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                 m->errorOut(e, "SharedUtil", "getSharedVectors");
  53                 exit(1);
  54         }
  55 }
  56 /**************************************************************************************************/
  57
  58 void SharedUtil::getSharedVectorswithReplacement(vector<string> Groups, vector<SharedRAbundVector*>& lookup, SharedOrderVector* order) {
  59         try {
  60
  61                 //delete each sharedrabundvector in lookup
  62                 for (int j = 0; j < lookup.size(); j++) {
  63                         delete lookup[j];
  64                 }
  65                 lookup.clear();
  66
  67                 //create and initialize vector of sharedvectors, one for each group
  68                 for (int i = 0; i < Groups.size(); i++) {
  69                         SharedRAbundVector* temp = new SharedRAbundVector(order->getNumBins());
  70                         temp->setLabel(order->getLabel());
  71                         temp->setGroup(Groups[i]);
  72                         lookup.push_back(temp);
  73                 }
  74
  75                 int numSeqs = order->size();
  76
  77                 //sample all the members
  78                 for(int i=0;i<numSeqs;i++){
  79                         //get random number
  80                         int random = int((float)(i+1) * (float)(rand()) / ((float)RAND_MAX+1.0));
  81                         individual chosen = order->get(random);
  82
  83                         int abundance;
  84                         //set info for sharedvector in chosens group
  85                         for (int j = 0; j < lookup.size(); j++) {
  86                                 if (chosen.group == lookup[j]->getGroup()) {
  87                                          abundance = lookup[j]->getAbundance(chosen.bin);
  88                                          lookup[j]->set(chosen.bin, (abundance + 1), chosen.group);
  89                                          break;
  90                                 }
  91                         }
  92                 }
  93
  94         }
  95         catch(exception& e) {
  96                 m->errorOut(e, "SharedUtil", "getSharedVectorswithReplacement");
  97                 exit(1);
  98         }
  99 }
 100
 101 /**************************************************************************************************/
 102 //need to have mode because different commands require different number of valid groups
 103 void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups) {
 104         try {
 105                 if (userGroups.size() != 0) {
 106                         if (userGroups[0] != "all") {
 107                                 //check that groups are valid
 108                                 for (int i = 0; i < userGroups.size(); i++) {
 109                                         if (isValidGroup(userGroups[i], allGroups) != true) {
 110                                                 m->mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
 111                                                 // erase the invalid group from userGroups
 112                                                 userGroups.erase(userGroups.begin()+i);
 113                                                 i--;
 114                                         }
 115                                 }
 116
 117                                 //if the user only entered invalid groups
 118                                 if (userGroups.size() == 0) {
 119                                         m->mothurOut("You provided no valid groups. I will run the command using all the groups in your groupfile."); m->mothurOutEndLine();
 120                                         for (int i = 0; i < allGroups.size(); i++) {
 121                                                 userGroups.push_back(allGroups[i]);
 122                                         }
 123                                 }
 124
 125                         }else{//user has enter "all" and wants the default groups
 126                                 userGroups.clear();
 127                                 for (int i = 0; i < allGroups.size(); i++) {
 128                                         userGroups.push_back(allGroups[i]);
 129                                 }
 130                         }
 131                 }else { //the user has not entered groups
 132                         for (int i = 0; i < allGroups.size(); i++) {
 133                                 userGroups.push_back(allGroups[i]);
 134                         }
 135                 }
 136
 137         }
 138         catch(exception& e) {
 139                 m->errorOut(e, "SharedUtil", "setGroups");
 140                 exit(1);
 141         }
 142 }
 143 /**************************************************************************************************/
 144 //need to have mode because different commands require different number of valid groups
 145 void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups, string mode) {
 146         try {
 147                 if (userGroups.size() != 0) {
 148                         if (userGroups[0] != "all") {
 149                                 //check that groups are valid
 150                                 for (int i = 0; i < userGroups.size(); i++) {
 151                                         if (isValidGroup(userGroups[i], allGroups) != true) {
 152                                                 m->mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
 153                                                 // erase the invalid group from userGroups
 154                                                 userGroups.erase(userGroups.begin()+i);
 155                                                 i--;
 156                                         }
 157                                 }
 158
 159                         }else{//user has enter "all" and wants the default groups
 160                                 userGroups.clear();
 161                                 for (int i = 0; i < allGroups.size(); i++) {
 162                                         userGroups.push_back(allGroups[i]);
 163                                 }
 164                         }
 165                 }else { //the user has not entered groups
 166                         for (int i = 0; i < allGroups.size(); i++) {
 167                                 userGroups.push_back(allGroups[i]);
 168                         }
 169                 }
 170
 171                 if ((mode == "collect") || (mode == "rarefact") || (mode == "summary") || (mode == "treegroup")) {
 172                                 //if the user only entered invalid groups
 173                                 if ((userGroups.size() == 0) || (userGroups.size() == 1)) {
 174                                         m->mothurOut("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."); m->mothurOutEndLine();
 175                                         for (int i = 0; i < allGroups.size(); i++) {
 176                                                 userGroups.push_back(allGroups[i]);
 177                                         }
 178                                 }
 179                 }
 180
 181         }
 182         catch(exception& e) {
 183                 m->errorOut(e, "SharedUtil", "setGroups");
 184                 exit(1);
 185         }
 186 }
 187
 188
 189 /**************************************************************************************/
 190 //for parsimony and unifrac commands you set pairwise groups as well as an allgroups in calc
 191 void SharedUtil::setGroups(vector<string>& userGroups, vector<string>& allGroups, string& label, int& numGroups, string mode){  //globaldata->Groups, your tree or group map, allgroups, mode
 192         try {
 193                 numGroups = 0;
 194                 label = "";
 195
 196                 //if the user has not entered specific groups to analyze then do them all
 197                 if (userGroups.size() != 0) {
 198                         if (userGroups[0] != "all") {
 199                                 //check that groups are valid
 200                                 for (int i = 0; i < userGroups.size(); i++) {
 201                                         if (isValidGroup(userGroups[i], allGroups) != true) {
 202                                                 m->mothurOut(userGroups[i] + " is not a valid group, and will be disregarded."); m->mothurOutEndLine();
 203                                                 // erase the invalid group from globaldata->Groups
 204                                                 userGroups.erase(userGroups.begin()+i);
 205                                                 i--;
 206                                         }
 207                                 }
 208                         }else { //users wants all groups
 209                                 userGroups.clear();
 210                                 for (int i=0; i < allGroups.size(); i++) {
 211                                         if (allGroups[i] != "xxx") {
 212                                                 userGroups.push_back(allGroups[i]);
 213                                         }
 214                                 }
 215                         }
 216                 }else { //the user has not entered groups
 217                         for (int i=0; i < allGroups.size(); i++) {
 218                                 if (allGroups[i] != "xxx") {
 219                                         if (mode == "weighted") {
 220                                                 userGroups.push_back(allGroups[i]);
 221                                         }else {
 222                                                 numGroups = 1;
 223                                                 label += allGroups[i] + "-";
 224                                         }
 225                                 }
 226                         }
 227                         //rip extra - off allgroups
 228                         label = label.substr(0, label.length()-1);
 229                         if ((mode != "weighted") && (allGroups.size() > 10)) {  label = "merged";  }
 230                 }
 231
 232                 if (mode == "weighted") {
 233                         //if the user only entered invalid groups
 234                         if (userGroups.size() == 0) {
 235                                 for (int i=0; i < allGroups.size(); i++) {
 236                                         if (allGroups[i] != "xxx") {
 237                                                 userGroups.push_back(allGroups[i]);
 238                                         }
 239                                 }
 240                                 m->mothurOut("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."); m->mothurOutEndLine();
 241                         }else if (userGroups.size() == 1) {
 242                                 m->mothurOut("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."); m->mothurOutEndLine();
 243                                 userGroups.clear();
 244                                 for (int i=0; i < allGroups.size(); i++) {
 245                                         if (allGroups[i] != "xxx") {
 246                                                 userGroups.push_back(allGroups[i]);
 247                                         }
 248                                 }
 249                         }
 250                         numGroups = userGroups.size();
 251
 252                 }else if ((mode == "unweighted") || (mode == "parsimony")) {
 253                                 //if the user only entered invalid groups
 254                                 if ((userGroups.size() == 0) && (numGroups == 0)) {
 255                                         m->mothurOut("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."); m->mothurOutEndLine();
 256                                         for (int i = 0; i < allGroups.size(); i++) {
 257                                                 if (allGroups[i] != "xxx") {
 258                                                         userGroups.push_back(allGroups[i]);
 259                                                 }
 260                                         }
 261                                 }
 262
 263                                 if (numGroups != 1) { numGroups = userGroups.size(); }
 264                 }
 265         }
 266         catch(exception& e) {
 267                 m->errorOut(e, "SharedUtil", "setGroups");
 268                 exit(1);
 269         }
 270 }
 271 /**************************************************************************************/
 272 void SharedUtil::getCombos(vector<string>& groupComb, vector<string> userGroups, int& numComp) { //groupcomb, globaldata->Groups, numcomb
 273         try {
 274                 //calculate number of comparisons i.e. with groups A,B,C = AB, AC, BC = 3;
 275                 numComp = 0;
 276                 for (int i=0; i< userGroups.size(); i++) {
 277                         numComp += i;
 278                         for (int l = i+1; l < userGroups.size(); l++) {
 279                                 //set group comparison labels
 280                                 groupComb.push_back(userGroups[i] + "-" + userGroups[l]);
 281                         }
 282                 }
 283         }
 284         catch(exception& e) {
 285                 m->errorOut(e, "SharedUtil", "getCombos");
 286                 exit(1);
 287         }
 288 }
 289 /**************************************************************************************/
 290 bool SharedUtil::isValidGroup(string groupname, vector<string> groups) {
 291         try {
 292                 for (int i = 0; i < groups.size(); i++) {
 293                         if (groupname == groups[i]) { return true; }
 294                 }
 295
 296                 return false;
 297         }
 298         catch(exception& e) {
 299                 m->errorOut(e, "SharedUtil", "isValidGroup");
 300                 exit(1);
 301         }
 302 }
 303
 304 /**************************************************************************************/
 305 void SharedUtil::updateGroupIndex(vector<string>& userGroups, map<string, int>& index) {
 306         try {
 307                 index.clear();
 308                 for (int i = 0; i < userGroups.size(); i++) {
 309                         index[userGroups[i]] = i;
 310                 }
 311         }
 312         catch(exception& e) {
 313                 m->errorOut(e, "SharedUtil", "updateGroupIndex");
 314                 exit(1);
 315         }
 316 }