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 m = MothurOut::getInstance();
16 groupFileName = filename;
17 m->openInputFile(filename, fileHandle);
21 /************************************************************/
22 GroupMap::~GroupMap(){}
24 /************************************************************/
25 int GroupMap::readMap() {
27 string seqName, seqGroup;
31 bool pairDone = false;
32 bool columnOne = true;
34 while (!fileHandle.eof()) {
35 if (m->control_pressed) { fileHandle.close(); return 1; }
37 fileHandle.read(buffer, 4096);
38 vector<string> pieces = m->splitWhiteSpace(rest, buffer, fileHandle.gcount());
40 for (int i = 0; i < pieces.size(); i++) {
41 if (columnOne) { seqName = pieces[i]; columnOne=false; }
42 else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
45 setNamesOfGroups(seqGroup);
47 it = groupmap.find(seqName);
49 if (it != groupmap.end()) { error = 1; m->mothurOut("Your groupfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
51 groupmap[seqName] = seqGroup; //store data in map
52 seqsPerGroup[seqGroup]++; //increment number of seqs in that group
60 m->setAllGroups(namesOfGroups);
64 m->errorOut(e, "GroupMap", "readMap");
68 /************************************************************/
69 int GroupMap::readDesignMap() {
71 string seqName, seqGroup;
75 bool pairDone = false;
76 bool columnOne = true;
78 while (!fileHandle.eof()) {
79 if (m->control_pressed) { fileHandle.close(); return 1; }
81 fileHandle.read(buffer, 4096);
82 vector<string> pieces = m->splitWhiteSpace(rest, buffer, fileHandle.gcount());
84 for (int i = 0; i < pieces.size(); i++) {
85 if (columnOne) { seqName = pieces[i]; columnOne=false; }
86 else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
89 setNamesOfGroups(seqGroup);
91 it = groupmap.find(seqName);
93 if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
95 groupmap[seqName] = seqGroup; //store data in map
96 seqsPerGroup[seqGroup]++; //increment number of seqs in that group
104 m->setAllGroups(namesOfGroups);
107 catch(exception& e) {
108 m->errorOut(e, "GroupMap", "readDesignMap");
112 /************************************************************/
113 int GroupMap::readDesignMap(string filename) {
115 groupFileName = filename;
116 m->openInputFile(filename, fileHandle);
118 string seqName, seqGroup;
122 bool pairDone = false;
123 bool columnOne = true;
125 while (!fileHandle.eof()) {
126 if (m->control_pressed) { fileHandle.close(); return 1; }
128 fileHandle.read(buffer, 4096);
129 vector<string> pieces = m->splitWhiteSpace(rest, buffer, fileHandle.gcount());
131 for (int i = 0; i < pieces.size(); i++) {
132 if (columnOne) { seqName = pieces[i]; columnOne=false; }
133 else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
136 setNamesOfGroups(seqGroup);
138 it = groupmap.find(seqName);
140 if (it != groupmap.end()) { error = 1; m->mothurOut("Your designfile contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
142 groupmap[seqName] = seqGroup; //store data in map
143 seqsPerGroup[seqGroup]++; //increment number of seqs in that group
151 m->setAllGroups(namesOfGroups);
154 catch(exception& e) {
155 m->errorOut(e, "GroupMap", "readDesignMap");
159 /************************************************************/
160 int GroupMap::getNumGroups() { return namesOfGroups.size(); }
161 /************************************************************/
163 string GroupMap::getGroup(string sequenceName) {
165 it = groupmap.find(sequenceName);
166 if (it != groupmap.end()) { //sequence name was in group file
173 /************************************************************/
175 void GroupMap::setGroup(string sequenceName, string groupN) {
176 setNamesOfGroups(groupN);
178 it = groupmap.find(sequenceName);
180 if (it != groupmap.end()) { m->mothurOut("Your groupfile contains more than 1 sequence named " + sequenceName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
182 groupmap[sequenceName] = groupN; //store data in map
183 seqsPerGroup[groupN]++; //increment number of seqs in that group
187 /************************************************************/
188 void GroupMap::setNamesOfGroups(string seqGroup) {
191 for (i=0; i<namesOfGroups.size(); i++) {
192 if (namesOfGroups[i] != seqGroup) {
193 count++; //you have not found this group
195 break; //you already have it
198 if (count == namesOfGroups.size()) {
199 namesOfGroups.push_back(seqGroup); //new group
200 seqsPerGroup[seqGroup] = 0;
201 groupIndex[seqGroup] = index;
205 /************************************************************/
206 bool GroupMap::isValidGroup(string groupname) {
208 for (int i = 0; i < namesOfGroups.size(); i++) {
209 if (groupname == namesOfGroups[i]) { return true; }
214 catch(exception& e) {
215 m->errorOut(e, "GroupMap", "isValidGroup");
219 /************************************************************/
220 int GroupMap::getNumSeqs(string group) {
223 map<string, int>::iterator itNum;
225 itNum = seqsPerGroup.find(group);
227 if (itNum == seqsPerGroup.end()) { return 0; }
229 return seqsPerGroup[group];
232 catch(exception& e) {
233 m->errorOut(e, "GroupMap", "getNumSeqs");
238 /************************************************************/
239 vector<string> GroupMap::getNamesSeqs(){
242 vector<string> names;
244 for (it = groupmap.begin(); it != groupmap.end(); it++) {
245 names.push_back(it->first);
250 catch(exception& e) {
251 m->errorOut(e, "GroupMap", "getNamesSeqs");
255 /************************************************************/
256 vector<string> GroupMap::getNamesSeqs(vector<string> picked){
259 vector<string> names;
261 for (it = groupmap.begin(); it != groupmap.end(); it++) {
262 //if you are belong to one the the groups in the picked vector add you
263 if (m->inUsersGroups(it->second, picked)) {
264 names.push_back(it->first);
270 catch(exception& e) {
271 m->errorOut(e, "GroupMap", "getNamesSeqs");
276 /************************************************************/