+++ /dev/null
-/*
- * getgroupcommand.cpp
- * Mothur
- *
- * Created by Thomas Ryabin on 2/2/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "getgroupcommand.h"
-#include "inputdata.h"
-
-//**********************************************************************************************************************
-vector<string> GetgroupCommand::setParameters(){
- try {
- CommandParameter pshared("shared", "InputTypes", "", "current", "none", "none", "none",false,true); parameters.push_back(pshared);
- CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
- CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
-
- vector<string> myArray;
- for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
- return myArray;
- }
- catch(exception& e) {
- m->errorOut(e, "GetgroupCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string GetgroupCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The get.group command parameter is shared and it's required if you have no valid current file.\n";
- //m->mothurOut("The get.group command outputs a .bootGroups file to you can use in addition to the tree file generated by the bootstrap.shared command to run the consensus command.\n");
- helpString += "You may not use any parameters with the get.group command.\n";
- helpString += "The get.group command should be in the following format: \n";
- helpString += "get.group()\n";
- helpString += "Example get.group().\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "GetgroupCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-GetgroupCommand::GetgroupCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- vector<string> tempOutNames;
- outputTypes["bootgroup"] = tempOutNames;
- }
- catch(exception& e) {
- m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-GetgroupCommand::GetgroupCommand(string option) {
- try {
- abort = false; calledHelp = false;
-
- //allow user to run help
- if(option == "help") { help(); abort = true; calledHelp = true; }
- else if(option == "citation") { citation(); abort = true; calledHelp = true;}
-
- else {
- vector<string> myArray = setParameters();
-
- OptionParser parser(option);
- map<string,string> parameters = parser.getParameters();
- map<string,string>::iterator it;
-
- ValidParameters validParameter;
- //check to make sure all parameters are valid for command
- for (it = parameters.begin(); it != parameters.end(); it++) {
- if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
- }
-
- //initialize outputTypes
- vector<string> tempOutNames;
- outputTypes["bootgroup"] = tempOutNames;
-
- //if the user changes the input directory command factory will send this info to us in the output parameter
- string inputDir = validParameter.validFile(parameters, "inputdir", false);
- if (inputDir == "not found"){ inputDir = ""; }
- else {
- string path;
- it = parameters.find("shared");
- //user has given a template file
- if(it != parameters.end()){
- path = m->hasPath(it->second);
- //if the user has not given a path then, add inputdir. else leave path alone.
- if (path == "") { parameters["shared"] = inputDir + it->second; }
- }
- }
-
- //get shared file
- sharedfile = validParameter.validFile(parameters, "shared", true);
- if (sharedfile == "not open") { sharedfile = ""; abort = true; }
- else if (sharedfile == "not found") {
- //if there is a current shared file, use it
- sharedfile = m->getSharedFile();
- if (sharedfile != "") { m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
- else { m->mothurOut("You have no current sharedfile and the shared parameter is required."); m->mothurOutEndLine(); abort = true; }
- }else { m->setSharedFile(sharedfile); }
-
-
- //if the user changes the output directory command factory will send this info to us in the output parameter
- outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(sharedfile); }
- }
- }
- catch(exception& e) {
- m->errorOut(e, "GetgroupCommand", "GetgroupCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int GetgroupCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- //open output file
- outputFile = outputDir + m->getRootName(m->getSimpleName(sharedfile)) + "bootGroups";
- m->openOutputFile(outputFile, out);
-
- InputData input(sharedfile, "sharedfile");
- vector<SharedRAbundVector*> lookup = input.getSharedRAbundVectors();
-
- for (int i = 0; i < lookup.size(); i++) {
- out << lookup[i]->getGroup() << '\t' << lookup[i]->getGroup() << endl;
- m->mothurOut(lookup[i]->getGroup()); m->mothurOutEndLine();
- delete lookup[i];
- }
-
- out.close();
-
- if (m->control_pressed) { m->mothurRemove(outputFile); return 0; }
-
- m->mothurOutEndLine();
- m->mothurOut("Output File Name: "); m->mothurOutEndLine();
- m->mothurOut(outputFile); m->mothurOutEndLine(); outputNames.push_back(outputFile); outputTypes["bootgroup"].push_back(outputFile);
- m->mothurOutEndLine();
-
- return 0;
- }
-
- catch(exception& e) {
- m->errorOut(e, "GetgroupCommand", "execute");
- exit(1);
- }
-}
-
-
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