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                 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
  63
  64                 else {
  65                         vector<string> myArray = setParameters();
  66
  67                         OptionParser parser(option);
  68                         map<string,string> parameters = parser.getParameters();
  69
  70                         ValidParameters validParameter;
  71                         //check to make sure all parameters are valid for command
  72                         for (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
  73                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
  74                         }
  75
  76                         clearTypes = validParameter.validFile(parameters, "clear", false);
  77                         if (clearTypes == "not found") { clearTypes = ""; }
  78                         else { m->splitAtDash(clearTypes, types);       }
  79                 }
  80
  81         }
  82         catch(exception& e) {
  83                 m->errorOut(e, "GetCurrentCommand", "GetCurrentCommand");
  84                 exit(1);
  85         }
  86 }
  87 //**********************************************************************************************************************
  88
  89 int GetCurrentCommand::execute(){
  90         try {
  91
  92                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
  93
  94                 cFactory = CommandFactory::getInstance();
  95
  96                 //user wants to clear a type
  97                 if (types.size() != 0) {
  98                         for (int i = 0; i < types.size(); i++) {
  99
 100                                 if (m->control_pressed) { break; }
 101
 102                                 //look for file types
 103                                 if (types[i] == "fasta") {
 104                                         m->setFastaFile("");
 105                                 }else if (types[i] == "qfile") {
 106                                         m->setQualFile("");
 107                                 }else if (types[i] == "phylip") {
 108                                         m->setPhylipFile("");
 109                                 }else if (types[i] == "column") {
 110                                         m->setColumnFile("");
 111                                 }else if (types[i] == "list") {
 112                                         m->setListFile("");
 113                                 }else if (types[i] == "rabund") {
 114                                         m->setRabundFile("");
 115                                 }else if (types[i] == "sabund") {
 116                                         m->setSabundFile("");
 117                                 }else if (types[i] == "name") {
 118                                         m->setNameFile("");
 119                                 }else if (types[i] == "group") {
 120                                         m->setGroupFile("");
 121                                 }else if (types[i] == "order") {
 122                                         m->setOrderFile("");
 123                                 }else if (types[i] == "ordergroup") {
 124                                         m->setOrderGroupFile("");
 125                                 }else if (types[i] == "tree") {
 126                                         m->setTreeFile("");
 127                                 }else if (types[i] == "shared") {
 128                                         m->setSharedFile("");
 129                                 }else if (types[i] == "relabund") {
 130                                         m->setRelAbundFile("");
 131                                 }else if (types[i] == "design") {
 132                                         m->setDesignFile("");
 133                                 }else if (types[i] == "sff") {
 134                                         m->setSFFFile("");
 135                                 }else if (types[i] == "oligos") {
 136                                         m->setOligosFile("");
 137                                 }else if (types[i] == "accnos") {
 138                                         m->setAccnosFile("");
 139                                 }else if (types[i] == "taxonomy") {
 140                                         m->setTaxonomyFile("");
 141                                 }else if (types[i] == "flow") {
 142                                         m->setFlowFile("");
 143                 }else if (types[i] == "biom") {
 144                                         m->setBiomFile("");
 145                 }else if (types[i] == "count") {
 146                                         m->setCountTableFile("");
 147                 }else if (types[i] == "summary") {
 148                                         m->setSummaryFile("");
 149                                 }else if (types[i] == "processors") {
 150                                         m->setProcessors("1");
 151                                 }else if (types[i] == "all") {
 152                                         m->clearCurrentFiles();
 153                                 }else {
 154                                         m->mothurOut("[ERROR]: mothur does not save a current file for " + types[i]); m->mothurOutEndLine();
 155                                 }
 156                         }
 157                 }
 158
 159                 if (m->hasCurrentFiles()) {
 160                         m->mothurOutEndLine(); m->mothurOut("Current files saved by mothur:"); m->mothurOutEndLine();
 161                         m->printCurrentFiles();
 162                 }
 163
 164         string inputDir = cFactory->getInputDir();
 165         if (inputDir != "") {
 166             m->mothurOutEndLine(); m->mothurOut("Current input directory saved by mothur: " + inputDir); m->mothurOutEndLine();
 167         }
 168
 169         string outputDir = cFactory->getOutputDir();
 170         if (outputDir != "") {
 171             m->mothurOutEndLine(); m->mothurOut("Current output directory saved by mothur: " + outputDir); m->mothurOutEndLine();
 172         }
 173         string defaultPath = m->getDefaultPath();
 174         if (defaultPath != "") {
 175             m->mothurOutEndLine(); m->mothurOut("Current default directory saved by mothur: " + defaultPath); m->mothurOutEndLine();
 176         }
 177
 178
 179         string temp = "./";
 180 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux) || (__linux__) || (__unix__) || (__unix)
 181 #else
 182             temp = ".\\";
 183 #endif
 184         temp = m->getFullPathName(temp);
 185         m->mothurOutEndLine(); m->mothurOut("Current working directory: " + temp); m->mothurOutEndLine();
 186
 187                 return 0;
 188         }
 189
 190         catch(exception& e) {
 191                 m->errorOut(e, "GetCurrentCommand", "execute");
 192                 exit(1);
 193         }
 194 }
 195
 196 //**********************************************************************************************************************
 197
 198
 199