rarefactsharedcommand.cpp

   1 /*
   2  *  rarefactsharedcommand.cpp
   3  *  Dotur
   4  *
   5  *  Created by Sarah Westcott on 1/6/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "rarefactsharedcommand.h"
  11 #include "sharedsobs.h"
  12 #include "sharednseqs.h"
  13
  14 //**********************************************************************************************************************
  15
  16 RareFactSharedCommand::RareFactSharedCommand(string option){
  17         try {
  18                 globaldata = GlobalData::getInstance();
  19
  20                 abort = false;
  21                 allLines = 1;
  22                 lines.clear();
  23                 labels.clear();
  24                 Estimators.clear();
  25                 Groups.clear();
  26
  27                 //allow user to run help
  28                 if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
  29
  30                 else {
  31                         //valid paramters for this command
  32                         string Array[] =  {"iters","line","label","calc","groups", "jumble"};
  33                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  34
  35                         OptionParser parser(option);
  36                         map<string,string> parameters = parser.getParameters();
  37
  38                         ValidParameters validParameter;
  39
  40                         //check to make sure all parameters are valid for command
  41                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  42                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  43                         }
  44
  45                         //make sure the user has already run the read.otu command
  46                         if (globaldata->getSharedFile() == "") {
  47                                 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; }
  48                                 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; }
  49                         }
  50
  51
  52                         //check for optional parameter and set defaults
  53                         // ...at some point should added some additional type checking...
  54                         line = validParameter.validFile(parameters, "line", false);
  55                         if (line == "not found") { line = "";  }
  56                         else {
  57                                 if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
  58                                 else { allLines = 1;  }
  59                         }
  60
  61                         label = validParameter.validFile(parameters, "label", false);
  62                         if (label == "not found") { label = ""; }
  63                         else {
  64                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  65                                 else { allLines = 1;  }
  66                         }
  67
  68                         //make sure user did not use both the line and label parameters
  69                         if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
  70                         //if the user has not specified any line or labels use the ones from read.otu
  71                         else if((line == "") && (label == "")) {
  72                                 allLines = globaldata->allLines;
  73                                 labels = globaldata->labels;
  74                                 lines = globaldata->lines;
  75                         }
  76
  77                         calc = validParameter.validFile(parameters, "calc", false);
  78                         if (calc == "not found") { calc = "sharedobserved";  }
  79                         else {
  80                                  if (calc == "default")  {  calc = "sharedobserved";  }
  81                         }
  82                         splitAtDash(calc, Estimators);
  83
  84                         groups = validParameter.validFile(parameters, "groups", false);
  85                         if (groups == "not found") { groups = ""; }
  86                         else {
  87                                 splitAtDash(groups, Groups);
  88                         }
  89                         globaldata->Groups = Groups;
  90
  91                         string temp;
  92                         temp = validParameter.validFile(parameters, "iters", false);                    if (temp == "not found") { temp = "1000"; }
  93                         convert(temp, nIters);
  94
  95                         temp = validParameter.validFile(parameters, "jumble", false);                   if (temp == "not found") { temp = "T"; }
  96                         if (isTrue(temp)) { jumble = true; }
  97                         else { jumble = false; }
  98                         globaldata->jumble = jumble;
  99
 100                         if (abort == false) {
 101
 102                                 string fileNameRoot = getRootName(globaldata->inputFileName);
 103 //                              format = globaldata->getFormat();
 104
 105
 106                                 validCalculator = new ValidCalculators();
 107
 108                                 for (int i=0; i<Estimators.size(); i++) {
 109                                         if (validCalculator->isValidCalculator("sharedrarefaction", Estimators[i]) == true) {
 110                                                 if (Estimators[i] == "sharedobserved") {
 111                                                         rDisplays.push_back(new RareDisplay(new SharedSobs(), new SharedThreeColumnFile(fileNameRoot+"shared.rarefaction", "")));
 112                                                 }else if (Estimators[i] == "sharednseqs") {
 113                                                         rDisplays.push_back(new RareDisplay(new SharedNSeqs(), new SharedThreeColumnFile(fileNameRoot+"shared.r_nseqs", "")));
 114                                                 }
 115                                         }
 116                                 }
 117                         }
 118
 119                 }
 120
 121         }
 122         catch(exception& e) {
 123                 errorOut(e, "RareFactSharedCommand", "RareFactSharedCommand");
 124                 exit(1);
 125         }
 126 }
 127
 128 //**********************************************************************************************************************
 129
 130 void RareFactSharedCommand::help(){
 131         try {
 132                 mothurOut("The rarefaction.shared command can only be executed after a successful read.otu command.\n");
 133                 mothurOut("The rarefaction.shared command parameters are label, line, iters, groups, jumble and calc.  No parameters are required, but you may not use \n");
 134                 mothurOut("both the line and label parameters at the same time. The rarefaction command should be in the following format: \n");
 135                 mothurOut("rarefaction.shared(label=yourLabel, line=yourLines, iters=yourIters, calc=yourEstimators, jumble=yourJumble, groups=yourGroups).\n");
 136                 mothurOut("Example rarefaction.shared(label=unique-.01-.03, line=0-5-10, iters=10000, groups=B-C, jumble=T, calc=sharedobserved).\n");
 137                 mothurOut("The default values for iters is 1000, freq is 100, and calc is sharedobserved which calculates the shared rarefaction curve for the observed richness.\n");
 138                 mothurOut("The default value for groups is all the groups in your groupfile, and jumble is true.\n");
 139                 validCalculator->printCalc("sharedrarefaction", cout);
 140                 mothurOut("The label and line parameters are used to analyze specific lines in your input.\n");
 141                 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");
 142                 mothurOut("Note: No spaces between parameter labels (i.e. freq), '=' and parameters (i.e.yourFreq).\n\n");
 143         }
 144         catch(exception& e) {
 145                 errorOut(e, "RareFactSharedCommand", "help");
 146                 exit(1);
 147         }
 148 }
 149
 150 //**********************************************************************************************************************
 151
 152 RareFactSharedCommand::~RareFactSharedCommand(){
 153         if (abort == false) {
 154                 delete input;   globaldata->ginput = NULL;
 155                 delete read;
 156                 delete validCalculator;
 157         }
 158 }
 159
 160 //**********************************************************************************************************************
 161
 162 int RareFactSharedCommand::execute(){
 163         try {
 164
 165                 if (abort == true) { return 0; }
 166
 167                 int count = 1;
 168
 169                 //if the users entered no valid calculators don't execute command
 170                 if (rDisplays.size() == 0) { return 0; }
 171
 172                 read = new ReadOTUFile(globaldata->inputFileName);
 173                 read->read(&*globaldata);
 174
 175                 input = globaldata->ginput;
 176                 lookup = input->getSharedRAbundVectors();
 177                 string lastLabel = lookup[0]->getLabel();
 178
 179                 if (lookup.size() < 2) {
 180                         mothurOut("I cannot run the command without at least 2 valid groups.");
 181                         for (int i = 0; i < lookup.size(); i++) { delete lookup[i]; }
 182                         return 0;
 183                 }
 184
 185                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 186                 set<string> processedLabels;
 187                 set<string> userLabels = labels;
 188                 set<int> userLines = lines;
 189
 190                 //as long as you are not at the end of the file or done wih the lines you want
 191                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 192
 193                         if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
 194
 195                                 rCurve = new Rarefact(lookup, rDisplays);
 196                                 rCurve->getSharedCurve(freq, nIters);
 197                                 delete rCurve;
 198
 199                                 mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 200                                 processedLabels.insert(lookup[0]->getLabel());
 201                                 userLabels.erase(lookup[0]->getLabel());
 202                                 userLines.erase(count);
 203                         }
 204
 205                         if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 206                                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 207                                         lookup = input->getSharedRAbundVectors(lastLabel);
 208
 209                                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 210                                         rCurve = new Rarefact(lookup, rDisplays);
 211                                         rCurve->getSharedCurve(freq, nIters);
 212                                         delete rCurve;
 213
 214                                         processedLabels.insert(lookup[0]->getLabel());
 215                                         userLabels.erase(lookup[0]->getLabel());
 216                         }
 217
 218
 219                         lastLabel = lookup[0]->getLabel();
 220
 221                         //get next line to process
 222                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 223                         lookup = input->getSharedRAbundVectors();
 224                         count++;
 225                 }
 226
 227                 //output error messages about any remaining user labels
 228                 set<string>::iterator it;
 229                 bool needToRun = false;
 230                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 231                         mothurOut("Your file does not include the label " + *it);
 232                         if (processedLabels.count(lastLabel) != 1) {
 233                                 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
 234                                 needToRun = true;
 235                         }else {
 236                                 mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
 237                         }
 238                 }
 239
 240                 //run last line if you need to
 241                 if (needToRun == true)  {
 242                         for (int i = 0; i < lookup.size(); i++) {  if (lookup[i] != NULL) {     delete lookup[i]; }  }
 243                         lookup = input->getSharedRAbundVectors(lastLabel);
 244
 245                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 246                         rCurve = new Rarefact(lookup, rDisplays);
 247                         rCurve->getSharedCurve(freq, nIters);
 248                         delete rCurve;
 249                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 250                 }
 251
 252                 for(int i=0;i<rDisplays.size();i++){    delete rDisplays[i];    }
 253
 254                 //reset groups parameter
 255                 globaldata->Groups.clear();
 256
 257                 return 0;
 258         }
 259         catch(exception& e) {
 260                 errorOut(e, "RareFactSharedCommand", "execute");
 261                 exit(1);
 262         }
 263 }
 264
 265
 266 //**********************************************************************************************************************