heatmapsimcommand.cpp

   1 /*
   2  *  heatmapsimcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 6/8/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "heatmapsimcommand.h"
  11 #include "sharedjabund.h"
  12 #include "sharedsorabund.h"
  13 #include "sharedjclass.h"
  14 #include "sharedsorclass.h"
  15 #include "sharedjest.h"
  16 #include "sharedsorest.h"
  17 #include "sharedthetayc.h"
  18 #include "sharedthetan.h"
  19 #include "sharedmorisitahorn.h"
  20 #include "sharedbraycurtis.h"
  21
  22
  23 //**********************************************************************************************************************
  24
  25 HeatMapSimCommand::HeatMapSimCommand(string option){
  26         try {
  27                 globaldata = GlobalData::getInstance();
  28                 abort = false;
  29                 allLines = 1;
  30                 lines.clear();
  31                 labels.clear();
  32                 Groups.clear();
  33                 Estimators.clear();
  34
  35                 //allow user to run help
  36                 if(option == "help") { validCalculator = new ValidCalculators(); help(); abort = true; }
  37
  38                 else {
  39                         //valid paramters for this command
  40                         string AlignArray[] =  {"groups","line","label", "calc"};
  41                         vector<string> myArray (AlignArray, AlignArray+(sizeof(AlignArray)/sizeof(string)));
  42
  43                         OptionParser parser(option);
  44                         map<string,string> parameters = parser.getParameters();
  45
  46                         ValidParameters validParameter;
  47
  48                         //check to make sure all parameters are valid for command
  49                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  50                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  51                         }
  52
  53                         //make sure the user has already run the read.otu command
  54                         if (globaldata->getSharedFile() == "") {
  55                                  cout << "You must read a list and a group, or a shared before you can use the heatmap.sim command." << endl; abort = true;
  56                         }
  57
  58                         //check for optional parameter and set defaults
  59                         // ...at some point should added some additional type checking...
  60                         line = validParameter.validFile(parameters, "line", false);
  61                         if (line == "not found") { line = "";  }
  62                         else {
  63                                 if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
  64                                 else { allLines = 1;  }
  65                         }
  66
  67                         label = validParameter.validFile(parameters, "label", false);
  68                         if (label == "not found") { label = ""; }
  69                         else {
  70                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  71                                 else { allLines = 1;  }
  72                         }
  73
  74                         //make sure user did not use both the line and label parameters
  75                         if ((line != "") && (label != "")) { cout << "You cannot use both the line and label parameters at the same time. " << endl; abort = true; }
  76                         //if the user has not specified any line or labels use the ones from read.otu
  77                         else if ((line == "") && (label == "")) {
  78                                 allLines = globaldata->allLines;
  79                                 labels = globaldata->labels;
  80                                 lines = globaldata->lines;
  81                         }
  82
  83                         calc = validParameter.validFile(parameters, "calc", false);
  84                         if (calc == "not found") { calc = "jest-thetayc";  }
  85                         else {
  86                                  if (calc == "default")  {  calc = "jest-thetayc";  }
  87                         }
  88                         splitAtDash(calc, Estimators);
  89
  90                         groups = validParameter.validFile(parameters, "groups", false);
  91                         if (groups == "not found") { groups = ""; }
  92                         else {
  93                                 splitAtDash(groups, Groups);
  94                                 globaldata->Groups = Groups;
  95                         }
  96
  97                         if (abort == false) {
  98                                 validCalculator = new ValidCalculators();
  99                                 heatmap = new HeatMapSim();
 100
 101                                 int i;
 102                                 for (i=0; i<Estimators.size(); i++) {
 103                                         if (validCalculator->isValidCalculator("heat", Estimators[i]) == true) {
 104                                                 if (Estimators[i] == "jabund") {
 105                                                         heatCalculators.push_back(new JAbund());
 106                                                 }else if (Estimators[i] == "sorabund") {
 107                                                         heatCalculators.push_back(new SorAbund());
 108                                                 }else if (Estimators[i] == "jclass") {
 109                                                         heatCalculators.push_back(new Jclass());
 110                                                 }else if (Estimators[i] == "sorclass") {
 111                                                         heatCalculators.push_back(new SorClass());
 112                                                 }else if (Estimators[i] == "jest") {
 113                                                         heatCalculators.push_back(new Jest());
 114                                                 }else if (Estimators[i] == "sorest") {
 115                                                         heatCalculators.push_back(new SorEst());
 116                                                 }else if (Estimators[i] == "thetayc") {
 117                                                         heatCalculators.push_back(new ThetaYC());
 118                                                 }else if (Estimators[i] == "thetan") {
 119                                                         heatCalculators.push_back(new ThetaN());
 120                                                 }else if (Estimators[i] == "morisitahorn") {
 121                                                         heatCalculators.push_back(new MorHorn());
 122                                                 }else if (Estimators[i] == "braycurtis") {
 123                                                         heatCalculators.push_back(new BrayCurtis());
 124                                                 }
 125                                         }
 126                                 }
 127
 128                         }
 129                 }
 130
 131
 132
 133         }
 134         catch(exception& e) {
 135                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSimCommand class Function HeatMapSimCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 136                 exit(1);
 137         }
 138         catch(...) {
 139                 cout << "An unknown error has occurred in the HeatMapSimCommand class function HeatMapSimCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 140                 exit(1);
 141         }
 142 }
 143
 144 //**********************************************************************************************************************
 145
 146 void HeatMapSimCommand::help(){
 147         try {
 148                 cout << "The heatmap.sim command can only be executed after a successful read.otu command." << "\n";
 149                 cout << "The heatmap.sim command parameters are groups, calc, line and label.  No parameters are required, but you may not use line and label at the same time." << "\n";
 150                 cout << "The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap." << "\n";
 151                 cout << "The group names are separated by dashes. The line and label allow you to select what distance levels you would like a heatmap created for, and are also separated by dashes." << "\n";
 152                 cout << "The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, line=yourLines, label=yourLabels)." << "\n";
 153                 cout << "Example heatmap.sim(groups=A-B-C, line=1-3-5, calc=jabund)." << "\n";
 154                 cout << "The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used." << "\n";
 155                 validCalculator->printCalc("heat", cout);
 156                 cout << "The default value for calc is jclass-thetayc." << "\n";
 157                 cout << "The heatmap.sim command outputs a .svg file for each calculator you choose at each line or label you specify." << "\n";
 158                 cout << "Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups)." << "\n" << "\n";
 159
 160         }
 161         catch(exception& e) {
 162                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSimCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 163                 exit(1);
 164         }
 165         catch(...) {
 166                 cout << "An unknown error has occurred in the HeatMapSimCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 167                 exit(1);
 168         }
 169 }
 170
 171 //**********************************************************************************************************************
 172
 173 HeatMapSimCommand::~HeatMapSimCommand(){
 174         if (abort == false) {
 175                 delete input;  globaldata->ginput = NULL;
 176                 delete read;
 177                 delete heatmap;
 178                 delete validCalculator;
 179         }
 180 }
 181
 182 //**********************************************************************************************************************
 183
 184 int HeatMapSimCommand::execute(){
 185         try {
 186
 187                 if (abort == true)  { return 0; }
 188
 189                 int count = 1;
 190
 191                 //if the users entered no valid calculators don't execute command
 192                 if (heatCalculators.size() == 0) { cout << "No valid calculators." << endl; return 0; }
 193
 194                 //you have groups
 195                 read = new ReadOTUFile(globaldata->inputFileName);
 196                 read->read(&*globaldata);
 197
 198                 input = globaldata->ginput;
 199                 lookup = input->getSharedRAbundVectors();
 200                 vector<SharedRAbundVector*> lastLookup = lookup;
 201
 202                 if (lookup.size() < 2) { cout << "You have not provided enough valid groups.  I cannot run the command." << endl; return 0;}
 203
 204                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 205                 set<string> processedLabels;
 206                 set<string> userLabels = labels;
 207                 set<int> userLines = lines;
 208
 209
 210                 //as long as you are not at the end of the file or done wih the lines you want
 211                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 212
 213                         if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
 214
 215                                 cout << lookup[0]->getLabel() << '\t' << count << endl;
 216                                 heatmap->getPic(lookup, heatCalculators);
 217
 218                                 processedLabels.insert(lookup[0]->getLabel());
 219                                 userLabels.erase(lookup[0]->getLabel());
 220                                 userLines.erase(count);
 221                         }
 222
 223                         if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLookup[0]->getLabel()) != 1)) {
 224                                 cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 225                                 heatmap->getPic(lastLookup, heatCalculators);
 226
 227                                 processedLabels.insert(lastLookup[0]->getLabel());
 228                                 userLabels.erase(lastLookup[0]->getLabel());
 229                         }
 230
 231                         //prevent memory leak
 232                         if (count != 1) { for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  } }
 233                         lastLookup = lookup;
 234
 235                         //get next line to process
 236                         lookup = input->getSharedRAbundVectors();
 237                         count++;
 238                 }
 239
 240                 //output error messages about any remaining user labels
 241                 set<string>::iterator it;
 242                 bool needToRun = false;
 243                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 244                         cout << "Your file does not include the label "<< *it;
 245                         if (processedLabels.count(lastLookup[0]->getLabel()) != 1) {
 246                                 cout << ". I will use " << lastLookup[0]->getLabel() << "." << endl;
 247                                 needToRun = true;
 248                         }else {
 249                                 cout << ". Please refer to " << lastLookup[0]->getLabel() << "." << endl;
 250                         }
 251                 }
 252
 253                 //run last line if you need to
 254                 if (needToRun == true)  {
 255                         cout << lastLookup[0]->getLabel() << '\t' << count << endl;
 256                         heatmap->getPic(lastLookup, heatCalculators);
 257                 }
 258
 259                 for (int i = 0; i < lastLookup.size(); i++) {  delete lastLookup[i];  }
 260
 261                 //reset groups parameter
 262                 globaldata->Groups.clear();
 263
 264                 return 0;
 265         }
 266         catch(exception& e) {
 267                 cout << "Standard Error: " << e.what() << " has occurred in the HeatMapSimCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 268                 exit(1);
 269         }
 270         catch(...) {
 271                 cout << "An unknown error has occurred in the HeatMapSimCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 272                 exit(1);
 273         }
 274 }
 275
 276 //**********************************************************************************************************************