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(){}
23 /************************************************************/
24 int GroupMap::readMap() {
26 string seqName, seqGroup;
30 bool pairDone = false;
31 bool columnOne = true;
33 while (!fileHandle.eof()) {
34 if (m->control_pressed) { fileHandle.close(); return 1; }
36 fileHandle.read(buffer, 4096);
37 vector<string> pieces = m->splitWhiteSpace(rest, buffer, fileHandle.gcount());
39 for (int i = 0; i < pieces.size(); i++) {
40 if (columnOne) { seqName = pieces[i]; columnOne=false; }
41 else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
44 setNamesOfGroups(seqGroup);
46 if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
47 m->checkName(seqName);
48 it = groupmap.find(seqName);
50 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(); }
52 groupmap[seqName] = seqGroup; //store data in map
53 seqsPerGroup[seqGroup]++; //increment number of seqs in that group
62 vector<string> pieces = m->splitWhiteSpace(rest);
64 for (int i = 0; i < pieces.size(); i++) {
65 if (columnOne) { seqName = pieces[i]; columnOne=false; }
66 else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
69 setNamesOfGroups(seqGroup);
71 if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
72 m->checkName(seqName);
73 it = groupmap.find(seqName);
75 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(); }
77 groupmap[seqName] = seqGroup; //store data in map
78 seqsPerGroup[seqGroup]++; //increment number of seqs in that group
85 m->setAllGroups(namesOfGroups);
89 m->errorOut(e, "GroupMap", "readMap");
93 /************************************************************/
94 int GroupMap::readDesignMap() {
96 string seqName, seqGroup;
100 bool pairDone = false;
101 bool columnOne = true;
103 while (!fileHandle.eof()) {
104 if (m->control_pressed) { fileHandle.close(); return 1; }
106 fileHandle.read(buffer, 4096);
107 vector<string> pieces = m->splitWhiteSpace(rest, buffer, fileHandle.gcount());
109 for (int i = 0; i < pieces.size(); i++) {
110 if (columnOne) { seqName = pieces[i]; columnOne=false; }
111 else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
114 setNamesOfGroups(seqGroup);
116 if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
117 m->checkName(seqName);
118 it = groupmap.find(seqName);
120 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(); }
122 groupmap[seqName] = seqGroup; //store data in map
123 seqsPerGroup[seqGroup]++; //increment number of seqs in that group
132 vector<string> pieces = m->splitWhiteSpace(rest);
134 for (int i = 0; i < pieces.size(); i++) {
135 if (columnOne) { seqName = pieces[i]; columnOne=false; }
136 else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
139 setNamesOfGroups(seqGroup);
141 if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
142 m->checkName(seqName);
143 it = groupmap.find(seqName);
145 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(); }
147 groupmap[seqName] = seqGroup; //store data in map
148 seqsPerGroup[seqGroup]++; //increment number of seqs in that group
156 m->setAllGroups(namesOfGroups);
159 catch(exception& e) {
160 m->errorOut(e, "GroupMap", "readDesignMap");
164 /************************************************************/
165 int GroupMap::readMap(string filename) {
167 groupFileName = filename;
168 m->openInputFile(filename, fileHandle);
170 string seqName, seqGroup;
174 bool pairDone = false;
175 bool columnOne = true;
177 while (!fileHandle.eof()) {
178 if (m->control_pressed) { fileHandle.close(); return 1; }
180 fileHandle.read(buffer, 4096);
181 vector<string> pieces = m->splitWhiteSpace(rest, buffer, fileHandle.gcount());
183 for (int i = 0; i < pieces.size(); i++) {
184 if (columnOne) { seqName = pieces[i]; columnOne=false; }
185 else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
188 setNamesOfGroups(seqGroup);
190 if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
191 m->checkName(seqName);
192 it = groupmap.find(seqName);
194 if (it != groupmap.end()) { error = 1; m->mothurOut("Your group file contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
196 groupmap[seqName] = seqGroup; //store data in map
197 seqsPerGroup[seqGroup]++; //increment number of seqs in that group
206 vector<string> pieces = m->splitWhiteSpace(rest);
208 for (int i = 0; i < pieces.size(); i++) {
209 if (columnOne) { seqName = pieces[i]; columnOne=false; }
210 else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
213 setNamesOfGroups(seqGroup);
215 if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
216 m->checkName(seqName);
217 it = groupmap.find(seqName);
219 if (it != groupmap.end()) { error = 1; m->mothurOut("Your group file contains more than 1 sequence named " + seqName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
221 groupmap[seqName] = seqGroup; //store data in map
222 seqsPerGroup[seqGroup]++; //increment number of seqs in that group
229 m->setAllGroups(namesOfGroups);
232 catch(exception& e) {
233 m->errorOut(e, "GroupMap", "readMap");
237 /************************************************************/
238 int GroupMap::readDesignMap(string filename) {
240 groupFileName = filename;
241 m->openInputFile(filename, fileHandle);
243 string seqName, seqGroup;
247 bool pairDone = false;
248 bool columnOne = true;
250 while (!fileHandle.eof()) {
251 if (m->control_pressed) { fileHandle.close(); return 1; }
253 fileHandle.read(buffer, 4096);
254 vector<string> pieces = m->splitWhiteSpace(rest, buffer, fileHandle.gcount());
256 for (int i = 0; i < pieces.size(); i++) {
257 if (columnOne) { seqName = pieces[i]; columnOne=false; }
258 else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
261 setNamesOfGroups(seqGroup);
263 if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
264 m->checkName(seqName);
265 it = groupmap.find(seqName);
267 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(); }
269 groupmap[seqName] = seqGroup; //store data in map
270 seqsPerGroup[seqGroup]++; //increment number of seqs in that group
279 vector<string> pieces = m->splitWhiteSpace(rest);
281 for (int i = 0; i < pieces.size(); i++) {
282 if (columnOne) { seqName = pieces[i]; columnOne=false; }
283 else { seqGroup = pieces[i]; pairDone = true; columnOne=true; }
286 setNamesOfGroups(seqGroup);
288 if (m->debug) { m->mothurOut("[DEBUG]: name = '" + seqName + "', group = '" + seqGroup + "'\n"); }
289 m->checkName(seqName);
290 it = groupmap.find(seqName);
292 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(); }
294 groupmap[seqName] = seqGroup; //store data in map
295 seqsPerGroup[seqGroup]++; //increment number of seqs in that group
302 m->setAllGroups(namesOfGroups);
305 catch(exception& e) {
306 m->errorOut(e, "GroupMap", "readDesignMap");
310 /************************************************************/
311 int GroupMap::getNumGroups() { return namesOfGroups.size(); }
312 /************************************************************/
314 string GroupMap::getGroup(string sequenceName) {
316 it = groupmap.find(sequenceName);
317 if (it != groupmap.end()) { //sequence name was in group file
320 //look for it in names of groups to see if the user accidently used the wrong file
321 if (m->inUsersGroups(sequenceName, namesOfGroups)) {
322 m->mothurOut("[WARNING]: Your group or design file contains a group named " + sequenceName + ". Perhaps you are used a group file instead of a design file? A common cause of this is using a tree file that relates your groups (created by the tree.shared command) with a group file that assigns sequences to a group."); m->mothurOutEndLine();
328 /************************************************************/
330 void GroupMap::setGroup(string sequenceName, string groupN) {
331 setNamesOfGroups(groupN);
332 m->checkName(sequenceName);
333 it = groupmap.find(sequenceName);
335 if (it != groupmap.end()) { m->mothurOut("Your groupfile contains more than 1 sequence named " + sequenceName + ", sequence names must be unique. Please correct."); m->mothurOutEndLine(); }
337 groupmap[sequenceName] = groupN; //store data in map
338 seqsPerGroup[groupN]++; //increment number of seqs in that group
342 /************************************************************/
343 void GroupMap::setNamesOfGroups(string seqGroup) {
346 for (i=0; i<namesOfGroups.size(); i++) {
347 if (namesOfGroups[i] != seqGroup) {
348 count++; //you have not found this group
350 break; //you already have it
353 if (count == namesOfGroups.size()) {
354 namesOfGroups.push_back(seqGroup); //new group
355 seqsPerGroup[seqGroup] = 0;
356 groupIndex[seqGroup] = index;
360 /************************************************************/
361 bool GroupMap::isValidGroup(string groupname) {
363 for (int i = 0; i < namesOfGroups.size(); i++) {
364 if (groupname == namesOfGroups[i]) { return true; }
369 catch(exception& e) {
370 m->errorOut(e, "GroupMap", "isValidGroup");
374 /************************************************************/
375 int GroupMap::getCopy(GroupMap* g) {
377 vector<string> names = g->getNamesSeqs();
378 for (int i = 0; i < names.size(); i++) {
379 if (m->control_pressed) { break; }
380 string group = g->getGroup(names[i]);
381 setGroup(names[i], group);
385 catch(exception& e) {
386 m->errorOut(e, "GroupMap", "getCopy");
390 /************************************************************/
391 int GroupMap::getNumSeqs(string group) {
394 map<string, int>::iterator itNum;
396 itNum = seqsPerGroup.find(group);
398 if (itNum == seqsPerGroup.end()) { return 0; }
400 return seqsPerGroup[group];
403 catch(exception& e) {
404 m->errorOut(e, "GroupMap", "getNumSeqs");
408 /************************************************************/
409 int GroupMap::renameSeq(string oldName, string newName) {
412 map<string, string>::iterator itName;
414 itName = groupmap.find(oldName);
416 if (itName == groupmap.end()) {
417 m->mothurOut("[ERROR]: cannot find " + toString(oldName) + " in group file");
418 m->control_pressed = true;
421 string group = itName->second;
422 groupmap.erase(itName);
423 groupmap[newName] = group;
429 catch(exception& e) {
430 m->errorOut(e, "GroupMap", "renameSeq");
434 /************************************************************/
435 int GroupMap::print(ofstream& out) {
438 for (map<string, string>::iterator itName = groupmap.begin(); itName != groupmap.end(); itName++) {
439 out << itName->first << '\t' << itName->second << endl;
445 catch(exception& e) {
446 m->errorOut(e, "GroupMap", "print");
450 /************************************************************/
451 int GroupMap::print(ofstream& out, vector<string> userGroups) {
454 for (map<string, string>::iterator itName = groupmap.begin(); itName != groupmap.end(); itName++) {
455 if (m->inUsersGroups(itName->second, userGroups)) {
456 out << itName->first << '\t' << itName->second << endl;
463 catch(exception& e) {
464 m->errorOut(e, "GroupMap", "print");
468 /************************************************************/
469 vector<string> GroupMap::getNamesSeqs(){
472 vector<string> names;
474 for (it = groupmap.begin(); it != groupmap.end(); it++) {
475 names.push_back(it->first);
480 catch(exception& e) {
481 m->errorOut(e, "GroupMap", "getNamesSeqs");
485 /************************************************************/
486 vector<string> GroupMap::getNamesSeqs(vector<string> picked){
489 vector<string> names;
491 for (it = groupmap.begin(); it != groupmap.end(); it++) {
492 //if you are belong to one the the groups in the picked vector add you
493 if (m->inUsersGroups(it->second, picked)) {
494 names.push_back(it->first);
500 catch(exception& e) {
501 m->errorOut(e, "GroupMap", "getNamesSeqs");
506 /************************************************************/