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                         OptionParser parser(option);
  29                         map<string, string> parameters = parser.getParameters();
  30
  31                         ValidParameters validParameter;
  32
  33                         //check to make sure all parameters are valid for command
  34                         for (map<string,string>::iterator 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 != "")) {
  68                         globaldata->setFormat("matrix"); }
  69
  70                         if ((phylipfile == "") && (columnfile == "")) { cout << "When executing a read.dist command you must enter a phylip or a column." << endl; abort = true; }
  71                         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; }
  72
  73                         if (columnfile != "") {
  74                                 if (namefile == "") {  cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }
  75                         }
  76
  77                         //check for optional parameter and set defaults
  78                         // ...at some point should added some additional type checking...
  79                         //get user cutoff and precision or use defaults
  80                         string temp;
  81                         temp = validParameter.validFile(parameters, "precision", false);                        if (temp == "not found") { temp = "100"; }
  82                         convert(temp, precision);
  83
  84                         temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "10"; }
  85                         convert(temp, cutoff);
  86                         cutoff += (5 / (precision * 10.0));
  87
  88                         if (abort == false) {
  89                                 distFileName = globaldata->inputFileName;
  90                                 format = globaldata->getFormat();
  91
  92                                 if (format == "column") { read = new ReadColumnMatrix(distFileName); }
  93                                 else if (format == "phylip") { read = new ReadPhylipMatrix(distFileName); }
  94                                 else if (format == "matrix") {
  95                                         groupMap = new GroupMap(groupfile);
  96                                         groupMap->readMap();
  97                                         if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap;  }
  98                                         globaldata->gGroupmap = groupMap;
  99                                 }
 100
 101                                 if (format != "matrix" ) {
 102                                         read->setCutoff(cutoff);
 103
 104                                         if(namefile != ""){
 105                                                 nameMap = new NameAssignment(namefile);
 106                                                 nameMap->readMap(1,2);
 107                                         }else{
 108                                                 nameMap = NULL;
 109                                         }
 110                                 }
 111                         }
 112
 113                 }
 114
 115         }
 116         catch(exception& e) {
 117                 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function ReadDistCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 118                 exit(1);
 119         }
 120         catch(...) {
 121                 cout << "An unknown error has occurred in the ReadDistCommand class function ReadDistCommand. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 122                 exit(1);
 123         }
 124 }
 125 //**********************************************************************************************************************
 126
 127 void ReadDistCommand::help(){
 128         try {
 129                 cout << "The read.dist command parameter options are phylip or column, group, name, cutoff and precision" << "\n";
 130                 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";
 131                 cout << "For this use the read.dist command should be in the following format: " << "\n";
 132                 cout << "read.dist(phylip=yourDistFile, name=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) " << "\n";
 133                 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";
 134                 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";
 135                 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";
 136                 cout << "For this use the read.dist command should be in the following format: " << "\n";
 137                 cout << "read.dist(phylip=yourPhylipfile, group=yourGroupFile). The cutoff and precision parameters are not valid with this use.  " << "\n";
 138                 cout << "Note: No spaces between parameter labels (i.e. phylip), '=' and parameters (i.e.yourPhylipfile)." << "\n" << "\n";
 139         }
 140         catch(exception& e) {
 141                 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 142                 exit(1);
 143         }
 144         catch(...) {
 145                 cout << "An unknown error has occurred in the ReadDistCommand class function help. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 146                 exit(1);
 147         }
 148 }
 149
 150 //**********************************************************************************************************************
 151
 152 ReadDistCommand::~ReadDistCommand(){
 153         if (abort == false) {
 154                 if (format != "matrix") { delete read; delete nameMap; }
 155         }
 156 }
 157
 158 //**********************************************************************************************************************
 159 int ReadDistCommand::execute(){
 160         try {
 161
 162                 if (abort == true) {    return 0;       }
 163
 164                 if (format == "matrix") {
 165                         ifstream in;
 166                         openInputFile(distFileName, in);
 167                         matrix = new FullMatrix(in); //reads the matrix file
 168                         in.close();
 169                         //memory leak prevention
 170                         if (globaldata->gMatrix != NULL) { delete globaldata->gMatrix;  }
 171                         globaldata->gMatrix = matrix; //save matrix for coverage commands
 172                 }else {
 173                         read->read(nameMap);
 174                         //to prevent memory leak
 175
 176                         if (globaldata->gListVector != NULL) {  delete globaldata->gListVector;  }
 177                         globaldata->gListVector = read->getListVector();
 178
 179                         if (globaldata->gSparseMatrix != NULL) { delete globaldata->gSparseMatrix;  }
 180                         globaldata->gSparseMatrix = read->getMatrix();
 181
 182                 }
 183                 return 0;
 184         }
 185         catch(exception& e) {
 186                 cout << "Standard Error: " << e.what() << " has occurred in the ReadDistCommand class Function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 187                 exit(1);
 188         }
 189         catch(...) {
 190                 cout << "An unknown error has occurred in the ReadDistCommand class function execute. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
 191                 exit(1);
 192         }
 193 }