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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. *
***************************************************************************/
#ifndef SUPERALIGNMENTUNLINKED_H
#define SUPERALIGNMENTUNLINKED_H
#include "superalignment.h"
class SuperAlignmentUnlinked : public SuperAlignment
{
public:
/** constructor initialize from a supertree */
SuperAlignmentUnlinked(Params ¶ms);
/** constructor initialize empty alignment */
SuperAlignmentUnlinked();
/**
initialize seq_names, taxon_index, buildPattern
*/
virtual void init(StrVector *sequence_names = NULL);
/**
* build all patterns of super alignent from partitions and taxa_index
* it is in form of a binary alignment, where 0 means absence and 1 means presence
* of a gene in a sequence
*/
virtual void buildPattern();
/**
determine if the pattern is constant. update the is_const variable.
*/
virtual void computeConst(Pattern &pat);
/* build seq_states containing set of states per sequence
* @param add_unobs_const TRUE to add all unobserved constant states (for +ASC model)
*/
// void buildSeqStates(bool add_unobs_const = false);
/** TRUE if all taxon sets are separate */
bool unlinked_taxa;
};
#endif
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