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//
// treereader.cpp
// Mothur
//
// Created by Sarah Westcott on 4/11/12.
// Copyright (c) 2012 Schloss Lab. All rights reserved.
//
#include "treereader.h"
#include "readtree.h"
#include "groupmap.h"
/***********************************************************************/
TreeReader::TreeReader(string tf, string cf) : treefile(tf), countfile(cf) {
try {
m = MothurOut::getInstance();
ct = new CountTable();
ct->readTable(cf, true, false);
Utils util;
Treenames = util.parseTreeFile(treefile); //fills treenames
//if no groupinfo in count file we need to add it
if (!ct->hasGroupInfo()) {
ct->addGroup("Group1");
vector<string> namesOfSeqs = ct->getNamesOfSeqs();
for (int i = 0; i < namesOfSeqs.size(); i++) {
ct->setAbund(namesOfSeqs[i], "Group1", ct->getNumSeqs(namesOfSeqs[i]));
}
}
namefile = "";
groupfile = "";
readTrees();
}
catch(exception& e) {
m->errorOut(e, "TreeReader", "TreeReader");
exit(1);
}
}
/***********************************************************************/
TreeReader::TreeReader(string tf, string gf, string nf) : treefile(tf), groupfile(gf), namefile(nf) {
try {
m = MothurOut::getInstance();
Utils util;
Treenames = util.parseTreeFile(treefile); //fills treenames
countfile = "";
ct = new CountTable();
if (namefile != "") { ct->createTable(namefile, groupfile, nullVector, true); }
else {
set<string> nameMap;
map<string, string> groupMap;
set<string> gps;
for (int i = 0; i < Treenames.size(); i++) { nameMap.insert(Treenames[i]); }
if (groupfile == "") { gps.insert("Group1"); for (int i = 0; i < Treenames.size(); i++) { groupMap[Treenames[i]] = "Group1"; } }
else {
GroupMap g(groupfile);
g.readMap();
vector<string> seqs = g.getNamesSeqs();
for (int i = 0; i < seqs.size(); i++) {
string group = g.getGroup(seqs[i]);
groupMap[seqs[i]] = group;
gps.insert(group);
}
}
ct->createTable(nameMap, groupMap, gps);
}
readTrees();
}
catch(exception& e) {
m->errorOut(e, "TreeReader", "TreeReader");
exit(1);
}
}
/***********************************************************************/
bool TreeReader::readTrees() {
try {
int numUniquesInName = ct->getNumUniqueSeqs();
ReadTree* read = new ReadNewickTree(treefile, Treenames);
int readOk = read->read(ct);
if (readOk != 0) { m->mothurOut("Read Terminated.\n"); delete read; m->setControl_pressed(true); return 0; }
read->AssembleTrees();
trees = read->getTrees();
delete read;
//make sure all files match
//if you provide a namefile we will use the numNames in the namefile as long as the number of unique match the tree names size.
int numNamesInTree;
if (namefile != "") {
if (numUniquesInName == Treenames.size()) { numNamesInTree = ct->getNumSeqs(); }
else { numNamesInTree = Treenames.size(); }
}else { numNamesInTree = Treenames.size(); }
//output any names that are in group file but not in tree
if (numNamesInTree < ct->getNumSeqs()) {
vector<string> namesSeqsCt = ct->getNamesOfSeqs();
for (int i = 0; i < namesSeqsCt.size(); i++) {
//is that name in the tree?
int count = 0;
for (int j = 0; j < Treenames.size(); j++) {
if (namesSeqsCt[i] == Treenames[j]) { break; } //found it
count++;
}
if (m->getControl_pressed()) { for (int i = 0; i < trees.size(); i++) { delete trees[i]; } return 0; }
//then you did not find it so report it
if (count == Treenames.size()) {
m->mothurOut(namesSeqsCt[i] + " is in your name or group file and not in your tree. It will be disregarded.\n");
ct->remove(namesSeqsCt[i]);
}
}
}
return true;
}
catch(exception& e) {
m->errorOut(e, "TreeReader", "readTrees");
exit(1);
}
}
/***********************************************************************/
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