com.hfg.bio.seq.genomic

Class Intron

java.lang.Object

com.hfg.chem.Molecule

com.hfg.bio.seq.BioSequenceImpl

com.hfg.bio.seq.BioSequencePlusImpl

com.hfg.bio.seq.NucleicAcid

com.hfg.bio.seq.genomic.Intron

All Implemented Interfaces:

BioSequence, BioSequencePlus, Matter, HfgXMLSerializable, Cloneable, Comparable

public class Intron
extends NucleicAcid

An intron in a gene.

Nested Class Summary

Nested classes/interfaces inherited from class com.hfg.bio.seq.BioSequenceImpl

BioSequenceImpl.SeqFilterReader

Field Summary

Fields inherited from class com.hfg.bio.seq.BioSequenceImpl

GAP_PATTERN

Fields inherited from class com.hfg.chem.Molecule

H2O, mLocked, mName, NaCl, NH3

Constructor Summary

Constructors

Constructor and Description
Intron()
Intron(XMLNode inXML)

Method Summary

Modifier and Type	Method and Description
String	getAcceptorSpliceSite()
String	getDonorSpliceSite()
GenomicLocation	getGenomicLocaiton()
Intron	setAcceptorSpliceSite(CharSequence inValue)
Intron	setDonorSpliceSite(CharSequence inValue)
Intron	setGenomicLocaiton(GenomicLocation inValue)
Intron	setSequence(String inValue)
XMLNode	toXMLNode()

Methods inherited from class com.hfg.bio.seq.NucleicAcid

clone, compareTo, getComplementSequence, getComplementSequenceReader, getComplementSequenceStream, getReverseComplementSequence, getReverseComplementSequenceReader, getReverseComplementSequenceStream, getReverseSequence, getReverseSequenceReader, getReverseSequenceStream, getSeqQualityScores, getType, setDescription, setID, setNCBITaxon, setSeqQualityScores, setSequence

Methods inherited from class com.hfg.bio.seq.BioSequencePlusImpl

addDbXref, addFeature, addKeyword, addKeywords, addKeywords, addParseException, addReference, clearDbXrefs, clearFeatures, clearKeywords, clearParseExceptions, clearReferences, getClone, getDbXrefs, getFeatures, getFeatures, getKeywords, getMolType, getNCBITaxon, getParseExceptions, getReferences, getRevisionDate, getSeqRepositoryDivision, getSeqTopology, setClone, setMolType, setReferences, setRevisionDate, setSeqRepositoryDivision, setSeqTopology

Methods inherited from class com.hfg.bio.seq.BioSequenceImpl

clearCalculatedProperties, clearElementalCompositionAndCalculatedProperties, containsGaps, countGaps, equals, getAverageMass, getChemicalFormula, getChemicalFormulaWithSubscripts, getComposition, getDescription, getElementalComposition, getID, getMD5Checksum, getMonoisotopicMass, getNumGaps, getOrganicAverageMass, getResidueComposition, getSequence, getSequenceReader, getSequenceStream, getSHA1Checksum, getSubSequence, getSubSequenceReader, getTerminiComposition, getTotalGapLength, getXLinkComposition, length, recalculateElementalComposition, residueAt, setCompressionThreshold, setNumGaps, setResidueAt, setSequence, setTotalGapLength, toString

Methods inherited from class com.hfg.chem.Molecule

add, add, addAtom, addAtoms, addAtoms, addAtoms, addElementalComposition, addElementalComposition, addElementalComposition, addKa, addKa, calculateMassFromElementalComposition, clearAttributes, clearElementalComposition, formatMassString, getAtoms, getAttribute, getAttributeNames, getKas, getLastAtom, getPhysicalProperty, hasAttribute, hasAttributes, hashCode, isLocked, lock, massesAreUserSet, name, remove, remove, removeAttribute, setAttribute, setAverageMass, setChemicalFormula, setElementalComposition, setMonoisotopicMass, setName, setOrganicAverageMass, setPhysicalProperty

Methods inherited from class java.lang.Object

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

Methods inherited from interface com.hfg.bio.seq.BioSequencePlus

hadParseExceptions

Methods inherited from interface com.hfg.bio.seq.BioSequence

getAttribute, getAttributeNames, getDescription, getID, getMD5Checksum, getSequence, getSequenceReader, getSequenceStream, getSHA1Checksum, getSubSequence, getSubSequenceReader, hasAttribute, instantiate, length, removeAttribute, residueAt, setAttribute, setSequence

Methods inherited from interface com.hfg.chem.Matter

getAverageMass, getChemicalFormula, getElementalComposition, getMonoisotopicMass, getOrganicAverageMass

Constructor Detail

Intron

public Intron()

Intron

public Intron(XMLNode inXML)

Method Detail

toXMLNode

public XMLNode toXMLNode()

Specified by:

toXMLNode in interface BioSequence

Specified by:

toXMLNode in interface HfgXMLSerializable

Overrides:

toXMLNode in class BioSequencePlusImpl

setGenomicLocaiton

public Intron setGenomicLocaiton(GenomicLocation inValue)

getGenomicLocaiton

public GenomicLocation getGenomicLocaiton()

setDonorSpliceSite

public Intron setDonorSpliceSite(CharSequence inValue)

getDonorSpliceSite

public String getDonorSpliceSite()

setAcceptorSpliceSite

public Intron setAcceptorSpliceSite(CharSequence inValue)

getAcceptorSpliceSite

public String getAcceptorSpliceSite()

setSequence

public Intron setSequence(String inValue)