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

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

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

Collaboration graph
List of all members.

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

References richInit().

Member Function Documentation

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

Definition at line 82 of file

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

Definition at line 158 of file

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

Definition at line 85 of file

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

Definition at line 88 of file

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

Definition at line 137 of file

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

Definition at line 103 of file

References accession.

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

Definition at line 73 of file

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

Definition at line 104 of file

References comments.

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

Definition at line 105 of file

References description.

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

Definition at line 106 of file

References division.

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

Definition at line 64 of file

References featureSet.

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

Definition at line 107 of file

References identifier.

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

Definition at line 76 of file

References intSymList.

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

Reimplemented from org::gel::mauve::format::DelegatingSequence.

Definition at line 108 of file

References bioname.

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

Definition at line 109 of file

References ns.

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

Definition at line 143 of file

References noteSet.

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

Definition at line 150 of file

References rankedCrossRefs.

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

Definition at line 110 of file

References rankedDocRefs.

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

Definition at line 111 of file

References relationships.

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

Definition at line 167 of file

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

Definition at line 58 of file

References seqVersion.

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

Definition at line 112 of file

References taxon.

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

Definition at line 113 of file

References bioVersion.

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

Definition at line 114 of file

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

Definition at line 162 of file

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

Definition at line 117 of file

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

Definition at line 120 of file

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

Definition at line 31 of file

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

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

Definition at line 123 of file

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

Definition at line 126 of file

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

Definition at line 67 of file

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

Definition at line 129 of file

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

Definition at line 144 of file

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

Definition at line 154 of file

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

Definition at line 61 of file

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

Definition at line 132 of file

Member Data Documentation

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

Definition at line 91 of file

Referenced by getAccession(), and richInit().

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

Definition at line 96 of file

Referenced by getName(), and richInit().

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

Definition at line 101 of file

Referenced by getVersion(), and richInit().

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

Definition at line 92 of file

Referenced by getComments(), and richInit().

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

Definition at line 93 of file

Referenced by getDescription(), and richInit().

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

Definition at line 94 of file

Referenced by getDivision(), and richInit().

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

Definition at line 53 of file

Referenced by getFeatureSet(), and richInit().

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

Definition at line 95 of file

Referenced by getIdentifier(), and richInit().

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

Definition at line 55 of file

Referenced by getInternalSymbolList(), and richInit().

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

Definition at line 142 of file

Referenced by getNoteSet(), and richInit().

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

Definition at line 97 of file

Referenced by getNamespace(), and richInit().

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

Definition at line 149 of file

Referenced by getRankedCrossRefs(), and richInit().

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

Definition at line 98 of file

Referenced by getRankedDocRefs(), and richInit().

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

Definition at line 99 of file

Referenced by getRelationships(), and richInit().

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

Definition at line 54 of file

Referenced by getSeqVersion(), and richInit().

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

Definition at line 100 of file

Referenced by getTaxon(), and richInit().

The documentation for this class was generated from the following file:
Generated on Mon Aug 19 06:04:01 2013 for Mauve by doxygen 1.3.6