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Marco Biasini authoredMarco Biasini authored
aligned_column.hh 2.25 KiB
//------------------------------------------------------------------------------
// This file is part of the OpenStructure project <www.openstructure.org>
//
// Copyright (C) 2008-2011 by the OpenStructure authors
//
// This library is free software; you can redistribute it and/or modify it under
// the terms of the GNU Lesser General Public License as published by the Free
// Software Foundation; either version 3.0 of the License, or (at your option)
// any later version.
// This library 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 Lesser General Public License for more
// details.
//
// You should have received a copy of the GNU Lesser General Public License
// along with this library; if not, write to the Free Software Foundation, Inc.,
// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
//------------------------------------------------------------------------------
#ifndef OST_SEQ_ALIGNED_COLUMN_HH
#define OST_SEQ_ALIGNED_COLUMN_HH
/*
Author: Marco Biasini
*/
#include <ost/seq/module_config.hh>
#include <ost/seq/alignment_handle.hh>
namespace ost { namespace seq {
/// \brief Provides access to a column in a \ref AlignedRegion "aligned region"
/// or a \ref AlignmentHandle "sequence alignment"
class DLLEXPORT_OST_SEQ AlignedColumn {
public:
AlignedColumn(const AlignmentHandle& aln, int index);
/// \brief construct empty (invalid) aligned column
AlignedColumn();
/// \brief get index of column
///
/// \sa AlignmentHandle::GetIndex()
int GetIndex() const;
char operator[](int row) const;
/// \brief get residue index at row
///
/// \sa AlignmentHandle::GetResidueIndex()
int GetResidueIndex(int row) const;
/// \brief get number of rows
///
/// \sa AlignmentHandle::GetCount()
int GetRowCount() const;
/// \brief get residue at row
///
/// \sa AlignmentHandle::GetResidue()
mol::ResidueView GetResidue(int row) const;
private:
void CheckRowValidity(int row) const;
AlignmentHandle aln_;
int index_;
};
DLLEXPORT_OST_SEQ std::ostream& operator<<(std::ostream& os,
const AlignedColumn& col);
}}
#endif