exit(1);
}
}
+/**************************************************************************************************/
+
+vector<string> PhyloTree::getSeqs(string seqTaxonomy){
+ try {
+ string taxCopy = seqTaxonomy;
+ vector<string> names;
+ map<string, int>::iterator childPointer;
+
+ int currentNode = 0;
+
+ m->removeConfidences(seqTaxonomy);
+
+ string taxon;
+ while(seqTaxonomy != ""){
+
+ if (m->control_pressed) { return names; }
+
+ taxon = getNextTaxon(seqTaxonomy, "");
+
+ if (m->debug) { m->mothurOut(taxon +'\n'); }
+
+ if (taxon == "") { m->mothurOut(taxCopy + " has an error in the taxonomy. This may be due to a ;;"); m->mothurOutEndLine(); break; }
+
+ childPointer = tree[currentNode].children.find(taxon);
+
+ if(childPointer != tree[currentNode].children.end()){ //if the node already exists, move on
+ currentNode = childPointer->second;
+ }
+ else{ //otherwise, error this taxonomy is not in tree
+ m->mothurOut("[ERROR]: " + taxCopy + " is not in taxonomy tree, please correct."); m->mothurOutEndLine(); m->control_pressed = true; return names;
+ }
+
+ if (seqTaxonomy == "") { names = tree[currentNode].accessions; }
+ }
+
+ return names;
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloTree", "getSeqs");
+ exit(1);
+ }
+}
/**************************************************************************************************/
//somehow the parent is getting one too many accnos
//use print to reassign the taxa id
taxon = getNextTaxon(seqTaxonomy, seqName);
+
+ if (m->debug) { m->mothurOut(seqName +'\t' + taxon +'\n'); }
if (taxon == "") { m->mothurOut(seqName + " has an error in the taxonomy. This may be due to a ;;"); m->mothurOutEndLine(); if (currentNode != 0) { uniqueTaxonomies.insert(currentNode); } break; }
int counter = 1;
for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
+
+ if (m->debug) { m->mothurOut(toString(index) +'\t' + tree[it->second].name +'\n'); }
+
tree[it->second].heirarchyID = tree[index].heirarchyID + '.' + toString(counter);
counter++;
tree[it->second].level = tree[index].level + 1;
}
}
+ if (m->debug) { m->mothurOut("maxLevel = " + toString(maxLevel) +'\n'); }
+
int copyNodes = copy.size();
//go through the seqs and if a sequence finest taxon is not the same level as the most finely defined taxon then classify it as unclassified where necessary
int level = copy[itLeaf->second].level;
int currentNode = itLeaf->second;
+
+ if (m->debug) { m->mothurOut(copy[currentNode].name +'\n'); }
//this sequence is unclassified at some levels
while(level < maxLevel){
level++;
+ if (m->debug) { m->mothurOut("level = " + toString(level) +'\n'); }
string taxon = "unclassified";