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