NCBI C++ ToolKit
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UnalignedSegReader Class Reference

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#include <algo/structure/cd_utils/cuResidueProfile.hpp>

+ Inheritance diagram for UnalignedSegReader:
+ Collaboration diagram for UnalignedSegReader:

Public Types

typedef pair< int, intSeg

Public Member Functions

 UnalignedSegReader ()
void setIndexSequence (string &seq)
string getIndexSequence ()
void read (ColumnResidueProfile &crp)
Seg getLongestSeg ()
int getLenOfLongestSeg ()
int getTotalUnaligned ()
int getTotal ()
int getLongUnalignedSegs (int length, vector< Seg > &segs)
string subtractLongestSeg (int threshold)
string subtractSeg (Seg seg, string &in)
- Public Member Functions inherited from ColumnReader
virtual ~ColumnReader ()

Private Member Functions

int getLen (Seg seg)

Private Attributes

Seg m_maxSeg
Seg m_curSeg
vector< Segm_unalignedSegs
int m_totalUnaligned
int m_pos
string m_indexSeq

Detailed Description

Definition at line 129 of file cuResidueProfile.hpp.

Member Typedef Documentation

◆ Seg

Definition at line 132 of file cuResidueProfile.hpp.

Constructor & Destructor Documentation

◆ UnalignedSegReader()

UnalignedSegReader::UnalignedSegReader ( )

Definition at line 888 of file cuResidueProfile.cpp.

References m_curSeg, and m_maxSeg.

Member Function Documentation

◆ getIndexSequence()

string UnalignedSegReader::getIndexSequence ( )

Definition at line 902 of file cuResidueProfile.cpp.

References m_indexSeq.

◆ getLen()

int UnalignedSegReader::getLen ( Seg  seg)

Definition at line 949 of file cuResidueProfile.cpp.

Referenced by getLenOfLongestSeg(), getLongUnalignedSegs(), and read().

◆ getLenOfLongestSeg()

int UnalignedSegReader::getLenOfLongestSeg ( )

Definition at line 912 of file cuResidueProfile.cpp.

References getLen(), and m_maxSeg.

Referenced by subtractLongestSeg().

◆ getLongestSeg()

UnalignedSegReader::Seg UnalignedSegReader::getLongestSeg ( )

Definition at line 907 of file cuResidueProfile.cpp.

References m_maxSeg.

◆ getLongUnalignedSegs()

int UnalignedSegReader::getLongUnalignedSegs ( int  length,
vector< Seg > &  segs 

Definition at line 927 of file cuResidueProfile.cpp.

References getLen(), i, and m_unalignedSegs.

Referenced by ResidueProfiles::skipUnalignedSeg().

◆ getTotal()

int UnalignedSegReader::getTotal ( )

Definition at line 142 of file cuResidueProfile.hpp.

References m_pos.

◆ getTotalUnaligned()

int UnalignedSegReader::getTotalUnaligned ( )

Definition at line 141 of file cuResidueProfile.hpp.

References m_totalUnaligned.

◆ read()

void UnalignedSegReader::read ( ColumnResidueProfile crp)

◆ setIndexSequence()

void UnalignedSegReader::setIndexSequence ( string seq)

Definition at line 897 of file cuResidueProfile.cpp.

References m_indexSeq.

Referenced by ResidueProfiles::countUnalignedConsensus().

◆ subtractLongestSeg()

string UnalignedSegReader::subtractLongestSeg ( int  threshold)

Definition at line 917 of file cuResidueProfile.cpp.

References getLenOfLongestSeg(), m_indexSeq, m_maxSeg, and subtractSeg().

◆ subtractSeg()

string UnalignedSegReader::subtractSeg ( Seg  seg,
string in 

Definition at line 954 of file cuResidueProfile.cpp.

References head, and in().

Referenced by subtractLongestSeg().

Member Data Documentation

◆ m_curSeg

Seg UnalignedSegReader::m_curSeg

Definition at line 149 of file cuResidueProfile.hpp.

Referenced by read(), and UnalignedSegReader().

◆ m_indexSeq

string UnalignedSegReader::m_indexSeq

Definition at line 153 of file cuResidueProfile.hpp.

Referenced by getIndexSequence(), setIndexSequence(), and subtractLongestSeg().

◆ m_maxSeg

Seg UnalignedSegReader::m_maxSeg

◆ m_pos

int UnalignedSegReader::m_pos

Definition at line 152 of file cuResidueProfile.hpp.

Referenced by getTotal(), and read().

◆ m_totalUnaligned

int UnalignedSegReader::m_totalUnaligned

Definition at line 151 of file cuResidueProfile.hpp.

Referenced by getTotalUnaligned(), and read().

◆ m_unalignedSegs

vector<Seg> UnalignedSegReader::m_unalignedSegs

Definition at line 150 of file cuResidueProfile.hpp.

Referenced by getLongUnalignedSegs(), and read().

The documentation for this class was generated from the following files:
Modified on Wed Jun 19 17:06:42 2024 by rev. 669887