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gnCompare Class Reference

#include <gnCompare.h>

Inheritance diagram for gnCompare:

gnClone List of all members.

Public Types

enum  gnCompareType { ProteinSeqCompareType, DNASeqCompareType, RNASeqCompareType }

Public Member Functions

 gnCompare ()
 gnCompare (const gnCompareType c_type)
 Creates a gnCompare for a predefined compare type.

 gnCompare (const gnCompare &sf)
 ~gnCompare ()
gnCompare * Clone () const
string GetName () const
void SetName (string name)
boolean LessThan (gnSeqC ch, gnSeqC ch2, boolean case_sensitive=false) const
boolean Contains (gnSeqC ch, gnSeqC ch2, boolean case_sensitive=false) const
 True if ch2 is equal to or contained within the scope of ch.

boolean LessThan (const gnSeqC *seq, const gnSeqC *seq2, const uint32 len, boolean case_sensitive=false) const
boolean Contains (const gnSeqC *seq, const gnSeqC *seq2, const uint32 len, boolean case_sensitive=false) const
boolean LessThan (const string &seq, const string &seq2, boolean case_sensitive=false) const
boolean Contains (const string &seq, const string &seq2, boolean case_sensitive=false) const
void SetSingle (const gnSeqC ch)
void SetPair (const gnSeqC ch, const gnSeqC ch2)
void SetContained (const gnSeqC ch, const gnSeqC ch2)
void RemoveSingle (const gnSeqC ch)
void RemovePair (const gnSeqC ch, const gnSeqC ch2)
void RemoveContained (const gnSeqC ch, const gnSeqC ch2)

Static Public Member Functions

const gnCompare * ProteinSeqCompare ()
 Returns a pointer to a ready to use Protein comparison object Do not delete the object when finished with it, it is a static object.

const gnCompare * DNASeqCompare ()
 Returns a pointer to a ready to use DNA comparison object This comparator can handle comparisons between ambiguous DNA sequences.

const gnCompare * RNASeqCompare ()
 Returns a pointer to a ready to use RNA comparison object This comparator can handle comparisons between ambiguous RNA sequences.


Private Member Functions

void CreateProteinComparator ()
void CreateDNAComparator ()
void CreateRNAComparator ()
void AddArrayEntry (gnSeqC *array[GNSEQC_MAX], const gnSeqC ch, const gnSeqC ch2)
void DelArrayEntry (gnSeqC *array[GNSEQC_MAX], const gnSeqC ch, const gnSeqC ch2)

Private Attributes

string m_name
boolean m_ignoreCase
gnSeqC * m_pairArray [GNSEQC_MAX]
gnSeqC * m_containArray [GNSEQC_MAX]

Member Enumeration Documentation

enum gnCompare::gnCompareType
 

Enumeration values:
ProteinSeqCompareType 
DNASeqCompareType 
RNASeqCompareType 

Definition at line 43 of file gnCompare.h.

Constructor & Destructor Documentation

gnCompare::gnCompare (    ) 
 

Definition at line 73 of file gnCompare.cpp.

References gnSeqC, GNSEQC_MAX, m_containArray, and m_pairArray.

Referenced by Clone(), DNASeqCompare(), ProteinSeqCompare(), and RNASeqCompare().

gnCompare::gnCompare (  const gnCompareType    c_type ) 
 

Creates a gnCompare for a predefined compare type.

Used by the static compare constructors to avoid the "static initialization order fiasco" For general use of a predefined comaprison type, you should use one of the static member functions to get a pointer to that comparison object.

Parameters:
c_type The type of comparator to create.
See also:
gnCompareType

Definition at line 29 of file gnCompare.cpp.

References CreateDNAComparator(), CreateProteinComparator(), CreateRNAComparator(), DNASeqCompareType, gnSeqC, GNSEQC_MAX, m_containArray, m_pairArray, ProteinSeqCompareType, and RNASeqCompareType.

gnCompare::gnCompare (  const gnCompare &    sf ) 
 

Definition at line 83 of file gnCompare.cpp.

References gnSeqC, GNSEQC_MAX, m_containArray, m_name, and m_pairArray.

gnCompare::~gnCompare (    ) 
 

Definition at line 93 of file gnCompare.cpp.

References gnSeqC, GNSEQC_MAX, m_containArray, and m_pairArray.

Member Function Documentation

void gnCompare::AddArrayEntry (  gnSeqC *    array[GNSEQC_MAX],
const gnSeqC    ch,
const gnSeqC    ch2
)  [private]
 

Definition at line 102 of file gnCompare.cpp.

References gnSeqC, and uint32.

Referenced by SetContained(), SetPair(), and SetSingle().

gnCompare * gnCompare::Clone (    )  const [inline, virtual]
 

Implements gnClone.

Definition at line 112 of file gnCompare.h.

References gnCompare().

boolean gnCompare::Contains (  const string &    seq,
const string &    seq2,
boolean    case_sensitive = false
)  const
 

Definition at line 67 of file gnCompare.cpp.

References Contains(), gnSeqC, and gnSeqI.

boolean gnCompare::Contains (  const gnSeqC *    seq,
const gnSeqC *    seq2,
const uint32    len,
boolean    case_sensitive = false
)  const
 

Definition at line 60 of file gnCompare.cpp.

References Contains(), and uint32.

boolean gnCompare::Contains (  gnSeqC    ch,
gnSeqC    ch2,
boolean    case_sensitive = false
)  const
 

True if ch2 is equal to or contained within the scope of ch.

Definition at line 49 of file gnCompare.cpp.

Referenced by Contains(), and gnTranslator::Filter().

void gnCompare::CreateDNAComparator (    )  [private]
 

Definition at line 182 of file gnCompare.cpp.

References SetContained(), SetName(), SetPair(), and SetSingle().

Referenced by gnCompare().

void gnCompare::CreateProteinComparator (    )  [private]
 

Definition at line 135 of file gnCompare.cpp.

References SetName(), and SetSingle().

Referenced by gnCompare().

void gnCompare::CreateRNAComparator (    )  [private]
 

Definition at line 438 of file gnCompare.cpp.

References SetContained(), SetName(), SetPair(), and SetSingle().

Referenced by gnCompare().

void gnCompare::DelArrayEntry (  gnSeqC *    array[GNSEQC_MAX],
const gnSeqC    ch,
const gnSeqC    ch2
)  [private]
 

Definition at line 112 of file gnCompare.cpp.

References gnSeqC, m_containArray, and uint32.

Referenced by RemoveContained(), RemovePair(), and RemoveSingle().

const gnCompare * gnCompare::DNASeqCompare (    )  [static]
 

Returns a pointer to a ready to use DNA comparison object This comparator can handle comparisons between ambiguous DNA sequences.

Do not delete the object when finished with it, it is a static object.

Definition at line 20 of file gnCompare.cpp.

References gnCompare().

Referenced by gnDNASequence::gnDNASequence(), and gnSequence::gnSequence().

string gnCompare::GetName (    )  const [inline]
 

Definition at line 117 of file gnCompare.h.

References m_name.

boolean gnCompare::LessThan (  const string &    seq,
const string &    seq2,
boolean    case_sensitive = false
)  const [inline]
 

Definition at line 151 of file gnCompare.h.

References gnSeqC, gnSeqI, and LessThan().

boolean gnCompare::LessThan (  const gnSeqC *    seq,
const gnSeqC *    seq2,
const uint32    len,
boolean    case_sensitive = false
)  const [inline]
 

Definition at line 142 of file gnCompare.h.

References LessThan(), and uint32.

boolean gnCompare::LessThan (  gnSeqC    ch,
gnSeqC    ch2,
boolean    case_sensitive = false
)  const [inline]
 

Definition at line 127 of file gnCompare.h.

Referenced by gnSequence::compare(), and LessThan().

const gnCompare * gnCompare::ProteinSeqCompare (    )  [static]
 

Returns a pointer to a ready to use Protein comparison object Do not delete the object when finished with it, it is a static object.

Definition at line 16 of file gnCompare.cpp.

References gnCompare().

Referenced by gnProteinSequence::gnProteinSequence().

void gnCompare::RemoveContained (  const gnSeqC    ch,
const gnSeqC    ch2
)  [inline]
 

Definition at line 186 of file gnCompare.h.

References DelArrayEntry().

void gnCompare::RemovePair (  const gnSeqC    ch,
const gnSeqC    ch2
)  [inline]
 

Definition at line 180 of file gnCompare.h.

References DelArrayEntry().

void gnCompare::RemoveSingle (  const gnSeqC    ch )  [inline]
 

Definition at line 174 of file gnCompare.h.

References DelArrayEntry().

const gnCompare * gnCompare::RNASeqCompare (    )  [static]
 

Returns a pointer to a ready to use RNA comparison object This comparator can handle comparisons between ambiguous RNA sequences.

Do not delete the object when finished with it, it is a static object.

Definition at line 24 of file gnCompare.cpp.

References gnCompare().

Referenced by gnRNASequence::gnRNASequence().

void gnCompare::SetContained (  const gnSeqC    ch,
const gnSeqC    ch2
)  [inline]
 

Definition at line 169 of file gnCompare.h.

References AddArrayEntry().

Referenced by CreateDNAComparator(), and CreateRNAComparator().

void gnCompare::SetName (  string    name )  [inline]
 

Definition at line 121 of file gnCompare.h.

References m_name.

Referenced by CreateDNAComparator(), CreateProteinComparator(), and CreateRNAComparator().

void gnCompare::SetPair (  const gnSeqC    ch,
const gnSeqC    ch2
)  [inline]
 

Definition at line 164 of file gnCompare.h.

References AddArrayEntry().

Referenced by CreateDNAComparator(), and CreateRNAComparator().

void gnCompare::SetSingle (  const gnSeqC    ch )  [inline]
 

Definition at line 159 of file gnCompare.h.

References AddArrayEntry().

Referenced by CreateDNAComparator(), CreateProteinComparator(), and CreateRNAComparator().

Member Data Documentation

gnSeqC* gnCompare::m_containArray[GNSEQC_MAX] [private]
 

Definition at line 107 of file gnCompare.h.

Referenced by DelArrayEntry(), gnCompare(), and ~gnCompare().

boolean gnCompare::m_ignoreCase [private]
 

Definition at line 104 of file gnCompare.h.

string gnCompare::m_name [private]
 

Definition at line 103 of file gnCompare.h.

Referenced by GetName(), gnCompare(), and SetName().

gnSeqC* gnCompare::m_pairArray[GNSEQC_MAX] [private]
 

Definition at line 106 of file gnCompare.h.

Referenced by gnCompare(), and ~gnCompare().

The documentation for this class was generated from the following files:
Generated on Mon Feb 3 02:34:44 2003 for libGenome by doxygen1.3-rc3