getsabundcommand.cpp

   1 /*
   2  *  getsabundcommand.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 "getsabundcommand.h"
  11
  12 //**********************************************************************************************************************
  13
  14 GetSAbundCommand::GetSAbundCommand(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() == "") && (globaldata->getRabundFile() == "")) { mothurOut("You must read a list or rabund before you can use the get.sabund 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) + "sabund";
  70                                 openOutputFile(filename, out);
  71                         }
  72                 }
  73
  74         }
  75         catch(exception& e) {
  76                 errorOut(e, "GetSAbundCommand", "GetSAbundCommand");
  77                 exit(1);
  78         }
  79 }
  80 //**********************************************************************************************************************
  81
  82 void GetSAbundCommand::help(){
  83         try {
  84                 mothurOut("The get.sabund command can only be executed after a successful read.otu of a listfile or rabundfile.\n");
  85                 mothurOut("The get.sabund 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 .sabund file, and are separated by dashes.\n");
  87                 mothurOut("The get.sabund command should be in the following format: get.sabund(line=yourLines, label=yourLabels).\n");
  88                 mothurOut("Example get.sabund(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.sabund command outputs a .sabund 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, "GetSAbundCommand", "help");
  95                 exit(1);
  96         }
  97 }
  98
  99 //**********************************************************************************************************************
 100
 101 GetSAbundCommand::~GetSAbundCommand(){
 102 }
 103
 104 //**********************************************************************************************************************
 105
 106 int GetSAbundCommand::execute(){
 107         try {
 108
 109                 if (abort == true) { return 0; }
 110
 111                 int count = 1;
 112
 113                 //using order vector so you don't have to distinguish between the list and rabund files
 114                 read = new ReadOTUFile(globaldata->inputFileName);
 115                 read->read(&*globaldata);
 116
 117                 order = globaldata->gorder;
 118                 string lastLabel = order->getLabel();
 119                 input = globaldata->ginput;
 120
 121                 //if the users enters label "0.06" and there is no "0.06" in their file use the next lowest label.
 122                 set<string> processedLabels;
 123                 set<string> userLabels = labels;
 124                 set<int> userLines = lines;
 125
 126
 127                 while((order != NULL) && ((allLines == 1) || (userLabels.size() != 0) || (userLines.size() != 0))) {
 128
 129                         if(allLines == 1 || lines.count(count) == 1 || labels.count(order->getLabel()) == 1){
 130                                         mothurOut(order->getLabel());  mothurOutEndLine();
 131                                         sabund = new SAbundVector();
 132                                         *sabund = (order->getSAbundVector());
 133                                         sabund->print(out);
 134                                         delete sabund;
 135
 136                                         processedLabels.insert(order->getLabel());
 137                                         userLabels.erase(order->getLabel());
 138                                         userLines.erase(count);
 139                         }
 140
 141                         if ((anyLabelsToProcess(order->getLabel(), userLabels, "") == true) && (processedLabels.count(lastLabel) != 1)) {
 142                                         delete order;
 143                                         order = (input->getOrderVector(lastLabel));
 144
 145                                         mothurOut(order->getLabel());  mothurOutEndLine();
 146                                         sabund = new SAbundVector();
 147                                         *sabund = (order->getSAbundVector());
 148                                         sabund->print(out);
 149                                         delete sabund;
 150
 151                                         processedLabels.insert(order->getLabel());
 152                                         userLabels.erase(order->getLabel());
 153                         }
 154
 155
 156                         lastLabel = order->getLabel();
 157
 158                         delete order;
 159                         order = (input->getOrderVector());
 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                         if (order != NULL) {    delete order;   }
 179                         order = (input->getOrderVector(lastLabel));
 180
 181                         mothurOut(order->getLabel());  mothurOutEndLine();
 182                         sabund = new SAbundVector();
 183                         *sabund = (order->getSAbundVector());
 184                         sabund->print(out);
 185                         delete sabund;
 186                         delete order;
 187                 }
 188                 globaldata->gorder = NULL;
 189
 190                 out.close();
 191                 return 0;
 192         }
 193
 194         catch(exception& e) {
 195                 errorOut(e, "GetSAbundCommand", "execute");
 196                 exit(1);
 197         }
 198 }
 199
 200 //**********************************************************************************************************************
 201
 202