com.hfg.bio.seq

Class BioSequenceImpl

java.lang.Object

com.hfg.chem.Molecule

com.hfg.bio.seq.BioSequenceImpl

All Implemented Interfaces:

BioSequence, Matter, HfgXMLSerializable, Cloneable, Comparable

Direct Known Subclasses:

BioSequencePlusImpl

public abstract class BioSequenceImpl
extends Molecule
implements Cloneable, BioSequence

Biological Protein, DNA, or RNA sequence.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	BioSequenceImpl.SeqFilterReader

Field Summary

Fields

Modifier and Type	Field and Description
protected static Pattern	GAP_PATTERN

Fields inherited from class com.hfg.chem.Molecule

H2O, mLocked, mName, NaCl, NH3

Constructor Summary

Constructors

Constructor and Description
BioSequenceImpl()
BioSequenceImpl(XMLNode inXML)

Method Summary

Modifier and Type	Method and Description
void	clearCalculatedProperties()
void	clearElementalCompositionAndCalculatedProperties()
BioSequenceImpl	clone() Returns an unlocked copy of the Molecule.
boolean	containsGaps()
protected void	countGaps()
boolean	equals(Object inObj2)
Double	getAverageMass()
String	getChemicalFormula() Returns a chemical formula String like 'C5H11NO'.
String	getChemicalFormulaWithSubscripts() Returns a chemical formula String like 'C₅H₁₁NO'.
protected Map<String,Integer>	getComposition() Returns a Map with 1-letter code Strings as keys and Integers as the values.
String	getDescription()
Map<Element,Float>	getElementalComposition() Returns an unmodifiable copy of the elemental composition Map.
String	getID()
byte[]	getMD5Checksum()
Double	getMonoisotopicMass()
Integer	getNumGaps()
Double	getOrganicAverageMass() Organic mass values used are from:
protected Map<Molecule,Integer>	getResidueComposition()
protected InputStream	getReverseSequenceStream()
String	getSequence()
Reader	getSequenceReader()
InputStream	getSequenceStream()
byte[]	getSHA1Checksum()
String	getSubSequence(SeqLocation inSeqLocation)
Reader	getSubSequenceReader(SeqLocation inSeqLocation)
protected Map<Molecule,Integer>	getTerminiComposition()
Integer	getTotalGapLength()
BioSequenceType	getType()
protected Map<? extends Molecule,Integer>	getXLinkComposition()
int	length()
protected void	recalculateElementalComposition()
char	residueAt(int inIndex) Returns the residue character at the specified (1-based) sequence location.
BioSequence	setCompressionThreshold(int inNumBytes)
BioSequence	setDescription(CharSequence inValue)
BioSequence	setID(String inValue) Sets the id or name for the sequence.
protected void	setNumGaps(Integer inValue)
void	setResidueAt(int inIndex, char inResidue) Specifies the residue to use at the specified (1-based) sequence location.
BioSequence	setSequence(CharSequence inValue)
BioSequence	setSequence(Reader inReader)
protected void	setTotalGapLength(Integer inValue)
String	toString()
XMLNode	toXMLNode()

Methods inherited from class com.hfg.chem.Molecule

add, add, addAtom, addAtoms, addAtoms, addAtoms, addElementalComposition, addElementalComposition, addElementalComposition, addKa, addKa, calculateMassFromElementalComposition, clearAttributes, clearElementalComposition, compareTo, 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.BioSequence

getAttribute, getAttributeNames, hasAttribute, instantiate, removeAttribute, setAttribute

Methods inherited from interface java.lang.Comparable

compareTo

Field Detail

GAP_PATTERN

protected static final Pattern GAP_PATTERN

Constructor Detail

BioSequenceImpl

public BioSequenceImpl()

BioSequenceImpl

public BioSequenceImpl(XMLNode inXML)

Method Detail

setCompressionThreshold

public BioSequence setCompressionThreshold(int inNumBytes)

getType

public BioSequenceType getType()

Specified by:

getType in interface BioSequence

toString

public String toString()

Overrides:

toString in class Molecule

clone

public BioSequenceImpl clone()

Description copied from class: Molecule

Returns an unlocked copy of the Molecule.

Specified by:

clone in interface BioSequence

Overrides:

clone in class Molecule

Returns:

an unlocked copy of the Molecule

equals

public boolean equals(Object inObj2)

Overrides:

equals in class Molecule

setID

public BioSequence 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

Parameters:

inValue - the id to use for this sequence

Returns:

this BioSequence to enable method chaining

getID

public String getID()

Specified by:

getID in interface BioSequence

setDescription

public BioSequence setDescription(CharSequence inValue)

Specified by:

setDescription in interface BioSequence

getDescription

public String getDescription()

Specified by:

getDescription in interface BioSequence

setSequence

public BioSequence setSequence(CharSequence inValue)

Specified by:

setSequence in interface BioSequence

setSequence

public BioSequence setSequence(Reader inReader)
                        throws SeqIOException

Specified by:

setSequence in interface BioSequence

Throws:

SeqIOException

getSequence

public String getSequence()

Specified by:

getSequence in interface BioSequence

getSequenceReader

public Reader getSequenceReader()

Specified by:

getSequenceReader in interface BioSequence

getSubSequenceReader

public Reader getSubSequenceReader(SeqLocation inSeqLocation)

Specified by:

getSubSequenceReader in interface BioSequence

getSequenceStream

public InputStream getSequenceStream()

Specified by:

getSequenceStream in interface BioSequence

getSubSequence

public String getSubSequence(SeqLocation inSeqLocation)

Specified by:

getSubSequence in interface BioSequence

getMD5Checksum

public byte[] getMD5Checksum()

Specified by:

getMD5Checksum in interface BioSequence

getSHA1Checksum

public byte[] getSHA1Checksum()

Specified by:

getSHA1Checksum in interface BioSequence

containsGaps

public boolean containsGaps()

getTotalGapLength

public Integer getTotalGapLength()

setNumGaps

protected void setNumGaps(Integer inValue)

setTotalGapLength

protected void setTotalGapLength(Integer inValue)

getNumGaps

public Integer getNumGaps()

countGaps

protected void countGaps()

length

public int length()

Specified by:

length in interface BioSequence

residueAt

public char residueAt(int inIndex)

Returns the residue character at the specified (1-based) sequence location.

Specified by:

residueAt in interface BioSequence

Parameters:

inIndex - the 1-based residue position

Returns:

the residue at the specified position

setResidueAt

public void setResidueAt(int inIndex,
                         char inResidue)

Specifies the residue to use at the specified (1-based) sequence location.

Parameters:

inIndex - the 1-based residue position

inResidue - the residue to place at the specified position

toXMLNode

public XMLNode toXMLNode()

Specified by:

toXMLNode in interface BioSequence

Specified by:

toXMLNode in interface HfgXMLSerializable

Overrides:

toXMLNode in class Molecule

getComposition

protected Map<String,Integer> getComposition()

Returns a Map with 1-letter code Strings as keys and Integers as the values. If a residue isn't present in the sequence, there won't be an entry for it in the map.

Returns:

Map with 1-letter code Strings as keys and Integers as the values

getElementalComposition

public Map<Element,Float> getElementalComposition()

Returns an unmodifiable copy of the elemental composition Map. The keys are Element objects and the values are Floats. Why Floats instead of Integers you ask? Because some amino acid codes such as B and Z are ambiguous averages.

Specified by:

getElementalComposition in interface Matter

Overrides:

getElementalComposition in class Molecule

Returns:

the elemental composition map

getChemicalFormula

public String getChemicalFormula()

Returns a chemical formula String like 'C5H11NO'. If carbon is present, it is listed first followed by the other elements in ascending mass order. Symbols for pure elements are enclosed in square brackets such as '[2H]2O' for deuterated water.

Specified by:

getChemicalFormula in interface Matter

Overrides:

getChemicalFormula in class Molecule

Returns:

the un-formatted chemical formula string

getChemicalFormulaWithSubscripts

public String getChemicalFormulaWithSubscripts()

Returns a chemical formula String like 'C₅H₁₁NO'. If carbon is present, it is listed first followed by the other elements in ascending mass order. Symbols for isotopes are enclosed in square brackets such as '[²H]₂O' for deuterated water.

Overrides:

getChemicalFormulaWithSubscripts in class Molecule

Returns:

the chemical formula string

getMonoisotopicMass

public Double getMonoisotopicMass()

Specified by:

getMonoisotopicMass in interface Matter

Overrides:

getMonoisotopicMass in class Molecule

getAverageMass

public Double getAverageMass()

Specified by:

getAverageMass in interface Matter

Overrides:

getAverageMass in class Molecule

getOrganicAverageMass

public Double getOrganicAverageMass()

Organic mass values used are from:

      Zhang Z, Pan H, Chen X. 2009. Mass spectrometry for structural characterization
      of therapeutic antibodies. Mass Spectrom Rev 28:147-176.
    

Specified by:

getOrganicAverageMass in interface Matter

Overrides:

getOrganicAverageMass in class Molecule

Returns:

the organic average mass for the sequence

clearCalculatedProperties

public void clearCalculatedProperties()

Overrides:

clearCalculatedProperties in class Molecule

clearElementalCompositionAndCalculatedProperties

public void clearElementalCompositionAndCalculatedProperties()

getResidueComposition

protected Map<Molecule,Integer> getResidueComposition()

getTerminiComposition

protected Map<Molecule,Integer> getTerminiComposition()

getXLinkComposition

protected Map<? extends Molecule,Integer> getXLinkComposition()

recalculateElementalComposition

protected void recalculateElementalComposition()

getReverseSequenceStream

protected InputStream getReverseSequenceStream()