com.hfg.bio.seq

Class NucleicAcid

java.lang.Object

com.hfg.chem.Molecule

com.hfg.bio.seq.BioSequenceImpl

com.hfg.bio.seq.BioSequencePlusImpl

com.hfg.bio.seq.NucleicAcid

All Implemented Interfaces:

BioSequence, BioSequencePlus, Matter, HfgXMLSerializable, Cloneable, Comparable

Direct Known Subclasses:

Intron

public class NucleicAcid
extends BioSequencePlusImpl

Biological DNA or RNA sequence.

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
NucleicAcid()
NucleicAcid(XMLNode inXML)

Method Summary

Modifier and Type	Method and Description
NucleicAcid	clone() Returns an unlocked copy of the Molecule.
int	compareTo(Object inObj2)
String	getComplementSequence()
Reader	getComplementSequenceReader()
InputStream	getComplementSequenceStream()
String	getReverseComplementSequence()
Reader	getReverseComplementSequenceReader()
InputStream	getReverseComplementSequenceStream()
String	getReverseSequence()
protected Reader	getReverseSequenceReader()
InputStream	getReverseSequenceStream()
SeqQualityScores	getSeqQualityScores()
BioSequenceType	getType()
NucleicAcid	setDescription(CharSequence inValue)
NucleicAcid	setID(String inValue) Sets the id or name for the sequence.
NucleicAcid	setNCBITaxon(NCBITaxon inValue)
NucleicAcid	setSeqQualityScores(SeqQualityScores inValue)
NucleicAcid	setSequence(CharSequence inValue)

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, toXMLNode

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

NucleicAcid

public NucleicAcid()

NucleicAcid

public NucleicAcid(XMLNode inXML)

Method Detail

clone

public NucleicAcid clone()

Description copied from class: Molecule

Returns an unlocked copy of the Molecule.

Specified by:

clone in interface BioSequence

Overrides:

clone in class BioSequencePlusImpl

Returns:

an unlocked copy of the Molecule

compareTo

public int compareTo(Object inObj2)

Specified by:

compareTo in interface Comparable

Overrides:

compareTo in class Molecule

getType

public BioSequenceType getType()

Specified by:

getType in interface BioSequence

Overrides:

getType in class BioSequenceImpl

setID

public NucleicAcid setID(String inValue)

Description copied from interface: BioSequence

Sets the id or name for the sequence. Returns 'this' which can be useful for method chaining.

Specified by:

setID in interface BioSequence

Overrides:

setID in class BioSequenceImpl

Parameters:

inValue - the id to use for this sequence

Returns:

this BioSequence to enable method chaining

setDescription

public NucleicAcid setDescription(CharSequence inValue)

Specified by:

setDescription in interface BioSequence

Overrides:

setDescription in class BioSequenceImpl

setNCBITaxon

public NucleicAcid setNCBITaxon(NCBITaxon inValue)

Specified by:

setNCBITaxon in interface BioSequencePlus

Overrides:

setNCBITaxon in class BioSequencePlusImpl

setSequence

public NucleicAcid setSequence(CharSequence inValue)

Specified by:

setSequence in interface BioSequence

Overrides:

setSequence in class BioSequenceImpl

getComplementSequence

public String getComplementSequence()

getReverseSequence

public String getReverseSequence()

getReverseComplementSequence

public String getReverseComplementSequence()

getComplementSequenceReader

public Reader getComplementSequenceReader()

getReverseSequenceReader

protected Reader getReverseSequenceReader()

getReverseComplementSequenceReader

public Reader getReverseComplementSequenceReader()

getComplementSequenceStream

public InputStream getComplementSequenceStream()

getReverseSequenceStream

public InputStream getReverseSequenceStream()

Overrides:

getReverseSequenceStream in class BioSequenceImpl

getReverseComplementSequenceStream

public InputStream getReverseComplementSequenceStream()

setSeqQualityScores

public NucleicAcid setSeqQualityScores(SeqQualityScores inValue)

getSeqQualityScores

public SeqQualityScores getSeqQualityScores()