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 //**********************************************************************************************************************
  14 vector<string> GetCurrentCommand::getValidParameters(){
  15         try {
  16                 string Array[] =  {"outputdir","inputdir","clear"};
  17                 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  18                 return myArray;
  19         }
  20         catch(exception& e) {
  21                 m->errorOut(e, "GetCurrentCommand", "getValidParameters");
  22                 exit(1);
  23         }
  24 }
  25 //**********************************************************************************************************************
  26 GetCurrentCommand::GetCurrentCommand(){
  27         try {
  28                 abort = true; calledHelp = true;
  29         }
  30         catch(exception& e) {
  31                 m->errorOut(e, "GetCurrentCommand", "GetCurrentCommand");
  32                 exit(1);
  33         }
  34 }
  35 //**********************************************************************************************************************
  36 vector<string> GetCurrentCommand::getRequiredParameters(){
  37         try {
  38                 vector<string> myArray;
  39                 return myArray;
  40         }
  41         catch(exception& e) {
  42                 m->errorOut(e, "GetCurrentCommand", "getRequiredParameters");
  43                 exit(1);
  44         }
  45 }
  46 //**********************************************************************************************************************
  47 vector<string> GetCurrentCommand::getRequiredFiles(){
  48         try {
  49                 vector<string> myArray;
  50                 return myArray;
  51         }
  52         catch(exception& e) {
  53                 m->errorOut(e, "GetCurrentCommand", "getRequiredFiles");
  54                 exit(1);
  55         }
  56 }
  57 //**********************************************************************************************************************
  58 GetCurrentCommand::GetCurrentCommand(string option)  {
  59         try {
  60                 abort = false; calledHelp = false;
  61
  62                 //allow user to run help
  63                 if(option == "help") { help(); abort = true; calledHelp = true; }
  64
  65                 else {
  66                         //valid paramters for this command
  67                         string Array[] =  {"outputdir","inputdir","clear"};
  68                         vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
  69
  70                         OptionParser parser(option);
  71                         map<string,string> parameters = parser.getParameters();
  72
  73                         ValidParameters validParameter;
  74                         //check to make sure all parameters are valid for command
  75                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  76                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  77                         }
  78
  79                         clearTypes = validParameter.validFile(parameters, "clear", false);
  80                         if (clearTypes == "not found") { clearTypes = ""; }
  81                         else { m->splitAtDash(clearTypes, types);       }
  82                 }
  83
  84         }
  85         catch(exception& e) {
  86                 m->errorOut(e, "GetCurrentCommand", "GetCurrentCommand");
  87                 exit(1);
  88         }
  89 }
  90 //**********************************************************************************************************************
  91
  92 void GetCurrentCommand::help(){
  93         try {
  94                 m->mothurOut("The get.current command outputs the current files saved by mothur.\n");
  95                 m->mothurOut("The get.current command has one parameter: clear.\n");
  96                 m->mothurOut("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");
  97                 m->mothurOut("The get.current command should be in the following format: \n");
  98                 m->mothurOut("get.current() or get.current(clear=fasta-name-accnos)\n");
  99
 100         }
 101         catch(exception& e) {
 102                 m->errorOut(e, "GetCurrentCommand", "help");
 103                 exit(1);
 104         }
 105 }
 106
 107 //**********************************************************************************************************************
 108 GetCurrentCommand::~GetCurrentCommand(){}
 109 //**********************************************************************************************************************
 110
 111 int GetCurrentCommand::execute(){
 112         try {
 113
 114                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
 115
 116                 //user wants to clear a type
 117                 if (types.size() != 0) {
 118                         for (int i = 0; i < types.size(); i++) {
 119
 120                                 if (m->control_pressed) { break; }
 121
 122                                 //look for file types
 123                                 if (types[i] == "fasta") {
 124                                         m->setFastaFile("");
 125                                 }else if (types[i] == "qfile") {
 126                                         m->setQualFile("");
 127                                 }else if (types[i] == "phylip") {
 128                                         m->setPhylipFile("");
 129                                 }else if (types[i] == "column") {
 130                                         m->setColumnFile("");
 131                                 }else if (types[i] == "list") {
 132                                         m->setListFile("");
 133                                 }else if (types[i] == "rabund") {
 134                                         m->setRabundFile("");
 135                                 }else if (types[i] == "sabund") {
 136                                         m->setSabundFile("");
 137                                 }else if (types[i] == "name") {
 138                                         m->setNameFile("");
 139                                 }else if (types[i] == "group") {
 140                                         m->setGroupFile("");
 141                                 }else if (types[i] == "order") {
 142                                         m->setOrderFile("");
 143                                 }else if (types[i] == "ordergroup") {
 144                                         m->setOrderGroupFile("");
 145                                 }else if (types[i] == "tree") {
 146                                         m->setTreeFile("");
 147                                 }else if (types[i] == "shared") {
 148                                         m->setSharedFile("");
 149                                 }else if (types[i] == "relabund") {
 150                                         m->setRelAbundFile("");
 151                                 }else if (types[i] == "design") {
 152                                         m->setDesignFile("");
 153                                 }else if (types[i] == "sff") {
 154                                         m->setSFFFile("");
 155                                 }else if (types[i] == "oligos") {
 156                                         m->setOligosFile("");
 157                                 }else if (types[i] == "accnos") {
 158                                         m->setAccnosFile("");
 159                                 }else if (types[i] == "taxonomy") {
 160                                                 m->setTaxonomyFile("");
 161                                 }else if (types[i] == "all") {
 162                                         m->clearCurrentFiles();
 163                                 }else {
 164                                         m->mothurOut("[ERROR]: mothur does not save a current file for " + types[i]); m->mothurOutEndLine();
 165                                 }
 166                         }
 167                 }
 168
 169                 m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
 170                 m->printCurrentFiles();
 171
 172                 return 0;
 173         }
 174
 175         catch(exception& e) {
 176                 m->errorOut(e, "GetCurrentCommand", "execute");
 177                 exit(1);
 178         }
 179 }
 180
 181 //**********************************************************************************************************************
 182
 183
 184