TreeMap::TreeMap(string filename) {
groupFileName = filename;
- openInputFile(filename, fileHandle);
+ m->openInputFile(filename, fileHandle);
}
/************************************************************/
while(fileHandle){
fileHandle >> seqName; //read from first column
fileHandle >> seqGroup; //read from second column
-
+
namesOfSeqs.push_back(seqName);
setNamesOfGroups(seqGroup);
-
+
treemap[seqName].groupname = seqGroup; //store data in map
it2 = seqsPerGroup.find(seqGroup);
seqsPerGroup[seqGroup]++;
}
- gobble(fileHandle);
+ m->gobble(fileHandle);
}
fileHandle.close();
}
/************************************************************/
+void TreeMap::addSeq(string seqName, string seqGroup) {
+
+ namesOfSeqs.push_back(seqName);
+ setNamesOfGroups(seqGroup);
+
+ treemap[seqName].groupname = seqGroup; //store data in map
+
+ it2 = seqsPerGroup.find(seqGroup);
+ if (it2 == seqsPerGroup.end()) { //if it's a new group
+ seqsPerGroup[seqGroup] = 1;
+ }else {//it's a group we already have
+ seqsPerGroup[seqGroup]++;
+ }
+}
+/************************************************************/
void TreeMap::removeSeq(string seqName) {
//erase name from namesOfSeqs
for (int i = 0; i < namesOfSeqs.size(); i++) {
if (namesOfSeqs[i] == seqName) {
- namesOfSeqs.erase (namesOfSeqs.begin()+i);
+ namesOfSeqs.erase(namesOfSeqs.begin()+i);
break;
}
}
//remove seq from treemap
it = treemap.find(seqName);
treemap.erase(it);
-
-
}
/************************************************************/
return false;
}
catch(exception& e) {
- errorOut(e, "TreeMap", "isValidGroup");
+ m->errorOut(e, "TreeMap", "isValidGroup");
exit(1);
}
}
}
}
catch(exception& e) {
- errorOut(e, "TreeMap", "print");
+ m->errorOut(e, "TreeMap", "print");
exit(1);
}
}
/************************************************************/
-void TreeMap::makeSim(GroupMap* groupmap) {
+void TreeMap::makeSim(vector<string> ThisnamesOfGroups) {
try {
//set names of groups
- namesOfGroups = groupmap->namesOfGroups;
+ namesOfGroups = ThisnamesOfGroups;
//set names of seqs to names of groups
- namesOfSeqs = groupmap->namesOfGroups;
+ namesOfSeqs = ThisnamesOfGroups;
// make map where key and value are both the group name since that what the tree.shared command wants
for (int i = 0; i < namesOfGroups.size(); i++) {
}
catch(exception& e) {
- errorOut(e, "TreeMap", "makeSim");
+ m->errorOut(e, "TreeMap", "makeSim");
exit(1);
}
}
}
catch(exception& e) {
- errorOut(e, "TreeMap", "makeSim");
+ m->errorOut(e, "TreeMap", "makeSim");
exit(1);
}
}