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/***************************************************************************
* Copyright (C) 2018 by BUI Quang Minh *
* m.bui@anu.edu.au *
* *
* This program is free software; you can redistribute it and/or modify *
* it under the terms of the GNU General Public License as published by *
* the Free Software Foundation; either version 2 of the License, or *
* (at your option) any later version. *
* *
* This program is distributed in the hope that it will be useful, *
* but WITHOUT ANY WARRANTY; without even the implied warranty of *
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
* GNU General Public License for more details. *
* *
* You should have received a copy of the GNU General Public License *
* along with this program; if not, write to the *
* Free Software Foundation, Inc., *
* 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA. *
***************************************************************************/
#include "superalignmentunlinked.h"
#include "utils/timeutil.h"
/** constructor initialize from a supertree */
SuperAlignmentUnlinked::SuperAlignmentUnlinked(Params ¶ms)
: SuperAlignment()
{
readFromParams(params);
init();
}
/** constructor initialize empty alignment */
SuperAlignmentUnlinked::SuperAlignmentUnlinked()
: SuperAlignment()
{
unlinked_taxa = true;
}
void SuperAlignmentUnlinked::init(StrVector *sequence_names) {
// start original code
max_num_states = 0;
// first build taxa_index and partitions
int part, seq, npart = partitions.size();
map<string, int> name2part;
vector<Alignment*>::iterator it;
unlinked_taxa = true;
for (it = partitions.begin(); it != partitions.end(); it++) {
// Make sure that all partitions have different seq names
for (auto sit = (*it)->seq_names.begin(); sit != (*it)->seq_names.end(); sit++) {
if (name2part.find(*sit) != name2part.end()) {
unlinked_taxa = false;
break;
}
name2part[*sit] = (it) - partitions.begin();
}
}
if (!unlinked_taxa) {
// if some taxon sets are overlapping
SuperAlignment::init(sequence_names);
cout << "Linked " << seq_names.size() << " total sequences" << endl;
return;
}
for (it = partitions.begin(); it != partitions.end(); it++) {
seq_names.insert(seq_names.end(), (*it)->seq_names.begin(), (*it)->seq_names.end());
}
cout << "Unlinked " << seq_names.size() << " total sequences" << endl;
/*
taxa_index.resize(total_seqs, IntVector(npart, -1));
for (it = partitions.begin(), part = 0, seq = 0; it != partitions.end(); it++, part++) {
int part_nseq = (*it)->getNSeq();
for (int part_seq = 0; part_seq < part_nseq; part_seq++, seq++) {
taxa_index[seq][part] = part_seq;
}
}
ASSERT(seq == total_seqs);
*/
// now the patterns of sequence-genes presence/absence
buildPattern();
}
void SuperAlignmentUnlinked::buildPattern() {
if (!unlinked_taxa) {
SuperAlignment::buildPattern();
return;
}
int part, seq, npart = partitions.size();
seq_type = SEQ_BINARY;
num_states = 2; // binary type because the super alignment presents the presence/absence of taxa in the partitions
STATE_UNKNOWN = 2;
site_pattern.resize(npart, -1);
clear();
pattern_index.clear();
/*
VerboseMode save_mode = verbose_mode;
verbose_mode = min(verbose_mode, VB_MIN); // to avoid printing gappy sites in addPattern
int nseq = getNSeq();
int start_seq = 0;
resize(npart, Pattern(nseq));
for (part = 0; part < npart; part++) {
Pattern *pat = &at(part);
for (seq = 0; seq < partitions[part]->getNSeq(); seq++)
pat->at(start_seq + seq) = 1;
//addPattern(pat, part);
computeConst(*pat);
// NOT USED FOR TOPO_UNLINKED
//pattern_index[*pat] = part;
site_pattern[part] = part;
start_seq += partitions[part]->getNSeq();
}
ASSERT(start_seq == nseq);
verbose_mode = save_mode;
*/
resize(1, Pattern(getNSeq(), npart));
computeConst(at(0));
for (part = 0; part < npart; part++) {
site_pattern[part] = 0;
}
countConstSite();
// buildSeqStates();
}
void SuperAlignmentUnlinked::computeConst(Pattern &pat) {
if (!unlinked_taxa) {
SuperAlignment::computeConst(pat);
return;
}
bool is_const = (partitions.size() == 1);
bool is_invariant = (partitions.size() == 1);
bool is_informative = (partitions.size() > 1);
pat.const_char = (is_const) ? 1 : (STATE_UNKNOWN+1);
pat.num_chars = (is_const) ? 1 : 2; // number of states with >= 1 appearance
pat.flag = 0;
if (is_const) pat.flag |= PAT_CONST;
if (is_invariant) pat.flag |= PAT_INVARIANT;
if (is_informative) pat.flag |= PAT_INFORMATIVE;
}
/*
void SuperAlignmentUnlinked::buildSeqStates(bool add_unobs_const) {
if (!unlinked_taxa) {
SuperAlignment::buildSeqStates(add_unobs_const);
return;
}
seq_states.clear();
if (add_unobs_const) {
seq_states.resize(getNSeq(), IntVector({0,1}));
} else {
if (partitions.size() == 1)
seq_states.resize(getNSeq(), IntVector({1}));
else
seq_states.resize(getNSeq(), IntVector({0,1}));
}
}
*/
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