/************************************************************/
GroupMap::GroupMap(string filename) {
+ m = MothurOut::getInstance();
groupFileName = filename;
openInputFile(filename, fileHandle);
index = 0;
}
/************************************************************/
- GroupMap::~GroupMap(){};
+ GroupMap::~GroupMap(){}
/************************************************************/
-void GroupMap::readMap() {
+int GroupMap::readMap() {
string seqName, seqGroup;
+ int error = 0;
while(fileHandle){
fileHandle >> seqName; //read from first column
fileHandle >> seqGroup; //read from second column
+ if (m->control_pressed) { fileHandle.close(); return 1; }
+
setNamesOfGroups(seqGroup);
-
- groupmap[seqName] = seqGroup; //store data in map
-
+
+ it = groupmap.find(seqName);
+
+ 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(); }
+ else {
+ groupmap[seqName] = seqGroup; //store data in map
+ seqsPerGroup[seqGroup]++; //increment number of seqs in that group
+ }
gobble(fileHandle);
}
fileHandle.close();
+ return error;
}
/************************************************************/
int GroupMap::getNumGroups() { return namesOfGroups.size(); }
}
if (count == namesOfGroups.size()) {
namesOfGroups.push_back(seqGroup); //new group
+ seqsPerGroup[seqGroup] = 0;
groupIndex[seqGroup] = index;
index++;
}
return false;
}
catch(exception& e) {
- cout << "Standard Error: " << e.what() << " has occurred in the GroupMap class Function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+ m->errorOut(e, "GroupMap", "isValidGroup");
exit(1);
}
- catch(...) {
- cout << "An unknown error has occurred in the GroupMap class function isValidGroup. Please contact Pat Schloss at pschloss@microbio.umass.edu." << "\n";
+}
+/************************************************************/
+int GroupMap::getNumSeqs(string group) {
+ try {
+
+ map<string, int>::iterator itNum;
+
+ itNum = seqsPerGroup.find(group);
+
+ if (itNum == seqsPerGroup.end()) { return 0; }
+
+ return seqsPerGroup[group];
+
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GroupMap", "getNumSeqs");
exit(1);
}
}
+
+/************************************************************/
+vector<string> GroupMap::getNamesSeqs(){
+ try {
+
+ vector<string> names;
+
+ for (it = groupmap.begin(); it != groupmap.end(); it++) {
+ names.push_back(it->first);
+ }
+
+ return names;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "GroupMap", "getNamesSeqs");
+ exit(1);
+ }
+}
+/************************************************************/
+