java.lang.Object

org.biojava.nbio.aaproperties.profeat.ProfeatPropertiesImpl

All Implemented Interfaces:: IProfeatProperties

public class ProfeatPropertiesImpl extends Object implements IProfeatProperties

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties
IProfeatProperties.ATTRIBUTE, IProfeatProperties.DISTRIBUTION, IProfeatProperties.GROUPING, IProfeatProperties.TRANSITION
Constructor Summary

Constructors

Constructor

Description

ProfeatPropertiesImpl()
Method Summary

Modifier and Type

Method

Description

Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Double>>

getComposition(ProteinSequence sequence)

Map<IProfeatProperties.GROUPING,Double>

getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)

double

getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group)

Returns the composition of the specific grouping for the given attribute.

Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>>

getDistributionPosition(ProteinSequence sequence)

Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>

getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)

Map<IProfeatProperties.DISTRIBUTION,Double>

getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group)

double

getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group, IProfeatProperties.DISTRIBUTION distribution)

Computes and return the position with respect to the sequence where the given distribution of the grouping can be found.
Example: "1111122222"
For the above example,
position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)

Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.TRANSITION,Double>>

getTransition(ProteinSequence sequence)

Map<IProfeatProperties.TRANSITION,Double>

getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)

double

getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.TRANSITION transition)

Returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details
- ProfeatPropertiesImpl
  
  public ProfeatPropertiesImpl()
Method Details
- getComposition
  
  public double getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws Exception
  
  Description copied from interface: IProfeatProperties
  
  Returns the composition of the specific grouping for the given attribute.
  
  Specified by:
  
  getComposition in interface IProfeatProperties
  
  Parameters:
  
  sequence - a protein sequence consisting of non-ambiguous characters only
  
  attribute - one of the seven attributes (Hydrophobicity, Volume, Polarity, Polarizability, Charge, SecondaryStructure or SolventAccessibility)
  
  group - the grouping to be computed
  
  Returns:
  
  returns the composition of the specific grouping for the given attribute
  
  Throws:
  
  Exception - throws Exception if attribute or group are unknown
- getTransition
  
  public double getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.TRANSITION transition) throws Exception
  
  Description copied from interface: IProfeatProperties
  
  Returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
  
  Specified by:
  
  getTransition in interface IProfeatProperties
  
  Parameters:
  
  sequence - a protein sequence consisting of non-ambiguous characters only
  
  attribute - one of the seven attributes (Hydrophobicity, Volume, Polarity, Polarizability, Charge, SecondaryStructure or SolventAccessibility)
  
  transition - the interested transition between the groups
  
  Returns:
  
  returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
  
  Throws:
  
  Exception - throws Exception if attribute or group are unknown
- getDistributionPosition
  
  public double getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group, IProfeatProperties.DISTRIBUTION distribution) throws Exception
  
  Description copied from interface: IProfeatProperties
  
  Computes and return the position with respect to the sequence where the given distribution of the grouping can be found.
  Example: "1111122222"
  For the above example,
  position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
  position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
  
  Specified by:
  
  getDistributionPosition in interface IProfeatProperties
  
  Parameters:
  
  sequence - a protein sequence consisting of non-ambiguous characters only
  
  attribute - one of the seven attributes (Hydrophobicity, Volume, Polarity, Polarizability, Charge, SecondaryStructure or SolventAccessibility)
  
  group - one the three groups for the attribute
  
  distribution - the distribution of the grouping
  
  Returns:
  
  the position with respect to the length of sequence where the given distribution of the grouping can be found.
  
  Throws:
  
  Exception - throws Exception if attribute or group are unknown
- getComposition
  
  public Map<IProfeatProperties.GROUPING,Double> getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws Exception
  
  Specified by:
  
  getComposition in interface IProfeatProperties
  
  Throws:
  
  Exception
- getComposition
  
  public Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Double>> getComposition(ProteinSequence sequence) throws Exception
  
  Specified by:
  
  getComposition in interface IProfeatProperties
  
  Throws:
  
  Exception
- getTransition
  
  public Map<IProfeatProperties.TRANSITION,Double> getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws Exception
  
  Specified by:
  
  getTransition in interface IProfeatProperties
  
  Throws:
  
  Exception
- getTransition
  
  public Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.TRANSITION,Double>> getTransition(ProteinSequence sequence) throws Exception
  
  Specified by:
  
  getTransition in interface IProfeatProperties
  
  Throws:
  
  Exception
- getDistributionPosition
  
  public Map<IProfeatProperties.DISTRIBUTION,Double> getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws Exception
  
  Specified by:
  
  getDistributionPosition in interface IProfeatProperties
  
  Throws:
  
  Exception
- getDistributionPosition
  
  public Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>> getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws Exception
  
  Specified by:
  
  getDistributionPosition in interface IProfeatProperties
  
  Throws:
  
  Exception
- getDistributionPosition
  
  public Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>> getDistributionPosition(ProteinSequence sequence) throws Exception
  
  Specified by:
  
  getDistributionPosition in interface IProfeatProperties
  
  Throws:
  
  Exception

Class ProfeatPropertiesImpl

Nested Class Summary

Nested classes/interfaces inherited from interface org.biojava.nbio.aaproperties.profeat.IProfeatProperties

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

ProfeatPropertiesImpl

Method Details

getComposition

getTransition

getDistributionPosition

getComposition

getComposition

getTransition

getTransition

getDistributionPosition

getDistributionPosition

getDistributionPosition