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                                  mothurOut("You must read a list and a group, or a shared before you can use the heatmap.sim command."); mothurOutEndLine(); 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 != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); 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                 errorOut(e, "HeatMapSimCommand", "HeatMapSimCommand");
 136                 exit(1);
 137         }
 138 }
 139
 140 //**********************************************************************************************************************
 141
 142 void HeatMapSimCommand::help(){
 143         try {
 144                 mothurOut("The heatmap.sim command can only be executed after a successful read.otu command.\n");
 145                 mothurOut("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");
 146                 mothurOut("The groups parameter allows you to specify which of the groups in your groupfile you would like included in your heatmap.\n");
 147                 mothurOut("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");
 148                 mothurOut("The heatmap.sim command should be in the following format: heatmap.sim(groups=yourGroups, calc=yourCalc, line=yourLines, label=yourLabels).\n");
 149                 mothurOut("Example heatmap.sim(groups=A-B-C, line=1-3-5, calc=jabund).\n");
 150                 mothurOut("The default value for groups is all the groups in your groupfile, and all lines in your inputfile will be used.\n");
 151                 validCalculator->printCalc("heat", cout);
 152                 mothurOut("The default value for calc is jclass-thetayc.\n");
 153                 mothurOut("The heatmap.sim command outputs a .svg file for each calculator you choose at each line or label you specify.\n");
 154                 mothurOut("Note: No spaces between parameter labels (i.e. groups), '=' and parameters (i.e.yourGroups).\n\n");
 155
 156         }
 157         catch(exception& e) {
 158                 errorOut(e, "HeatMapSimCommand", "help");
 159                 exit(1);
 160         }
 161 }
 162
 163 //**********************************************************************************************************************
 164
 165 HeatMapSimCommand::~HeatMapSimCommand(){
 166         if (abort == false) {
 167                 delete input;  globaldata->ginput = NULL;
 168                 delete read;
 169                 delete heatmap;
 170                 delete validCalculator;
 171         }
 172 }
 173
 174 //**********************************************************************************************************************
 175
 176 int HeatMapSimCommand::execute(){
 177         try {
 178
 179                 if (abort == true)  { return 0; }
 180
 181                 int count = 1;
 182
 183                 //if the users entered no valid calculators don't execute command
 184                 if (heatCalculators.size() == 0) { mothurOut("No valid calculators."); mothurOutEndLine(); return 0; }
 185
 186                 //you have groups
 187                 read = new ReadOTUFile(globaldata->inputFileName);
 188                 read->read(&*globaldata);
 189
 190                 input = globaldata->ginput;
 191                 lookup = input->getSharedRAbundVectors();
 192                 string lastLabel = lookup[0]->getLabel();
 193
 194                 if (lookup.size() < 2) { mothurOut("You have not provided enough valid groups.  I cannot run the command."); mothurOutEndLine(); return 0;}
 195
 196                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 197                 set<string> processedLabels;
 198                 set<string> userLabels = labels;
 199                 set<int> userLines = lines;
 200
 201
 202                 //as long as you are not at the end of the file or done wih the lines you want
 203                 while((lookup[0] != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 204
 205                         if(allLines == 1 || lines.count(count) == 1 || labels.count(lookup[0]->getLabel()) == 1){
 206
 207                                 mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 208                                 heatmap->getPic(lookup, heatCalculators);
 209
 210                                 processedLabels.insert(lookup[0]->getLabel());
 211                                 userLabels.erase(lookup[0]->getLabel());
 212                                 userLines.erase(count);
 213                         }
 214
 215                         if ((anyLabelsToProcess(lookup[0]->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 216
 217                                 for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 218                                 lookup = input->getSharedRAbundVectors(lastLabel);
 219
 220                                 mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 221                                 heatmap->getPic(lookup, heatCalculators);
 222
 223                                 processedLabels.insert(lookup[0]->getLabel());
 224                                 userLabels.erase(lookup[0]->getLabel());
 225                         }
 226
 227                         //prevent memory leak
 228
 229                         lastLabel = lookup[0]->getLabel();
 230
 231                         //get next line to process
 232                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 233                         lookup = input->getSharedRAbundVectors();
 234                         count++;
 235                 }
 236
 237                 //output error messages about any remaining user labels
 238                 set<string>::iterator it;
 239                 bool needToRun = false;
 240                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 241                         mothurOut("Your file does not include the label " + *it);
 242                         if (processedLabels.count(lastLabel) != 1) {
 243                                 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
 244                                 needToRun = true;
 245                         }else {
 246                                 mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
 247                         }
 248                 }
 249
 250                 //run last line if you need to
 251                 if (needToRun == true)  {
 252                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 253                         lookup = input->getSharedRAbundVectors(lastLabel);
 254
 255                         mothurOut(lookup[0]->getLabel()); mothurOutEndLine();
 256                         heatmap->getPic(lookup, heatCalculators);
 257                         for (int i = 0; i < lookup.size(); i++) {  delete lookup[i];  }
 258                 }
 259
 260
 261                 //reset groups parameter
 262                 globaldata->Groups.clear();
 263
 264                 return 0;
 265         }
 266         catch(exception& e) {
 267                 errorOut(e, "HeatMapSimCommand", "execute");
 268                 exit(1);
 269         }
 270 }
 271
 272 //**********************************************************************************************************************