5 * Created by Sarah Westcott on 1/23/09.
6 * Copyright 2009 Schloss Lab UMASS Amherst. All rights reserved.
10 #include "readtreecommand.h"
12 //**********************************************************************************************************************
13 ReadTreeCommand::ReadTreeCommand(string option){
15 globaldata = GlobalData::getInstance();
18 //allow user to run help
19 if(option == "help") { help(); abort = true; }
22 //valid paramters for this command
23 string Array[] = {"tree","group","name","outputdir","inputdir"};
24 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
26 OptionParser parser(option);
27 map<string, string> parameters = parser.getParameters();
29 ValidParameters validParameter;
30 map<string, string>::iterator it;
32 //check to make sure all parameters are valid for command
33 for (it = parameters.begin(); it != parameters.end(); it++) {
34 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
37 globaldata->newRead();
39 //if the user changes the input directory command factory will send this info to us in the output parameter
40 string inputDir = validParameter.validFile(parameters, "inputdir", false);
41 if (inputDir == "not found"){ inputDir = ""; }
44 it = parameters.find("tree");
45 //user has given a template file
46 if(it != parameters.end()){
47 path = hasPath(it->second);
48 //if the user has not given a path then, add inputdir. else leave path alone.
49 if (path == "") { parameters["tree"] = inputDir + it->second; }
52 it = parameters.find("group");
53 //user has given a template file
54 if(it != parameters.end()){
55 path = hasPath(it->second);
56 //if the user has not given a path then, add inputdir. else leave path alone.
57 if (path == "") { parameters["group"] = inputDir + it->second; }
60 it = parameters.find("name");
61 //user has given a template file
62 if(it != parameters.end()){
63 path = hasPath(it->second);
64 //if the user has not given a path then, add inputdir. else leave path alone.
65 if (path == "") { parameters["name"] = inputDir + it->second; }
71 //check for required parameters
72 treefile = validParameter.validFile(parameters, "tree", true);
73 if (treefile == "not open") { abort = true; }
74 else if (treefile == "not found") { treefile = ""; mothurOut("tree is a required parameter for the read.tree command."); mothurOutEndLine(); abort = true; }
75 else { globaldata->setTreeFile(treefile); globaldata->setFormat("tree"); }
77 groupfile = validParameter.validFile(parameters, "group", true);
78 if (groupfile == "not open") { abort = true; }
79 else if (groupfile == "not found") { groupfile = ""; mothurOut("group is a required parameter for the read.tree command."); mothurOutEndLine(); abort = true; }
81 globaldata->setGroupFile(groupfile);
82 //read in group map info.
83 treeMap = new TreeMap(groupfile);
85 globaldata->gTreemap = treeMap;
88 namefile = validParameter.validFile(parameters, "name", true);
89 if (namefile == "not open") { abort = true; }
90 else if (namefile == "not found") { treefile = ""; }
91 else { readNamesFile(); }
95 read = new ReadNewickTree(filename);
100 catch(exception& e) {
101 errorOut(e, "ReadTreeCommand", "ReadTreeCommand");
105 //**********************************************************************************************************************
107 void ReadTreeCommand::help(){
109 mothurOut("The read.tree command must be run before you execute a unifrac.weighted, unifrac.unweighted. \n");
110 mothurOut("It also must be run before using the parsimony command, unless you are using the randomtree parameter.\n");
111 mothurOut("The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile).\n");
112 mothurOut("The tree and group parameters are both required.\n");
113 mothurOut("Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n");
115 catch(exception& e) {
116 errorOut(e, "ReadTreeCommand", "help");
121 //**********************************************************************************************************************
123 ReadTreeCommand::~ReadTreeCommand(){
124 if (abort == false) { delete read; }
127 //**********************************************************************************************************************
129 int ReadTreeCommand::execute(){
132 if (abort == true) { return 0; }
136 readOk = read->read();
138 if (readOk != 0) { mothurOut("Read Terminated."); mothurOutEndLine(); globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
140 vector<Tree*> T = globaldata->gTree;
142 //assemble users trees
143 for (int i = 0; i < T.size(); i++) {
144 T[i]->assembleTree();
147 //output any names that are in group file but not in tree
148 if (globaldata->Treenames.size() < treeMap->getNumSeqs()) {
149 for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) {
150 //is that name in the tree?
152 for (int j = 0; j < globaldata->Treenames.size(); j++) {
153 if (treeMap->namesOfSeqs[i] == globaldata->Treenames[j]) { break; } //found it
157 //then you did not find it so report it
158 if (count == globaldata->Treenames.size()) {
159 //if it is in your namefile then don't remove
160 map<string, string>::iterator it = nameMap.find(treeMap->namesOfSeqs[i]);
162 if (it == nameMap.end()) {
163 mothurOut(treeMap->namesOfSeqs[i] + " is in your groupfile and not in your tree. It will be disregarded."); mothurOutEndLine();
164 treeMap->removeSeq(treeMap->namesOfSeqs[i]);
172 catch(exception& e) {
173 errorOut(e, "ReadTreeCommand", "execute");
177 /*****************************************************************/
178 int ReadTreeCommand::readNamesFile() {
180 globaldata->names.clear();
183 openInputFile(namefile, in);
185 string first, second;
186 map<string, string>::iterator itNames;
189 in >> first >> second; gobble(in);
191 itNames = globaldata->names.find(first);
192 if (itNames == globaldata->names.end()) {
193 globaldata->names[first] = second;
195 //we need a list of names in your namefile to use above when removing extra seqs above so we don't remove them
196 vector<string> dupNames;
197 splitAtComma(second, dupNames);
199 for (int i = 0; i < dupNames.size(); i++) { nameMap[dupNames[i]] = dupNames[i]; }
200 }else { mothurOut(first + " has already been seen in namefile, disregarding names file."); mothurOutEndLine(); in.close(); globaldata->names.clear(); return 1; }
206 catch(exception& e) {
207 errorOut(e, "ReadTreeCommand", "readNamesFile");
212 //**********************************************************************************************************************