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 //**********************************************************************************************************************
  16 ReadDistCommand::ReadDistCommand(string option) {
  17         try {
  18                 abort = false; calledHelp = false;
  19
  20                 //allow user to run help
  21                 if(option == "help") { help(); abort = true; calledHelp = true; }
  22                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  23
  24                 else {
  25                         /*//valid paramters for this command
  26                         string Array[] =  {"phylip", "column", "name", "cutoff", "precision", "group","outputdir","inputdir","sim"};
  27                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  28
  29                         OptionParser parser(option);
  30                         map<string, string> parameters = parser.getParameters();
  31
  32                         ValidParameters validParameter;
  33                         map<string,string>::iterator it;
  34
  35                         //check to make sure all parameters are valid for command
  36                         for (it = parameters.begin(); it != parameters.end(); it++) {
  37                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  38                         }
  39
  40                         globaldata->newRead();
  41
  42                         //if the user changes the input directory command factory will send this info to us in the output parameter
  43                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  44                         if (inputDir == "not found"){   inputDir = "";          }
  45                         else {
  46                                 string path;
  47                                 it = parameters.find("phylip");
  48                                 //user has given a template file
  49                                 if(it != parameters.end()){
  50                                         path = m->hasPath(it->second);
  51                                         //if the user has not given a path then, add inputdir. else leave path alone.
  52                                         if (path == "") {       parameters["phylip"] = inputDir + it->second;           }
  53                                 }
  54
  55                                 it = parameters.find("column");
  56                                 //user has given a template file
  57                                 if(it != parameters.end()){
  58                                         path = m->hasPath(it->second);
  59                                         //if the user has not given a path then, add inputdir. else leave path alone.
  60                                         if (path == "") {       parameters["column"] = inputDir + it->second;           }
  61                                 }
  62
  63                                 it = parameters.find("name");
  64                                 //user has given a template file
  65                                 if(it != parameters.end()){
  66                                         path = m->hasPath(it->second);
  67                                         //if the user has not given a path then, add inputdir. else leave path alone.
  68                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
  69                                 }
  70
  71                                 it = parameters.find("group");
  72                                 //user has given a template file
  73                                 if(it != parameters.end()){
  74                                         path = m->hasPath(it->second);
  75                                         //if the user has not given a path then, add inputdir. else leave path alone.
  76                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
  77                                 }
  78                         }
  79
  80                         //if the user changes the output directory command factory will send this info to us in the output parameter
  81                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = ""; }
  82
  83                         //check for required parameters
  84                         phylipfile = validParameter.validFile(parameters, "phylip", true);
  85                         if (phylipfile == "not open") { abort = true; }
  86                         else if (phylipfile == "not found") { phylipfile = ""; }
  87                         else {  globaldata->setPhylipFile(phylipfile);  globaldata->setFormat("phylip");        }
  88
  89                         columnfile = validParameter.validFile(parameters, "column", true);
  90                         if (columnfile == "not open") { abort = true; }
  91                         else if (columnfile == "not found") { columnfile = ""; }
  92                         else {  globaldata->setColumnFile(columnfile); globaldata->setFormat("column"); }
  93
  94                         groupfile = validParameter.validFile(parameters, "group", true);
  95                         if (groupfile == "not open") { abort = true; }
  96                         else if (groupfile == "not found") { groupfile = ""; }
  97                         else {
  98                                 globaldata->setGroupFile(groupfile);
  99                                 //groupMap = new GroupMap(groupfile);
 100                                 //groupMap->readMap();
 101                         }
 102
 103                         namefile = validParameter.validFile(parameters, "name", true);
 104                         if (namefile == "not open") { abort = true; }
 105                         else if (namefile == "not found") { namefile = ""; }
 106                         else {  globaldata->setNameFile(namefile);      }
 107
 108                         //you are doing a list and group shared
 109                         if ((phylipfile != "") && (groupfile != "")) {
 110                         globaldata->setFormat("matrix"); }
 111
 112                         if ((phylipfile == "") && (columnfile == "")) { m->mothurOut("When executing a read.dist command you must enter a phylip or a column."); m->mothurOutEndLine(); abort = true; }
 113                         else if ((phylipfile != "") && (columnfile != "")) { m->mothurOut("When executing a read.dist command you must enter ONLY ONE of the following: phylip or column."); m->mothurOutEndLine(); abort = true; }
 114
 115                         if (columnfile != "") {
 116                                 if (namefile == "") {  cout << "You need to provide a namefile if you are going to use the column format." << endl; abort = true; }
 117                         }
 118
 119                         //check for optional parameter and set defaults
 120                         // ...at some point should added some additional type checking...
 121                         //get user cutoff and precision or use defaults
 122                         string temp;
 123                         temp = validParameter.validFile(parameters, "precision", false);                if (temp == "not found") { temp = "100"; }
 124                         m->mothurConvert(temp, precision);
 125
 126                         temp = validParameter.validFile(parameters, "sim", false);                              if (temp == "not found") { temp = "F"; }
 127                         sim = m->isTrue(temp);
 128                         globaldata->sim = sim;
 129
 130                         temp = validParameter.validFile(parameters, "cutoff", false);                   if (temp == "not found") { temp = "10"; }
 131                         convert(temp, cutoff);
 132                         cutoff += (5 / (precision * 10.0));
 133
 134                         if (abort == false) {
 135                                 distFileName = globaldata->inputFileName;
 136                                 format = globaldata->getFormat();
 137
 138                                 if (format == "column") { read = new ReadColumnMatrix(distFileName); }
 139                                 else if (format == "phylip") { read = new ReadPhylipMatrix(distFileName); }
 140                                 else if (format == "matrix") {
 141                                         groupMap = new GroupMap(groupfile);
 142                                         int error = groupMap->readMap();
 143                                         if (error == 1) { delete groupMap; abort = true; }
 144                                         else {
 145                                                 if (globaldata->gGroupmap != NULL) { delete globaldata->gGroupmap;  }
 146                                                 globaldata->gGroupmap = groupMap;
 147                                         }
 148                                 }
 149
 150                                 if (format != "matrix" ) {
 151                                         read->setCutoff(cutoff);
 152
 153                                         if(namefile != ""){
 154                                                 nameMap = new NameAssignment(namefile);
 155                                                 nameMap->readMap();
 156                                         }else{
 157                                                 nameMap = NULL;
 158                                         }
 159                                 }
 160                         }
 161 */
 162                 }
 163
 164         }
 165         catch(exception& e) {
 166                 m->errorOut(e, "ReadDistCommand", "ReadDistCommand");
 167                 exit(1);
 168         }
 169 }
 170 //**********************************************************************************************************************
 171 int ReadDistCommand::execute(){
 172         try {
 173
 174                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 175                 m->mothurOut(getHelpString()); m->mothurOutEndLine();
 176 /*
 177                 time_t start = time(NULL);
 178                 size_t numDists = 0;
 179
 180                 if (format == "matrix") {
 181                         ifstream in;
 182                         m->openInputFile(distFileName, in);
 183                         matrix = new FullMatrix(in); //reads the matrix file
 184                         in.close();
 185
 186                         if (m->control_pressed) { delete groupMap; delete matrix; return 0; }
 187
 188                         //if files don't match...
 189                         if (matrix->getNumSeqs() < groupMap->getNumSeqs()) {
 190                                 m->mothurOut("Your distance file contains " + toString(matrix->getNumSeqs()) + " sequences, and your group file contains " + toString(groupMap->getNumSeqs()) + " sequences.");  m->mothurOutEndLine();
 191                                 //create new group file
 192                                 if(outputDir == "") { outputDir += m->hasPath(groupfile); }
 193
 194                                 string newGroupFile = outputDir + m->getRootName(m->getSimpleName(groupfile)) + "editted.groups";
 195                                 outputNames.push_back(newGroupFile);
 196                                 ofstream outGroups;
 197                                 m->openOutputFile(newGroupFile, outGroups);
 198
 199                                 for (int i = 0; i < matrix->getNumSeqs(); i++) {
 200                                         if (m->control_pressed) { delete groupMap; delete matrix; outGroups.close(); m->mothurRemove(newGroupFile); return 0; }
 201
 202                                         Names temp = matrix->getRowInfo(i);
 203                                         outGroups << temp.seqName << '\t' << temp.groupName << endl;
 204                                 }
 205                                 outGroups.close();
 206
 207                                 m->mothurOut(newGroupFile + " is a new group file containing only the sequence that are in your distance file. I will read this file instead."); m->mothurOutEndLine();
 208
 209                                 //read new groupfile
 210                                 delete groupMap; groupMap = NULL;
 211                                 groupfile = newGroupFile;
 212                                 globaldata->setGroupFile(groupfile);
 213
 214                                 groupMap = new GroupMap(groupfile);
 215                                 groupMap->readMap();
 216
 217                                 if (m->control_pressed) { delete groupMap; delete matrix; m->mothurRemove(newGroupFile); return 0; }
 218
 219                                 globaldata->gGroupmap = groupMap;
 220                         }
 221
 222                         //memory leak prevention
 223                         if (globaldata->gMatrix != NULL) { delete globaldata->gMatrix;  }
 224                         globaldata->gMatrix = matrix; //save matrix for coverage commands
 225                         numDists = matrix->getSizes()[1];
 226                 } else {
 227                         read->read(nameMap);
 228                         //to prevent memory leak
 229
 230                         if (m->control_pressed) {  return 0; }
 231
 232                         if (globaldata->gListVector != NULL) {  delete globaldata->gListVector;  }
 233                         globaldata->gListVector = read->getListVector();
 234
 235                         if (globaldata->gSparseMatrix != NULL) { delete globaldata->gSparseMatrix;  }
 236                         globaldata->gSparseMatrix = read->getMatrix();
 237                         numDists = globaldata->gSparseMatrix->getNNodes();
 238                 }
 239
 240                 if (m->control_pressed) {  return 0; }
 241
 242                 if (outputNames.size() != 0) {
 243                         m->mothurOutEndLine();
 244                         m->mothurOut("Output File Name: "); m->mothurOutEndLine();
 245                         for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 246                         m->mothurOutEndLine();
 247                 }
 248
 249                 m->mothurOut("It took " + toString(time(NULL) - start) + " secs to read "); m->mothurOutEndLine();
 250  */
 251                 return 0;
 252
 253         }
 254         catch(exception& e) {
 255                 m->errorOut(e, "ReadDistCommand", "execute");
 256                 exit(1);
 257         }
 258 }