 while((d=filehandle.get()) != EOF){
  36
  37                         //is d a number meaning its square
  38                         if(isalnum(d)){
  39                                 square = true;
  40                                 filehandle.putback(d);
  41                                 for(int i=0;i<numSeqs;i++){
  42                                         filehandle >> matrix[0][i];
  43                                 }
  44                                 break;
  45                         }
  46
  47                         //is d a line return meaning its lower triangle
  48                         if(d == '\n'){
  49                                 square = false;
  50                                 break;
  51                         }
  52                 }
  53
  54                 //read rest of matrix
  55                 if (square == true) { readSquareMatrix(filehandle); }
  56                 else { readLTMatrix(filehandle); }
  57
  58
  59
  60         printMatrix(cout);
  61                 //sort sequences so they are gathered in groups for processing
  62                 sortGroups();
  63                 cout << "after sort" << endl;
  64         printMatrix(cout);
  65
  66         }
  67         catch(exception& e) {
  68                 cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function FullMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  69                 exit(1);
  70         }
  71         catch(...) {
  72                 cout << "An unknown error has occurred in the FullMatrix class function FullMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  73                 exit(1);
  74         }
  75 }
  76 /**************************************************************************/
  77 void FullMatrix::readSquareMatrix(ifstream& filehandle) {
  78         try {
  79
  80                 Progress* reading;
  81                 reading = new Progress("Reading matrix:    ", numSeqs * numSeqs);
  82
  83                 int count = 0;
  84                 float distance;
  85                 string group, name;
  86
  87                 for(int i=1;i<numSeqs;i++){
  88                         filehandle >> name;
  89
  90                         group = groupmap->getGroup(name);
  91                         index[i] = group;
  92
  93                         if(group == "not found") {      cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl; exit(1); }
  94
  95                         for(int j=0;j<numSeqs;j++){
  96                                 filehandle >> distance;
  97
  98                                 matrix[i][j] = distance;
  99                                 count++;
 100                                 reading->update(count);
 101                         }
 102                 }
 103                 reading->finish();
 104                 delete reading;
 105         }
 106         catch(exception& e) {
 107                 cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function readSquareMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 108                 exit(1);
 109         }
 110         catch(...) {
 111                 cout << "An unknown error has occurred in the FullMatrix class function readSquareMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 112                 exit(1);
 113         }
 114
 115 }
 116 /**************************************************************************/
 117 void FullMatrix::readLTMatrix(ifstream& filehandle) {
 118         try {
 119                 Progress* reading;
 120                 reading = new Progress("Reading matrix:    ", numSeqs * (numSeqs - 1) / 2);
 121
 122                 int count = 0;
 123                 float distance;
 124                 string group, name;
 125
 126                 for(int i=1;i<numSeqs;i++){
 127                         filehandle >> name;
 128
 129                         group = groupmap->getGroup(name);
 130                         index[i] = group;
 131
 132                         if(group == "not found") {      cout << "Error: Sequence '" << name << "' was not found in the group file, please correct." << endl;  exit(1); }
 133
 134                         for(int j=0;j<i;j++){
 135                                 filehandle >> distance;
 136
 137                                 matrix[i][j] = distance;  matrix[j][i] = distance;
 138                                 count++;
 139                                 reading->update(count);
 140                         }
 141                 }
 142                 reading->finish();
 143                 delete reading;
 144         }
 145         catch(exception& e) {
 146                 cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function readLTMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 147                 exit(1);
 148         }
 149         catch(...) {
 150                 cout << "An unknown error has occurred in the FullMatrix class function readLTMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 151                 exit(1);
 152         }
 153
 154 }
 155
 156 /**************************************************************************/
 157 void FullMatrix::sortGroups(){
 158         try{
 159                 //sort each row by group and when you do, swap rows too.
 160                 for (int i = 0; i < numSeqs; i++) {
 161                         quicksort(0, numSeqs-1, i);
 162                 }
 163         }
 164         catch(exception& e) {
 165                 cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function sortGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 166                 exit(1);
 167         }
 168         catch(...) {
 169                 cout << "An unknown error has occurred in the FullMatrix class function sortGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 170                 exit(1);
 171         }
 172
 173 }
 174 /**************************************************************************/
 175 //this is a version of quicksort taken from http://www.c.happycodings.com/Sorting_Searching/code13.html
 176 /* sort everything inbetween `low' <-> `high' */
 177 void FullMatrix::quicksort(int low, int high, int row) {
 178         try {
 179                 int i = low;
 180                 int j = high;
 181                 int y = 0;
 182
 183                 /* compare value */
 184                 //what group does this row belong to
 185                 string z = index[(low + high) / 2];
 186
 187                 /* partition */
 188                 do {
 189                         /* find member above ... */
 190                         while(index[i] < z) i++;
 191
 192                         /* find element below ... */
 193                         while(index[j] > z) j--;
 194
 195                         if(i <= j) {
 196                                 /* swap two elements in row*/
 197                                 y = matrix[row][i];
 198                                 matrix[row][i] = matrix[row][j];
 199                                 matrix[row][j] = y;
 200
 201                                 /* swap two elements in column*/
 202                                 y = matrix[i][row];
 203                                 matrix[i][row] = matrix[j][row];
 204                                 matrix[j][row] = y;
 205
 206                                 //swap map elements
 207                                 z = index[i];
 208                                 index[i] = index[j];
 209                                 index[j] = z;
 210
 211                                 i++;
 212                                 j--;
 213 //cout << "swapping elements " << i << " " << j << endl;
 214 //printMatrix(cout); cout << endl;
 215                         }
 216                 } while(i <= j);
 217
 218                 /* recurse */
 219                 if(low < j)
 220                 quicksort(low, j, row);
 221
 222                 if(i < high)
 223                 quicksort(i, high, row);
 224         }
 225         catch(exception& e) {
 226                 cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function quicksort. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 227                 exit(1);
 228         }
 229         catch(...) {
 230                 cout << "An unknown error has occurred in the FullMatrix class function quicksort. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 231                 exit(1);
 232         }
 233 }
 234
 235 /**************************************************************************/
 236 int FullMatrix::getNumSeqs(){ return numSeqs; }
 237 /**************************************************************************/
 238 //print out matrix
 239 void FullMatrix::printMatrix(ostream& out) {
 240         try{
 241                 for (int i = 0; i < numSeqs; i++) {
 242                         out << "row " << i << " group = " << index[i] << endl;
 243                         for (int j = 0; j < numSeqs; j++) {
 244                                 out << matrix[i][j] << " ";
 245                         }
 246                         out << endl;
 247                 }
 248         }
 249         catch(exception& e) {
 250                 cout << "Standard Error: " << e.what() << " has occurred in the FullMatrix class Function printMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 251                 exit(1);
 252         }
 253         catch(...) {
 254                 cout << "An unknown error has occurred in the FullMatrix class function printMatrix. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 255                 exit(1);
 256         }
 257
 258 }
 259 /**************************************************************************/
 260