5 * Created by Thomas Ryabin on 1/30/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "getlabelcommand.h"
13 //**********************************************************************************************************************
14 vector<string> GetlabelCommand::setParameters(){
16 CommandParameter plist("list", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(plist);
17 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(prabund);
18 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none","",false,false, true); parameters.push_back(psabund);
19 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(pinputdir);
20 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "","",false,false); parameters.push_back(poutputdir);
22 vector<string> myArray;
23 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
27 m->errorOut(e, "GetlabelCommand", "setParameters");
31 //**********************************************************************************************************************
32 GetlabelCommand::GetlabelCommand(){
34 abort = true; calledHelp = true;
38 m->errorOut(e, "GetlabelCommand", "CollectCommand");
42 //**********************************************************************************************************************
43 string GetlabelCommand::getHelpString(){
45 string helpString = "";
46 helpString += "The get.label command parameters are list, sabund and rabund file. \n";
47 helpString += "The get.label command should be in the following format: \n";
48 helpString += "get.label()\n";
49 helpString += "Example get.label().\n";
53 m->errorOut(e, "GetlabelCommand", "getHelpString");
57 //**********************************************************************************************************************
59 GetlabelCommand::GetlabelCommand(string option) {
61 abort = false; calledHelp = false;
63 //allow user to run help
64 if(option == "help") { help(); abort = true; calledHelp = true; }
65 else if(option == "citation") { citation(); abort = true; calledHelp = true;}
68 vector<string> myArray = setParameters();
70 OptionParser parser(option);
71 map<string,string> parameters = parser.getParameters();
72 map<string,string>::iterator it;
74 ValidParameters validParameter;
76 //check to make sure all parameters are valid for command
77 for (it = parameters.begin(); it != parameters.end(); it++) {
78 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
81 //if the user changes the input directory command factory will send this info to us in the output parameter
82 string inputDir = validParameter.validFile(parameters, "inputdir", false);
83 if (inputDir == "not found"){ inputDir = ""; }
87 it = parameters.find("rabund");
88 //user has given a template file
89 if(it != parameters.end()){
90 path = m->hasPath(it->second);
91 //if the user has not given a path then, add inputdir. else leave path alone.
92 if (path == "") { parameters["rabund"] = inputDir + it->second; }
95 it = parameters.find("sabund");
96 //user has given a template file
97 if(it != parameters.end()){
98 path = m->hasPath(it->second);
99 //if the user has not given a path then, add inputdir. else leave path alone.
100 if (path == "") { parameters["sabund"] = inputDir + it->second; }
103 it = parameters.find("list");
104 //user has given a template file
105 if(it != parameters.end()){
106 path = m->hasPath(it->second);
107 //if the user has not given a path then, add inputdir. else leave path alone.
108 if (path == "") { parameters["list"] = inputDir + it->second; }
112 //check for required parameters
113 listfile = validParameter.validFile(parameters, "list", true);
114 if (listfile == "not open") { listfile = ""; abort = true; }
115 else if (listfile == "not found") { listfile = ""; }
116 else { format = "list"; inputfile = listfile; m->setListFile(listfile); }
118 sabundfile = validParameter.validFile(parameters, "sabund", true);
119 if (sabundfile == "not open") { sabundfile = ""; abort = true; }
120 else if (sabundfile == "not found") { sabundfile = ""; }
121 else { format = "sabund"; inputfile = sabundfile; m->setSabundFile(sabundfile); }
123 rabundfile = validParameter.validFile(parameters, "rabund", true);
124 if (rabundfile == "not open") { rabundfile = ""; abort = true; }
125 else if (rabundfile == "not found") { rabundfile = ""; }
126 else { format = "rabund"; inputfile = rabundfile; m->setRabundFile(rabundfile); }
128 if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) {
129 //is there are current file available for any of these?
130 //give priority to list, then rabund, then sabund
131 //if there is a current shared file, use it
133 listfile = m->getListFile();
134 if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
136 rabundfile = m->getRabundFile();
137 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
139 sabundfile = m->getSabundFile();
140 if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
142 m->mothurOut("No valid current files. You must provide a list, sabund or rabund file."); m->mothurOutEndLine();
151 catch(exception& e) {
152 m->errorOut(e, "GetlabelCommand", "GetlabelCommand");
156 //**********************************************************************************************************************
158 int GetlabelCommand::execute(){
161 if (abort == true) { if (calledHelp) { return 0; } return 2; }
163 InputData* input = new InputData(inputfile, format);
164 OrderVector* order = input->getOrderVector();
165 string label = order->getLabel();
167 while (order != NULL) {
169 if (m->control_pressed) { delete input; delete order; return 0; }
171 label = order->getLabel();
173 m->mothurOut(label); m->mothurOutEndLine();
176 order = input->getOrderVector();
184 catch(exception& e) {
185 m->errorOut(e, "GetlabelCommand", "execute");
189 //**********************************************************************************************************************