getcurrentcommand.cpp

   1 /*
   2  *  getcurrentcommand.cpp
   3  *  Mothur
   4  *
   5  *  Created by westcott on 3/16/11.
   6  *  Copyright 2011 Schloss Lab. All rights reserved.
   7  *
   8  */
   9
  10 #include "getcurrentcommand.h"
  11
  12 //**********************************************************************************************************************
  13 vector<string> GetCurrentCommand::setParameters(){
  14         try {
  15                 CommandParameter pclear("clear", "String", "", "", "", "", "",false,false); parameters.push_back(pclear);
  16                 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
  17                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
  18
  19                 vector<string> myArray;
  20                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
  21                 return myArray;
  22         }
  23         catch(exception& e) {
  24                 m->errorOut(e, "GetCurrentCommand", "setParameters");
  25                 exit(1);
  26         }
  27 }
  28 //**********************************************************************************************************************
  29 string GetCurrentCommand::getHelpString(){
  30         try {
  31                 string helpString = "";
  32                 helpString += "The get.current command outputs the current files saved by mothur.\n";
  33                 helpString += "The get.current command has one parameter: clear.\n";
  34                 helpString += "The clear paramter is used to indicate which file types you would like to clear values for, multiple types can be separated by dashes.\n";
  35                 helpString += "The get.current command should be in the following format: \n";
  36                 helpString += "get.current() or get.current(clear=fasta-name-accnos)\n";
  37                 return helpString;
  38         }
  39         catch(exception& e) {
  40                 m->errorOut(e, "GetCurrentCommand", "getHelpString");
  41                 exit(1);
  42         }
  43 }
  44 //**********************************************************************************************************************
  45 GetCurrentCommand::GetCurrentCommand(){
  46         try {
  47                 abort = true; calledHelp = true;
  48                 setParameters();
  49         }
  50         catch(exception& e) {
  51                 m->errorOut(e, "GetCurrentCommand", "GetCurrentCommand");
  52                 exit(1);
  53         }
  54 }
  55 //**********************************************************************************************************************
  56 GetCurrentCommand::GetCurrentCommand(string option)  {
  57         try {
  58                 abort = false; calledHelp = false;
  59
  60                 //allow user to run help
  61                 if(option == "help") { help(); abort = true; calledHelp = true; }
  62
  63                 else {
  64                         vector<string> myArray = setParameters();
  65
  66                         OptionParser parser(option);
  67                         map<string,string> parameters = parser.getParameters();
  68
  69                         ValidParameters validParameter;
  70                         //check to make sure all parameters are valid for command
  71                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  72                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  73                         }
  74
  75                         clearTypes = validParameter.validFile(parameters, "clear", false);
  76                         if (clearTypes == "not found") { clearTypes = ""; }
  77                         else { m->splitAtDash(clearTypes, types);       }
  78                 }
  79
  80         }
  81         catch(exception& e) {
  82                 m->errorOut(e, "GetCurrentCommand", "GetCurrentCommand");
  83                 exit(1);
  84         }
  85 }
  86 //**********************************************************************************************************************
  87
  88 int GetCurrentCommand::execute(){
  89         try {
  90
  91                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
  92
  93                 //user wants to clear a type
  94                 if (types.size() != 0) {
  95                         for (int i = 0; i < types.size(); i++) {
  96
  97                                 if (m->control_pressed) { break; }
  98
  99                                 //look for file types
 100                                 if (types[i] == "fasta") {
 101                                         m->setFastaFile("");
 102                                 }else if (types[i] == "qfile") {
 103                                         m->setQualFile("");
 104                                 }else if (types[i] == "phylip") {
 105                                         m->setPhylipFile("");
 106                                 }else if (types[i] == "column") {
 107                                         m->setColumnFile("");
 108                                 }else if (types[i] == "list") {
 109                                         m->setListFile("");
 110                                 }else if (types[i] == "rabund") {
 111                                         m->setRabundFile("");
 112                                 }else if (types[i] == "sabund") {
 113                                         m->setSabundFile("");
 114                                 }else if (types[i] == "name") {
 115                                         m->setNameFile("");
 116                                 }else if (types[i] == "group") {
 117                                         m->setGroupFile("");
 118                                 }else if (types[i] == "order") {
 119                                         m->setOrderFile("");
 120                                 }else if (types[i] == "ordergroup") {
 121                                         m->setOrderGroupFile("");
 122                                 }else if (types[i] == "tree") {
 123                                         m->setTreeFile("");
 124                                 }else if (types[i] == "shared") {
 125                                         m->setSharedFile("");
 126                                 }else if (types[i] == "relabund") {
 127                                         m->setRelAbundFile("");
 128                                 }else if (types[i] == "design") {
 129                                         m->setDesignFile("");
 130                                 }else if (types[i] == "sff") {
 131                                         m->setSFFFile("");
 132                                 }else if (types[i] == "oligos") {
 133                                         m->setOligosFile("");
 134                                 }else if (types[i] == "accnos") {
 135                                         m->setAccnosFile("");
 136                                 }else if (types[i] == "taxonomy") {
 137                                         m->setTaxonomyFile("");
 138                                 }else if (types[i] == "all") {
 139                                         m->clearCurrentFiles();
 140                                 }else {
 141                                         m->mothurOut("[ERROR]: mothur does not save a current file for " + types[i]); m->mothurOutEndLine();
 142                                 }
 143                         }
 144                 }
 145
 146                 m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
 147                 m->printCurrentFiles();
 148
 149                 return 0;
 150         }
 151
 152         catch(exception& e) {
 153                 m->errorOut(e, "GetCurrentCommand", "execute");
 154                 exit(1);
 155         }
 156 }
 157
 158 //**********************************************************************************************************************
 159
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