gnRNASequence Class Reference

gnRNASequence 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 <gnRNASequence.h>

Inheritance diagram for gnRNASequence:

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Collaboration diagram for gnRNASequence:

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List of all members.

Public Member Functions

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

Private Attributes

const gnComparecomparator
list< const gnBaseFilter * > filter_list
gnGenomeSpecspec

Detailed Description

gnRNASequence 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 gnRNASequence.h.


Constructor & Destructor Documentation

gnRNASequence::gnRNASequence  )  [inline]
 

Empty Constructor, creates an empty gnRNASequence.

Definition at line 78 of file gnRNASequence.h.

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

gnRNASequence::gnRNASequence const gnSeqC seq  )  [inline]
 

Creates a gnRNASequence 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 gnRNASequence.h.

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

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

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

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

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

gnRNASequence::gnRNASequence const gnGenomeSpec gngs  )  [inline]
 

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

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

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

gnRNASequence::gnRNASequence const gnFragmentSpec gnfs  )  [inline]
 

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

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

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

gnRNASequence::gnRNASequence const gnContigSpec gncs  )  [inline]
 

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

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

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

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

Creates a gnRNASequence 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 gnRNASequence.h.

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

gnRNASequence::gnRNASequence const gnRNASequence seq  )  [inline]
 

Copies the gnRNASequence "seq".

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

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


Member Data Documentation

const gnCompare* gnRNASequence::comparator [private]
 

Reimplemented from gnSequence.

Definition at line 74 of file gnRNASequence.h.

Referenced by gnRNASequence().

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

Reimplemented from gnSequence.

Definition at line 73 of file gnRNASequence.h.

Referenced by gnRNASequence().

gnGenomeSpec* gnRNASequence::spec [private]
 

Reimplemented from gnSequence.

Definition at line 72 of file gnRNASequence.h.


The documentation for this class was generated from the following file:
Generated on Mon Feb 14 19:29:56 2005 for libGenome by doxygen 1.3.8