1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
|
/*
* deuniquetreecommand.cpp
* Mothur
*
* Created by westcott on 5/27/11.
* Copyright 2011 Schloss Lab. All rights reserved.
*
*/
#include "deuniquetreecommand.h"
#include "treereader.h"
//**********************************************************************************************************************
vector<string> DeuniqueTreeCommand::setParameters(){
try {
CommandParameter ptree("tree", "InputTypes", "", "", "none", "none", "none","tree",false,true,true); parameters.push_back(ptree);
CommandParameter pname("name", "InputTypes", "", "", "none", "none", "none","",false,true,true); parameters.push_back(pname);
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, "DeuniqueTreeCommand", "setParameters");
exit(1);
}
}
//**********************************************************************************************************************
string DeuniqueTreeCommand::getHelpString(){
try {
string helpString = "";
helpString += "The deunique.tree command parameters are tree and name. Both parameters are required unless you have valid current files.\n";
helpString += "The deunique.tree command should be in the following format: deunique.tree(tree=yourTreeFile, name=yourNameFile).\n";
helpString += "Example deunique.tree(tree=abrecovery.tree, name=abrecovery.names).\n";
helpString += "Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreeFile).\n";
return helpString;
}
catch(exception& e) {
m->errorOut(e, "DeuniqueTreeCommand", "getHelpString");
exit(1);
}
}
//**********************************************************************************************************************
string DeuniqueTreeCommand::getOutputPattern(string type) {
try {
string pattern = "";
if (type == "tree") { pattern = "[filename],deunique.tre"; }
else { m->mothurOut("[ERROR]: No definition for type " + type + " output pattern.\n"); m->control_pressed = true; }
return pattern;
}
catch(exception& e) {
m->errorOut(e, "DeuniqueTreeCommand", "getOutputPattern");
exit(1);
}
}
//**********************************************************************************************************************
DeuniqueTreeCommand::DeuniqueTreeCommand(){
try {
abort = true; calledHelp = true;
setParameters();
vector<string> tempOutNames;
outputTypes["tree"] = tempOutNames;
}
catch(exception& e) {
m->errorOut(e, "DeuniqueTreeCommand", "DeuniqueTreeCommand");
exit(1);
}
}
/***********************************************************/
DeuniqueTreeCommand::DeuniqueTreeCommand(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 (map<string,string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
}
//initialize outputTypes
vector<string> tempOutNames;
outputTypes["tree"] = 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("tree");
//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["tree"] = inputDir + it->second; }
}
it = parameters.find("name");
//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["name"] = inputDir + it->second; }
}
}
//check for required parameters
treefile = validParameter.validFile(parameters, "tree", true);
if (treefile == "not open") { abort = true; }
else if (treefile == "not found") { //if there is a current design file, use it
treefile = m->getTreeFile();
if (treefile != "") { m->mothurOut("Using " + treefile + " as input file for the tree parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current tree file and the tree parameter is required."); m->mothurOutEndLine(); abort = true; }
}else { m->setTreeFile(treefile); }
namefile = validParameter.validFile(parameters, "name", true);
if (namefile == "not open") { abort = true; }
else if (namefile == "not found") { //if there is a current design file, use it
namefile = m->getNameFile();
if (namefile != "") { m->mothurOut("Using " + namefile + " as input file for the name parameter."); m->mothurOutEndLine(); }
else { m->mothurOut("You have no current name file and the name parameter is required."); m->mothurOutEndLine(); abort = true; }
}else { m->setNameFile(namefile); }
outputDir = validParameter.validFile(parameters, "outputdir", false); if (outputDir == "not found"){ outputDir = m->hasPath(treefile); }
}
}
catch(exception& e) {
m->errorOut(e, "DeuniqueTreeCommand", "DeuniqueTreeCommand");
exit(1);
}
}
/***********************************************************/
int DeuniqueTreeCommand::execute() {
try {
if (abort == true) { if (calledHelp) { return 0; } return 2; }
m->setTreeFile(treefile);
TreeReader* reader = new TreeReader(treefile, "", namefile);
vector<Tree*> T = reader->getTrees();
map<string, string> nameMap;
m->readNames(namefile, nameMap);
delete reader;
//print new Tree
map<string, string> variables;
variables["[filename]"] = outputDir + m->getRootName(m->getSimpleName(treefile));
string outputFile = getOutputFileName("tree", variables);
outputNames.push_back(outputFile); outputTypes["tree"].push_back(outputFile);
ofstream out;
m->openOutputFile(outputFile, out);
T[0]->print(out, nameMap);
out.close();
delete (T[0]->getCountTable());
for (int i = 0; i < T.size(); i++) { delete T[i]; }
//set phylip file as new current phylipfile
string current = "";
itTypes = outputTypes.find("tree");
if (itTypes != outputTypes.end()) {
if ((itTypes->second).size() != 0) { current = (itTypes->second)[0]; m->setTreeFile(current); }
}
m->mothurOutEndLine();
m->mothurOut("Output File Names: "); m->mothurOutEndLine();
for (int i = 0; i < outputNames.size(); i++) { m->mothurOut(outputNames[i]); m->mothurOutEndLine(); }
m->mothurOutEndLine();
return 0;
}
catch(exception& e) {
m->errorOut(e, "DeuniqueTreeCommand", "execute");
exit(1);
}
}
/***********************************************************/
|
