clusterclassic.cpp

   1 /*
   2  *  clusterclassic.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 10/29/10.
   6  *  Copyright 2010 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "clusterclassic.h"
  11 #include "progress.hpp"
  12
  13 /***********************************************************************/
  14 ClusterClassic::ClusterClassic(float c, string f, bool s) : method(f), smallDist(1e6), nseqs(0), sim(s) {
  15         try {
  16                 mapWanted = false;  //set to true by mgcluster to speed up overlap merge
  17
  18                 //save so you can modify as it changes in average neighbor
  19                 cutoff = c;
  20                 aboveCutoff = cutoff + 10000.0;
  21                 m = MothurOut::getInstance();
  22         if(method == "furthest")        {   tag = "fn";   }
  23         else if (method == "average")   {   tag = "an";   }
  24         else if (method == "weighted")  {   tag = "wn";   }
  25         else if (method == "nearest")   {   tag = "nn";   }
  26         }
  27         catch(exception& e) {
  28                 m->errorOut(e, "ClusterClassic", "ClusterClassic");
  29                 exit(1);
  30         }
  31 }
  32 /***********************************************************************/
  33 int ClusterClassic::readPhylipFile(string filename, NameAssignment* nameMap) {
  34         try {
  35                 double distance;
  36                 int square;
  37                 string name;
  38                 vector<string> matrixNames;
  39
  40                 ifstream fileHandle;
  41                 m->openInputFile(filename, fileHandle);
  42
  43         string numTest;
  44                 fileHandle >> numTest >> name;
  45
  46         if (!m->isContainingOnlyDigits(numTest)) { m->mothurOut("[ERROR]: expected a number and got " + numTest + ", quitting."); m->mothurOutEndLine(); exit(1); }
  47         else { convert(numTest, nseqs); }
  48
  49
  50                 matrixNames.push_back(name);
  51
  52                 if(nameMap == NULL){
  53                                 list = new ListVector(nseqs);
  54                                 list->set(0, name);
  55                 }
  56                 else{
  57                                 list = new ListVector(nameMap->getListVector());
  58                                 if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
  59                 }
  60
  61                 //initialize distance matrix to cutoff
  62                 dMatrix.resize(nseqs);
  63                 //colDist temp(0, 0, aboveCutoff);
  64                 //rowSmallDists.resize(nseqs, temp);
  65                 for (int i = 1; i < nseqs; i++) {
  66                         dMatrix[i].resize(i, aboveCutoff);
  67                 }
  68
  69
  70                 char d;
  71                 while((d=fileHandle.get()) != EOF){
  72
  73                                 if(isalnum(d)){
  74                                                 square = 1;
  75                                                 fileHandle.putback(d);
  76                                                 for(int i=0;i<nseqs;i++){
  77                                                                 fileHandle >> distance;
  78                                                 }
  79                                                 break;
  80                                 }
  81                                 if(d == '\n'){
  82                                                 square = 0;
  83                                                 break;
  84                                 }
  85                 }
  86
  87                 Progress* reading;
  88
  89                 if(square == 0){
  90
  91                                 reading = new Progress("Reading matrix:     ", nseqs * (nseqs - 1) / 2);
  92
  93                                 int        index = 0;
  94
  95                                 for(int i=1;i<nseqs;i++){
  96                                                 if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
  97
  98                                                 fileHandle >> name;
  99                                                 matrixNames.push_back(name);
 100
 101
 102                                                 //there's A LOT of repeated code throughout this method...
 103                                                 if(nameMap == NULL){
 104                                                                 list->set(i, name);
 105
 106                                                                 for(int j=0;j<i;j++){
 107
 108                                                                                 if (m->control_pressed) { delete reading; fileHandle.close(); return 0;  }
 109
 110                                                                                 fileHandle >> distance;
 111
 112                                                                                 if (distance == -1) { distance = 1000000; }
 113                                                                                 else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
 114
 115                                                                                 //if(distance < cutoff){
 116                                                                                         dMatrix[i][j] = distance;
 117                                                                                         if (distance < smallDist) { smallDist = distance; }
 118                                                                                         //if (rowSmallDists[i].dist > distance) {  rowSmallDists[i].dist = distance; rowSmallDists[i].col = j; rowSmallDists[i].row = i; }
 119                                                                                         //if (rowSmallDists[j].dist > distance) {  rowSmallDists[j].dist = distance; rowSmallDists[j].col = i; rowSmallDists[j].row = j; }
 120                                                                                 //}
 121                                                                                 index++;
 122                                                                                 reading->update(index);
 123                                                                 }
 124
 125                                                 }
 126                                                 else{
 127                                                                 if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
 128
 129                                                                 for(int j=0;j<i;j++){
 130                                                                                 fileHandle >> distance;
 131
 132                                                                                 if (m->control_pressed) { delete reading; fileHandle.close(); return 0;  }
 133
 134                                                                                 if (distance == -1) { distance = 1000000; }
 135                                                                                 else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
 136
 137                                                                                 //if(distance < cutoff){
 138                                                                                         if (distance < smallDist) { smallDist = distance; }
 139
 140                                                                                         int row = nameMap->get(matrixNames[i]);
 141                                                                                         int col = nameMap->get(matrixNames[j]);
 142
 143                                                                                         if (row < col) {  dMatrix[col][row] = distance; }
 144                                                                                         else { dMatrix[row][col] = distance; }
 145
 146                                                                                         //if (rowSmallDists[row].dist > distance) {  rowSmallDists[row].dist = distance; rowSmallDists[row].col = col; rowSmallDists[row].row = row; }
 147                                                                                         //if (rowSmallDists[col].dist > distance) {  rowSmallDists[col].dist = distance; rowSmallDists[col].col = row; rowSmallDists[col].row = col; }
 148                                                                                 //}
 149                                                                                 index++;
 150                                                                                 reading->update(index);
 151                                                                 }
 152                                                 }
 153                                 }
 154                 }
 155                 else{
 156
 157                                 reading = new Progress("Reading matrix:     ", nseqs * nseqs);
 158
 159                                 int index = nseqs;
 160
 161                                 for(int i=1;i<nseqs;i++){
 162                                                 fileHandle >> name;
 163                                                 matrixNames.push_back(name);
 164
 165                                                 if(nameMap == NULL){
 166                                                                 list->set(i, name);
 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(j < i){
 176                                                                                         if (distance < smallDist) { smallDist = distance; }
 177
 178                                                                                         dMatrix[i][j] = distance;
 179                                                                                         //if (rowSmallDists[i].dist > distance) {  rowSmallDists[i].dist = distance; rowSmallDists[i].col = j; rowSmallDists[i].row = i; }
 180                                                                                         //if (rowSmallDists[j].dist > distance) {  rowSmallDists[j].dist = distance; rowSmallDists[j].col = i; rowSmallDists[j].row = j; }
 181                                                                                 }
 182                                                                                 index++;
 183                                                                                 reading->update(index);
 184                                                                 }
 185
 186                                                 }
 187                                                 else{
 188                                                                 if(nameMap->count(name)==0){        m->mothurOut("Error: Sequence '" + name + "' was not found in the names file, please correct"); m->mothurOutEndLine(); }
 189
 190                                                                 for(int j=0;j<nseqs;j++){
 191                                                                                 fileHandle >> distance;
 192
 193                                                                                 if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
 194
 195                                                                            if (distance == -1) { distance = 1000000; }
 196                                                                                 else if (sim) { distance = 1.0 - distance;  }  //user has entered a sim matrix that we need to convert.
 197
 198                                                                                 if(j < i){
 199                                                                                         if (distance < smallDist) { smallDist = distance; }
 200
 201                                                                                         int row = nameMap->get(matrixNames[i]);
 202                                                                                         int col = nameMap->get(matrixNames[j]);
 203
 204                                                                                         if (row < col) {  dMatrix[col][row] = distance; }
 205                                                                                         else { dMatrix[row][col] = distance; }
 206
 207                                                                                         //if (rowSmallDists[row].dist > distance) {  rowSmallDists[row].dist = distance; rowSmallDists[row].col = col; rowSmallDists[row].row = row; }
 208                                                                                         //if (rowSmallDists[col].dist > distance) {  rowSmallDists[col].dist = distance; rowSmallDists[col].col = row; rowSmallDists[col].row = col; }
 209                                                                                 }
 210                                                                                 index++;
 211                                                                                 reading->update(index);
 212                                                                 }
 213                                                 }
 214                                 }
 215                 }
 216
 217                 if (m->control_pressed) {  fileHandle.close();  delete reading; return 0; }
 218
 219                 reading->finish();
 220                 delete reading;
 221
 222                 list->setLabel("0");
 223                 rabund = new RAbundVector(list->getRAbundVector());
 224
 225                 fileHandle.close();
 226
 227                 return 0;
 228         }
 229         catch(exception& e) {
 230                 m->errorOut(e, "ClusterClassic", "readPhylipFile");
 231                 exit(1);
 232         }
 233
 234 }
 235 /***********************************************************************/
 236 //sets smallCol and smallRow, returns distance
 237 double ClusterClassic::getSmallCell() {
 238         try {
 239
 240                 smallDist = aboveCutoff;
 241                 smallRow = 1;
 242                 smallCol = 0;
 243
 244                 vector<colDist> mins;
 245
 246                 for(int i=1;i<nseqs;i++){
 247                         for(int j=0;j<i;j++){
 248                                 if (dMatrix[i][j] < smallDist) {
 249                                         mins.clear();
 250                                         colDist temp(i, j, dMatrix[i][j]);
 251                                         mins.push_back(temp);
 252                                         smallDist = dMatrix[i][j];
 253                                 }else if (dMatrix[i][j] == smallDist) {
 254                                         colDist temp(i, j, dMatrix[i][j]);
 255                                         mins.push_back(temp);
 256
 257                                 }
 258                         }
 259                 }
 260
 261                 if (mins.size() > 0) {
 262                         int zrand = 0;
 263                         if (mins.size() > 1) {
 264                                 //pick random number between 0 and mins.size()
 265                                 zrand = (int)((float)(rand()) / (RAND_MAX / (mins.size()-1) + 1));
 266                         }
 267
 268                         smallRow = mins[zrand].row;
 269                         smallCol = mins[zrand].col;
 270
 271                 }
 272         //cout << smallRow << '\t' << smallCol << '\t' << smallDist << endl;
 273                 //eliminate smallCell
 274                 if (smallRow < smallCol) { dMatrix[smallCol][smallRow] = aboveCutoff; }
 275                 else { dMatrix[smallRow][smallCol] = aboveCutoff; }
 276
 277                 return smallDist;
 278
 279         }
 280         catch(exception& e) {
 281                 m->errorOut(e, "ClusterClassic", "getSmallCell");
 282                 exit(1);
 283         }
 284 }
 285 /***********************************************************************/
 286 void ClusterClassic::clusterBins(){
 287         try {
 288         //      cout << smallCol << '\t' << smallRow << '\t' << smallDist << '\t' << rabund->get(smallRow) << '\t' << rabund->get(smallCol);
 289
 290                 rabund->set(smallRow, rabund->get(smallRow)+rabund->get(smallCol));
 291                 rabund->set(smallCol, 0);
 292                 /*for (int i = smallCol+1; i < rabund->size(); i++) {
 293                         rabund->set((i-1), rabund->get(i));
 294                 }
 295                 rabund->resize((rabund->size()-1));*/
 296                 rabund->setLabel(toString(smallDist));
 297
 298         //      cout << '\t' << rabund->get(smallRow) << '\t' << rabund->get(smallCol) << endl;
 299         }
 300         catch(exception& e) {
 301                 m->errorOut(e, "ClusterClassic", "clusterBins");
 302                 exit(1);
 303         }
 304 }
 305 /***********************************************************************/
 306 void ClusterClassic::clusterNames(){
 307         try {
 308         //      cout << smallCol << '\t' << smallRow << '\t' << smallDist << '\t' << list->get(smallRow) << '\t' << list->get(smallCol);
 309                 if (mapWanted) {  updateMap();  }
 310
 311                 list->set(smallRow, list->get(smallRow)+','+list->get(smallCol));
 312                 list->set(smallCol, "");
 313                 /*for (int i = smallCol+1; i < list->size(); i++) {
 314                         list->set((i-1), list->get(i));
 315                 }
 316                 list->resize((list->size()-1));*/
 317                 list->setLabel(toString(smallDist));
 318
 319         //      cout << '\t' << list->get(smallRow) << '\t' << list->get(smallCol) << endl;
 320     }
 321         catch(exception& e) {
 322                 m->errorOut(e, "ClusterClassic", "clusterNames");
 323                 exit(1);
 324         }
 325 }
 326 /***********************************************************************/
 327 void ClusterClassic::update(double& cutOFF){
 328         try {
 329 //print();
 330                 getSmallCell();
 331
 332                 int r, c;
 333                 r = smallRow; c = smallCol;
 334
 335                 for(int i=0;i<nseqs;i++){
 336                         if(i != r && i != c){
 337                                 double distRow, distCol, newDist;
 338                                 if (i > r) { distRow = dMatrix[i][r]; }
 339                                 else { distRow =  dMatrix[r][i]; }
 340
 341                                 if (i > c) { distCol = dMatrix[i][c]; dMatrix[i][c] = aboveCutoff; } //like removeCell
 342                                 else { distCol =  dMatrix[c][i]; dMatrix[c][i] = aboveCutoff; }
 343
 344                                 if(method == "furthest"){
 345                                         newDist = max(distRow, distCol);
 346                                 }
 347                                 else if (method == "average"){
 348                                         int rowBin = rabund->get(r);
 349                                         int colBin = rabund->get(c);
 350                                         newDist = (colBin * distCol + rowBin * distRow) / (rowBin + colBin);
 351                                 }
 352                                 else if (method == "weighted"){
 353                                         newDist = (distCol + distRow) / 2.0;
 354                                 }
 355                                 else if (method == "nearest"){
 356                                         newDist = min(distRow, distCol);
 357                                 }
 358                                 //cout << "newDist = " << newDist << endl;
 359                                 if (i > r) { dMatrix[i][r] = newDist; }
 360                                 else { dMatrix[r][i] = newDist; }
 361
 362                         }
 363                 }
 364
 365                 clusterBins();
 366                 clusterNames();
 367
 368                 //resize each row
 369                 /*for(int i=0;i<nseqs;i++){
 370                         for(int j=c+1;j<dMatrix[i].size();j++){
 371                                 dMatrix[i][j-1]=dMatrix[i][j];
 372                         }
 373                 }
 374
 375                 //resize each col
 376                 for(int i=c+1;i<nseqs;i++){
 377                         for(int j=0;j < dMatrix[i-1].size();j++){
 378                                 dMatrix[i-1][j]=dMatrix[i][j];
 379                         }
 380                 }
 381
 382                 nseqs--;
 383                 dMatrix.pop_back();*/
 384
 385         }
 386         catch(exception& e) {
 387                 m->errorOut(e, "ClusterClassic", "update");
 388                 exit(1);
 389         }
 390 }
 391 /***********************************************************************/
 392 void ClusterClassic::setMapWanted(bool f)  {
 393         try {
 394                 mapWanted = f;
 395
 396                 //initialize map
 397                 for (int i = 0; i < list->getNumBins(); i++) {
 398
 399                         //parse bin
 400                         string names = list->get(i);
 401                         while (names.find_first_of(',') != -1) {
 402                                 //get name from bin
 403                                 string name = names.substr(0,names.find_first_of(','));
 404                                 //save name and bin number
 405                                 seq2Bin[name] = i;
 406                                 names = names.substr(names.find_first_of(',')+1, names.length());
 407                         }
 408
 409                         //get last name
 410                         seq2Bin[names] = i;
 411                 }
 412
 413         }
 414         catch(exception& e) {
 415                 m->errorOut(e, "ClusterClassic", "setMapWanted");
 416                 exit(1);
 417         }
 418 }
 419 /***********************************************************************/
 420 void ClusterClassic::updateMap() {
 421 try {
 422                 //update location of seqs in smallRow since they move to smallCol now
 423                 string names = list->get(smallRow);
 424                 while (names.find_first_of(',') != -1) {
 425                         //get name from bin
 426                         string name = names.substr(0,names.find_first_of(','));
 427                         //save name and bin number
 428                         seq2Bin[name] = smallCol;
 429                         names = names.substr(names.find_first_of(',')+1, names.length());
 430                 }
 431
 432                 //get last name
 433                 seq2Bin[names] = smallCol;
 434
 435         }
 436         catch(exception& e) {
 437                 m->errorOut(e, "ClusterClassic", "updateMap");
 438                 exit(1);
 439         }
 440 }
 441 /***********************************************************************/
 442 void ClusterClassic::print() {
 443 try {
 444                 //update location of seqs in smallRow since they move to smallCol now
 445                 for (int i = 0; i < dMatrix.size(); i++) {
 446                         m->mothurOut("row = " + toString(i) + "\t");
 447                         for (int j = 0; j < dMatrix[i].size(); j++) {
 448                                 m->mothurOut(toString(dMatrix[i][j]) + "\t");
 449                         }
 450                         m->mothurOutEndLine();
 451                 }
 452         }
 453         catch(exception& e) {
 454                 m->errorOut(e, "ClusterClassic", "updateMap");
 455                 exit(1);
 456         }
 457 }
 458 /***********************************************************************/
 459