collectsharedcommand.cpp

   1 /*
   2  *  collectsharedcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/2/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "collectsharedcommand.h"
  11 #include "sharedsobscollectsummary.h"
  12 #include "sharedchao1.h"
  13 #include "sharedace.h"
  14 #include "sharedjabund.h"
  15 #include "sharedsorabund.h"
  16 #include "sharedjclass.h"
  17 #include "sharedsorclass.h"
  18 #include "sharedjest.h"
  19 #include "sharedsorest.h"
  20 #include "sharedthetayc.h"
  21 #include "sharedthetan.h"
  22 #include "sharedkstest.h"
  23 #include "whittaker.h"
  24 #include "sharednseqs.h"
  25 #include "sharedochiai.h"
  26 #include "sharedanderbergs.h"
  27 #include "sharedkulczynski.h"
  28 #include "sharedkulczynskicody.h"
  29 #include "sharedlennon.h"
  30 #include "sharedmorisitahorn.h"
  31 #include "sharedbraycurtis.h"
  32 #include "sharedjackknife.h"
  33 #include "whittaker.h"
  34
  35
  36
  37 //**********************************************************************************************************************
  38
  39 CollectSharedCommand::CollectSharedCommand(string option){
  40         try {
  41                 globaldata = GlobalData::getInstance();
  42                 abort = false;
  43                 allLines = 1;
  44                 labels.clear();
  45                 Estimators.clear();
  46                 Groups.clear();
  47
  48                 //allow user to run help
  49                 if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
  50
  51                 else {
  52                         //valid paramters for this command
  53                         string Array[] =  {"freq","label","calc","groups"};
  54                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  55
  56                         OptionParser parser(option);
  57                         map<string,string> parameters=parser.getParameters();
  58
  59                         ValidParameters validParameter;
  60
  61                         //check to make sure all parameters are valid for command
  62                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  63                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  64                         }
  65
  66                         //make sure the user has already run the read.otu command
  67                         if (globaldata->getSharedFile() == "") {
  68                                 if (globaldata->getListFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); mothurOutEndLine(); abort = true; }
  69                                 else if (globaldata->getGroupFile() == "") { mothurOut("You must read a list and a group, or a shared before you can use the collect.shared command."); mothurOutEndLine(); abort = true; }
  70                         }
  71
  72
  73                         //check for optional parameter and set defaults
  74                         // ...at some point should added some additional type checking..
  75                         label = validParameter.validFile(parameters, "label", false);
  76                         if (label == "not found") { label = ""; }
  77                         else {
  78                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  79                                 else { allLines = 1;  }
  80                         }
  81
  82                         //if the user has not specified any labels use the ones from read.otu
  83                         if(label == "") {
  84                                 allLines = globaldata->allLines;
  85                                 labels = globaldata->labels;
  86                         }
  87
  88                         calc = validParameter.validFile(parameters, "calc", false);
  89                         if (calc == "not found") { calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan";  }
  90                         else {
  91                                  if (calc == "default")  {  calc = "sharedsobs-sharedchao-sharedace-jabund-sorabund-jclass-sorclass-jest-sorest-thetayc-thetan";  }
  92                         }
  93                         splitAtDash(calc, Estimators);
  94
  95                         groups = validParameter.validFile(parameters, "groups", false);
  96                         if (groups == "not found") { groups = ""; }
  97                         else {
  98                                 splitAtDash(groups, Groups);
  99                         }
 100                         globaldata->Groups = Groups;
 101
 102                         string temp;
 103                         temp = validParameter.validFile(parameters, "freq", false);                     if (temp == "not found") { temp = "100"; }
 104                         convert(temp, freq);
 105
 106                         if (abort == false) {
 107
 108                                 string fileNameRoot = getRootName(globaldata->inputFileName);
 109                                 format = globaldata->getFormat();
 110                                 int i;
 111
 112                                 validCalculator = new ValidCalculators();
 113                                 util = new SharedUtil();
 114
 115                                 for (i=0; i<Estimators.size(); i++) {
 116                                         if (validCalculator->isValidCalculator("shared", Estimators[i]) == true) {
 117                                                 if (Estimators[i] == "sharedchao") {
 118                                                         cDisplays.push_back(new CollectDisplay(new SharedChao1(), new SharedOneColumnFile(fileNameRoot+"shared.chao")));
 119                                                 }else if (Estimators[i] == "sharedsobs") {
 120                                                         cDisplays.push_back(new CollectDisplay(new SharedSobsCS(), new SharedOneColumnFile(fileNameRoot+"shared.sobs")));
 121                                                 }else if (Estimators[i] == "sharedace") {
 122                                                         cDisplays.push_back(new CollectDisplay(new SharedAce(), new SharedOneColumnFile(fileNameRoot+"shared.ace")));
 123                                                 }else if (Estimators[i] == "jabund") {
 124                                                         cDisplays.push_back(new CollectDisplay(new JAbund(), new SharedOneColumnFile(fileNameRoot+"jabund")));
 125                                                 }else if (Estimators[i] == "sorabund") {
 126                                                         cDisplays.push_back(new CollectDisplay(new SorAbund(), new SharedOneColumnFile(fileNameRoot+"sorabund")));
 127                                                 }else if (Estimators[i] == "jclass") {
 128                                                         cDisplays.push_back(new CollectDisplay(new Jclass(), new SharedOneColumnFile(fileNameRoot+"jclass")));
 129                                                 }else if (Estimators[i] == "sorclass") {
 130                                                         cDisplays.push_back(new CollectDisplay(new SorClass(), new SharedOneColumnFile(fileNameRoot+"sorclass")));
 131                                                 }else if (Estimators[i] == "jest") {
 132                                                         cDisplays.push_back(new CollectDisplay(new Jest(), new SharedOneColumnFile(fileNameRoot+"jest")));
 133                                                 }else if (Estimators[i] == "sorest") {
 134                                                         cDisplays.push_back(new CollectDisplay(new SorEst(), new SharedOneColumnFile(fileNameRoot+"sorest")));
 135                                                 }else if (Estimators[i] == "thetayc") {
 136                                                         cDisplays.push_back(new CollectDisplay(new ThetaYC(), new SharedOneColumnFile(fileNameRoot+"thetayc")));
 137                                                 }else if (Estimators[i] == "thetan") {
 138                                                         cDisplays.push_back(new CollectDisplay(new ThetaN(), new SharedOneColumnFile(fileNameRoot+"thetan")));
 139                                                 }else if (Estimators[i] == "kstest") {
 140                                                         cDisplays.push_back(new CollectDisplay(new KSTest(), new SharedOneColumnFile(fileNameRoot+"kstest")));
 141                                                 }else if (Estimators[i] == "whittaker") {
 142                                                         cDisplays.push_back(new CollectDisplay(new Whittaker(), new SharedOneColumnFile(fileNameRoot+"whittaker")));
 143                                                 }else if (Estimators[i] == "sharednseqs") {
 144                                                         cDisplays.push_back(new CollectDisplay(new SharedNSeqs(), new SharedOneColumnFile(fileNameRoot+"shared.nseqs")));
 145                                                 }else if (Estimators[i] == "ochiai") {
 146                                                         cDisplays.push_back(new CollectDisplay(new Ochiai(), new SharedOneColumnFile(fileNameRoot+"ochiai")));
 147                                                 }else if (Estimators[i] == "anderberg") {
 148                                                         cDisplays.push_back(new CollectDisplay(new Anderberg(), new SharedOneColumnFile(fileNameRoot+"anderberg")));
 149                                                 }else if (Estimators[i] == "skulczynski") {
 150                                                         cDisplays.push_back(new CollectDisplay(new Kulczynski(), new SharedOneColumnFile(fileNameRoot+"kulczynski")));
 151                                                 }else if (Estimators[i] == "kulczynskicody") {
 152                                                         cDisplays.push_back(new CollectDisplay(new KulczynskiCody(), new SharedOneColumnFile(fileNameRoot+"kulczynskicody")));
 153                                                 }else if (Estimators[i] == "lennon") {
 154                                                         cDisplays.push_back(new CollectDisplay(new Lennon(), new SharedOneColumnFile(fileNameRoot+"lennon")));
 155                                                 }else if (Estimators[i] == "morisitahorn") {
 156                                                         cDisplays.push_back(new CollectDisplay(new MorHorn(), new SharedOneColumnFile(fileNameRoot+"morisitahorn")));
 157                                                 }else if (Estimators[i] == "braycurtis") {
 158                                                         cDisplays.push_back(new CollectDisplay(new BrayCurtis(), new SharedOneColumnFile(fileNameRoot+"braycurtis")));
 159                                                 }
 160                                         }
 161                                 }
 162                         }
 163                 }
 164
 165         }
 166         catch(exception& e) {
 167                 errorOut(e, "CollectSharedCommand", "CollectSharedCommand");
 168                 exit(1);
 169         }
 170 }
 171 //**********************************************************************************************************************
 172
 173 void CollectSharedCommand::help(){
 174         try {
 175                 mothurOut("The collect.shared command can only be executed after a successful read.otu command.\n");
 176                 mothurOut("The collect.shared command parameters are label, freq, calc and groups.  No parameters are required \n");
 177                 mothurOut("The collect.shared command should be in the following format: \n");
 178                 mothurOut("collect.shared(label=yourLabel, freq=yourFreq, calc=yourEstimators, groups=yourGroups).\n");
 179                 mothurOut("Example collect.shared(label=unique-.01-.03, freq=10, groups=B-C, calc=sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan).\n");
 180                 mothurOut("The default values for freq is 100 and calc are sharedsobs-sharedchao-sharedace-jabund-sorensonabund-jclass-sorclass-jest-sorest-thetayc-thetan.\n");
 181                 mothurOut("The default value for groups is all the groups in your groupfile.\n");
 182                 validCalculator->printCalc("shared", cout);
 183                 mothurOut("The label parameter is used to analyze specific labels in your input.\n");
 184                 mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like analyzed.  You must enter at least 2 valid groups.\n");
 185                 mothurOut("Note: No spaces between parameter labels (i.e. list), '=' and parameters (i.e.yourListfile).\n\n");
 186
 187         }
 188         catch(exception& e) {
 189                 errorOut(e, "CollectSharedCommand", "help");
 190                 exit(1);
 191         }
 192 }
 193
 194 //**********************************************************************************************************************
 195
 196 CollectSharedCommand::~CollectSharedCommand(){
 197         if (abort == false) {
 198                 delete input; globaldata->ginput = NULL;
 199                 delete read;
 200                 delete util;
 201                 delete validCalculator;
 202                 globaldata->gorder = NULL;
 203         }
 204 }
 205
 206 //**********************************************************************************************************************
 207
 208 int CollectSharedCommand::execute(){
 209         try {
 210
 211                 if (abort == true) {    return 0;       }
 212
 213                 //if the users entered no valid calculators don't execute command
 214                 if (cDisplays.size() == 0) { return 0; }
 215
 216                 read = new ReadOTUFile(globaldata->inputFileName);
 217                 read->read(&*globaldata);
 218
 219                 input = globaldata->ginput;
 220                 order = input->getSharedOrderVector();
 221                 string lastLabel = order->getLabel();
 222
 223                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 224                 set<string> processedLabels;
 225                 set<string> userLabels = labels;
 226
 227                 //set users groups
 228                 util->setGroups(globaldata->Groups, globaldata->gGroupmap->namesOfGroups, "collect");
 229                 util->updateGroupIndex(globaldata->Groups, globaldata->gGroupmap->groupIndex);
 230
 231                 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0))) {
 232
 233                         if(allLines == 1 || labels.count(order->getLabel()) == 1){
 234
 235                                 //create collectors curve
 236                                 cCurve = new Collect(order, cDisplays);
 237                                 cCurve->getSharedCurve(freq);
 238                                 delete cCurve;
 239
 240                                 mothurOut(order->getLabel()); mothurOutEndLine();
 241                                 processedLabels.insert(order->getLabel());
 242                                 userLabels.erase(order->getLabel());
 243                         }
 244
 245                         //you have a label the user want that is smaller than this label and the last label has not already been processed
 246                         if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 247                                 string saveLabel = order->getLabel();
 248
 249                                 delete order;
 250                                 order = input->getSharedOrderVector(lastLabel);
 251
 252                                 //create collectors curve
 253                                 cCurve = new Collect(order, cDisplays);
 254                                 cCurve->getSharedCurve(freq);
 255                                 delete cCurve;
 256
 257                                 mothurOut(order->getLabel()); mothurOutEndLine();
 258                                 processedLabels.insert(order->getLabel());
 259                                 userLabels.erase(order->getLabel());
 260
 261                                 //restore real lastlabel to save below
 262                                 order->setLabel(saveLabel);
 263                         }
 264
 265
 266                         lastLabel = order->getLabel();
 267
 268                         //get next line to process
 269                         delete order;
 270                         order = input->getSharedOrderVector();
 271                 }
 272
 273                 //output error messages about any remaining user labels
 274                 set<string>::iterator it;
 275                 bool needToRun = false;
 276                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 277                         mothurOut("Your file does not include the label " + *it);
 278                         if (processedLabels.count(lastLabel) != 1) {
 279                                 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
 280                                 needToRun = true;
 281                         }else {
 282                                 mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
 283                         }
 284                 }
 285
 286                 //run last label if you need to
 287                 if (needToRun == true)  {
 288                         if (order != NULL) {  delete order;  }
 289                         order = input->getSharedOrderVector(lastLabel);
 290
 291                         cCurve = new Collect(order, cDisplays);
 292                         cCurve->getSharedCurve(freq);
 293                         delete cCurve;
 294
 295                         mothurOut(order->getLabel()); mothurOutEndLine();
 296                         delete order;
 297                 }
 298
 299                 for(int i=0;i<cDisplays.size();i++){    delete cDisplays[i];    }
 300
 301                 //reset groups parameter
 302                 globaldata->Groups.clear();
 303
 304                 return 0;
 305         }
 306         catch(exception& e) {
 307                 errorOut(e, "CollectSharedCommand", "execute");
 308                 exit(1);
 309         }
 310 }
 311
 312 /***********************************************************/