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java.lang.Objectorg.biojava3.aaproperties.PeptidePropertiesImpl
public class PeptidePropertiesImpl
This class contains the actual implementation of IPeptideProperties and is wrapped around by PeptideProperties for ease of use.
IPeptideProperties
,
PeptideProperties
Constructor Summary | |
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PeptidePropertiesImpl()
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Method Summary | |
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Map<AminoAcidCompound,Double> |
getAAComposition(ProteinSequence sequence)
Returns the composition of the 20 standard amino acid in the sequence. |
double |
getAbsorbance(ProteinSequence sequence,
boolean assumeCysReduced)
Returns the absorbance (optical density) of sequence. |
double |
getApliphaticIndex(ProteinSequence sequence)
Returns the apliphatic index of sequence. |
double |
getAvgHydropathy(ProteinSequence sequence)
Returns the average hydropathy value of sequence. |
double |
getEnrichment(ProteinSequence sequence,
AminoAcidCompound aminoAcidCode)
Returns the composition of specified amino acid in the sequence. |
double |
getExtinctionCoefficient(ProteinSequence sequence,
boolean assumeCysReduced)
Returns the extinction coefficient of sequence. |
double |
getInstabilityIndex(ProteinSequence sequence)
Returns the instability index of sequence. |
double |
getIsoelectricPoint(ProteinSequence sequence)
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double |
getIsoelectricPoint(ProteinSequence sequence,
boolean useExpasyValues)
Returns the isoelectric point of sequence. |
double |
getMolecularWeight(ProteinSequence sequence)
Returns the molecular weight of sequence. |
double |
getMolecularWeight(ProteinSequence sequence,
File aminoAcidCompositionFile)
Returns the molecular weight of sequence. |
double |
getMolecularWeight(ProteinSequence sequence,
File elementMassFile,
File aminoAcidCompositionFile)
Returns the molecular weight of sequence. |
double |
getMolecularWeightBasedOnXML(ProteinSequence sequence,
AminoAcidCompositionTable aminoAcidCompositionTable)
Returns the molecular weight of sequence. |
double |
getNetCharge(ProteinSequence sequence)
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double |
getNetCharge(ProteinSequence sequence,
boolean useExpasyValues)
|
double |
getNetCharge(ProteinSequence sequence,
boolean useExpasyValues,
double pHPoint)
Returns the net charge of sequence at pH 7. |
AminoAcidCompositionTable |
obtainAminoAcidCompositionTable(File aminoAcidCompositionFile)
This method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable). |
AminoAcidCompositionTable |
obtainAminoAcidCompositionTable(File elementMassFile,
File aminoAcidCompositionFile)
This method would initialize amino acid composition table based on the input xml files and stores the table for usage in future calls to IPeptideProperties.getMolecularWeightBasedOnXML(ProteinSequence, AminoAcidCompositionTable). |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public PeptidePropertiesImpl()
Method Detail |
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public double getMolecularWeight(ProteinSequence sequence)
IPeptideProperties
getMolecularWeight
in interface IPeptideProperties
sequence
- a protein sequence consisting of non-ambiguous characters only
ProteinSequence
public double getMolecularWeight(ProteinSequence sequence, File aminoAcidCompositionFile) throws JAXBException, FileNotFoundException
IPeptideProperties
getMolecularWeight
in interface IPeptideProperties
sequence
- a protein sequence consisting of non-ambiguous characters only
xml file that details the mass of each elements and isotopesaminoAcidCompositionFile
- xml file that details the composition of amino acids
JAXBException
- thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
FileNotFoundException
- thrown if either elementMassFile or aminoAcidCompositionFile are not foundpublic double getMolecularWeight(ProteinSequence sequence, File elementMassFile, File aminoAcidCompositionFile) throws JAXBException, FileNotFoundException
IPeptideProperties
getMolecularWeight
in interface IPeptideProperties
sequence
- a protein sequence consisting of non-ambiguous characters onlyelementMassFile
- xml file that details the mass of each elements and isotopesaminoAcidCompositionFile
- xml file that details the composition of amino acids
JAXBException
- thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
FileNotFoundException
- thrown if either elementMassFile or aminoAcidCompositionFile are not foundpublic double getMolecularWeightBasedOnXML(ProteinSequence sequence, AminoAcidCompositionTable aminoAcidCompositionTable)
IPeptideProperties
getMolecularWeightBasedOnXML
in interface IPeptideProperties
sequence
- a protein sequence consisting of non-ambiguous characters onlyaminoAcidCompositionTable
- a amino acid composition table obtained by calling IPeptideProperties.obtainAminoAcidCompositionTable
public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File aminoAcidCompositionFile) throws JAXBException, FileNotFoundException
IPeptideProperties
obtainAminoAcidCompositionTable
in interface IPeptideProperties
aminoAcidCompositionFile
- xml file that details the composition of amino acids
JAXBException
- thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
FileNotFoundException
- thrown if either elementMassFile or aminoAcidCompositionFile are not foundpublic AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMassFile, File aminoAcidCompositionFile) throws JAXBException, FileNotFoundException
IPeptideProperties
obtainAminoAcidCompositionTable
in interface IPeptideProperties
elementMassFile
- xml file that details the mass of each elements and isotopesaminoAcidCompositionFile
- xml file that details the composition of amino acids
JAXBException
- thrown if unable to properly parse either elementMassFile or aminoAcidCompositionFile
FileNotFoundException
- thrown if either elementMassFile or aminoAcidCompositionFile are not foundpublic double getExtinctionCoefficient(ProteinSequence sequence, boolean assumeCysReduced)
IPeptideProperties
getExtinctionCoefficient
in interface IPeptideProperties
sequence
- a protein sequence consisting of non-ambiguous characters onlyassumeCysReduced
- true if Cys are assumed to be reduced and false if Cys are
assumed to form cystines
ProteinSequence
public double getAbsorbance(ProteinSequence sequence, boolean assumeCysReduced)
IPeptideProperties
getAbsorbance
in interface IPeptideProperties
sequence
- a protein sequence consisting of non-ambiguous characters onlyassumeCysReduced
- true if Cys are assumed to be reduced and false if Cys are
assumed to form cystines
ProteinSequence
public double getInstabilityIndex(ProteinSequence sequence)
IPeptideProperties
getInstabilityIndex
in interface IPeptideProperties
sequence
- a protein sequence consisting of non-ambiguous characters only
ProteinSequence
public double getApliphaticIndex(ProteinSequence sequence)
IPeptideProperties
getApliphaticIndex
in interface IPeptideProperties
sequence
- a protein sequence consisting of non-ambiguous characters only
ProteinSequence
public double getAvgHydropathy(ProteinSequence sequence)
IPeptideProperties
getAvgHydropathy
in interface IPeptideProperties
sequence
- a protein sequence consisting of non-ambiguous characters only
ProteinSequence
public double getIsoelectricPoint(ProteinSequence sequence, boolean useExpasyValues)
IPeptideProperties
getIsoelectricPoint
in interface IPeptideProperties
sequence
- a protein sequence consisting of non-ambiguous characters onlyuseExpasyValues
- whether to use Expasy values (Default) or Innovagen values
ProteinSequence
public double getIsoelectricPoint(ProteinSequence sequence)
getIsoelectricPoint
in interface IPeptideProperties
public double getNetCharge(ProteinSequence sequence)
getNetCharge
in interface IPeptideProperties
public double getNetCharge(ProteinSequence sequence, boolean useExpasyValues)
getNetCharge
in interface IPeptideProperties
public double getNetCharge(ProteinSequence sequence, boolean useExpasyValues, double pHPoint)
IPeptideProperties
getNetCharge
in interface IPeptideProperties
sequence
- a protein sequence consisting of non-ambiguous characters onlyuseExpasyValues
- whether to use Expasy values (Default) or Innovagen valuespHPoint
- the pH value to use for computation of the net charge. Default at 7.
ProteinSequence
public double getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAcidCode)
IPeptideProperties
getEnrichment
in interface IPeptideProperties
sequence
- a protein sequence consisting of non-ambiguous characters onlyaminoAcidCode
- the code of the amino acid to compute
ProteinSequence
,
AminoAcidCompound
public Map<AminoAcidCompound,Double> getAAComposition(ProteinSequence sequence)
IPeptideProperties
getAAComposition
in interface IPeptideProperties
sequence
- a protein sequence consisting of non-ambiguous characters only
ProteinSequence
,
AminoAcidCompound
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