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); parameters.push_back(plist);
17 CommandParameter prabund("rabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(prabund);
18 CommandParameter psabund("sabund", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(psabund);
19 CommandParameter pshared("shared", "InputTypes", "", "", "LRSS", "LRSS", "none",false,false); parameters.push_back(pshared);
20 CommandParameter pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
21 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
23 vector<string> myArray;
24 for (int i = 0; i < parameters.size(); i++) { myArray.push_back(parameters[i].name); }
28 m->errorOut(e, "GetlabelCommand", "setParameters");
32 //**********************************************************************************************************************
33 GetlabelCommand::GetlabelCommand(){
35 abort = true; calledHelp = true;
39 m->errorOut(e, "GetlabelCommand", "CollectCommand");
43 //**********************************************************************************************************************
44 string GetlabelCommand::getHelpString(){
46 string helpString = "";
47 helpString += "The get.label command parameters are list, sabund, rabund and shared file. \n";
48 helpString += "The get.label command should be in the following format: \n";
49 helpString += "get.label()\n";
50 helpString += "Example get.label().\n";
54 m->errorOut(e, "GetlabelCommand", "getHelpString");
58 //**********************************************************************************************************************
60 GetlabelCommand::GetlabelCommand(string option) {
62 abort = false; calledHelp = false;
64 //allow user to run help
65 if(option == "help") { help(); 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 = ""; }
86 it = parameters.find("shared");
87 //user has given a template file
88 if(it != parameters.end()){
89 path = m->hasPath(it->second);
90 //if the user has not given a path then, add inputdir. else leave path alone.
91 if (path == "") { parameters["shared"] = inputDir + it->second; }
94 it = parameters.find("rabund");
95 //user has given a template file
96 if(it != parameters.end()){
97 path = m->hasPath(it->second);
98 //if the user has not given a path then, add inputdir. else leave path alone.
99 if (path == "") { parameters["rabund"] = inputDir + it->second; }
102 it = parameters.find("sabund");
103 //user has given a template file
104 if(it != parameters.end()){
105 path = m->hasPath(it->second);
106 //if the user has not given a path then, add inputdir. else leave path alone.
107 if (path == "") { parameters["sabund"] = inputDir + it->second; }
110 it = parameters.find("list");
111 //user has given a template file
112 if(it != parameters.end()){
113 path = m->hasPath(it->second);
114 //if the user has not given a path then, add inputdir. else leave path alone.
115 if (path == "") { parameters["list"] = inputDir + it->second; }
119 //check for required parameters
120 listfile = validParameter.validFile(parameters, "list", true);
121 if (listfile == "not open") { listfile = ""; abort = true; }
122 else if (listfile == "not found") { listfile = ""; }
123 else { format = "list"; inputfile = listfile; }
125 sabundfile = validParameter.validFile(parameters, "sabund", true);
126 if (sabundfile == "not open") { sabundfile = ""; abort = true; }
127 else if (sabundfile == "not found") { sabundfile = ""; }
128 else { format = "sabund"; inputfile = sabundfile; }
130 rabundfile = validParameter.validFile(parameters, "rabund", true);
131 if (rabundfile == "not open") { rabundfile = ""; abort = true; }
132 else if (rabundfile == "not found") { rabundfile = ""; }
133 else { format = "rabund"; inputfile = rabundfile; }
135 sharedfile = validParameter.validFile(parameters, "shared", true);
136 if (sharedfile == "not open") { sharedfile = ""; abort = true; }
137 else if (sharedfile == "not found") { sharedfile = ""; }
138 else { format = "sharedfile"; inputfile = sharedfile; }
140 if ((sharedfile == "") && (listfile == "") && (rabundfile == "") && (sabundfile == "")) {
141 //is there are current file available for any of these?
142 //give priority to shared, then list, then rabund, then sabund
143 //if there is a current shared file, use it
144 sharedfile = m->getSharedFile();
145 if (sharedfile != "") { inputfile = sharedfile; format = "sharedfile"; m->mothurOut("Using " + sharedfile + " as input file for the shared parameter."); m->mothurOutEndLine(); }
147 listfile = m->getListFile();
148 if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
150 rabundfile = m->getRabundFile();
151 if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
153 sabundfile = m->getSabundFile();
154 if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
156 m->mothurOut("No valid current files. You must provide a list, sabund, rabund or shared file before you can use the collect.single command."); m->mothurOutEndLine();
167 catch(exception& e) {
168 m->errorOut(e, "GetlabelCommand", "GetlabelCommand");
172 //**********************************************************************************************************************
174 int GetlabelCommand::execute(){
177 if (abort == true) { if (calledHelp) { return 0; } return 2; }
179 InputData* input = new InputData(inputfile, format);
180 OrderVector* order = input->getOrderVector();
181 string label = order->getLabel();
183 while (order != NULL) {
185 if (m->control_pressed) { delete input; delete order; return 0; }
187 m->mothurOut(label); m->mothurOutEndLine();
189 label = order->getLabel();
192 order = input->getOrderVector();
200 catch(exception& e) {
201 m->errorOut(e, "GetlabelCommand", "execute");
205 //**********************************************************************************************************************