BioSequenceImpl (com.hfg API Documentation)

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

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

Fields
Modifier and Type	Field and Description
`protected static Pattern`	`GAP_PATTERN`

Constructor Summary

Constructors
Constructor and Description

BioSequenceImpl()

BioSequenceImpl(XMLNode inXML)

Constructors
Constructor and Description
`BioSequenceImpl()`
`BioSequenceImpl(XMLNode inXML)`

Method Summary

All Methods Instance Methods Concrete Methods
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 'Câ‚…Hâ‚â‚NO'.
`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 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 'Câ‚…Hâ‚â‚NO'. 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 '[Â²H]â‚‚O' 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()
```

Class BioSequenceImpl

Nested Class Summary

Field Summary

Fields inherited from class com.hfg.chem.Molecule

Constructor Summary

Method Summary

Methods inherited from class com.hfg.chem.Molecule

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Comparable

Field Detail

GAP_PATTERN

Constructor Detail

BioSequenceImpl

BioSequenceImpl

Method Detail

setCompressionThreshold

getType

toString

clone

equals

setID

getID

setDescription

getDescription

setSequence

setSequence

getSequence

getSequenceReader

getSubSequenceReader

getSequenceStream

getSubSequence

getMD5Checksum

getSHA1Checksum

containsGaps

getTotalGapLength

setNumGaps

setTotalGapLength

getNumGaps

countGaps

length

residueAt

setResidueAt

toXMLNode

getComposition

getElementalComposition

getChemicalFormula

getChemicalFormulaWithSubscripts

getMonoisotopicMass

getAverageMass

getOrganicAverageMass

clearCalculatedProperties

clearElementalCompositionAndCalculatedProperties

getResidueComposition

getTerminiComposition

getXLinkComposition

recalculateElementalComposition

getReverseSequenceStream