int PhyloTree::addSeqToTree(string seqName, string seqTaxonomy){
try {
numSeqs++;
map<string, int>::iterator childPointer;
int currentNode = 0;
int level = 0;
tree[0].accessions.push_back(seqName);
m->removeConfidences(seqTaxonomy);
string taxon;// = getNextTaxon(seqTaxonomy);
while(seqTaxonomy != ""){
level++;
if (m->control_pressed) { return 0; }
//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; }
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;
currentNode = tree[currentNode].children[taxon];
tree[currentNode].accessions.push_back(seqName);
name2Taxonomy[seqName] = currentNode;
}
if (seqTaxonomy == "") { uniqueTaxonomies.insert(currentNode); }
}
//save maxLevel for binning the unclassified seqs
if (level > maxLevel) { maxLevel = level; }
return 0;
}
catch(exception& e) {
m->errorOut(e, "PhyloTree", "addSeqToTree");
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);
}
}
int PhyloSummary::addSeqToTree(string seqTaxonomy, map<string, bool> containsGroup){
try {
numSeqs++;
map<string, int>::iterator childPointer;
int currentNode = 0;
string taxon;
int level = 0;
//are there confidence scores, if so remove them
if (seqTaxonomy.find_first_of('(') != -1) { m->removeConfidences(seqTaxonomy); }
while (seqTaxonomy != "") {
level++;
if (m->control_pressed) { return 0; }
//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, update count and move on
for (map<string, bool>::iterator itGroup = containsGroup.begin(); itGroup != containsGroup.end(); itGroup++) {
if (itGroup->second == true) {
tree[childPointer->second].groupCount[itGroup->first]++;
}
}
tree[childPointer->second].total++;
currentNode = childPointer->second;
}else{
if (ignore) {
tree.push_back(rawTaxNode(taxon));
int index = tree.size() - 1;
tree[index].parent = currentNode;
tree[index].level = level;
tree[index].total = 1;
tree[currentNode].children[taxon] = index;
for (map<string, bool>::iterator itGroup = containsGroup.begin(); itGroup != containsGroup.end(); itGroup++) {
if (itGroup->second == true) {
tree[index].groupCount[itGroup->first]++;
}
}
currentNode = index;
}else{ //otherwise, error
m->mothurOut("Warning: cannot find taxon " + taxon + " in reference taxonomy tree at level " + toString(tree[currentNode].level) + ". This may cause totals of daughter levels not to add up in summary file."); m->mothurOutEndLine();
break;
}
}
}
if (level > maxLevel) { maxLevel = level; }
return 0;
}
catch(exception& e) {
m->errorOut(e, "PhyloSummary", "addSeqToTree");
exit(1);
}
}
int PhyloSummary::addSeqToTree(string seqName, string seqTaxonomy){
try {
numSeqs++;
map<string, int>::iterator childPointer;
int currentNode = 0;
string taxon;
int level = 0;
//are there confidence scores, if so remove them
if (seqTaxonomy.find_first_of('(') != -1) { m->removeConfidences(seqTaxonomy); }
while (seqTaxonomy != "") {
level++;
if (m->control_pressed) { return 0; }
//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, update count and move on
int thisCount = 1;
if (groupmap != NULL) {
//find out the sequences group
string group = groupmap->getGroup(seqName);
if (group == "not found") { m->mothurOut("[WARNING]: " + seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine(); }
//do you have a count for this group?
map<string, int>::iterator itGroup = tree[childPointer->second].groupCount.find(group);
//if yes, increment it - there should not be a case where we can't find it since we load group in read
if (itGroup != tree[childPointer->second].groupCount.end()) {
tree[childPointer->second].groupCount[group]++;
}
}else if (ct != NULL) {
if (ct->hasGroupInfo()) {
vector<int> groupCounts = ct->getGroupCounts(seqName);
vector<string> groups = ct->getNamesOfGroups();
for (int i = 0; i < groups.size(); i++) {
if (groupCounts[i] != 0) {
//do you have a count for this group?
map<string, int>::iterator itGroup = tree[childPointer->second].groupCount.find(groups[i]);
//if yes, increment it - there should not be a case where we can't find it since we load group in read
if (itGroup != tree[childPointer->second].groupCount.end()) {
tree[childPointer->second].groupCount[groups[i]] += groupCounts[i];
}
}
}
}
thisCount = ct->getNumSeqs(seqName);
}
tree[childPointer->second].total += thisCount;
currentNode = childPointer->second;
}else{
if (ignore) {
tree.push_back(rawTaxNode(taxon));
int index = tree.size() - 1;
tree[index].parent = currentNode;
tree[index].level = level;
tree[currentNode].children[taxon] = index;
int thisCount = 1;
//initialize groupcounts
if (groupmap != NULL) {
vector<string> mGroups = groupmap->getNamesOfGroups();
for (int j = 0; j < mGroups.size(); j++) {
tree[index].groupCount[mGroups[j]] = 0;
}
//find out the sequences group
string group = groupmap->getGroup(seqName);
if (group == "not found") { m->mothurOut("[WARNING]: " + seqName + " is not in your groupfile, and will be included in the overall total, but not any group total."); m->mothurOutEndLine(); }
//do you have a count for this group?
map<string, int>::iterator itGroup = tree[index].groupCount.find(group);
//if yes, increment it - there should not be a case where we can't find it since we load group in read
if (itGroup != tree[index].groupCount.end()) {
tree[index].groupCount[group]++;
}
}else if (ct != NULL) {
if (ct->hasGroupInfo()) {
vector<string> mGroups = ct->getNamesOfGroups();
for (int j = 0; j < mGroups.size(); j++) {
tree[index].groupCount[mGroups[j]] = 0;
}
vector<int> groupCounts = ct->getGroupCounts(seqName);
vector<string> groups = ct->getNamesOfGroups();
for (int i = 0; i < groups.size(); i++) {
if (groupCounts[i] != 0) {
//do you have a count for this group?
map<string, int>::iterator itGroup = tree[index].groupCount.find(groups[i]);
//if yes, increment it - there should not be a case where we can't find it since we load group in read
if (itGroup != tree[index].groupCount.end()) {
tree[index].groupCount[groups[i]]+=groupCounts[i];
}
}
}
}
thisCount = ct->getNumSeqs(seqName);
}
tree[index].total = thisCount;
currentNode = index;
}else{ //otherwise, error
m->mothurOut("Warning: cannot find taxon " + taxon + " in reference taxonomy tree at level " + toString(tree[currentNode].level) + " for " + seqName + ". This may cause totals of daughter levels not to add up in summary file."); m->mothurOutEndLine();
break;
}
}
}
if (level > maxLevel) { maxLevel = level; }
return 0;
}
catch(exception& e) {
m->errorOut(e, "PhyloSummary", "addSeqToTree");
exit(1);
}
}
