PhyloSummary::PhyloSummary(string refTfile, GroupMap* g, bool r, int p){
try {
m = MothurOut::getInstance();
maxLevel = 0;
ignore = false;
numSeqs = 0;
relabund = r;
printlevel = p;
groupmap = g;
ct = NULL;
//check for necessary files
string taxFileNameTest = m->getFullPathName((refTfile.substr(0,refTfile.find_last_of(".")+1) + "tree.sum"));
ifstream FileTest(taxFileNameTest.c_str());
if (!FileTest) {
m->mothurOut("Error: can't find " + taxFileNameTest + "."); m->mothurOutEndLine(); exit(1);
}else{
readTreeStruct(FileTest);
}
tree[0].rank = "0";
assignRank(0);
}
catch(exception& e) {
m->errorOut(e, "PhyloSummary", "PhyloSummary");
exit(1);
}
}
PhyloSummary::PhyloSummary(string refTfile, CountTable* c){
try {
m = MothurOut::getInstance();
maxLevel = 0;
ignore = false;
numSeqs = 0;
ct = c;
groupmap = NULL;
//check for necessary files
if (refTfile == "saved") { ReferenceDB* rdb = ReferenceDB::getInstance(); refTfile = rdb->getSavedTaxonomy(); }
string taxFileNameTest = m->getFullPathName((refTfile.substr(0,refTfile.find_last_of(".")+1) + "tree.sum"));
ifstream FileTest(taxFileNameTest.c_str());
if (!FileTest) {
m->mothurOut("Error: can't find " + taxFileNameTest + "."); m->mothurOutEndLine(); exit(1);
}else{
readTreeStruct(FileTest);
}
tree[0].rank = "0";
assignRank(0);
}
catch(exception& e) {
m->errorOut(e, "PhyloSummary", "PhyloSummary");
exit(1);
}
}
void PhyloSummary::print(ofstream& out, bool relabund){
try {
if (ignore) { assignRank(0); }
int totalChildrenInTree = 0;
map<string, int>::iterator itGroup;
map<string,int>::iterator it;
for(it=tree[0].children.begin();it!=tree[0].children.end();it++){
if (tree[it->second].total != 0) {
totalChildrenInTree++;
tree[0].total += tree[it->second].total;
if (groupmap != NULL) {
vector<string> mGroups = groupmap->getNamesOfGroups();
for (int i = 0; i < mGroups.size(); i++) { tree[0].groupCount[mGroups[i]] += tree[it->second].groupCount[mGroups[i]]; }
}else if ( ct != NULL) {
vector<string> mGroups = ct->getNamesOfGroups();
if (ct->hasGroupInfo()) { for (int i = 0; i < mGroups.size(); i++) { tree[0].groupCount[mGroups[i]] += tree[it->second].groupCount[mGroups[i]]; } }
}
}
}
//print root
out << tree[0].name << "\t" << "1.0000" << "\t"; //root relative abundance is 1, everyone classifies to root
/*
if (groupmap != NULL) {
for (int i = 0; i < mGroups.size(); i++) { out << tree[0].groupCount[mGroups[i]] << '\t'; }
}else if ( ct != NULL) {
if (ct->hasGroupInfo()) { for (int i = 0; i < mGroups.size(); i++) { out << tree[0].groupCount[mGroups[i]] << '\t'; } }
}*/
if (groupmap != NULL) {
vector<string> mGroups = groupmap->getNamesOfGroups();
for (int i = 0; i < mGroups.size(); i++) { out << "1.0000" << '\t'; }
}else if ( ct != NULL) {
vector<string> mGroups = ct->getNamesOfGroups();
if (ct->hasGroupInfo()) { for (int i = 0; i < mGroups.size(); i++) { out << "1.0000" << '\t'; } }
}
out << endl;
//print rest
print(0, out, relabund);
}
catch(exception& e) {
m->errorOut(e, "PhyloSummary", "print");
exit(1);
}
}
void PhyloSummary::assignRank(int index){
try {
map<string,int>::iterator it;
int counter = 1;
for(it=tree[index].children.begin();it!=tree[index].children.end();it++){
tree[it->second].rank = tree[index].rank + '.' + toString(counter);
counter++;
assignRank(it->second);
}
}
catch(exception& e) {
m->errorOut(e, "PhyloSummary", "assignRank");
exit(1);
}
}
void PhyloSummary::print(ofstream& out, string output){
try {
if (ignore) { assignRank(0); }
vector<string> mGroups;
//print labels
if (output == "detail") { out << "taxlevel\trankID\ttaxon\tdaughterlevels\ttotal"; }
else { out << "taxonomy\ttotal"; }
if (printlevel == -1) { printlevel = maxLevel; }
else if (printlevel > maxLevel) { m->mothurOut("[WARNING]: Your printlevel is greater than your maxlevel, adjusting your printlevel to " + toString(maxLevel) + "\n"); printlevel = maxLevel; }
if (groupmap != NULL) {
//so the labels match the counts below, since the map sorts them automatically...
//sort(groupmap->namesOfGroups.begin(), groupmap->namesOfGroups.end());
mGroups = groupmap->getNamesOfGroups();
for (int i = 0; i < mGroups.size(); i++) {
out << '\t' << mGroups[i];
}
}else if (ct != NULL) {
if (ct->hasGroupInfo()) {
mGroups = ct->getNamesOfGroups();
for (int i = 0; i < mGroups.size(); i++) {
out << '\t' << mGroups[i];
}
}
}
out << endl;
int totalChildrenInTree = 0;
map<string, int>::iterator itGroup;
map<string,int>::iterator it;
for(it=tree[0].children.begin();it!=tree[0].children.end();it++){
if (tree[it->second].total != 0) {
totalChildrenInTree++;
tree[0].total += tree[it->second].total;
if (groupmap != NULL) {
for (int i = 0; i < mGroups.size(); i++) { tree[0].groupCount[mGroups[i]] += tree[it->second].groupCount[mGroups[i]]; }
}else if ( ct != NULL) {
if (ct->hasGroupInfo()) { for (int i = 0; i < mGroups.size(); i++) { tree[0].groupCount[mGroups[i]] += tree[it->second].groupCount[mGroups[i]]; } }
}
}
}
//print root
if (relabund) {
out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
if (output == "detail") {
out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << (tree[0].total/(double) tree[0].total);
}else{
out << tree[0].name << "\t" << (tree[0].total/(double) tree[0].total);
}
if (groupmap != NULL) {
for (int i = 0; i < mGroups.size(); i++) {
double thisNum = tree[0].groupCount[mGroups[i]];
thisNum /= (double) groupmap->getNumSeqs(mGroups[i]);
out << '\t' << thisNum;
}
}else if ( ct != NULL) {
if (ct->hasGroupInfo()) {
for (int i = 0; i < mGroups.size(); i++) {
double thisNum = tree[0].groupCount[mGroups[i]];
thisNum /= (double) ct->getGroupCount(mGroups[i]);
out << '\t' << thisNum;
}
}
}
out << endl;
}else {
if (output == "detail") {
out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << tree[0].total;
}else{
out << tree[0].name << '\t' << tree[0].total;
}
if (groupmap != NULL) {
for (int i = 0; i < mGroups.size(); i++) { out << '\t'<< tree[0].groupCount[mGroups[i]]; }
}else if ( ct != NULL) {
if (ct->hasGroupInfo()) { for (int i = 0; i < mGroups.size(); i++) { out << '\t' << tree[0].groupCount[mGroups[i]]; } }
}
out << endl;
}
//print rest
print(0, out, output);
}
catch(exception& e) {
m->errorOut(e, "PhyloSummary", "print");
exit(1);
}
}
void PhyloSummary::print(ofstream& out){
try {
if (ignore) { assignRank(0); }
vector<string> mGroups;
//print labels
out << "taxlevel\t rankID\t taxon\t daughterlevels\t total\t";
if (groupmap != NULL) {
//so the labels match the counts below, since the map sorts them automatically...
//sort(groupmap->namesOfGroups.begin(), groupmap->namesOfGroups.end());
mGroups = groupmap->getNamesOfGroups();
for (int i = 0; i < mGroups.size(); i++) {
out << mGroups[i] << '\t';
}
}else if (ct != NULL) {
if (ct->hasGroupInfo()) {
mGroups = ct->getNamesOfGroups();
for (int i = 0; i < mGroups.size(); i++) {
out << mGroups[i] << '\t';
}
}
}
out << endl;
int totalChildrenInTree = 0;
map<string, int>::iterator itGroup;
map<string,int>::iterator it;
for(it=tree[0].children.begin();it!=tree[0].children.end();it++){
if (tree[it->second].total != 0) {
totalChildrenInTree++;
tree[0].total += tree[it->second].total;
if (groupmap != NULL) {
for (int i = 0; i < mGroups.size(); i++) { tree[0].groupCount[mGroups[i]] += tree[it->second].groupCount[mGroups[i]]; }
}else if ( ct != NULL) {
if (ct->hasGroupInfo()) { for (int i = 0; i < mGroups.size(); i++) { tree[0].groupCount[mGroups[i]] += tree[it->second].groupCount[mGroups[i]]; } }
}
}
}
//print root
out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << tree[0].total << "\t";
if (groupmap != NULL) {
for (int i = 0; i < mGroups.size(); i++) { out << tree[0].groupCount[mGroups[i]] << '\t'; }
}else if ( ct != NULL) {
if (ct->hasGroupInfo()) { for (int i = 0; i < mGroups.size(); i++) { out << tree[0].groupCount[mGroups[i]] << '\t'; } }
}
out << endl;
//print rest
print(0, out);
}
catch(exception& e) {
m->errorOut(e, "PhyloSummary", "print");
exit(1);
}
}