gnProteinSequence Class Reference

gnProteinSequence is a special kind of gnSequence which can be used for RNA sequences It sets the default filters and comparators to the RNA filters and comparators. More...

#include <gnProteinSequence.h>

Inheritance diagram for gnProteinSequence:

Inheritance graph
[legend]
Collaboration diagram for gnProteinSequence:

Collaboration graph
[legend]
List of all members.

Public Member Functions

 gnProteinSequence (const gnProteinSequence &seq)
 Copies the gnProteinSequence "seq".
 gnProteinSequence (gnSeqC *bases, const gnSeqI length)
 Creates a gnProteinSequence with a single contig containing the bases in "bases".
 gnProteinSequence (const gnContigSpec &gncs)
 Creates a gnProteinSequence with the contigs stored in "gncs".
 gnProteinSequence (const gnFragmentSpec &gnfs)
 Creates a gnProteinSequence with the contigs stored in "gnfs".
 gnProteinSequence (const gnGenomeSpec &gngs)
 Creates a gnProteinSequence with the contigs stored in "gngs".
 gnProteinSequence (const string &str)
 Creates a gnProteinSequence with a single contig containing the bases in "str".
 gnProteinSequence (const gnSeqC *seq)
 Creates a gnProteinSequence with a single contig containing the bases in "seq".
 gnProteinSequence ()
 Empty Constructor, creates an empty gnProteinSequence.

Private Attributes

const gnComparecomparator
list< const gnBaseFilter * > filter_list
gnGenomeSpecspec

Detailed Description

gnProteinSequence is a special kind of gnSequence which can be used for RNA sequences It sets the default filters and comparators to the RNA filters and comparators.

Definition at line 28 of file gnProteinSequence.h.


Constructor & Destructor Documentation

gnProteinSequence::gnProteinSequence  )  [inline]
 

Empty Constructor, creates an empty gnProteinSequence.

Definition at line 78 of file gnProteinSequence.h.

References comparator, filter_list, and gnCompare::ProteinSeqCompare().

gnProteinSequence::gnProteinSequence const gnSeqC seq  )  [inline]
 

Creates a gnProteinSequence with a single contig containing the bases in "seq".

Parameters:
seq The null terminated array of base pairs to use.
Definition at line 83 of file gnProteinSequence.h.

References comparator, filter_list, gnSeqC, and gnCompare::ProteinSeqCompare().

gnProteinSequence::gnProteinSequence const string &  str  )  [inline]
 

Creates a gnProteinSequence with a single contig containing the bases in "str".

Parameters:
str The base pairs to use.
Definition at line 88 of file gnProteinSequence.h.

References comparator, filter_list, and gnCompare::ProteinSeqCompare().

gnProteinSequence::gnProteinSequence const gnGenomeSpec gngs  )  [inline]
 

Creates a gnProteinSequence with the contigs stored in "gngs".

Parameters:
gngs the gnGenomeSpec to get contigs from.
Definition at line 93 of file gnProteinSequence.h.

References comparator, filter_list, and gnCompare::ProteinSeqCompare().

gnProteinSequence::gnProteinSequence const gnFragmentSpec gnfs  )  [inline]
 

Creates a gnProteinSequence with the contigs stored in "gnfs".

Parameters:
gnfs the gnFragmentSpec to get contigs from.
Definition at line 98 of file gnProteinSequence.h.

References comparator, filter_list, and gnCompare::ProteinSeqCompare().

gnProteinSequence::gnProteinSequence const gnContigSpec gncs  )  [inline]
 

Creates a gnProteinSequence with the contigs stored in "gncs".

Parameters:
gncs the gnContigSpec to get contigs from.
Definition at line 103 of file gnProteinSequence.h.

References comparator, filter_list, and gnCompare::ProteinSeqCompare().

gnProteinSequence::gnProteinSequence gnSeqC bases,
const gnSeqI  length
[inline]
 

Creates a gnProteinSequence with a single contig containing the bases in "bases".

Parameters:
bases The base pairs to use
length The length of the base pair array.
Definition at line 108 of file gnProteinSequence.h.

References comparator, filter_list, gnSeqC, gnSeqI, and gnCompare::ProteinSeqCompare().

gnProteinSequence::gnProteinSequence const gnProteinSequence seq  )  [inline]
 

Copies the gnProteinSequence "seq".

Parameters:
seq The gnProteinSequence to copy.
Definition at line 113 of file gnProteinSequence.h.

References comparator, filter_list, and gnCompare::ProteinSeqCompare().


Member Data Documentation

const gnCompare* gnProteinSequence::comparator [private]
 

Reimplemented from gnSequence.

Definition at line 74 of file gnProteinSequence.h.

Referenced by gnProteinSequence().

list<const gnBaseFilter*> gnProteinSequence::filter_list [private]
 

Reimplemented from gnSequence.

Definition at line 73 of file gnProteinSequence.h.

Referenced by gnProteinSequence().

gnGenomeSpec* gnProteinSequence::spec [private]
 

Reimplemented from gnSequence.

Definition at line 72 of file gnProteinSequence.h.


The documentation for this class was generated from the following file:
Generated on Mon Feb 14 19:29:55 2005 for libGenome by doxygen 1.3.8