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1 /*
2  *  GetlabelCommand.cpp
3  *  Mothur
4  *
5  *  Created by Thomas Ryabin on 1/30/09.
6  *  Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
7  *
8  */
9
10 #include "getlabelcommand.h"
11
12
13 //**********************************************************************************************************************
14 vector<string> GetlabelCommand::setParameters(){        
15         try {
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 pinputdir("inputdir", "String", "", "", "", "", "",false,false); parameters.push_back(pinputdir);
20                 CommandParameter poutputdir("outputdir", "String", "", "", "", "", "",false,false); parameters.push_back(poutputdir);
21                 
22                 vector<string> myArray;
23                 for (int i = 0; i < parameters.size(); i++) {   myArray.push_back(parameters[i].name);          }
24                 return myArray;
25         }
26         catch(exception& e) {
27                 m->errorOut(e, "GetlabelCommand", "setParameters");
28                 exit(1);
29         }
30 }
31 //**********************************************************************************************************************
32 GetlabelCommand::GetlabelCommand(){     
33         try {
34                 abort = true; calledHelp = true; 
35                 setParameters();
36         }
37         catch(exception& e) {
38                 m->errorOut(e, "GetlabelCommand", "CollectCommand");
39                 exit(1);
40         }
41 }
42 //**********************************************************************************************************************
43 string GetlabelCommand::getHelpString(){        
44         try {
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";
50                 return helpString;
51         }
52         catch(exception& e) {
53                 m->errorOut(e, "GetlabelCommand", "getHelpString");
54                 exit(1);
55         }
56 }
57 //**********************************************************************************************************************
58
59 GetlabelCommand::GetlabelCommand(string option)  {
60         try {
61                 abort = false; calledHelp = false;   
62                 
63                 //allow user to run help
64                 if(option == "help") { help(); abort = true; calledHelp = true; }
65                 
66                 else {
67                         vector<string> myArray = setParameters();
68                         
69                         OptionParser parser(option);
70                         map<string,string> parameters = parser.getParameters();
71                         map<string,string>::iterator it;
72                         
73                         ValidParameters validParameter;
74                         
75                         //check to make sure all parameters are valid for command
76                         for (it = parameters.begin(); it != parameters.end(); it++) { 
77                                 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) {  abort = true;  }
78                         }
79                         
80                         //if the user changes the input directory command factory will send this info to us in the output parameter 
81                         string inputDir = validParameter.validFile(parameters, "inputdir", false);              
82                         if (inputDir == "not found"){   inputDir = "";          }
83                         else {
84                                 string path;
85                                 
86                                 it = parameters.find("rabund");
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["rabund"] = inputDir + it->second;           }
92                                 }
93                                 
94                                 it = parameters.find("sabund");
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["sabund"] = inputDir + it->second;           }
100                                 }
101                                 
102                                 it = parameters.find("list");
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["list"] = inputDir + it->second;             }
108                                 }
109                         }
110                         
111                         //check for required parameters
112                         listfile = validParameter.validFile(parameters, "list", true);
113                         if (listfile == "not open") { listfile = ""; abort = true; }
114                         else if (listfile == "not found") { listfile = ""; }
115                         else {  format = "list"; inputfile = listfile; }
116                         
117                         sabundfile = validParameter.validFile(parameters, "sabund", true);
118                         if (sabundfile == "not open") { sabundfile = ""; abort = true; }        
119                         else if (sabundfile == "not found") { sabundfile = ""; }
120                         else {  format = "sabund"; inputfile = sabundfile; }
121                         
122                         rabundfile = validParameter.validFile(parameters, "rabund", true);
123                         if (rabundfile == "not open") { rabundfile = ""; abort = true; }        
124                         else if (rabundfile == "not found") { rabundfile = ""; }
125                         else {  format = "rabund"; inputfile = rabundfile; }
126                         
127                         if ((listfile == "") && (rabundfile == "") && (sabundfile == "")) { 
128                                 //is there are current file available for any of these?
129                                 //give priority to list, then rabund, then sabund
130                                 //if there is a current shared file, use it
131                                 
132                                 listfile = m->getListFile(); 
133                                 if (listfile != "") { inputfile = listfile; format = "list"; m->mothurOut("Using " + listfile + " as input file for the list parameter."); m->mothurOutEndLine(); }
134                                 else { 
135                                         rabundfile = m->getRabundFile(); 
136                                         if (rabundfile != "") { inputfile = rabundfile; format = "rabund"; m->mothurOut("Using " + rabundfile + " as input file for the rabund parameter."); m->mothurOutEndLine(); }
137                                         else { 
138                                                 sabundfile = m->getSabundFile(); 
139                                                 if (sabundfile != "") { inputfile = sabundfile; format = "sabund"; m->mothurOut("Using " + sabundfile + " as input file for the sabund parameter."); m->mothurOutEndLine(); }
140                                                 else { 
141                                                         m->mothurOut("No valid current files. You must provide a list, sabund or rabund file."); m->mothurOutEndLine(); 
142                                                         abort = true;
143                                                 }
144                                         }
145                                 }
146                         }
147                 }
148
149         }
150         catch(exception& e) {
151                 m->errorOut(e, "GetlabelCommand", "GetlabelCommand");
152                 exit(1);
153         }
154 }
155 //**********************************************************************************************************************
156
157 int GetlabelCommand::execute(){
158         try {
159                 
160                 if (abort == true) { if (calledHelp) { return 0; }  return 2;   }
161                 
162                 InputData* input = new InputData(inputfile, format);
163                 OrderVector* order = input->getOrderVector();
164                 string label = order->getLabel();
165                 
166                 while (order != NULL) {
167                         
168                         if (m->control_pressed) { delete input;  delete order; return 0; }
169                         
170                         label = order->getLabel();      
171                         
172                         m->mothurOut(label); m->mothurOutEndLine();
173                         
174                         delete order;           
175                         order = input->getOrderVector();
176                 }
177                 
178                 delete input; 
179                 
180                 return 0;       
181         }
182
183         catch(exception& e) {
184                 m->errorOut(e, "GetlabelCommand", "execute");
185                 exit(1);
186         }
187 }
188 //**********************************************************************************************************************
189
190