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"};
24 vector<string> myArray (Array, Array+(sizeof(Array)/sizeof(string)));
26 OptionParser parser(option);
27 map<string, string> parameters = parser.getParameters();
29 ValidParameters validParameter;
31 //check to make sure all parameters are valid for command
32 for (map<string, string>::iterator it = parameters.begin(); it != parameters.end(); it++) {
33 if (validParameter.isValidParameter(it->first, myArray, it->second) != true) { abort = true; }
36 globaldata->newRead();
38 //check for required parameters
39 treefile = validParameter.validFile(parameters, "tree", true);
40 if (treefile == "not open") { abort = true; }
41 else if (treefile == "not found") { treefile = ""; mothurOut("tree is a required parameter for the read.tree command."); mothurOutEndLine(); abort = true; }
42 else { globaldata->setTreeFile(treefile); globaldata->setFormat("tree"); }
44 groupfile = validParameter.validFile(parameters, "group", true);
45 if (groupfile == "not open") { abort = true; }
46 else if (groupfile == "not found") { groupfile = ""; mothurOut("group is a required parameter for the read.tree command."); mothurOutEndLine(); abort = true; }
48 globaldata->setGroupFile(groupfile);
49 //read in group map info.
50 treeMap = new TreeMap(groupfile);
52 globaldata->gTreemap = treeMap;
57 read = new ReadNewickTree(filename);
63 errorOut(e, "ReadTreeCommand", "ReadTreeCommand");
67 //**********************************************************************************************************************
69 void ReadTreeCommand::help(){
71 mothurOut("The read.tree command must be run before you execute a unifrac.weighted, unifrac.unweighted. \n");
72 mothurOut("It also must be run before using the parsimony command, unless you are using the randomtree parameter.\n");
73 mothurOut("The read.tree command should be in the following format: read.tree(tree=yourTreeFile, group=yourGroupFile).\n");
74 mothurOut("The tree and group parameters are both required.\n");
75 mothurOut("Note: No spaces between parameter labels (i.e. tree), '=' and parameters (i.e.yourTreefile).\n\n");
78 errorOut(e, "ReadTreeCommand", "help");
83 //**********************************************************************************************************************
85 ReadTreeCommand::~ReadTreeCommand(){
86 if (abort == false) { delete read; }
89 //**********************************************************************************************************************
91 int ReadTreeCommand::execute(){
94 if (abort == true) { return 0; }
98 readOk = read->read();
100 if (readOk != 0) { mothurOut("Read Terminated."); mothurOutEndLine(); globaldata->gTree.clear(); delete globaldata->gTreemap; return 0; }
102 vector<Tree*> T = globaldata->gTree;
104 //assemble users trees
105 for (int i = 0; i < T.size(); i++) {
106 T[i]->assembleTree();
109 //output any names that are in names file but not in tree
110 if (globaldata->Treenames.size() < treeMap->getNumSeqs()) {
111 for (int i = 0; i < treeMap->namesOfSeqs.size(); i++) {
112 //is that name in the tree?
114 for (int j = 0; j < globaldata->Treenames.size(); j++) {
115 if (treeMap->namesOfSeqs[i] == globaldata->Treenames[j]) { break; } //found it
119 //then you did not find it so report it
120 if (count == globaldata->Treenames.size()) {
121 mothurOut(treeMap->namesOfSeqs[i] + " is in your namefile and not in your tree. It will be disregarded."); mothurOutEndLine();
128 catch(exception& e) {
129 errorOut(e, "ReadTreeCommand", "execute");
134 //**********************************************************************************************************************