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CNWFormatter Class Reference

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#include <algo/align/nw/nw_formatter.hpp>

+ Inheritance diagram for CNWFormatter:
+ Collaboration diagram for CNWFormatter:

List of all members.

Classes

struct  SSegment

Public Types

enum  ETextFormatType {
  eFormatType1, eFormatType2, eFormatAsn, eFormatFastA,
  eFormatExonTable, eFormatExonTableEx
}
enum  ESeqAlignFormatFlags { eSAFF_None = 0, eSAFF_DynProgScore = 1, eSAFF_Identity = 2 }

Public Member Functions

 CNWFormatter (const CNWAligner &aligner)
void SetSeqIds (CConstRef< objects::CSeq_id > id1, CConstRef< objects::CSeq_id > id2)
void AsText (string *output, ETextFormatType type, size_t line_width=100) const
CRef< objects::CSeq_align > AsSeqAlign (TSeqPos query_start, objects::ENa_strand query_strand, TSeqPos subj_start, objects::ENa_strand subj_strand, ESeqAlignFormatFlags flags=eSAFF_None) const
void MakeSegments (deque< SSegment > *psegments) const

Private Member Functions

size_t x_ApplyTranscript (vector< char > *seq1_transformed, vector< char > *seq2_transformed) const

Private Attributes

const CNWAlignerm_aligner
CConstRef< objects::CSeq_id > m_Seq1Id
CConstRef< objects::CSeq_id > m_Seq2Id

Detailed Description

Definition at line 56 of file nw_formatter.hpp.


Member Enumeration Documentation

Enumerator:
eSAFF_None 
eSAFF_DynProgScore 
eSAFF_Identity 

Definition at line 73 of file nw_formatter.hpp.

Enumerator:
eFormatType1 
eFormatType2 
eFormatAsn 
eFormatFastA 
eFormatExonTable 
eFormatExonTableEx 

Definition at line 63 of file nw_formatter.hpp.


Constructor & Destructor Documentation


Member Function Documentation

CRef< CSeq_align > CNWFormatter::AsSeqAlign ( TSeqPos  query_start,
objects::ENa_strand  query_strand,
TSeqPos  subj_start,
objects::ENa_strand  subj_strand,
ESeqAlignFormatFlags  flags = eSAFF_None 
) const
void CNWFormatter::AsText ( string output,
ETextFormatType  type,
size_t  line_width = 100 
) const
void CNWFormatter::MakeSegments ( deque< SSegment > *  psegments) const
void CNWFormatter::SetSeqIds ( CConstRef< objects::CSeq_id >  id1,
CConstRef< objects::CSeq_id >  id2 
)

Definition at line 61 of file nw_formatter.cpp.

References m_Seq1Id, and m_Seq2Id.

Referenced by CAppNWA::x_RunOnPair().

size_t CNWFormatter::x_ApplyTranscript ( vector< char > *  seq1_transformed,
vector< char > *  seq2_transformed 
) const [private]

Definition at line 1216 of file nw_formatter.cpp.


Member Data Documentation

Definition at line 154 of file nw_formatter.hpp.

Referenced by AsSeqAlign(), AsText(), and MakeSegments().

CConstRef<objects::CSeq_id> CNWFormatter::m_Seq1Id [private]

Definition at line 155 of file nw_formatter.hpp.

Referenced by AsSeqAlign(), AsText(), CNWFormatter(), and SetSeqIds().

CConstRef<objects::CSeq_id> CNWFormatter::m_Seq2Id [private]

Definition at line 155 of file nw_formatter.hpp.

Referenced by AsSeqAlign(), AsText(), CNWFormatter(), and SetSeqIds().


The documentation for this class was generated from the following files:
Modified on Sun Jul 13 17:39:50 2014 by modify_doxy.py rev. 426318