/**************************************************************************************************/
PhyloTree::PhyloTree(){
-
- numNodes = 1;
- numSeqs = 0;
- tree.push_back(TaxNode("Root"));
- tree[0].heirarchyID = "0";
+ try {
+ numNodes = 1;
+ numSeqs = 0;
+ tree.push_back(TaxNode("Root"));
+ tree[0].heirarchyID = "0";
+ }
+ catch(exception& e) {
+ errorOut(e, "PhyloTree", "PhyloTree");
+ exit(1);
+ }
}
/**************************************************************************************************/
string PhyloTree::getNextTaxon(string& heirarchy){
-
- string currentLevel = "";
- if(heirarchy != ""){
- currentLevel=heirarchy.substr(0,heirarchy.find_first_of(';'));
- heirarchy=heirarchy.substr(heirarchy.find_first_of(';')+1);
+ try {
+ string currentLevel = "";
+ if(heirarchy != ""){
+ currentLevel=heirarchy.substr(0,heirarchy.find_first_of(';'));
+ heirarchy=heirarchy.substr(heirarchy.find_first_of(';')+1);
+ }
+ return currentLevel;
+ }
+ catch(exception& e) {
+ errorOut(e, "PhyloTree", "getNextTaxon");
+ exit(1);
}
- return currentLevel;
-
}
/**************************************************************************************************/
void PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
-
- numSeqs++;
-
- map<string, int>::iterator childPointer;
-
- int currentNode = 0;
- int level = 1;
-
- tree[0].accessions.push_back(seqName);
- string taxon;// = getNextTaxon(seqTaxonomy);
-
- while(seqTaxonomy != ""){
-
- level++;
-
-//somehow the parent is getting one too many accnos
-//use print to reassign the taxa id
- taxon = getNextTaxon(seqTaxonomy);
-
- childPointer = tree[currentNode].children.find(taxon);
-
- if(childPointer != tree[currentNode].children.end()){ //if the node already exists, move on
- currentNode = childPointer->second;
- tree[currentNode].accessions.push_back(seqName);
- name2Taxonomy[seqName] = currentNode;
- }
- else{ //otherwise, create it
- tree.push_back(TaxNode(taxon));
- numNodes++;
- tree[currentNode].children[taxon] = numNodes-1;
- tree[numNodes-1].parent = currentNode;
-
-// int numChildren = tree[currentNode].children.size();
-// string heirarchyID = tree[currentNode].heirarchyID;
-// tree[currentNode].accessions.push_back(seqName);
+ try {
+ numSeqs++;
+
+ map<string, int>::iterator childPointer;
+
+ int currentNode = 0;
+ int level = 1;
+
+ tree[0].accessions.push_back(seqName);
+ string taxon;// = getNextTaxon(seqTaxonomy);
+
+ while(seqTaxonomy != ""){
- currentNode = tree[currentNode].children[taxon];
- tree[currentNode].accessions.push_back(seqName);
- name2Taxonomy[seqName] = currentNode;
-// tree[currentNode].level = level;
-// tree[currentNode].childNumber = numChildren;
-// tree[currentNode].heirarchyID = heirarchyID + '.' + toString(tree[currentNode].childNumber);
- }
+ level++;
+
+ //somehow the parent is getting one too many accnos
+ //use print to reassign the taxa id
+ taxon = getNextTaxon(seqTaxonomy);
+
+ childPointer = tree[currentNode].children.find(taxon);
+
+ if(childPointer != tree[currentNode].children.end()){ //if the node already exists, move on
+ currentNode = childPointer->second;
+ tree[currentNode].accessions.push_back(seqName);
+ name2Taxonomy[seqName] = currentNode;
+ }
+ else{ //otherwise, create it
+ tree.push_back(TaxNode(taxon));
+ numNodes++;
+ tree[currentNode].children[taxon] = numNodes-1;
+ tree[numNodes-1].parent = currentNode;
+
+ // int numChildren = tree[currentNode].children.size();
+ // string heirarchyID = tree[currentNode].heirarchyID;
+ // tree[currentNode].accessions.push_back(seqName);
+
+ currentNode = tree[currentNode].children[taxon];
+ tree[currentNode].accessions.push_back(seqName);
+ name2Taxonomy[seqName] = currentNode;
+ // tree[currentNode].level = level;
+ // tree[currentNode].childNumber = numChildren;
+ // tree[currentNode].heirarchyID = heirarchyID + '.' + toString(tree[currentNode].childNumber);
+ }
- if (seqTaxonomy == "") { uniqueTaxonomies[currentNode] = currentNode; }
+ if (seqTaxonomy == "") { uniqueTaxonomies[currentNode] = currentNode; }
+ }
+
+ }
+ catch(exception& e) {
+ errorOut(e, "PhyloTree", "addSeqToTree");
+ exit(1);
}
}
/**************************************************************************************************/
/**************************************************************************************************/
void PhyloTree::assignHeirarchyIDs(int index){
-
- map<string,int>::iterator it;
- int counter = 1;
-
- for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
- tree[it->second].heirarchyID = tree[index].heirarchyID + '.' + toString(counter);
- counter++;
- tree[it->second].level = tree[index].level + 1;
- assignHeirarchyIDs(it->second);
+ try {
+ map<string,int>::iterator it;
+ int counter = 1;
+
+ for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
+ tree[it->second].heirarchyID = tree[index].heirarchyID + '.' + toString(counter);
+ counter++;
+ tree[it->second].level = tree[index].level + 1;
+ assignHeirarchyIDs(it->second);
+ }
+ }
+ catch(exception& e) {
+ errorOut(e, "PhyloTree", "assignHeirarchyIDs");
+ exit(1);
}
}
/**************************************************************************************************/
void PhyloTree::print(ofstream& out){
-
- out << tree[0].level << '\t'<< tree[0].heirarchyID << '\t' << tree[0].name << '\t' << tree[0].children.size() << '\t' << tree[0].accessions.size() << endl;
- print(0, out);
-
-
+ try {
+ out << tree[0].level << '\t'<< tree[0].heirarchyID << '\t' << tree[0].name << '\t' << tree[0].children.size() << '\t' << tree[0].accessions.size() << endl;
+ print(0, out);
+ }
+ catch(exception& e) {
+ errorOut(e, "PhyloTree", "print");
+ exit(1);
+ }
}
/**************************************************************************************************/
void PhyloTree::print(int i, ofstream& out){
-
- map<string,int>::iterator it;
- for(it=tree[i].children.begin();it!=tree[i].children.end();it++){
- out <<tree[it->second].level << '\t' << tree[it->second].heirarchyID << '\t' << tree[it->second].name << '\t' << tree[it->second].children.size() << '\t' << tree[it->second].accessions.size() << endl;
- print(it->second, out);
+ try {
+ map<string,int>::iterator it;
+ for(it=tree[i].children.begin();it!=tree[i].children.end();it++){
+ out <<tree[it->second].level << '\t' << tree[it->second].heirarchyID << '\t' << tree[it->second].name << '\t' << tree[it->second].children.size() << '\t' << tree[it->second].accessions.size() << endl;
+ print(it->second, out);
+ }
+ }
+ catch(exception& e) {
+ errorOut(e, "PhyloTree", "print");
+ exit(1);
}
-
}
/**************************************************************************************************/
projects / mothur.git / blobdiff