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include
ost
seq
aligned_region.hh
Go to the documentation of this file.
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//------------------------------------------------------------------------------
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// This file is part of the OpenStructure project <www.openstructure.org>
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//
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// Copyright (C) 2008-2011 by the OpenStructure authors
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//
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// This library is free software; you can redistribute it and/or modify it under
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// the terms of the GNU Lesser General Public License as published by the Free
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// Software Foundation; either version 3.0 of the License, or (at your option)
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// any later version.
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// This library is distributed in the hope that it will be useful, but WITHOUT
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// ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
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// FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
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// details.
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//
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// You should have received a copy of the GNU Lesser General Public License
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// along with this library; if not, write to the Free Software Foundation, Inc.,
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// 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
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//------------------------------------------------------------------------------
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#ifndef OST_SEQ_ALIGNED_REGION_HH
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#define OST_SEQ_ALIGNED_REGION_HH
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/*
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Author: Marco Biasini
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*/
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#include <
ost/seq/module_config.hh
>
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#include <
ost/seq/alignment_handle.hh
>
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#include <
ost/seq/aligned_column_iterator.hh
>
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namespace
ost {
namespace
seq {
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class
DLLEXPORT_OST_SEQ
AlignedRegion
{
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public
:
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typedef
AlignedColumnIterator
iterator
;
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AlignedRegion
(
const
AlignmentHandle
& aln,
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int
start,
int
end
,
int
master=-1);
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int
GetEnd()
const
;
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int
GetStart()
const
;
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int
GetMaster()
const
;
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void
SetMaster(
int
master);
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void
Delete();
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void
Replace(
const
AlignedRegion
& aln_r);
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void
ShiftLeft(
int
n);
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void
ShiftRight(
int
n);
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int
GetLength()
const
;
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AlignmentHandle
GetAlignmentHandle()
const
;
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AlignedColumn
operator[](
int
index)
const
;
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AlignedColumnIterator
begin
();
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AlignedColumnIterator
end
();
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bool
operator==
(
const
AlignedRegion
& rhs)
const
;
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bool
operator!=
(
const
AlignedRegion
& rhs)
const
;
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private
:
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AlignmentHandle
aln_;
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int
start_;
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int
end_ ;
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int
master_;
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};
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typedef
std::vector<AlignedRegion>
AlignedRegionList
;
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}}
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#endif
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