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
  21                 else {
  22                         /*
  23                         //valid paramters for this command
  24                         string Array[] =  {"tree","group","name","outputdir","inputdir"};
  25                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  26
  27                         OptionParser parser(option);
  28                         map<string, string> parameters = parser.getParameters();
  29
  30                         ValidParameters validParameter;
  31                         map<string, string>::iterator it;
  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                         //if the user changes the input directory command factory will send this info to us in the output parameter
  41                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
  42                         if (inputDir == "not found"){   inputDir = "";          }
  43                         else {
  44                                 string path;
  45                                 it = parameters.find("tree");
  46                                 //user has given a template file
  47                                 if(it != parameters.end()){
  48                                         path = m->hasPath(it->second);
  49                                         //if the user has not given a path then, add inputdir. else leave path alone.
  50                                         if (path == "") {       parameters["tree"] = inputDir + it->second;             }
  51                                 }
  52
  53                                 it = parameters.find("group");
  54                                 //user has given a template file
  55                                 if(it != parameters.end()){
  56                                         path = m->hasPath(it->second);
  57                                         //if the user has not given a path then, add inputdir. else leave path alone.
  58                                         if (path == "") {       parameters["group"] = inputDir + it->second;            }
  59                                 }
  60
  61                                 it = parameters.find("name");
  62                                 //user has given a template file
  63                                 if(it != parameters.end()){
  64                                         path = m->hasPath(it->second);
  65                                         //if the user has not given a path then, add inputdir. else leave path alone.
  66                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
  67                                 }
  68
  69                         }
  70
  71
  72                         //check for required parameters
  73                         treefile = validParameter.validFile(parameters, "tree", true);
  74                         if (treefile == "not open") { abort = true; }
  75                         else if (treefile == "not found") { treefile = ""; m->mothurOut("tree is a required parameter for the read.tree command."); m->mothurOutEndLine(); abort = true;  }
  76
  77                         groupfile = validParameter.validFile(parameters, "group", true);
  78                         if (groupfile == "not open") { abort = true; }
  79                         else if (groupfile == "not found") {
  80                                 groupfile = "";
  81
  82                                 m->mothurOut("You have not provided a group file. I am assumming all sequence are from the same group."); m->mothurOutEndLine();
  83
  84                                 if (treefile != "") {  Tree* tree = new Tree(treefile); delete tree;  } //extracts names from tree to make faked out groupmap
  85
  86                                 //read in group map info.
  87                                 treeMap = new TreeMap();
  88                                 for (int i = 0; i < m->Treenames.size(); i++) { treeMap->addSeq(m->Treenames[i], "Group1"); }
  89
  90                         }else {
  91                                 //read in group map info.
  92                                 treeMap = new TreeMap(groupfile);
  93                                 treeMap->readMap();
  94                         }
  95
  96                         namefile = validParameter.validFile(parameters, "name", true);
  97                         if (namefile == "not open") { abort = true; }
  98                         else if (namefile == "not found") { namefile = ""; }
  99                         else { readNamesFile(); }
 100
 101                         if (abort == false) {
 102                                 filename = treefile;
 103                                 read = new ReadNewickTree(filename);
 104                         }
 105                         */
 106                 }
 107         }
 108         catch(exception& e) {
 109                 m->errorOut(e, "ReadTreeCommand", "ReadTreeCommand");
 110                 exit(1);
 111         }
 112 }
 113 //**********************************************************************************************************************
 114
 115 int ReadTreeCommand::execute(){
 116         try {
 117
 118                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 119                 m->mothurOut(getHelpString()); m->mothurOutEndLine();
 120                 /*
 121                 int readOk;
 122
 123                 readOk = read->read(treeMap);
 124
 125                 if (readOk != 0) { m->mothurOut("Read Terminated."); m->mothurOutEndLine(); globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
 126
 127                 vector<Tree*> T = read->gTree;
 128
 129                 //assemble users trees
 130                 for (int i = 0; i < T.size(); i++) {
 131                         if (m->control_pressed) {
 132                                 for (int i = 0; i < T.size(); i++) {  delete T[i];  }
 133                                 globaldata->gTree.clear();
 134                                 delete globaldata->gTreemap;
 135                                 return 0;
 136                         }
 137
 138                         T[i]->assembleTree();
 139                 }
 140
 141
 142                 //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.
 143                 int numNamesInTree;
 144                 if (namefile != "")  {
 145                         if (numUniquesInName == globaldata->Treenames.size()) {  numNamesInTree = nameMap.size();  }
 146                         else {   numNamesInTree = globaldata->Treenames.size();  }
 147                 }else {  numNamesInTree = globaldata->Treenames.size();  }
 148
 149
 150                 //output any names that are in group file but not in tree
 151                 if (numNamesInTree < treeMap->getNumSeqs()) {
 152                         for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) {
 153                                 //is that name in the tree?
 154                                 int count = 0;
 155                                 for (int j = 0; j < globaldata->Treenames.size(); j++) {
 156                                         if (treeMap->namesOfSeqs[i] == globaldata->Treenames[j]) { break; } //found it
 157                                         count++;
 158                                 }
 159
 160                                 if (m->control_pressed) {
 161                                         for (int i = 0; i < T.size(); i++) {  delete T[i];  }
 162                                         globaldata->gTree.clear();
 163                                         delete globaldata->gTreemap;
 164                                         return 0;
 165                                 }
 166
 167                                 //then you did not find it so report it
 168                                 if (count == globaldata->Treenames.size()) {
 169                                         //if it is in your namefile then don't remove
 170                                         map<string, string>::iterator it = nameMap.find(treeMap->namesOfSeqs[i]);
 171
 172                                         if (it == nameMap.end()) {
 173                                                 m->mothurOut(treeMap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); m->mothurOutEndLine();
 174                                                 treeMap->removeSeq(treeMap->namesOfSeqs[i]);
 175                                                 i--; //need this because removeSeq removes name from namesOfSeqs
 176                                         }
 177                                 }
 178                         }
 179
 180                         globaldata->gTreemap = treeMap;
 181                 }
 182                  */
 183                 return 0;
 184         }
 185         catch(exception& e) {
 186                 m->errorOut(e, "ReadTreeCommand", "execute");
 187                 exit(1);
 188         }
 189 }
 190 /*****************************************************************/
 191 int ReadTreeCommand::readNamesFile() {
 192         try {
 193                 /*
 194                 m->names.clear();
 195                 numUniquesInName = 0;
 196
 197                 ifstream in;
 198                 m->openInputFile(namefile, in);
 199
 200                 string first, second;
 201                 map<string, string>::iterator itNames;
 202
 203                 while(!in.eof()) {
 204                         in >> first >> second; m->gobble(in);
 205
 206                         numUniquesInName++;
 207
 208                         itNames = m->names.find(first);
 209                         if (itNames == globaldata->names.end()) {
 210                                 globaldata->names[first] = second;
 211
 212                                 //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
 213                                 vector<string> dupNames;
 214                                 m->splitAtComma(second, dupNames);
 215
 216                                 for (int i = 0; i < dupNames.size(); i++) {     nameMap[dupNames[i]] = dupNames[i];  if ((groupfile == "") && (i != 0)) { globaldata->gTreemap->addSeq(dupNames[i], "Group1"); }  }
 217                         }else {  m->mothurOut(first + " has already been seen in namefile, disregarding names file."); m->mothurOutEndLine(); in.close(); globaldata->names.clear(); namefile = ""; return 1; }
 218                 }
 219                 in.close();
 220                 */
 221                 return 0;
 222         }
 223         catch(exception& e) {
 224                 m->errorOut(e, "ReadTreeCommand", "readNamesFile");
 225                 exit(1);
 226         }
 227 }
 228
 229 //**********************************************************************************************************************