NCBI C++ ToolKit
genomic_compart.hpp
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1 #ifndef ALGO_ALIGN_UTIL___GENOMIC_COMPART__HPP
2 #define ALGO_ALIGN_UTIL___GENOMIC_COMPART__HPP
3 
4 /* $Id: genomic_compart.hpp 72046 2016-04-13 15:59:55Z mozese2 $
5  * ===========================================================================
6  *
7  * PUBLIC DOMAIN NOTICE
8  * National Center for Biotechnology Information
9  *
10  * This software/database is a "United States Government Work" under the
11  * terms of the United States Copyright Act. It was written as part of
12  * the author's official duties as a United States Government employee and
13  * thus cannot be copyrighted. This software/database is freely available
14  * to the public for use. The National Library of Medicine and the U.S.
15  * Government have not placed any restriction on its use or reproduction.
16  *
17  * Although all reasonable efforts have been taken to ensure the accuracy
18  * and reliability of the software and data, the NLM and the U.S.
19  * Government do not and cannot warrant the performance or results that
20  * may be obtained by using this software or data. The NLM and the U.S.
21  * Government disclaim all warranties, express or implied, including
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25  * Please cite the author in any work or product based on this material.
26  *
27  * ===========================================================================
28  *
29  * Authors: Mike DiCuccio
30  *
31  * File Description:
32  *
33  */
34 
35 #include <corelib/ncbistd.hpp>
38 
41 
42 
51 
54 
56 };
57 typedef int TCompartOptions;
58 
60 FindCompartments(const list< CRef<CSeq_align> >& aligns,
61  list< CRef<CSeq_align_set> >& align_sets,
63  float diff_len_filter=3.0f);
64 
65 // Join compartment, which is represented by Seq-align-set into
66 // one or more disc Seq-aligns which is suitable for nice graphical
67 // representation.
68 // It relies on a compartment structure - that is that alignments in
69 // the align set are sorted along query. It breaks the set into several
70 // alignments by gaps, longer than the gap_ratio*total_alignment_length
72 JoinCompartment(const CRef<CSeq_align_set>& compartment,
73  float gap_ratio,
74  list< CRef<CSeq_align> >& aligns);
75 
76 
79 
80 
81 #endif // ALGO_ALIGN_UTIL___GENOMIC_COMPART__HPP
Include a standard set of the NCBI C++ Toolkit most basic headers.
void FindCompartments(const list< CRef< CSeq_align > > &aligns, list< CRef< CSeq_align_set > > &align_sets, TCompartOptions options=fCompart_Defaults, float diff_len_filter=3.0f)
void JoinCompartment(const CRef< CSeq_align_set > &compartment, float gap_ratio, list< CRef< CSeq_align > > &aligns)
int TCompartOptions
ECompartOptions
@ fCompart_Defaults
@ fCompart_SortByScore
@ fCompart_AllowIntersectionsSubject
@ fCompart_SortByPctIdent
@ fCompart_FilterByDiffLen
@ fCompart_AllowIntersectionsBoth
@ fCompart_AllowIntersections
@ fCompart_AllowIntersectionsQuery
@ fCompart_AllowInconsistentIntersection
#define END_NCBI_SCOPE
End previously defined NCBI scope.
Definition: ncbistl.hpp:103
#define END_SCOPE(ns)
End the previously defined scope.
Definition: ncbistl.hpp:75
#define BEGIN_NCBI_SCOPE
Define ncbi namespace.
Definition: ncbistl.hpp:100
#define BEGIN_SCOPE(ns)
Define a new scope.
Definition: ncbistl.hpp:72
#define NCBI_XALGOALIGN_EXPORT
Definition: ncbi_export.h:985
Modified on Tue May 28 05:54:20 2024 by modify_doxy.py rev. 669887