readdistcommand.cpp

   1 /*
   2  *  readdistcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 1/20/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "readdistcommand.h"
  11 #include "readphylip.h"
  12 #include "readcolumn.h"
  13 #include "readmatrix.hpp"
  14
  15 ReadDistCommand::ReadDistCommand(string option){
  16         try {
  17                 globaldata = GlobalData::getInstance();
  18                 abort = false;
  19
  20                 //allow user to run help
  21                 if(option == "help") { help(); abort = true; }
  22
  23                 else {
  24                         //valid paramters for this command
  25                         string Array[] =  {"phylip","column", "name","cutoff","precision", "group"};
  26                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  27
  28                         parser = new OptionParser();
  29                         parser->parse(option, parameters);  delete parser;
  30
  31                         ValidParameters* validParameter = new ValidParameters();
  32
  33                         //check to make sure all parameters are valid for command
  34                         for (it = parameters.begin(); it != parameters.end(); it++) {
  35                                 if (validParameter->isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  36                         }
  37
  38                         globaldata->newRead();
  39
  40                         //check for required parameters
  41                         phylipfile = validParameter->validFile(parameters, "phylip", true);
  42                         if (phylipfile == "not open") { abort = true; }
  43                         else if (phylipfile == "not found") { phylipfile = ""; }
  44                         else {  globaldata->setPhylipFile(phylipfile);  globaldata->setFormat("phylip");        }
  45
  46                         columnfile = validParameter->validFile(parameters, "column", true);
  47                         if (columnfile == "not open") { abort = true; }
  48                         else if (columnfile == "not found") { columnfile = ""; }
  49                         else {  globaldata->setColumnFile(columnfile); globaldata->setFormat("column"); }
  50
  51                         groupfile = validParameter->validFile(parameters, "group", true);
  52                         if (groupfile == "not open") { abort = true; }
  53                         else if (groupfile == "not found") { groupfile = ""; }
  54                         else {
  55                                 globaldata->setGroupFile(groupfile);
  56                                 groupMap = new GroupMap(groupfile);
  57                                 groupMap->readMap();
  58                         }
  59
  60                         namefile = validParameter->validFile(parameters, "name", true);
  61                         if (namefile == "not open") { abort = true; }
  62                         else if (namefile == "not found") { namefile = ""; }
  63                         else {  globaldata->setNameFile(namefile);      }
  64
  65
  66                         //you are doing a list and group shared
  67                         if ((phylipfile != "") && (groupfile != "")) { globaldata->setFormat("matrix"); }
  68
  69                         if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist command you must enter a phylip or a column." << endl; abort = true; }
  70                         else if ((phylipfile != "") && (columnfile != "")) { cout << "When executing a read.dist command you must enter ONLY ONE of the following: phylip or column." << endl; abort = true; }
  71
  72                         if (columnfile != "") {
  73                                 if (namefile == "") {  cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }
  74                         }
  75
  76                         //check for optional parameter and set defaults
  77                         // ...at some point should added some additional type checking...
  78                         //get user cutoff and precision or use defaults
  79                         string temp;
  80                         temp = validParameter->validFile(parameters, "precision", false);                       if (temp == "not found") { temp = "100"; }
  81                         convert(temp, precision);
  82
  83                         temp = validParameter->validFile(parameters, "cutoff", false);                  if (temp == "not found") { temp = "10"; }
  84                         convert(temp, cutoff);
  85                         cutoff += (5 / (precision * 10.0));
  86
  87                         delete validParameter;
  88
  89                         if (abort == false) {
  90                                 filename = globaldata->inputFileName;
  91                                 format = globaldata->getFormat();
  92
  93                                 if (format == "column") { read = new ReadColumnMatrix(filename); }
  94                                 else if (format == "phylip") { read = new ReadPhylipMatrix(filename); }
  95                                 else if (format == "matrix") {
  96                                         groupMap = new GroupMap(groupfile);
  97                                         groupMap->readMap();
  98                                         if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap;  }
  99                                         globaldata->gGroupmap = groupMap;
 100                                 }
 101
 102                                 if (format != "matrix" ) {
 103                                         read->setCutoff(cutoff);
 104
 105                                         if(namefile != ""){
 106                                                 nameMap = new NameAssignment(namefile);
 107                                                 nameMap->readMap(1,2);
 108                                         }else{
 109                                                 nameMap = NULL;
 110                                         }
 111                                 }
 112                         }
 113
 114                 }
 115
 116         }
 117         catch(exception& e) {
 118                 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function ReadDistCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 119                 exit(1);
 120         }
 121         catch(...) {
 122                 cout << "An unknown error has occurred in the ReadDistCommand class function ReadDistCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 123                 exit(1);
 124         }
 125 }
 126 //**********************************************************************************************************************
 127
 128 void ReadDistCommand::help(){
 129         try {
 130                 cout << "The read.dist command parameter options are phylip or column, group, name, cutoff and precision" << "\n";
 131                 cout << "The read.dist command can be used in two ways.  The first is to read a phylip or column and run the cluster command" << "\n";
 132                 cout << "For this use the read.dist command should be in the following format: " << "\n";
 133                 cout << "read.dist(phylip=yourDistFile, name=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) " << "\n";
 134                 cout << "The phylip or column parameter is required, but only one may be used.  If you use a column file the name filename is required. " << "\n";
 135                 cout << "If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed." << "\n";
 136                 cout << "The second way to use the read.dist command is to read a phylip or column and a group, so you can use the libshuff command." << "\n";
 137                 cout << "For this use the read.dist command should be in the following format: " << "\n";
 138                 cout << "read.dist(phylip=yourPhylipfile, group=yourGroupFile). The cutoff and precision parameters are not valid with this use.  " << "\n";
 139                 cout << "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourPhylipfile)." << "\n" << "\n";
 140         }
 141         catch(exception& e) {
 142                 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 143                 exit(1);
 144         }
 145         catch(...) {
 146                 cout << "An unknown error has occurred in the ReadDistCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 147                 exit(1);
 148         }
 149 }
 150
 151 //**********************************************************************************************************************
 152 ReadDistCommand::~ReadDistCommand(){
 153         delete read;
 154         delete nameMap;
 155 }
 156
 157 //**********************************************************************************************************************
 158 int ReadDistCommand::execute(){
 159         try {
 160
 161                 if (abort == true) {    return 0;       }
 162
 163                 if (format == "matrix") {
 164                         ifstream in;
 165                         openInputFile(filename, in);
 166                         matrix = new FullMatrix(in); //reads the matrix file
 167                         //memory leak prevention
 168                         //if (globaldata->gMatrix != NULL) { delete globaldata->gMatrix;  }
 169                         globaldata->gMatrix = matrix; //save matrix for coverage commands
 170                 }else {
 171                         read->read(nameMap);
 172                         //to prevent memory leak
 173                         if (globaldata->gListVector != NULL) { delete globaldata->gListVector;  }
 174                         globaldata->gListVector = read->getListVector();
 175                         if (globaldata->gSparseMatrix != NULL) { delete globaldata->gSparseMatrix;  }
 176                         globaldata->gSparseMatrix = read->getMatrix();
 177                 }
 178                 return 0;
 179         }
 180         catch(exception& e) {
 181                 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 182                 exit(1);
 183         }
 184         catch(...) {
 185                 cout << "An unknown error has occurred in the ReadDistCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 186                 exit(1);
 187         }
 188 }