org::gel::mauve::format::RichDelegatingSequence Class Reference

Inheritance diagram for org::gel::mauve::format::RichDelegatingSequence:

[legend]Collaboration diagram for org::gel::mauve::format::RichDelegatingSequence:


Public Member Functions
void	addComment (Comment comment) throws ChangeVetoException
void	addRankedCrossRef (RankedCrossRef crossref) throws ChangeVetoException
void	addRankedDocRef (RankedDocRef docref) throws ChangeVetoException
void	addRelationship (BioEntryRelationship relation) throws ChangeVetoException
int	compareTo (Object o)
String	getAccession ()
boolean	getCircular ()
Set	getComments ()
String	getDescription ()
String	getDivision ()
Set	getFeatureSet ()
String	getIdentifier ()
SymbolList	getInternalSymbolList ()
String	getName ()
Namespace	getNamespace ()
Set	getNoteSet ()
Set	getRankedCrossRefs ()
Set	getRankedDocRefs ()
Set	getRelationships ()
RichAnnotation	getRichAnnotation ()
Double	getSeqVersion ()
NCBITaxon	getTaxon ()
int	getVersion ()
void	removeComment (Comment comment) throws ChangeVetoException
void	removeRankedCrossRef (RankedCrossRef crossref) throws ChangeVetoException
void	removeRankedDocRef (RankedDocRef docref) throws ChangeVetoException
void	removeRelationship (BioEntryRelationship relation) throws ChangeVetoException
	RichDelegatingSequence (Sequence s, SupportedFormat format, File source, int index) throws FileNotFoundException
void	setCircular (boolean circular) throws ChangeVetoException
void	setDescription (String description) throws ChangeVetoException
void	setDivision (String division) throws ChangeVetoException
void	setFeatureSet (Set s) throws ChangeVetoException
void	setIdentifier (String identifier) throws ChangeVetoException
void	setNoteSet (Set notes) throws ChangeVetoException
void	setRankedCrossRefs (Set refs) throws ChangeVetoException
void	setSeqVersion (Double version) throws ChangeVetoException
void	setTaxon (NCBITaxon taxon) throws ChangeVetoException
Package Functions
void	richInit (Sequence s)
Package Attributes
String	accession = null
String	bioname = null
int	bioVersion = 0
Set	comments = null
String	description = null
String	division = null
Set	featureSet = null
String	identifier = null
SymbolList	intSymList = null
Set	noteSet = null
Namespace	ns = null
Set	rankedCrossRefs = null
Set	rankedDocRefs = null
Set	relationships = null
Double	seqVersion = null
NCBITaxon	taxon = null

Constructor & Destructor Documentation

org::gel::mauve::format::RichDelegatingSequence::RichDelegatingSequence ( Sequence s,

SupportedFormat format,

File source,

int index

) throws FileNotFoundException [inline]

Definition at line 25 of file RichDelegatingSequence.java.
References richInit().

Member Function Documentation

void org::gel::mauve::format::RichDelegatingSequence::addComment ( Comment comment ) throws ChangeVetoException [inline]

Definition at line 82 of file RichDelegatingSequence.java.

void org::gel::mauve::format::RichDelegatingSequence::addRankedCrossRef ( RankedCrossRef crossref ) throws ChangeVetoException [inline]

Definition at line 158 of file RichDelegatingSequence.java.

void org::gel::mauve::format::RichDelegatingSequence::addRankedDocRef ( RankedDocRef docref ) throws ChangeVetoException [inline]

Definition at line 85 of file RichDelegatingSequence.java.

void org::gel::mauve::format::RichDelegatingSequence::addRelationship ( BioEntryRelationship relation ) throws ChangeVetoException [inline]

Definition at line 88 of file RichDelegatingSequence.java.

int org::gel::mauve::format::RichDelegatingSequence::compareTo ( Object o ) [inline]

Definition at line 137 of file RichDelegatingSequence.java.

String org::gel::mauve::format::RichDelegatingSequence::getAccession ( ) [inline]

Definition at line 103 of file RichDelegatingSequence.java.
References accession.

boolean org::gel::mauve::format::RichDelegatingSequence::getCircular ( ) [inline]

Definition at line 73 of file RichDelegatingSequence.java.

Set org::gel::mauve::format::RichDelegatingSequence::getComments ( ) [inline]

Definition at line 104 of file RichDelegatingSequence.java.
References comments.

String org::gel::mauve::format::RichDelegatingSequence::getDescription ( ) [inline]

Definition at line 105 of file RichDelegatingSequence.java.
References description.

String org::gel::mauve::format::RichDelegatingSequence::getDivision ( ) [inline]

Definition at line 106 of file RichDelegatingSequence.java.
References division.

Set org::gel::mauve::format::RichDelegatingSequence::getFeatureSet ( ) [inline]

Definition at line 64 of file RichDelegatingSequence.java.
References featureSet.

String org::gel::mauve::format::RichDelegatingSequence::getIdentifier ( ) [inline]

Definition at line 107 of file RichDelegatingSequence.java.
References identifier.

SymbolList org::gel::mauve::format::RichDelegatingSequence::getInternalSymbolList ( ) [inline]

Definition at line 76 of file RichDelegatingSequence.java.
References intSymList.

String org::gel::mauve::format::RichDelegatingSequence::getName ( ) [inline]

Reimplemented from org::gel::mauve::format::DelegatingSequence.
Definition at line 108 of file RichDelegatingSequence.java.
References bioname.

Namespace org::gel::mauve::format::RichDelegatingSequence::getNamespace ( ) [inline]

Definition at line 109 of file RichDelegatingSequence.java.
References ns.

Set org::gel::mauve::format::RichDelegatingSequence::getNoteSet ( ) [inline]

Definition at line 143 of file RichDelegatingSequence.java.
References noteSet.

Set org::gel::mauve::format::RichDelegatingSequence::getRankedCrossRefs ( ) [inline]

Definition at line 150 of file RichDelegatingSequence.java.
References rankedCrossRefs.

Set org::gel::mauve::format::RichDelegatingSequence::getRankedDocRefs ( ) [inline]

Definition at line 110 of file RichDelegatingSequence.java.
References rankedDocRefs.

Set org::gel::mauve::format::RichDelegatingSequence::getRelationships ( ) [inline]

Definition at line 111 of file RichDelegatingSequence.java.
References relationships.

RichAnnotation org::gel::mauve::format::RichDelegatingSequence::getRichAnnotation ( ) [inline]

Definition at line 167 of file RichDelegatingSequence.java.

Double org::gel::mauve::format::RichDelegatingSequence::getSeqVersion ( ) [inline]

Definition at line 58 of file RichDelegatingSequence.java.
References seqVersion.

NCBITaxon org::gel::mauve::format::RichDelegatingSequence::getTaxon ( ) [inline]

Definition at line 112 of file RichDelegatingSequence.java.
References taxon.

int org::gel::mauve::format::RichDelegatingSequence::getVersion ( ) [inline]

Definition at line 113 of file RichDelegatingSequence.java.
References bioVersion.

void org::gel::mauve::format::RichDelegatingSequence::removeComment ( Comment comment ) throws ChangeVetoException [inline]

Definition at line 114 of file RichDelegatingSequence.java.

void org::gel::mauve::format::RichDelegatingSequence::removeRankedCrossRef ( RankedCrossRef crossref ) throws ChangeVetoException [inline]

Definition at line 162 of file RichDelegatingSequence.java.

void org::gel::mauve::format::RichDelegatingSequence::removeRankedDocRef ( RankedDocRef docref ) throws ChangeVetoException [inline]

Definition at line 117 of file RichDelegatingSequence.java.

void org::gel::mauve::format::RichDelegatingSequence::removeRelationship ( BioEntryRelationship relation ) throws ChangeVetoException [inline]

Definition at line 120 of file RichDelegatingSequence.java.

void org::gel::mauve::format::RichDelegatingSequence::richInit ( Sequence s ) [inline, package]

Definition at line 31 of file RichDelegatingSequence.java.
References accession, bioname, bioVersion, comments, description, division, featureSet, identifier, intSymList, noteSet, ns, rankedCrossRefs, rankedDocRefs, relationships, seqVersion, and taxon.
Referenced by RichDelegatingSequence().

void org::gel::mauve::format::RichDelegatingSequence::setCircular ( boolean circular ) throws ChangeVetoException [inline]

Definition at line 70 of file RichDelegatingSequence.java.

void org::gel::mauve::format::RichDelegatingSequence::setDescription ( String description ) throws ChangeVetoException [inline]

Definition at line 123 of file RichDelegatingSequence.java.

void org::gel::mauve::format::RichDelegatingSequence::setDivision ( String division ) throws ChangeVetoException [inline]

Definition at line 126 of file RichDelegatingSequence.java.

void org::gel::mauve::format::RichDelegatingSequence::setFeatureSet ( Set s ) throws ChangeVetoException [inline]

Definition at line 67 of file RichDelegatingSequence.java.

void org::gel::mauve::format::RichDelegatingSequence::setIdentifier ( String identifier ) throws ChangeVetoException [inline]

Definition at line 129 of file RichDelegatingSequence.java.

void org::gel::mauve::format::RichDelegatingSequence::setNoteSet ( Set notes ) throws ChangeVetoException [inline]

Definition at line 144 of file RichDelegatingSequence.java.

void org::gel::mauve::format::RichDelegatingSequence::setRankedCrossRefs ( Set refs ) throws ChangeVetoException [inline]

Definition at line 154 of file RichDelegatingSequence.java.

void org::gel::mauve::format::RichDelegatingSequence::setSeqVersion ( Double version ) throws ChangeVetoException [inline]

Definition at line 61 of file RichDelegatingSequence.java.

void org::gel::mauve::format::RichDelegatingSequence::setTaxon ( NCBITaxon taxon ) throws ChangeVetoException [inline]

Definition at line 132 of file RichDelegatingSequence.java.

Member Data Documentation

String org::gel::mauve::format::RichDelegatingSequence::accession = null [package]

Definition at line 91 of file RichDelegatingSequence.java.
Referenced by getAccession(), and richInit().

String org::gel::mauve::format::RichDelegatingSequence::bioname = null [package]

Definition at line 96 of file RichDelegatingSequence.java.
Referenced by getName(), and richInit().

int org::gel::mauve::format::RichDelegatingSequence::bioVersion = 0 [package]

Definition at line 101 of file RichDelegatingSequence.java.
Referenced by getVersion(), and richInit().

Set org::gel::mauve::format::RichDelegatingSequence::comments = null [package]

Definition at line 92 of file RichDelegatingSequence.java.
Referenced by getComments(), and richInit().

String org::gel::mauve::format::RichDelegatingSequence::description = null [package]

Definition at line 93 of file RichDelegatingSequence.java.
Referenced by getDescription(), and richInit().

String org::gel::mauve::format::RichDelegatingSequence::division = null [package]

Definition at line 94 of file RichDelegatingSequence.java.
Referenced by getDivision(), and richInit().

Set org::gel::mauve::format::RichDelegatingSequence::featureSet = null [package]

Definition at line 53 of file RichDelegatingSequence.java.
Referenced by getFeatureSet(), and richInit().

String org::gel::mauve::format::RichDelegatingSequence::identifier = null [package]

Definition at line 95 of file RichDelegatingSequence.java.
Referenced by getIdentifier(), and richInit().

SymbolList org::gel::mauve::format::RichDelegatingSequence::intSymList = null [package]

Definition at line 55 of file RichDelegatingSequence.java.
Referenced by getInternalSymbolList(), and richInit().

Set org::gel::mauve::format::RichDelegatingSequence::noteSet = null [package]

Definition at line 142 of file RichDelegatingSequence.java.
Referenced by getNoteSet(), and richInit().

Namespace org::gel::mauve::format::RichDelegatingSequence::ns = null [package]

Definition at line 97 of file RichDelegatingSequence.java.
Referenced by getNamespace(), and richInit().

Set org::gel::mauve::format::RichDelegatingSequence::rankedCrossRefs = null [package]

Definition at line 149 of file RichDelegatingSequence.java.
Referenced by getRankedCrossRefs(), and richInit().

Set org::gel::mauve::format::RichDelegatingSequence::rankedDocRefs = null [package]

Definition at line 98 of file RichDelegatingSequence.java.
Referenced by getRankedDocRefs(), and richInit().

Set org::gel::mauve::format::RichDelegatingSequence::relationships = null [package]

Definition at line 99 of file RichDelegatingSequence.java.
Referenced by getRelationships(), and richInit().

Double org::gel::mauve::format::RichDelegatingSequence::seqVersion = null [package]

Definition at line 54 of file RichDelegatingSequence.java.
Referenced by getSeqVersion(), and richInit().

NCBITaxon org::gel::mauve::format::RichDelegatingSequence::taxon = null [package]

Definition at line 100 of file RichDelegatingSequence.java.
Referenced by getTaxon(), and richInit().

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

src/org/gel/mauve/format/RichDelegatingSequence.java

Generated on Sun May 19 06:21:27 2013 for Mauve by

1.3.6

org::gel::mauve::format::RichDelegatingSequence Class Reference

Public Member Functions

Package Functions

Package Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation