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include
ost
seq
alignment_handle.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_ALIGNMENT_HANDLE_HH
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#define OST_SEQ_ALIGNMENT_HANDLE_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/impl/sequence_list_impl_fw.hh
>
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#include <
ost/seq/sequence_handle.hh
>
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#include <
ost/seq/sequence_list.hh
>
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namespace
ost {
namespace
seq {
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class
SequenceList
;
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class
AlignedRegion;
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class
AlignedColumn;
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class
AlignedColumnIterator;
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class
DLLEXPORT_OST_SEQ
AlignmentHandle
{
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public
:
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typedef
AlignedColumnIterator
iterator
;
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AlignmentHandle
();
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int
GetPos(
int
seq_index,
int
residue_index)
const
;
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int
GetResidueIndex(
int
seq_index,
int
pos)
const
;
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mol::ResidueView
GetResidue(
int
seq_index,
int
pos)
const
;
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char
GetOneLetterCode(
int
seq_index,
int
pos)
const
;
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void
AddSequence(
const
ConstSequenceHandle
& sequence);
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ConstSequenceHandle
GetSequence(
int
seq_id)
const
;
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void
RemoveSequence(
int
seq_index);
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String
ToString(
int
width=80)
const
;
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int
GetLength()
const
;
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AlignmentHandle
Copy()
const
;
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ConstSequenceHandle
FindSequence(
const
String
& name)
const
;
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int
FindSequenceIndex(
const
String
& name)
const
;
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void
AttachView(
int
seq_index,
const
mol::EntityView
& view);
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void
AttachView(
int
seq_index,
const
mol::EntityView
& view,
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const
String
& chain_name);
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mol::EntityViewPair
GetMatchingBackboneViews(
int
idx0=0,
int
idx1=1)
const
;
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void
SetSequenceName(
int
seq_index,
const
String
& name);
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void
SetSequenceOffset(
int
seq_index,
int
offset);
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int
GetSequenceOffset(
int
seq_index);
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ConstSequenceList
GetSequences()
const
;
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AlignedRegion
MakeRegion(
int
start,
int
n,
int
master=-1)
const
;
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int
GetCount()
const
;
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bool
operator==
(
const
AlignmentHandle
& rhs)
const
;
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bool
operator!=
(
const
AlignmentHandle
& rhs)
const
;
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AlignedColumn
operator[](
int
index)
const
;
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AlignmentHandle
(
const
impl::SequenceListImplPtr
& impl);
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void
Cut(
int
start,
int
end
);
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void
Replace(
const
AlignedRegion
& rhs,
int
start,
int
end
);
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void
ShiftRegion(
int
start,
int
end
,
int
amount,
int
master=-1);
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iterator
begin
()
const
;
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iterator
end
()
const
;
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bool
IsValid
()
const
{
return
impl_.get()!=0; }
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Real
GetCoverage(
int
seq_index)
const
;
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const
String
& GetSequenceRole(
int
seq_index);
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void
SetSequenceRole(
int
seq_index,
const
String
& role);
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private
:
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void
CheckValidity()
const
;
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impl::SequenceListImplPtr
impl_;
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};
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AlignmentHandle
DLLEXPORT_OST_SEQ
CreateAlignment
();
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AlignmentHandle
DLLEXPORT_OST_SEQ
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AlignmentFromSequenceList
(
const
SequenceList
& seq_list);
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typedef
std::vector<AlignmentHandle>
AlignmentList
;
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}}
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#endif
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