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                 errorOut(e, "Unweighted", "getValues");
 185                 exit(1);
 186         }
 187 }
 188
 189 /**************************************************************************************************/
 190
 191 EstOutput Unweighted::getValues(Tree* t, string groupA, string groupB) {
 192  try {
 193         globaldata = GlobalData::getInstance();
 194
 195                 vector<string> groups;
 196                 double UniqueBL;  //a branch length is unique if it's chidren are from the same group
 197                 double totalBL; //all branch lengths
 198                 double UW;              //Unweighted Value = UniqueBL / totalBL;
 199                 map<string, int>::iterator it;  //iterator to traverse pgroups
 200                 map<string, int> copyIpcount;
 201                 copyTree = new Tree;
 202
 203                 //if the users enters no groups then give them the score of all groups
 204                 int numGroups = globaldata->Groups.size();
 205
 206                 //calculate number of comparsions
 207                 int numComp = 0;
 208                 for (int r=0; r<numGroups; r++) {
 209                         for (int l = r+1; l < numGroups; l++) {
 210                                 numComp++;
 211                         }
 212                 }
 213
 214                 //numComp+1 for AB, AC, BC, ABC
 215                 data.resize(numComp+1,0);
 216
 217                 int count = 0;
 218                 for (int a=0; a<numGroups; a++) {
 219                         for (int l = a+1; l < numGroups; l++) {
 220                                 UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
 221                                 totalBL = 0.00; //all branch lengths
 222                                 UW = 0.00;              //Unweighted Value = UniqueBL / totalBL;
 223                                 copyIpcount.clear();
 224
 225                                 //copy random tree passed in
 226                                 copyTree->getCopy(t);
 227
 228                                 //groups in this combo
 229                                 groups.push_back(globaldata->Groups[a]); groups.push_back(globaldata->Groups[l]);
 230
 231                                 //swap labels in the groups you want to compare
 232                                 copyTree->assembleRandomUnifracTree(groups[0], groups[1]);
 233
 234                                 //copyTree->createNewickFile("random"+groupA+toString(count));
 235
 236                                 for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
 237
 238                                         int lc = copyTree->tree[i].getLChild();  //lc = vector index of left child
 239                                         int rc = copyTree->tree[i].getRChild();  //rc = vector index of right child
 240
 241                                         /**********************************************************************/
 242                                         //This section adds in all lengths that are non leaf
 243
 244                                         copyIpcount = copyTree->tree[i].pcount;
 245                                         for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
 246                                                 if (inUsersGroups(it->first, groups) != true) { copyIpcount.erase(it->first);   }
 247                                         }
 248
 249                                         //if i's children are from the same group then i's pcount size will be 1
 250                                         //if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
 251                                         if (copyIpcount.size() == 0) { }
 252                                         else if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) {  UniqueBL += abs(copyTree->tree[i].getBranchLength());     }
 253
 254                                         //add i's BL to total if it is from the groups the user wants
 255                                         if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
 256                                                 totalBL += abs(copyTree->tree[i].getBranchLength());
 257                                         }
 258
 259                                         /**********************************************************************/
 260                                         //This section adds in all lengths that are leaf
 261
 262                                         //if i's chidren are leaves
 263                                         if (copyTree->tree[rc].getRChild() == -1) {
 264                                                 //if rc is a valid group and rc has a BL
 265                                                 if ((inUsersGroups(copyTree->tree[rc].getGroup(), groups) == true) && (copyTree->tree[rc].getBranchLength() != -1)) {
 266                                                         UniqueBL += abs(copyTree->tree[rc].getBranchLength());
 267                                                         totalBL += abs(copyTree->tree[rc].getBranchLength());
 268                                                 }
 269                                         }
 270
 271                                         if (copyTree->tree[lc].getLChild() == -1) {
 272                                                 //if lc is a valid group and lc has a BL
 273                                                 if ((inUsersGroups(copyTree->tree[lc].getGroup(), groups) == true) && (copyTree->tree[lc].getBranchLength() != -1)) {
 274                                                         UniqueBL += abs(copyTree->tree[lc].getBranchLength());
 275                                                         totalBL += abs(copyTree->tree[lc].getBranchLength());
 276                                                 }
 277                                         }
 278
 279                                         /**********************************************************************/
 280                                 }
 281
 282                                 UW = (UniqueBL / totalBL);
 283
 284                                 if (isnan(UW) || isinf(UW)) { UW = 0; }
 285
 286                                 data[count] = UW;
 287                                 count++;
 288                                 groups.clear();
 289                         }
 290                 }
 291
 292
 293                 if (numComp != 1) {
 294                         if (numGroups == 0) {
 295                                 //get score for all users groups
 296                                 for (int i = 0; i < tmap->namesOfGroups.size(); i++) {
 297                                         if (tmap->namesOfGroups[i] != "xxx") {
 298                                                 groups.push_back(tmap->namesOfGroups[i]);
 299                                         }
 300                                 }
 301                         }else {
 302                                 for (int i = 0; i < globaldata->Groups.size(); i++) {
 303                                         groups.push_back(globaldata->Groups[i]);
 304                                 }
 305                         }
 306
 307                         UniqueBL=0.0000;  //a branch length is unique if it's chidren are from the same group
 308                         totalBL = 0.00; //all branch lengths
 309                         UW = 0.00;              //Unweighted Value = UniqueBL / totalBL;
 310                         copyIpcount.clear();
 311
 312                         //copy random tree passed in
 313                         copyTree->getCopy(t);
 314
 315                         //swap labels in all the groups you want to compare
 316                         copyTree->assembleRandomUnifracTree(groups);
 317
 318                         for(int i=copyTree->getNumLeaves();i<copyTree->getNumNodes();i++){
 319
 320                                 int lc = copyTree->tree[i].getLChild();  //lc = vector index of left child
 321                                 int rc = copyTree->tree[i].getRChild();  //rc = vector index of right child
 322
 323                                 /**********************************************************************/
 324                                 //This section adds in all lengths that are non leaf
 325
 326                                 copyIpcount = copyTree->tree[i].pcount;
 327                                 for (it = copyIpcount.begin(); it != copyIpcount.end(); it++) {
 328                                         if (inUsersGroups(it->first, groups) != true) { copyIpcount.erase(it->first);   }
 329                                 }
 330
 331                                 //if i's children are from the same group then i's pcount size will be 1
 332                                 //if copyIpcount.size() = 0 they are from a branch that is entirely from a group the user doesn't want
 333                                 if (copyIpcount.size() == 0) { }
 334                                 else if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() == 1)) {  abs(UniqueBL += copyTree->tree[i].getBranchLength());     }
 335
 336                                 //add i's BL to total if it is from the groups the user wants
 337                                 if ((copyTree->tree[i].getBranchLength() != -1) && (copyIpcount.size() != 0)) {
 338                                         totalBL += abs(copyTree->tree[i].getBranchLength());
 339                                 }
 340
 341                                 /**********************************************************************/
 342                                 //This section adds in all lengths that are leaf
 343
 344                                 //if i's chidren are leaves
 345                                 if (copyTree->tree[rc].getRChild() == -1) {
 346                                         //if rc is a valid group and rc has a BL
 347                                         if ((inUsersGroups(copyTree->tree[rc].getGroup(), groups) == true) && (copyTree->tree[rc].getBranchLength() != -1)) {
 348                                                 UniqueBL += abs(copyTree->tree[rc].getBranchLength());
 349                                                 totalBL += abs(copyTree->tree[rc].getBranchLength());
 350                                         }
 351                                 }
 352
 353                                 if (copyTree->tree[lc].getLChild() == -1) {
 354                                         //if lc is a valid group and lc has a BL
 355                                         if ((inUsersGroups(copyTree->tree[lc].getGroup(), groups) == true) && (copyTree->tree[lc].getBranchLength() != -1)) {
 356                                                 UniqueBL += abs(copyTree->tree[lc].getBranchLength());
 357                                                 totalBL += abs(copyTree->tree[lc].getBranchLength());
 358                                         }
 359                                 }
 360
 361                                 /**********************************************************************/
 362                         }
 363
 364                         UW = (UniqueBL / totalBL);
 365
 366                         if (isnan(UW) || isinf(UW)) { UW = 0; }
 367
 368                         data[count] = UW;
 369                 }
 370
 371                 delete copyTree;
 372
 373                 return data;
 374
 375         }
 376         catch(exception& e) {
 377                 errorOut(e, "Unweighted", "getValues");
 378                 exit(1);
 379         }
 380 }
 381
 382
 383
 384