deuniquetreecommand.cpp

   1 /*
   2  *  deuniquetreecommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 5/27/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "deuniquetreecommand.h"
  11 #include "treereader.h"
  12
  13 //**********************************************************************************************************************
  14 vector<string> DeuniqueTreeCommand::setParameters(){
  15         try {
  16                 CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","tree",false,true,true); parameters.push_back(ptree);
  17                 CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pname);
  18                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
  19                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
  20
  21                 vector<string> myArray;
  22                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  23                 return myArray;
  24         }
  25         catch(exception& e) {
  26                 m->errorOut(e, "DeuniqueTreeCommand", "setParameters");
  27                 exit(1);
  28         }
  29 }
  30 //**********************************************************************************************************************
  31 string DeuniqueTreeCommand::getHelpString(){
  32         try {
  33                 string helpString = "";
  34                 helpString += "The deunique.tree command parameters are tree and name.  Both parameters are required unless you have valid current files.\n";
  35                 helpString += "The deunique.tree command should be in the following format: deunique.tree(tree=yourTreeFile, name=yourNameFile).\n";
  36                 helpString += "Example deunique.tree(tree=abrecovery.tree, name=abrecovery.names).\n";
  37                 helpString += "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreeFile).\n";
  38                 return helpString;
  39         }
  40         catch(exception& e) {
  41                 m->errorOut(e, "DeuniqueTreeCommand", "getHelpString");
  42                 exit(1);
  43         }
  44 }
  45 //**********************************************************************************************************************
  46 string DeuniqueTreeCommand::getOutputPattern(string type) {
  47     try {
  48         string pattern = "";
  49
  50         if (type == "tree") {  pattern = "[filename],deunique.tre"; }
  51         else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true;  }
  52
  53         return pattern;
  54     }
  55     catch(exception& e) {
  56         m->errorOut(e, "DeuniqueTreeCommand", "getOutputPattern");
  57         exit(1);
  58     }
  59 }
  60 //**********************************************************************************************************************
  61 DeuniqueTreeCommand::DeuniqueTreeCommand(){
  62         try {
  63                 abort = true; calledHelp = true;
  64                 setParameters();
  65                 vector<string> tempOutNames;
  66                 outputTypes["tree"] = tempOutNames;
  67         }
  68         catch(exception& e) {
  69                 m->errorOut(e, "DeuniqueTreeCommand", "DeuniqueTreeCommand");
  70                 exit(1);
  71         }
  72 }
  73 /***********************************************************/
  74 DeuniqueTreeCommand::DeuniqueTreeCommand(string option)  {
  75         try {
  76                 abort = false; calledHelp = false;
  77
  78                 //allow user to run help
  79                 if(option == "help") { help(); abort = true; calledHelp = true; }
  80                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  81
  82                 else {
  83                         vector<string> myArray = setParameters();
  84
  85                         OptionParser parser(option);
  86                         map<string,string> parameters = parser.getParameters();
  87                         map<string,string>::iterator it;
  88
  89                         ValidParameters validParameter;
  90
  91                         //check to make sure all parameters are valid for command
  92                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  93                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  94                         }
  95
  96                         //initialize outputTypes
  97                         vector<string> tempOutNames;
  98                         outputTypes["tree"] = tempOutNames;
  99
 100                         //if the user changes the input directory command factory will send this info to us in the output parameter
 101                         string inputDir = validParameter.validFile(parameters, "inputdir", false);
 102                         if (inputDir == "not found"){   inputDir = "";          }
 103                         else {
 104                                 string path;
 105                                 it = parameters.find("tree");
 106                                 //user has given a template file
 107                                 if(it != parameters.end()){
 108                                         path = m->hasPath(it->second);
 109                                         //if the user has not given a path then, add inputdir. else leave path alone.
 110                                         if (path == "") {       parameters["tree"] = inputDir + it->second;             }
 111                                 }
 112
 113                                 it = parameters.find("name");
 114                                 //user has given a template file
 115                                 if(it != parameters.end()){
 116                                         path = m->hasPath(it->second);
 117                                         //if the user has not given a path then, add inputdir. else leave path alone.
 118                                         if (path == "") {       parameters["name"] = inputDir + it->second;             }
 119                                 }
 120                         }
 121
 122             //check for required parameters
 123                         treefile = validParameter.validFile(parameters, "tree", true);
 124                         if (treefile == "not open") { abort = true; }
 125                         else if (treefile == "not found") {                             //if there is a current design file, use it
 126                                 treefile = m->getTreeFile();
 127                                 if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
 128                                 else {  m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
 129                         }else { m->setTreeFile(treefile); }
 130
 131                         namefile = validParameter.validFile(parameters, "name", true);
 132                         if (namefile == "not open") { abort = true; }
 133                         else if (namefile == "not found") {                             //if there is a current design file, use it
 134                                 namefile = m->getNameFile();
 135                                 if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
 136                                 else {  m->mothurOut("You have no current name file and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
 137                         }else { m->setNameFile(namefile); }
 138
 139                         outputDir = validParameter.validFile(parameters, "outputdir", false);           if (outputDir == "not found"){  outputDir = m->hasPath(treefile);       }
 140                 }
 141
 142         }
 143         catch(exception& e) {
 144                 m->errorOut(e, "DeuniqueTreeCommand", "DeuniqueTreeCommand");
 145                 exit(1);
 146         }
 147 }
 148
 149 /***********************************************************/
 150 int DeuniqueTreeCommand::execute() {
 151         try {
 152
 153                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 154
 155                 m->setTreeFile(treefile);
 156
 157                 TreeReader* reader = new TreeReader(treefile, "", namefile);
 158         vector<Tree*> T = reader->getTrees();
 159         map<string, string> nameMap;
 160         m->readNames(namefile, nameMap);
 161         delete reader;
 162
 163                 //print new Tree
 164         map<string, string> variables;
 165         variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(treefile));
 166                 string outputFile = getOutputFileName("tree", variables);
 167                 outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
 168                 ofstream out;
 169                 m->openOutputFile(outputFile, out);
 170                 T[0]->print(out, nameMap);
 171                 out.close();
 172
 173         delete (T[0]->getCountTable());
 174                 for (int i = 0; i < T.size(); i++) { delete T[i]; }
 175
 176                 //set phylip file as new current phylipfile
 177                 string current = "";
 178                 itTypes = outputTypes.find("tree");
 179                 if (itTypes != outputTypes.end()) {
 180                         if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
 181                 }
 182
 183                 m->mothurOutEndLine();
 184                 m->mothurOut("Output File Names: "); m->mothurOutEndLine();
 185                 for (int i = 0; i < outputNames.size(); i++) {  m->mothurOut(outputNames[i]); m->mothurOutEndLine();    }
 186                 m->mothurOutEndLine();
 187
 188                 return 0;
 189
 190         }
 191         catch(exception& e) {
 192                 m->errorOut(e, "DeuniqueTreeCommand", "execute");
 193                 exit(1);
 194         }
 195 }
 196 /***********************************************************/
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