unweighted.cpp

   1 /*
   2  *  unweighted.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 2/9/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "unweighted.h"
  11
  12 /**************************************************************************************************/
  13
  14 EstOutput Unweighted::getValues(Tree* t) {
  15         try {
  16                 globaldata = GlobalData::getInstance();
  17
  18                 vector<string> groups;
  19                 double UniqueBL;  //a branch length is unique if it's chidren are from the same group
  20                 double totalBL; //all branch lengths
  21                 double UW;              //Unweighted Value = UniqueBL / totalBL;
  22                 map<string, int>::iterator it;  //iterator to traverse pgroups
  23                 map<string, int> copyIpcount;
  24
  25
  26                 //if the users enters no groups then give them the score of all groups
  27                 int numGroups = globaldata->Groups.size();
  28
  29                 //calculate number of comparsions
  30                 int numComp = 0;
  31                 for (int r=0; r<numGroups; r++) {
  32                         for (int l = r+1; l < numGroups; l++) {
  33                                 numComp++;
  34                         }
  35                 }
  36
  37                 //numComp+1 for AB, AC, BC, ABC
  38                 data.resize(numComp+1,0);
  39
  40                 int count = 0;
  41                 for (int a=0; a<numGroups; a++) {
  42                         for (int l = a+1; l < numGroups; l++) {
  43                                 UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
  44                                 totalBL = 0.00; //all branch lengths
  45                                 UW = 0.00;              //Unweighted Value = UniqueBL / totalBL;
  46                                 copyIpcount.clear();
  47
  48                                 //groups in this combo
  49                                 groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
  50
  51                                 for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
  52
  53                                         int lc = t->tree[i].getLChild();  //lc = vector index of left child
  54                                         int rc = t->tree[i].getRChild();  //rc = vector index of right child
  55
  56                                         /**********************************************************************/
  57                                         //This section adds in all lengths that are non leaf
  58
  59                                         copyIpcount = t->tree[i].pcount;
  60                                         for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
  61                                                 if (inUsersGroups(it->first, groups) != true) { copyIpcount.erase(it->first);   }
  62                                         }
  63
  64                                         //if i's children are from the same group then i's pcount size will be 1
  65                                         //if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
  66                                         if (copyIpcount.size() == 0) { }
  67                                         else if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) {  UniqueBL += abs(t->tree[i].getBranchLength());   }
  68
  69                                         //add i's BL to total if it is from the groups the user wants
  70                                         if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
  71                                                 totalBL += abs(t->tree[i].getBranchLength());
  72                                         }
  73
  74                                         /**********************************************************************/
  75                                         //This section adds in all lengths that are leaf
  76
  77                                         //if i's chidren are leaves
  78                                         if (t->tree[rc].getRChild() == -1) {
  79                                                 //if rc is a valid group and rc has a BL
  80                                                 if ((inUsersGroups(t->tree[rc].getGroup(), groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
  81                                                         UniqueBL += abs(t->tree[rc].getBranchLength());
  82                                                         totalBL += abs(t->tree[rc].getBranchLength());
  83                                                 }
  84                                         }
  85
  86                                         if (t->tree[lc].getLChild() == -1) {
  87                                                 //if lc is a valid group and lc has a BL
  88                                                 if ((inUsersGroups(t->tree[lc].getGroup(), groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
  89                                                         UniqueBL += abs(t->tree[lc].getBranchLength());
  90                                                         totalBL += abs(t->tree[lc].getBranchLength());
  91                                                 }
  92                                         }
  93
  94                                         /**********************************************************************/
  95                                 }
  96
  97                                 UW = (UniqueBL / totalBL);
  98
  99                                 if (isnan(UW) || isinf(UW)) { UW = 0; }
 100
 101                                 data[count] = UW;
 102                                 count++;
 103                                 groups.clear();
 104                         }
 105                 }
 106
 107
 108                 if (numComp != 1) {
 109                         if (numGroups == 0) {
 110                                 //get score for all users groups
 111                                 for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 112                                         if (tmap->namesOfGroups[i] != "xxx") {
 113                                                 groups.push_back(tmap->namesOfGroups[i]);
 114                                         }
 115                                 }
 116                         }else {
 117                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 118                                         groups.push_back(globaldata->Groups[i]);
 119                                 }
 120                         }
 121
 122                         UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
 123                         totalBL = 0.00; //all branch lengths
 124                         UW = 0.00;              //Unweighted Value = UniqueBL / totalBL;
 125                         copyIpcount.clear();
 126
 127                         for(int i=t->getNumLeaves();i<t->getNumNodes();i++){
 128
 129                                 int lc = t->tree[i].getLChild();  //lc = vector index of left child
 130                                 int rc = t->tree[i].getRChild();  //rc = vector index of right child
 131
 132                                 /**********************************************************************/
 133                                 //This section adds in all lengths that are non leaf
 134
 135                                 copyIpcount = t->tree[i].pcount;
 136                                 for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
 137                                         if (inUsersGroups(it->first, groups) != true) { copyIpcount.erase(it->first);   }
 138                                 }
 139
 140                                 //if i's children are from the same group then i's pcount size will be 1
 141                                 //if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
 142                                 if (copyIpcount.size() == 0) { }
 143                                 else if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) {  UniqueBL += abs(t->tree[i].getBranchLength());   }
 144
 145                                 //add i's BL to total if it is from the groups the user wants
 146                                 if ((t->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
 147                                         totalBL += abs(t->tree[i].getBranchLength());
 148                                 }
 149
 150                                 /**********************************************************************/
 151                                 //This section adds in all lengths that are leaf
 152
 153                                 //if i's chidren are leaves
 154                                 if (t->tree[rc].getRChild() == -1) {
 155                                         //if rc is a valid group and rc has a BL
 156                                         if ((inUsersGroups(t->tree[rc].getGroup(), groups) == true) && (t->tree[rc].getBranchLength() != -1)) {
 157                                                 UniqueBL += abs(t->tree[rc].getBranchLength());
 158                                                 totalBL += abs(t->tree[rc].getBranchLength());
 159                                         }
 160                                 }
 161
 162                                 if (t->tree[lc].getLChild() == -1) {
 163                                         //if lc is a valid group and lc has a BL
 164                                         if ((inUsersGroups(t->tree[lc].getGroup(), groups) == true) && (t->tree[lc].getBranchLength() != -1)) {
 165                                                 UniqueBL += abs(t->tree[lc].getBranchLength());
 166                                                 totalBL += abs(t->tree[lc].getBranchLength());
 167                                         }
 168                                 }
 169
 170                                 /**********************************************************************/
 171                         }
 172
 173                         UW = (UniqueBL / totalBL);
 174
 175                         if (isnan(UW) || isinf(UW)) { UW = 0; }
 176
 177                         data[count] = UW;
 178                 }
 179
 180                 return data;
 181
 182         }
 183         catch(exception& e) {
 184                 cout << "Standard Error: " << e.what() << " has occurred in the Unweighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 185                 exit(1);
 186         }
 187         catch(...) {
 188                 cout << "An unknown error has occurred in the Unweighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 189                 exit(1);
 190         }
 191
 192 }
 193
 194 /**************************************************************************************************/
 195
 196 EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) {
 197  try {
 198         globaldata = GlobalData::getInstance();
 199
 200                 vector<string> groups;
 201                 double UniqueBL;  //a branch length is unique if it's chidren are from the same group
 202                 double totalBL; //all branch lengths
 203                 double UW;              //Unweighted Value = UniqueBL / totalBL;
 204                 map<string, int>::iterator it;  //iterator to traverse pgroups
 205                 map<string, int> copyIpcount;
 206                 copyTree = new Tree;
 207
 208                 //if the users enters no groups then give them the score of all groups
 209                 int numGroups = globaldata->Groups.size();
 210
 211                 //calculate number of comparsions
 212                 int numComp = 0;
 213                 for (int r=0; r<numGroups; r++) {
 214                         for (int l = r+1; l < numGroups; l++) {
 215                                 numComp++;
 216                         }
 217                 }
 218
 219                 //numComp+1 for AB, AC, BC, ABC
 220                 data.resize(numComp+1,0);
 221
 222                 int count = 0;
 223                 for (int a=0; a<numGroups; a++) {
 224                         for (int l = a+1; l < numGroups; l++) {
 225                                 UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
 226                                 totalBL = 0.00; //all branch lengths
 227                                 UW = 0.00;              //Unweighted Value = UniqueBL / totalBL;
 228                                 copyIpcount.clear();
 229
 230                                 //copy random tree passed in
 231                                 copyTree->getCopy(t);
 232
 233                                 //groups in this combo
 234                                 groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
 235
 236                                 //swap labels in the groups you want to compare
 237                                 copyTree->assembleRandomUnifracTree(groups[0], groups[1]);
 238
 239                                 //copyTree->createNewickFile("random"+groupA+toString(count));
 240
 241                                 for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
 242
 243                                         int lc = copyTree->tree[i].getLChild();  //lc = vector index of left child
 244                                         int rc = copyTree->tree[i].getRChild();  //rc = vector index of right child
 245
 246                                         /**********************************************************************/
 247                                         //This section adds in all lengths that are non leaf
 248
 249                                         copyIpcount = copyTree->tree[i].pcount;
 250                                         for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
 251                                                 if (inUsersGroups(it->first, groups) != true) { copyIpcount.erase(it->first);   }
 252                                         }
 253
 254                                         //if i's children are from the same group then i's pcount size will be 1
 255                                         //if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
 256                                         if (copyIpcount.size() == 0) { }
 257                                         else if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) {  UniqueBL += abs(copyTree->tree[i].getBranchLength());     }
 258
 259                                         //add i's BL to total if it is from the groups the user wants
 260                                         if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
 261                                                 totalBL += abs(copyTree->tree[i].getBranchLength());
 262                                         }
 263
 264                                         /**********************************************************************/
 265                                         //This section adds in all lengths that are leaf
 266
 267                                         //if i's chidren are leaves
 268                                         if (copyTree->tree[rc].getRChild() == -1) {
 269                                                 //if rc is a valid group and rc has a BL
 270                                                 if ((inUsersGroups(copyTree->tree[rc].getGroup(), groups) == true) && (copyTree->tree[rc].getBranchLength() != -1)) {
 271                                                         UniqueBL += abs(copyTree->tree[rc].getBranchLength());
 272                                                         totalBL += abs(copyTree->tree[rc].getBranchLength());
 273                                                 }
 274                                         }
 275
 276                                         if (copyTree->tree[lc].getLChild() == -1) {
 277                                                 //if lc is a valid group and lc has a BL
 278                                                 if ((inUsersGroups(copyTree->tree[lc].getGroup(), groups) == true) && (copyTree->tree[lc].getBranchLength() != -1)) {
 279                                                         UniqueBL += abs(copyTree->tree[lc].getBranchLength());
 280                                                         totalBL += abs(copyTree->tree[lc].getBranchLength());
 281                                                 }
 282                                         }
 283
 284                                         /**********************************************************************/
 285                                 }
 286
 287                                 UW = (UniqueBL / totalBL);
 288
 289                                 if (isnan(UW) || isinf(UW)) { UW = 0; }
 290
 291                                 data[count] = UW;
 292                                 count++;
 293                                 groups.clear();
 294                         }
 295                 }
 296
 297
 298                 if (numComp != 1) {
 299                         if (numGroups == 0) {
 300                                 //get score for all users groups
 301                                 for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 302                                         if (tmap->namesOfGroups[i] != "xxx") {
 303                                                 groups.push_back(tmap->namesOfGroups[i]);
 304                                         }
 305                                 }
 306                         }else {
 307                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 308                                         groups.push_back(globaldata->Groups[i]);
 309                                 }
 310                         }
 311
 312                         UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
 313                         totalBL = 0.00; //all branch lengths
 314                         UW = 0.00;              //Unweighted Value = UniqueBL / totalBL;
 315                         copyIpcount.clear();
 316
 317                         //copy random tree passed in
 318                         copyTree->getCopy(t);
 319
 320                         //swap labels in all the groups you want to compare
 321                         copyTree->assembleRandomUnifracTree(groups);
 322
 323                         for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
 324
 325                                 int lc = copyTree->tree[i].getLChild();  //lc = vector index of left child
 326                                 int rc = copyTree->tree[i].getRChild();  //rc = vector index of right child
 327
 328                                 /**********************************************************************/
 329                                 //This section adds in all lengths that are non leaf
 330
 331                                 copyIpcount = copyTree->tree[i].pcount;
 332                                 for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
 333                                         if (inUsersGroups(it->first, groups) != true) { copyIpcount.erase(it->first);   }
 334                                 }
 335
 336                                 //if i's children are from the same group then i's pcount size will be 1
 337                                 //if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
 338                                 if (copyIpcount.size() == 0) { }
 339                                 else if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) {  abs(UniqueBL += copyTree->tree[i].getBranchLength());     }
 340
 341                                 //add i's BL to total if it is from the groups the user wants
 342                                 if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
 343                                         totalBL += abs(copyTree->tree[i].getBranchLength());
 344                                 }
 345
 346                                 /**********************************************************************/
 347                                 //This section adds in all lengths that are leaf
 348
 349                                 //if i's chidren are leaves
 350                                 if (copyTree->tree[rc].getRChild() == -1) {
 351                                         //if rc is a valid group and rc has a BL
 352                                         if ((inUsersGroups(copyTree->tree[rc].getGroup(), groups) == true) && (copyTree->tree[rc].getBranchLength() != -1)) {
 353                                                 UniqueBL += abs(copyTree->tree[rc].getBranchLength());
 354                                                 totalBL += abs(copyTree->tree[rc].getBranchLength());
 355                                         }
 356                                 }
 357
 358                                 if (copyTree->tree[lc].getLChild() == -1) {
 359                                         //if lc is a valid group and lc has a BL
 360                                         if ((inUsersGroups(copyTree->tree[lc].getGroup(), groups) == true) && (copyTree->tree[lc].getBranchLength() != -1)) {
 361                                                 UniqueBL += abs(copyTree->tree[lc].getBranchLength());
 362                                                 totalBL += abs(copyTree->tree[lc].getBranchLength());
 363                                         }
 364                                 }
 365
 366                                 /**********************************************************************/
 367                         }
 368
 369                         UW = (UniqueBL / totalBL);
 370
 371                         if (isnan(UW) || isinf(UW)) { UW = 0; }
 372
 373                         data[count] = UW;
 374                 }
 375
 376                 delete copyTree;
 377
 378                 return data;
 379
 380         }
 381         catch(exception& e) {
 382                 cout << "Standard Error: " << e.what() << " has occurred in the Unweighted class Function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 383                 exit(1);
 384         }
 385         catch(...) {
 386                 cout << "An unknown error has occurred in the Unweighted class function getValues. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 387                 exit(1);
 388         }
 389 }
 390
 391
 392
 393