sharedutilities.cpp

   1 /*
   2  *  sharedutilities.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 4/9/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "sharedutilities.h"
  11 #include "sharedrabundvector.h"
  12 #include "sharedordervector.h"
  13
  14 /**************************************************************************************************/
  15
  16 void SharedUtil::getSharedVectors(vector<string> Groups, vector<SharedRAbundVector*>& lookup, SharedOrderVector* order) {
  17         try {
  18
  19                 //delete each sharedrabundvector in lookup
  20                 for (int j = 0; j < lookup.size(); j++) {
  21                         delete lookup[j];
  22                 }
  23
  24                 lookup.clear();
  25
  26                 //create and initialize vector of sharedvectors, one for each group
  27                 for (int i = 0; i < Groups.size(); i++) {
  28                         SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
  29                         temp->setLabel(order->getLabel());
  30                         temp->setGroup(Groups[i]);
  31                         lookup.push_back(temp);
  32                 }
  33
  34                 int numSeqs = order->size();
  35                 //sample all the members
  36                 for(int i=0;i<numSeqs;i++){
  37                         //get first sample
  38                         individual chosen = order->get(i);
  39                         int abundance;
  40
  41                         //set info for sharedvector in chosens group
  42                         for (int j = 0; j < lookup.size(); j++) {
  43                                 if (chosen.group == lookup[j]->getGroup()) {
  44                                          abundance = lookup[j]->getAbundance(chosen.bin);
  45                                          lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
  46                                          break;
  47                                 }
  48                         }
  49                 }
  50         }
  51         catch(exception& e) {
  52                 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  53                 exit(1);
  54         }
  55         catch(...) {
  56                 cout << "An unknown error has occurred in the SharedUtil class function getSharedVectors. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
  57                 exit(1);
  58         }
  59 }
  60 /**************************************************************************************************/
  61
  62 void SharedUtil::getSharedVectorswithReplacement(vector<string> Groups, vector<SharedRAbundVector*>& lookup, SharedOrderVector* order) {
  63         try {
  64
  65                 //delete each sharedrabundvector in lookup
  66                 for (int j = 0; j < lookup.size(); j++) {
  67                         delete lookup[j];
  68                 }
  69
  70                 lookup.clear();
  71
  72                 //create and initialize vector of sharedvectors, one for each group
  73                 for (int i = 0; i < Groups.size(); i++) {
  74                         SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
  75                         temp->setLabel(order->getLabel());
  76                         temp->setGroup(Groups[i]);
  77                         lookup.push_back(temp);
  78                 }
  79
  80                 int numSeqs = order->size();
  81
  82                 //sample all the members
  83                 for(int i=0;i<numSeqs;i++){
  84                         //get random number
  85                         int random = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
  86                         individual chosen = order->get(random);
  87
  88                         int abundance;
  89                         //set info for sharedvector in chosens group
  90                         for (int j = 0; j < lookup.size(); j++) {
  91                                 if (chosen.group == lookup[j]->getGroup()) {
  92                                          abundance = lookup[j]->getAbundance(chosen.bin);
  93                                          lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
  94                                          break;
  95                                 }
  96                         }
  97                 }
  98
  99         }
 100         catch(exception& e) {
 101                 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function getSharedVectorswithReplacement. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 102                 exit(1);
 103         }
 104         catch(...) {
 105                 cout << "An unknown error has occurred in the SharedUtil class function getSharedVectorswithReplacement. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 106                 exit(1);
 107         }
 108 }
 109
 110 /**************************************************************************************************/
 111 //need to have mode because different commands require different number of valid groups
 112 void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups) {
 113         try {
 114 //cout << "groups size" << userGroups.size() << endl;
 115                 if (userGroups.size() != 0) {
 116                         if (userGroups[0] != "all") {
 117                                 //check that groups are valid
 118                                 for (int i = 0; i < userGroups.size(); i++) {
 119                                         if (isValidGroup(userGroups[i], allGroups) != true) {
 120                                                 cout << userGroups[i] << " is not a valid group, and will be disregarded." << endl;
 121                                                 // erase the invalid group from userGroups
 122                                                 userGroups.erase(userGroups.begin()+i);
 123                                                 i--;
 124                                         }
 125                                 }
 126
 127                                 //if the user only entered invalid groups
 128                                 if (userGroups.size() == 0) {
 129                                         cout << "You provided no valid groups. I will run the command using all the groups in your groupfile." << endl;
 130                                         for (int i = 0; i < allGroups.size(); i++) {
 131                                                 userGroups.push_back(allGroups[i]);
 132                                         }
 133                                 }
 134
 135                         }else{//user has enter "all" and wants the default groups
 136                                 userGroups.clear();
 137                                 for (int i = 0; i < allGroups.size(); i++) {
 138                                         userGroups.push_back(allGroups[i]);
 139                                 }
 140                         }
 141                 }else { //the user has not entered groups
 142                         for (int i = 0; i < allGroups.size(); i++) {
 143                                 userGroups.push_back(allGroups[i]);
 144                         }
 145                 }
 146
 147         }
 148         catch(exception& e) {
 149                 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function setGroups. 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 SharedUtil class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 154                 exit(1);
 155         }
 156
 157 }
 158 /**************************************************************************************************/
 159 //need to have mode because different commands require different number of valid groups
 160 void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups, string mode) {
 161         try {
 162                 if (userGroups.size() != 0) {
 163                         if (userGroups[0] != "all") {
 164                                 //check that groups are valid
 165                                 for (int i = 0; i < userGroups.size(); i++) {
 166                                         if (isValidGroup(userGroups[i], allGroups) != true) {
 167                                                 cout << userGroups[i] << " is not a valid group, and will be disregarded." << endl;
 168                                                 // erase the invalid group from userGroups
 169                                                 userGroups.erase(userGroups.begin()+i);
 170                                                 i--;
 171                                         }
 172                                 }
 173
 174                         }else{//user has enter "all" and wants the default groups
 175                                 userGroups.clear();
 176                                 for (int i = 0; i < allGroups.size(); i++) {
 177                                         userGroups.push_back(allGroups[i]);
 178                                 }
 179                         }
 180                 }else { //the user has not entered groups
 181                         for (int i = 0; i < allGroups.size(); i++) {
 182                                 userGroups.push_back(allGroups[i]);
 183                         }
 184                 }
 185
 186                 if ((mode == "collect") || (mode == "rarefact") || (mode == "summary") || (mode == "treegroup")) {
 187                                 //if the user only entered invalid groups
 188                                 if ((userGroups.size() == 0) || (userGroups.size() == 1)) {
 189                                         cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
 190                                         for (int i = 0; i < allGroups.size(); i++) {
 191                                                 userGroups.push_back(allGroups[i]);
 192                                         }
 193                                 }
 194                 }
 195
 196         }
 197         catch(exception& e) {
 198                 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 199                 exit(1);
 200         }
 201         catch(...) {
 202                 cout << "An unknown error has occurred in the SharedUtil class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 203                 exit(1);
 204         }
 205
 206 }
 207
 208
 209 /**************************************************************************************/
 210 //for parsimony and unifrac commands you set pairwise groups as well as an allgroups in calc
 211 void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups, string& label, int& numGroups, string mode){  //globaldata->Groups, your tree or group map, allgroups, mode
 212         try {
 213                 numGroups = 0;
 214                 label = "";
 215                 //if the user has not entered specific groups to analyze then do them all
 216                 if (userGroups.size() != 0) {
 217                         if (userGroups[0] != "all") {
 218                                 //check that groups are valid
 219                                 for (int i = 0; i < userGroups.size(); i++) {
 220                                         if (isValidGroup(userGroups[i], allGroups) != true) {
 221                                                 cout << userGroups[i] << " is not a valid group, and will be disregarded." << endl;
 222                                                 // erase the invalid group from globaldata->Groups
 223                                                 userGroups.erase(userGroups.begin()+i);
 224                                                 i--;
 225                                         }
 226                                 }
 227                         }else { //users wants all groups
 228                                 userGroups.clear();
 229                                 for (int i=0; i < allGroups.size(); i++) {
 230                                         if (allGroups[i] != "xxx") {
 231                                                 userGroups.push_back(allGroups[i]);
 232                                         }
 233                                 }
 234                         }
 235                 }else { //the user has not entered groups
 236                         for (int i=0; i < allGroups.size(); i++) {
 237                                 if (allGroups[i] != "xxx") {
 238                                         if (mode == "weighted") {
 239                                                 userGroups.push_back(allGroups[i]);
 240                                         }else {
 241                                                 numGroups = 1;
 242                                                 label += allGroups[i] + "-";
 243                                         }
 244                                 }
 245                         }
 246                         //rip extra - off allgroups
 247                         label = label.substr(0, label.length()-1);
 248                 }
 249
 250                 if (mode == "weighted") {
 251                         //if the user only entered invalid groups
 252                         if (userGroups.size() == 0) {
 253                                 for (int i=0; i < allGroups.size(); i++) {
 254                                         if (allGroups[i] != "xxx") {
 255                                                 userGroups.push_back(allGroups[i]);
 256                                         }
 257                                 }
 258                                 cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
 259                         }else if (userGroups.size() == 1) {
 260                                 cout << "When using the groups parameter you must have at least 2 valid groups. I will run the command using all the groups in your groupfile." << endl;
 261                                 userGroups.clear();
 262                                 for (int i=0; i < allGroups.size(); i++) {
 263                                         if (allGroups[i] != "xxx") {
 264                                                 userGroups.push_back(allGroups[i]);
 265                                         }
 266                                 }
 267                         }
 268                         numGroups = userGroups.size();
 269
 270                 }else if ((mode == "unweighted") || (mode == "parsimony")) {
 271                                 //if the user only entered invalid groups
 272                                 if ((userGroups.size() == 0) && (numGroups == 0)) {
 273                                         cout << "When using the groups parameter you must have at least 1 valid group. I will run the command using all the groups in your groupfile." << endl;
 274                                         for (int i = 0; i < allGroups.size(); i++) {
 275                                                 if (allGroups[i] != "xxx") {
 276                                                         userGroups.push_back(allGroups[i]);
 277                                                 }
 278                                         }
 279                                 }
 280
 281                                 if (numGroups != 1) { numGroups = userGroups.size(); }
 282                 }
 283         }
 284         catch(exception& e) {
 285                 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 286                 exit(1);
 287         }
 288         catch(...) {
 289                 cout << "An unknown error has occurred in the SharedUtil class function setGroups. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 290                 exit(1);
 291         }
 292 }
 293 /**************************************************************************************/
 294 void SharedUtil::getCombos(vector<string>& groupComb, vector<string> userGroups, int& numComp) { //groupcomb, globaldata->Groups, numcomb
 295         try {
 296                 //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
 297                 numComp = 0;
 298                 for (int i=0; i< userGroups.size(); i++) {
 299                         numComp += i;
 300                         for (int l = i+1; l < userGroups.size(); l++) {
 301                                 //set group comparison labels
 302                                 groupComb.push_back(userGroups[i] + "-" + userGroups[l]);
 303                         }
 304                 }
 305         }
 306         catch(exception& e) {
 307                 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function getCombos. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 308                 exit(1);
 309         }
 310         catch(...) {
 311                 cout << "An unknown error has occurred in the SharedUtil class function getCombos. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 312                 exit(1);
 313         }
 314 }
 315 /**************************************************************************************/
 316 bool SharedUtil::isValidGroup(string groupname, vector<string> groups) {
 317         try {
 318                 for (int i = 0; i < groups.size(); i++) {
 319                         if (groupname == groups[i]) { return true; }
 320                 }
 321
 322                 return false;
 323         }
 324         catch(exception& e) {
 325                 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 326                 exit(1);
 327         }
 328         catch(...) {
 329                 cout << "An unknown error has occurred in the SharedUtil class function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 330                 exit(1);
 331         }
 332 }
 333
 334 /**************************************************************************************/
 335 void SharedUtil::updateGroupIndex(vector<string>& userGroups, map<string, int>& index) {
 336         try {
 337                 index.clear();
 338                 for (int i = 0; i < userGroups.size(); i++) {
 339                         index[userGroups[i]] = i;
 340                 }
 341         }
 342         catch(exception& e) {
 343                 cout << "Standard Error: " << e.what() << " has occurred in the SharedUtil class Function updateGroupIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 344                 exit(1);
 345         }
 346         catch(...) {
 347                 cout << "An unknown error has occurred in the SharedUtil class function updateGroupIndex. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 348                 exit(1);
 349         }
 350 }