getrabundcommand.cpp

   1 /*
   2  *  getrabundcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 6/2/09.
   6  *  Copyright 2009 Schloss Lab Umass Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "getrabundcommand.h"
  11
  12 //**********************************************************************************************************************
  13
  14 GetRAbundCommand::GetRAbundCommand(string option){
  15         try {
  16                 globaldata = GlobalData::getInstance();
  17                 abort = false;
  18                 allLines = 1;
  19                 lines.clear();
  20                 labels.clear();
  21
  22                 //allow user to run help
  23                 if(option == "help") { help(); abort = true; }
  24
  25                 else {
  26                         //valid paramters for this command
  27                         string Array[] =  {"line","label"};
  28                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  29
  30                         OptionParser parser(option);
  31                         map<string,string> parameters = parser.getParameters();
  32
  33                         ValidParameters validParameter;
  34
  35                         //check to make sure all parameters are valid for command
  36                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  37                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  38                         }
  39
  40                         //make sure the user has already run the read.otu command
  41                         if (globaldata->getListFile() == "") { mothurOut("You must read a listfile before you can use the get.rabund command."); mothurOutEndLine(); abort = true; }
  42
  43                         //check for optional parameter and set defaults
  44                         // ...at some point should added some additional type checking...
  45                         line = validParameter.validFile(parameters, "line", false);
  46                         if (line == "not found") { line = "";  }
  47                         else {
  48                                 if(line != "all") {  splitAtDash(line, lines);  allLines = 0;  }
  49                                 else { allLines = 1;  }
  50                         }
  51
  52                         label = validParameter.validFile(parameters, "label", false);
  53                         if (label == "not found") { label = ""; }
  54                         else {
  55                                 if(label != "all") {  splitAtDash(label, labels);  allLines = 0;  }
  56                                 else { allLines = 1;  }
  57                         }
  58
  59                         //make sure user did not use both the line and label parameters
  60                         if ((line != "") && (label != "")) { mothurOut("You cannot use both the line and label parameters at the same time. "); mothurOutEndLine(); abort = true; }
  61                         //if the user has not specified any line or labels use the ones from read.otu
  62                         else if((line == "") && (label == "")) {
  63                                 allLines = globaldata->allLines;
  64                                 labels = globaldata->labels;
  65                                 lines = globaldata->lines;
  66                         }
  67
  68                         if (abort == false) {
  69                                 filename = getRootName(globaldata->inputFileName) + "rabund";
  70                                 openOutputFile(filename, out);
  71                         }
  72                 }
  73
  74         }
  75         catch(exception& e) {
  76                 errorOut(e, "GetRAbundCommand", "GetRAbundCommand");
  77                 exit(1);
  78         }
  79 }
  80 //**********************************************************************************************************************
  81
  82 void GetRAbundCommand::help(){
  83         try {
  84                 mothurOut("The get.rabund command can only be executed after a successful read.otu of a listfile.\n");
  85                 mothurOut("The get.rabund command parameters are line and label.  No parameters are required, and you may not use line and label at the same time.\n");
  86                 mothurOut("The line and label allow you to select what distance levels you would like included in your .rabund file, and are separated by dashes.\n");
  87                 mothurOut("The get.rabund command should be in the following format: get.rabund(line=yourLines, label=yourLabels).\n");
  88                 mothurOut("Example get.rabund(line=1-3-5).\n");
  89                 mothurOut("The default value for line and label are all lines in your inputfile.\n");
  90                 mothurOut("The get.rabund command outputs a .rabund file containing the lines you selected.\n");
  91                 mothurOut("Note: No spaces between parameter labels (i.e. line), '=' and parameters (i.e.yourLines).\n\n");
  92         }
  93         catch(exception& e) {
  94                 errorOut(e, "GetRAbundCommand", "help");
  95                 exit(1);
  96         }
  97 }
  98
  99 //**********************************************************************************************************************
 100
 101 GetRAbundCommand::~GetRAbundCommand(){
 102         if (abort == false) {  globaldata->gListVector = NULL; }
 103 }
 104
 105 //**********************************************************************************************************************
 106
 107 int GetRAbundCommand::execute(){
 108         try {
 109
 110                 if (abort == true) { return 0; }
 111
 112                 int count = 1;
 113
 114                 //read first line
 115                 read = new ReadOTUFile(globaldata->inputFileName);
 116                 read->read(&*globaldata);
 117
 118                 input = globaldata->ginput;
 119                 list = globaldata->gListVector;
 120                 string lastLabel = list->getLabel();
 121
 122                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 123                 set<string> processedLabels;
 124                 set<string> userLabels = labels;
 125                 set<int> userLines = lines;
 126
 127
 128                 while((list != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 129
 130                         if(allLines == 1 || lines.count(count) == 1 || labels.count(list->getLabel()) == 1){
 131                                         mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
 132                                         rabund = new RAbundVector();
 133                                         *rabund = (list->getRAbundVector());
 134                                         rabund->print(out);
 135                                         delete rabund;
 136
 137                                         processedLabels.insert(list->getLabel());
 138                                         userLabels.erase(list->getLabel());
 139                                         userLines.erase(count);
 140                         }
 141
 142                         if ((anyLabelsToProcess(list->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 143                                         delete list;
 144                                         list = input->getListVector(lastLabel);
 145
 146                                         mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
 147                                         rabund = new RAbundVector();
 148                                         *rabund = (list->getRAbundVector());
 149                                         rabund->print(out);
 150                                         delete rabund;
 151
 152                                         processedLabels.insert(list->getLabel());
 153                                         userLabels.erase(list->getLabel());
 154                         }
 155
 156                         lastLabel = list->getLabel();
 157
 158                         delete list;
 159                         list = input->getListVector();
 160                         count++;
 161                 }
 162
 163                 //output error messages about any remaining user labels
 164                 set<string>::iterator it;
 165                 bool needToRun = false;
 166                 for (it = userLabels.begin(); it != userLabels.end(); it++) {
 167                         mothurOut("Your file does not include the label " + *it);
 168                         if (processedLabels.count(lastLabel) != 1) {
 169                                 mothurOut(". I will use " + lastLabel + "."); mothurOutEndLine();
 170                                 needToRun = true;
 171                         }else {
 172                                 mothurOut(". Please refer to " + lastLabel + "."); mothurOutEndLine();
 173                         }
 174                 }
 175
 176                 //run last line if you need to
 177                 if (needToRun == true)  {
 178                         delete list;
 179                         list = input->getListVector(lastLabel);
 180
 181                         mothurOut(list->getLabel() + "\t" + toString(count)); mothurOutEndLine();
 182                         rabund = new RAbundVector();
 183                         *rabund = (list->getRAbundVector());
 184                         rabund->print(out);
 185                         delete rabund;
 186                         delete list;
 187                 }
 188
 189                 out.close();
 190                 return 0;
 191         }
 192
 193         catch(exception& e) {
 194                 errorOut(e, "GetRAbundCommand", "execute");
 195                 exit(1);
 196         }
 197 }
 198
 199 //**********************************************************************************************************************
 200
 201