gnDNASequence Class Reference

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

#include <gnDNASequence.h>

Inheritance diagram for gnDNASequence:

[legend]Collaboration diagram for gnDNASequence:

[legend]List of all members.

Public Member Functions
	gnDNASequence (const gnDNASequence &seq)
	Copies the gnDNASequence "seq".
	gnDNASequence (gnSeqC *bases, const gnSeqI length)
	Creates a gnDNASequence with a single contig containing the bases in "bases".
	gnDNASequence (const gnContigSpec &gncs)
	Creates a gnDNASequence with the contigs stored in "gncs".
	gnDNASequence (const gnFragmentSpec &gnfs)
	Creates a gnDNASequence with the contigs stored in "gnfs".
	gnDNASequence (const gnGenomeSpec &gngs)
	Creates a gnDNASequence with the contigs stored in "gngs".
	gnDNASequence (const string &str)
	Creates a gnDNASequence with a single contig containing the bases in "str".
	gnDNASequence (const gnSeqC *seq)
	Creates a gnDNASequence with a single contig containing the bases in "seq".
	gnDNASequence ()
	Empty Constructor, creates an empty gnDNASequence.
Private Attributes
const gnCompare *	comparator
list< const gnBaseFilter * >	filter_list
gnGenomeSpec *	spec

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Detailed Description

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

Definition at line 27 of file gnDNASequence.h.

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Constructor & Destructor Documentation

gnDNASequence::gnDNASequence (   )  [inline]

Empty Constructor, creates an empty gnDNASequence. Definition at line 77 of file gnDNASequence.h. References comparator, gnCompare::DNASeqCompare(), and filter_list.

gnDNASequence::gnDNASequence (  const gnSeqC *  seq  )  [inline]

Creates a gnDNASequence with a single contig containing the bases in "seq". Parameters: seq  The null terminated array of base pairs to use. Definition at line 82 of file gnDNASequence.h. References comparator, gnCompare::DNASeqCompare(), filter_list, and gnSeqC.

gnDNASequence::gnDNASequence (  const string &  str  )  [inline]

Creates a gnDNASequence with a single contig containing the bases in "str". Parameters: str  The base pairs to use. Definition at line 87 of file gnDNASequence.h. References comparator, gnCompare::DNASeqCompare(), and filter_list.

gnDNASequence::gnDNASequence (  const gnGenomeSpec &  gngs  )  [inline]

Creates a gnDNASequence with the contigs stored in "gngs". Parameters: gngs  the gnGenomeSpec to get contigs from. Definition at line 92 of file gnDNASequence.h. References comparator, gnCompare::DNASeqCompare(), and filter_list.

gnDNASequence::gnDNASequence (  const gnFragmentSpec &  gnfs  )  [inline]

Creates a gnDNASequence with the contigs stored in "gnfs". Parameters: gnfs  the gnFragmentSpec to get contigs from. Definition at line 97 of file gnDNASequence.h. References comparator, gnCompare::DNASeqCompare(), and filter_list.

gnDNASequence::gnDNASequence (  const gnContigSpec &  gncs  )  [inline]

Creates a gnDNASequence with the contigs stored in "gncs". Parameters: gncs  the gnContigSpec to get contigs from. Definition at line 102 of file gnDNASequence.h. References comparator, gnCompare::DNASeqCompare(), and filter_list.

gnDNASequence::gnDNASequence (  gnSeqC *  bases, const gnSeqI  length )  [inline]

Creates a gnDNASequence 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 107 of file gnDNASequence.h. References comparator, gnCompare::DNASeqCompare(), filter_list, gnSeqC, and gnSeqI.

gnDNASequence::gnDNASequence (  const gnDNASequence &  seq  )  [inline]

Copies the gnDNASequence "seq". Parameters: seq  The gnDNASequence to copy. Definition at line 112 of file gnDNASequence.h. References comparator, gnCompare::DNASeqCompare(), and filter_list.

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Member Data Documentation

const gnCompare* gnDNASequence::comparator [private]

Reimplemented from gnSequence. Definition at line 73 of file gnDNASequence.h. Referenced by gnDNASequence().

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

Reimplemented from gnSequence. Definition at line 72 of file gnDNASequence.h. Referenced by gnDNASequence().

gnGenomeSpec* gnDNASequence::spec [private]

Reimplemented from gnSequence. Definition at line 71 of file gnDNASequence.h.

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The documentation for this class was generated from the following file:

• include/gn/gnDNASequence.h

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