+++ /dev/null
-/*
- * GetlabelCommand.cpp
- * Mothur
- *
- * Created by Thomas Ryabin on 1/30/09.
- * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
- *
- */
-
-#include "getlabelcommand.h"
-
-
-//**********************************************************************************************************************
-vector<string> GetlabelCommand::setParameters(){
- try {
- CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(plist);
- CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
- CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
- 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, "GetlabelCommand", "setParameters");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-GetlabelCommand::GetlabelCommand(){
- try {
- abort = true; calledHelp = true;
- setParameters();
- }
- catch(exception& e) {
- m->errorOut(e, "GetlabelCommand", "CollectCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-string GetlabelCommand::getHelpString(){
- try {
- string helpString = "";
- helpString += "The get.label command parameters are list, sabund and rabund file. \n";
- helpString += "The get.label command should be in the following format: \n";
- helpString += "get.label()\n";
- helpString += "Example get.label().\n";
- return helpString;
- }
- catch(exception& e) {
- m->errorOut(e, "GetlabelCommand", "getHelpString");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-GetlabelCommand::GetlabelCommand(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; }
- }
-
- //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("rabund");
- //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["rabund"] = inputDir + it->second; }
- }
-
- it = parameters.find("sabund");
- //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["sabund"] = inputDir + it->second; }
- }
-
- it = parameters.find("list");
- //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["list"] = inputDir + it->second; }
- }
- }
-
- //check for required parameters
- listfile = validParameter.validFile(parameters, "list", true);
- if (listfile == "not open") { listfile = ""; abort = true; }
- else if (listfile == "not found") { listfile = ""; }
- else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
-
- sabundfile = validParameter.validFile(parameters, "sabund", true);
- if (sabundfile == "not open") { sabundfile = ""; abort = true; }
- else if (sabundfile == "not found") { sabundfile = ""; }
- else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
-
- rabundfile = validParameter.validFile(parameters, "rabund", true);
- if (rabundfile == "not open") { rabundfile = ""; abort = true; }
- else if (rabundfile == "not found") { rabundfile = ""; }
- else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
-
- if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) {
- //is there are current file available for any of these?
- //give priority to list, then rabund, then sabund
- //if there is a current shared file, use it
-
- listfile = m->getListFile();
- if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
- else {
- rabundfile = m->getRabundFile();
- if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
- else {
- sabundfile = m->getSabundFile();
- if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
- else {
- m->mothurOut("No valid current files. You must provide a list, sabund or rabund file."); m->mothurOutEndLine();
- abort = true;
- }
- }
- }
- }
- }
-
- }
- catch(exception& e) {
- m->errorOut(e, "GetlabelCommand", "GetlabelCommand");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-int GetlabelCommand::execute(){
- try {
-
- if (abort == true) { if (calledHelp) { return 0; } return 2; }
-
- InputData* input = new InputData(inputfile, format);
- OrderVector* order = input->getOrderVector();
- string label = order->getLabel();
-
- while (order != NULL) {
-
- if (m->control_pressed) { delete input; delete order; return 0; }
-
- label = order->getLabel();
-
- m->mothurOut(label); m->mothurOutEndLine();
-
- delete order;
- order = input->getOrderVector();
- }
-
- delete input;
-
- return 0;
- }
-
- catch(exception& e) {
- m->errorOut(e, "GetlabelCommand", "execute");
- exit(1);
- }
-}
-//**********************************************************************************************************************
-
-
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