5 * Created by Sarah Westcott on 12/1/08.
6 * Copyright 2008 Schloss Lab UMASS Amherst. All rights reserved.
12 /************************************************************/
14 GroupMap::GroupMap(string filename) {
15 groupFileName = filename;
16 openInputFile(filename, fileHandle);
20 /************************************************************/
21 GroupMap::~GroupMap(){}
23 /************************************************************/
24 void GroupMap::readMap() {
25 string seqName, seqGroup;
28 fileHandle >> seqName; //read from first column
29 fileHandle >> seqGroup; //read from second column
31 setNamesOfGroups(seqGroup);
33 groupmap[seqName] = seqGroup; //store data in map
34 seqsPerGroup[seqGroup]++; //increment number of seqs in that group
40 /************************************************************/
41 int GroupMap::getNumGroups() { return namesOfGroups.size(); }
42 /************************************************************/
44 string GroupMap::getGroup(string sequenceName) {
46 it = groupmap.find(sequenceName);
47 if (it != groupmap.end()) { //sequence name was in group file
54 /************************************************************/
55 void GroupMap::setGroup(string sequenceName, string groupN) {
56 groupmap[sequenceName] = groupN;
58 /************************************************************/
59 void GroupMap::setNamesOfGroups(string seqGroup) {
62 for (i=0; i<namesOfGroups.size(); i++) {
63 if (namesOfGroups[i] != seqGroup) {
64 count++; //you have not found this group
66 break; //you already have it
69 if (count == namesOfGroups.size()) {
70 namesOfGroups.push_back(seqGroup); //new group
71 seqsPerGroup[seqGroup] = 0;
72 groupIndex[seqGroup] = index;
76 /************************************************************/
77 bool GroupMap::isValidGroup(string groupname) {
79 for (int i = 0; i < namesOfGroups.size(); i++) {
80 if (groupname == namesOfGroups[i]) { return true; }
86 errorOut(e, "GroupMap", "isValidGroup");
90 /************************************************************/
91 int GroupMap::getNumSeqs(string group) {
94 map<string, int>::iterator itNum;
96 itNum = seqsPerGroup.find(group);
98 if (itNum == seqsPerGroup.end()) { return 0; }
100 return seqsPerGroup[group];
103 catch(exception& e) {
104 errorOut(e, "GroupMap", "getNumSeqs");
109 /************************************************************/
110 vector<string> GroupMap::getNamesSeqs(){
113 vector<string> names;
115 for (it = groupmap.begin(); it != groupmap.end(); it++) {
116 names.push_back(it->first);
121 catch(exception& e) {
122 errorOut(e, "GroupMap", "getNamesSeqs");
126 /************************************************************/