readtreecommand.cpp

   1 /*
   2  *  readtreecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by Sarah Westcott on 1/23/09.
   6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
   7  *
   8  */
   9
  10 #include "readtreecommand.h"
  11
  12
  13 //**********************************************************************************************************************
  14 ReadTreeCommand::ReadTreeCommand(string option)  {
  15         try {
  16                 abort = false; calledHelp = false;
  17
  18                 //allow user to run help
  19                 if(option == "help") { help(); abort = true; calledHelp = true; }
  20                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  21
  22                 else {
  23                         /*
  24                         //valid paramters for this command
  25                         string Array[] =  {"tree","group","name","outputdir","inputdir"};
  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                         map<string, string>::iterator it;
  33
  34                         //check to make sure all parameters are valid for command
  35                         for (it = parameters.begin(); it != parameters.end(); it++) {
  36                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  37                         }
  38
  39                         globaldata->newRead();
  40
  41                         //if the user changes the input directory command factory will send this info to us in the output parameter
  42                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  43                         if (inputDir == "not found"){   inputDir = "";          }
  44                         else {
  45                                 string path;
  46                                 it = parameters.find("tree");
  47                                 //user has given a template file
  48                                 if(it != parameters.end()){
  49                                         path = m->hasPath(it->second);
  50                                         //if the user has not given a path then, add inputdir. else leave path alone.
  51                                         if (path == "") {       parameters["tree"] = inputDir + it->second;             }
  52                                 }
  53
  54                                 it = parameters.find("group");
  55                                 //user has given a template file
  56                                 if(it != parameters.end()){
  57                                         path = m->hasPath(it->second);
  58                                         //if the user has not given a path then, add inputdir. else leave path alone.
  59                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
  60                                 }
  61
  62                                 it = parameters.find("name");
  63                                 //user has given a template file
  64                                 if(it != parameters.end()){
  65                                         path = m->hasPath(it->second);
  66                                         //if the user has not given a path then, add inputdir. else leave path alone.
  67                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
  68                                 }
  69
  70                         }
  71
  72
  73                         //check for required parameters
  74                         treefile = validParameter.validFile(parameters, "tree", true);
  75                         if (treefile == "not open") { abort = true; }
  76                         else if (treefile == "not found") { treefile = ""; m->mothurOut("tree is a required parameter for the read.tree command."); m->mothurOutEndLine(); abort = true;  }
  77
  78                         groupfile = validParameter.validFile(parameters, "group", true);
  79                         if (groupfile == "not open") { abort = true; }
  80                         else if (groupfile == "not found") {
  81                                 groupfile = "";
  82
  83                                 m->mothurOut("You have not provided a group file. I am assumming all sequence are from the same group."); m->mothurOutEndLine();
  84
  85                                 if (treefile != "") {  Tree* tree = new Tree(treefile); delete tree;  } //extracts names from tree to make faked out groupmap
  86
  87                                 //read in group map info.
  88                                 treeMap = new TreeMap();
  89                                 for (int i = 0; i < m->Treenames.size(); i++) { treeMap->addSeq(m->Treenames[i], "Group1"); }
  90
  91                         }else {
  92                                 //read in group map info.
  93                                 treeMap = new TreeMap(groupfile);
  94                                 treeMap->readMap();
  95                         }
  96
  97                         namefile = validParameter.validFile(parameters, "name", true);
  98                         if (namefile == "not open") { abort = true; }
  99                         else if (namefile == "not found") { namefile = ""; }
 100                         else { readNamesFile(); }
 101
 102                         if (abort == false) {
 103                                 filename = treefile;
 104                                 read = new ReadNewickTree(filename);
 105                         }
 106                         */
 107                 }
 108         }
 109         catch(exception& e) {
 110                 m->errorOut(e, "ReadTreeCommand", "ReadTreeCommand");
 111                 exit(1);
 112         }
 113 }
 114 //**********************************************************************************************************************
 115
 116 int ReadTreeCommand::execute(){
 117         try {
 118
 119                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 120                 m->mothurOut(getHelpString()); m->mothurOutEndLine();
 121                 /*
 122                 int readOk;
 123
 124                 readOk = read->read(treeMap);
 125
 126                 if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
 127
 128                 vector<Tree*> T = read->gTree;
 129
 130                 //assemble users trees
 131                 for (int i = 0; i < T.size(); i++) {
 132                         if (m->control_pressed) {
 133                                 for (int i = 0; i < T.size(); i++) {  delete T[i];  }
 134                                 globaldata->gTree.clear();
 135                                 delete globaldata->gTreemap;
 136                                 return 0;
 137                         }
 138
 139                         T[i]->assembleTree();
 140                 }
 141
 142
 143                 //if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
 144                 int numNamesInTree;
 145                 if (namefile != "")  {
 146                         if (numUniquesInName == globaldata->Treenames.size()) {  numNamesInTree = nameMap.size();  }
 147                         else {   numNamesInTree = globaldata->Treenames.size();  }
 148                 }else {  numNamesInTree = globaldata->Treenames.size();  }
 149
 150
 151                 //output any names that are in group file but not in tree
 152                 if (numNamesInTree < treeMap->getNumSeqs()) {
 153                         for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) {
 154                                 //is that name in the tree?
 155                                 int count = 0;
 156                                 for (int j = 0; j < globaldata->Treenames.size(); j++) {
 157                                         if (treeMap->namesOfSeqs[i] == globaldata->Treenames[j]) { break; } //found it
 158                                         count++;
 159                                 }
 160
 161                                 if (m->control_pressed) {
 162                                         for (int i = 0; i < T.size(); i++) {  delete T[i];  }
 163                                         globaldata->gTree.clear();
 164                                         delete globaldata->gTreemap;
 165                                         return 0;
 166                                 }
 167
 168                                 //then you did not find it so report it
 169                                 if (count == globaldata->Treenames.size()) {
 170                                         //if it is in your namefile then don't remove
 171                                         map<string, string>::iterator it = nameMap.find(treeMap->namesOfSeqs[i]);
 172
 173                                         if (it == nameMap.end()) {
 174                                                 m->mothurOut(treeMap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
 175                                                 treeMap->removeSeq(treeMap->namesOfSeqs[i]);
 176                                                 i--; //need this because removeSeq removes name from namesOfSeqs
 177                                         }
 178                                 }
 179                         }
 180
 181                         globaldata->gTreemap = treeMap;
 182                 }
 183                  */
 184                 return 0;
 185         }
 186         catch(exception& e) {
 187                 m->errorOut(e, "ReadTreeCommand", "execute");
 188                 exit(1);
 189         }
 190 }
 191 /*****************************************************************/
 192 int ReadTreeCommand::readNamesFile() {
 193         try {
 194                 /*
 195                 m->names.clear();
 196                 numUniquesInName = 0;
 197
 198                 ifstream in;
 199                 m->openInputFile(namefile, in);
 200
 201                 string first, second;
 202                 map<string, string>::iterator itNames;
 203
 204                 while(!in.eof()) {
 205                         in >> first >> second; m->gobble(in);
 206
 207                         numUniquesInName++;
 208
 209                         itNames = m->names.find(first);
 210                         if (itNames == globaldata->names.end()) {
 211                                 globaldata->names[first] = second;
 212
 213                                 //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
 214                                 vector<string> dupNames;
 215                                 m->splitAtComma(second, dupNames);
 216
 217                                 for (int i = 0; i < dupNames.size(); i++) {     nameMap[dupNames[i]] = dupNames[i];  if ((groupfile == "") && (i != 0)) { globaldata->gTreemap->addSeq(dupNames[i], "Group1"); }  }
 218                         }else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); globaldata->names.clear(); namefile = ""; return 1; }
 219                 }
 220                 in.close();
 221                 */
 222                 return 0;
 223         }
 224         catch(exception& e) {
 225                 m->errorOut(e, "ReadTreeCommand", "readNamesFile");
 226                 exit(1);
 227         }
 228 }
 229
 230 //**********************************************************************************************************************