Package org.biojavax.bio.seq

Class SimpleRichSequence

java.lang.Object

org.biojava.utils.AbstractChangeable

org.biojavax.bio.SimpleBioEntry

org.biojavax.bio.seq.ThinRichSequence

org.biojavax.bio.seq.SimpleRichSequence

All Implemented Interfaces:

Comparable, Annotatable, FeatureHolder, Sequence, SymbolList, Changeable, BioEntry, RichSequence, RankedCrossRefable, RichAnnotatable

public class SimpleRichSequence
extends ThinRichSequence

A simple implementation of RichSequence.

Since:

1.5

Author:

Richard Holland, Bubba Puryear

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder

FeatureHolder.EmptyFeatureHolder

Nested classes/interfaces inherited from interface org.biojavax.bio.seq.RichSequence

RichSequence.IOTools, RichSequence.Terms, RichSequence.Tools

Field Summary

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Fields inherited from interface org.biojavax.bio.BioEntry

COMMENT, DESCRIPTION, DIVISION, IDENTIFIER, RANKEDCROSSREF, RANKEDDOCREF, RELATIONS, SEQVERSION, TAXON

Fields inherited from interface org.biojava.bio.seq.FeatureHolder

EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

Fields inherited from interface org.biojavax.bio.seq.RichSequence

CIRCULAR, SYMLISTVERSION

Fields inherited from interface org.biojava.bio.symbol.SymbolList

EDIT, EMPTY_LIST

Constructor Summary

Constructors

Modifier	Constructor	Description
protected	SimpleRichSequence()
	SimpleRichSequence(Namespace ns, String name, String accession, int version, SymbolList symList, Double seqversion)	Creates a new instance of SimpleRichSequence.

Method Summary

Modifier and Type	Method	Description
SymbolList	getInternalSymbolList()	A special function that returns the SymbolList that this RichSequence is based around.
protected int	getSequenceLength()
protected String	getStringSequence()
int	length()	The number of symbols in this SymbolList.
protected void	setAlphabetName(String alphaname)
protected void	setSequenceLength(int length)
protected void	setStringSequence(String seq)

Methods inherited from class org.biojavax.bio.seq.ThinRichSequence

containsFeature, countFeatures, createFeature, edit, features, filter, filter, getAlphabet, getAlphabetName, getCircular, getFeatureSet, getSchema, getSeqVersion, getURN, iterator, removeFeature, seqString, setCircular, setFeatureSet, setSeqVersion, subList, subStr, symbolAt, toList

Methods inherited from class org.biojavax.bio.SimpleBioEntry

addComment, addRankedCrossRef, addRankedDocRef, addRelationship, compareTo, equals, getAccession, getAnnotation, getComments, getDescription, getDivision, getId, getIdentifier, getName, getNamespace, getNoteSet, getRankedCrossRefs, getRankedDocRefs, getRelationships, getRichAnnotation, getTaxon, getVersion, hashCode, removeComment, removeRankedCrossRef, removeRankedDocRef, removeRelationship, setDescription, setDivision, setId, setIdentifier, setNoteSet, setRankedCrossRefs, setTaxon, toString

Methods inherited from class org.biojava.utils.AbstractChangeable

addChangeListener, addChangeListener, generateChangeSupport, getChangeSupport, hasListeners, hasListeners, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojavax.bio.BioEntry

addComment, addRankedDocRef, addRelationship, getAccession, getComments, getDescription, getDivision, getIdentifier, getName, getNamespace, getRankedDocRefs, getRelationships, getTaxon, getVersion, removeComment, removeRankedDocRef, removeRelationship, setDescription, setDivision, setIdentifier, setTaxon

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface java.lang.Comparable

compareTo

Methods inherited from interface org.biojavax.RankedCrossRefable

addRankedCrossRef, getRankedCrossRefs, removeRankedCrossRef, setRankedCrossRefs

Methods inherited from interface org.biojavax.RichAnnotatable

getNoteSet, getRichAnnotation, setNoteSet

Methods inherited from interface org.biojava.bio.seq.Sequence

getName

Constructor Detail

SimpleRichSequence

public SimpleRichSequence(Namespace ns,
                          String name,
                          String accession,
                          int version,
                          SymbolList symList,
                          Double seqversion)

Creates a new instance of SimpleRichSequence. Note the use of Double for seqversion, which indicates that it is nullable.

Parameters:

ns - the namespace for this sequence.

name - the name of the sequence.

accession - the accession of the sequence.

version - the version of the sequence.

symList - the symbols for the sequence.

seqversion - the version of the symbols for the sequence.

SimpleRichSequence

protected SimpleRichSequence()

Method Detail

setAlphabetName

protected void setAlphabetName(String alphaname)
                        throws IllegalSymbolException,
                               BioException

Overrides:

setAlphabetName in class ThinRichSequence

Throws:

IllegalSymbolException

BioException

setStringSequence

protected void setStringSequence(String seq)
                          throws IllegalSymbolException,
                                 BioException

Throws:

IllegalSymbolException

BioException

getStringSequence

protected String getStringSequence()

length

public int length()

The number of symbols in this SymbolList.

Specified by:

length in interface SymbolList

Overrides:

length in class ThinRichSequence

Returns:

the length

setSequenceLength

protected void setSequenceLength(int length)

Overrides:

setSequenceLength in class ThinRichSequence

getSequenceLength

protected int getSequenceLength()

Overrides:

getSequenceLength in class ThinRichSequence

getInternalSymbolList

public SymbolList getInternalSymbolList()

A special function that returns the SymbolList that this RichSequence is based around. This should _not_ be the RichSequence object itself, as this function is used to perform actions on the symbol list without referring to the RichSequence object directly.

Specified by:

getInternalSymbolList in interface RichSequence

Overrides:

getInternalSymbolList in class ThinRichSequence

Returns:

the internal SymbolList of the RichSequence, NOT the RichSequence object itself.