*/
#include "phylosummary.h"
+#include "referencedb.h"
/**************************************************************************************************/
-PhyloSummary::PhyloSummary(string refTfile, CountTable* c){
+PhyloSummary::PhyloSummary(string refTfile, CountTable* c, bool r){
try {
m = MothurOut::getInstance();
maxLevel = 0;
ignore = false;
numSeqs = 0;
+ relabund = r;
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());
/**************************************************************************************************/
-PhyloSummary::PhyloSummary(CountTable* c){
+PhyloSummary::PhyloSummary(CountTable* c, bool r){
try {
m = MothurOut::getInstance();
maxLevel = 0;
ignore = true;
numSeqs = 0;
+ relabund = r;
ct = c;
groupmap = NULL;
}
}
/**************************************************************************************************/
-PhyloSummary::PhyloSummary(string refTfile, GroupMap* g){
+PhyloSummary::PhyloSummary(string refTfile, GroupMap* g, bool r){
try {
m = MothurOut::getInstance();
maxLevel = 0;
ignore = false;
numSeqs = 0;
+ relabund = r;
groupmap = g;
ct = 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());
/**************************************************************************************************/
-PhyloSummary::PhyloSummary(GroupMap* g){
+PhyloSummary::PhyloSummary(GroupMap* g, bool r){
try {
m = MothurOut::getInstance();
maxLevel = 0;
ignore = true;
numSeqs = 0;
+ relabund = r;
groupmap = g;
ct = NULL;
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);
}
}
void PhyloSummary::print(ofstream& out){
try {
- if (ignore) { assignRank(0); }
+ if (ignore) { assignRank(0); }
vector<string> mGroups;
//print labels
out << "taxlevel\t rankID\t taxon\t daughterlevels\t total\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) {
}
//print root
- out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << tree[0].total << "\t";
+ if (relabund) {
+ out.setf(ios::fixed, ios::floatfield); out.setf(ios::showpoint);
+ out << tree[0].level << "\t" << tree[0].rank << "\t" << tree[0].name << "\t" << totalChildrenInTree << "\t" << (tree[0].total/(double) tree[0].total) << '\t';
+
+ 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 << thisNum << '\t';
+ }
+ }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 << thisNum << '\t';
+ }
+ }
+ }
+ out << endl;
+ }else {
+ 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);
+ }
+}
+/**************************************************************************************************/
+
+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'; }
+ 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);
+ print(0, out, relabund);
}
catch(exception& e) {
exit(1);
}
}
-
/**************************************************************************************************/
void PhyloSummary::print(int i, ofstream& out){
+ try {
+ map<string,int>::iterator it;
+ for(it=tree[i].children.begin();it!=tree[i].children.end();it++){
+
+ if (tree[it->second].total != 0) {
+
+ int totalChildrenInTree = 0;
+
+ map<string,int>::iterator it2;
+ for(it2=tree[it->second].children.begin();it2!=tree[it->second].children.end();it2++){
+ if (tree[it2->second].total != 0) { totalChildrenInTree++; }
+ }
+
+ if (relabund) {
+ out << tree[it->second].level << "\t" << tree[it->second].rank << "\t" << tree[it->second].name << "\t" << totalChildrenInTree << "\t" << (tree[it->second].total/(double) tree[0].total) << "\t";
+ }else {
+ out << tree[it->second].level << "\t" << tree[it->second].rank << "\t" << tree[it->second].name << "\t" << totalChildrenInTree << "\t" << tree[it->second].total << "\t";
+ }
+
+ if (relabund) {
+ map<string, int>::iterator itGroup;
+ if (groupmap != NULL) {
+ vector<string> mGroups = groupmap->getNamesOfGroups();
+ for (int i = 0; i < mGroups.size(); i++) { out << (tree[it->second].groupCount[mGroups[i]]/(double)groupmap->getNumSeqs(mGroups[i])) << '\t'; }
+ }else if (ct != NULL) {
+ if (ct->hasGroupInfo()) {
+ vector<string> mGroups = ct->getNamesOfGroups();
+ for (int i = 0; i < mGroups.size(); i++) { out << (tree[it->second].groupCount[mGroups[i]]/(double)ct->getGroupCount(mGroups[i])) << '\t'; }
+ }
+ }
+ }else {
+ map<string, int>::iterator itGroup;
+ if (groupmap != NULL) {
+ vector<string> mGroups = groupmap->getNamesOfGroups();
+ for (int i = 0; i < mGroups.size(); i++) { out << tree[it->second].groupCount[mGroups[i]] << '\t'; }
+ }else if (ct != NULL) {
+ if (ct->hasGroupInfo()) {
+ vector<string> mGroups = ct->getNamesOfGroups();
+ for (int i = 0; i < mGroups.size(); i++) { out << tree[it->second].groupCount[mGroups[i]] << '\t'; }
+ }
+ }
+
+ }
+ out << endl;
+
+ }
+
+ print(it->second, out);
+ }
+ }
+ catch(exception& e) {
+ m->errorOut(e, "PhyloSummary", "print");
+ exit(1);
+ }
+}
+
+/**************************************************************************************************/
+
+void PhyloSummary::print(int i, ofstream& out, bool relabund){
try {
map<string,int>::iterator it;
for(it=tree[i].children.begin();it!=tree[i].children.end();it++){
for(it2=tree[it->second].children.begin();it2!=tree[it->second].children.end();it2++){
if (tree[it2->second].total != 0) { totalChildrenInTree++; }
}
-
- out << tree[it->second].level << "\t" << tree[it->second].rank << "\t" << tree[it->second].name << "\t" << totalChildrenInTree << "\t" << tree[it->second].total << "\t";
+
+ string nodeName = "";
+ int thisNode = it->second;
+ while (tree[thisNode].rank != "0") { //while you are not at top
+ if (m->control_pressed) { break; }
+ nodeName = tree[thisNode].name + "|" + nodeName;
+ thisNode = tree[thisNode].parent;
+ }
+ if (nodeName != "") { nodeName = nodeName.substr(0, nodeName.length()-1); }
+
+ out << nodeName << "\t" << (tree[it->second].total / (float)tree[i].total) << "\t";
map<string, int>::iterator itGroup;
if (groupmap != NULL) {
- //for (itGroup = tree[it->second].groupCount.begin(); itGroup != tree[it->second].groupCount.end(); itGroup++) {
- // out << itGroup->second << '\t';
- //}
vector<string> mGroups = groupmap->getNamesOfGroups();
- for (int i = 0; i < mGroups.size(); i++) { out << tree[it->second].groupCount[mGroups[i]] << '\t'; }
+ for (int j = 0; j < mGroups.size(); j++) {
+ if (tree[i].groupCount[mGroups[j]] == 0) {
+ out << 0 << '\t';
+ }else { out << (tree[it->second].groupCount[mGroups[j]] / (float)tree[i].groupCount[mGroups[j]]) << '\t'; }
+ }
}else if (ct != NULL) {
if (ct->hasGroupInfo()) {
vector<string> mGroups = ct->getNamesOfGroups();
- for (int i = 0; i < mGroups.size(); i++) { out << tree[it->second].groupCount[mGroups[i]] << '\t'; }
+ for (int j = 0; j < mGroups.size(); j++) {
+ if (tree[i].groupCount[mGroups[j]] == 0) {
+ out << 0 << '\t';
+ }else { out << (tree[it->second].groupCount[mGroups[j]] / (float)tree[i].groupCount[mGroups[j]]) << '\t'; }
+ }
}
}
out << endl;
}
- print(it->second, out);
+ print(it->second, out, relabund);
}
}
catch(exception& e) {
projects / mothur.git / blobdiff