java.lang.Object

org.biojava.nbio.aaproperties.profeat.ProfeatProperties

public class ProfeatProperties extends Object

This is an adaptor class which enable the ease of generating profeat properties. At least one adaptor method is written for each available properties provided in IProfeatProperties.

Since:

3.0.2

Version:

2011.06.16

Author:

kohchuanhock

See Also:

Constructor Summary

Constructors

Constructor

Description

ProfeatProperties()
Method Summary

Modifier and Type

Method

Description

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

getComposition(String sequence)

static Map<IProfeatProperties.GROUPING,Double>

getComposition(String sequence, IProfeatProperties.ATTRIBUTE attribute)

static double

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

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

getComposition(ProteinSequence sequence)

static Map<IProfeatProperties.GROUPING,Double>

getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)

static double

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

An adaptor method which returns the composition of the specific grouping for the given attribute.

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

getDistributionPosition(String sequence)

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

getDistributionPosition(String sequence, IProfeatProperties.ATTRIBUTE attribute)

static Map<IProfeatProperties.DISTRIBUTION,Double>

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

static double

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

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

getDistributionPosition(ProteinSequence sequence)

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

getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)

static Map<IProfeatProperties.DISTRIBUTION,Double>

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

static double

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

An adaptor method which 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)

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

getTransition(String sequence)

static Map<IProfeatProperties.TRANSITION,Double>

getTransition(String sequence, IProfeatProperties.ATTRIBUTE attribute)

static double

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

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

getTransition(ProteinSequence sequence)

static Map<IProfeatProperties.TRANSITION,Double>

getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)

static double

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

An adaptor method which 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
- ProfeatProperties
  
  public ProfeatProperties()
Method Details
- getComposition
  
  public static double getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws Exception
  
  An adaptor method which returns the composition of the specific grouping for the given attribute.
  
  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
- getComposition
  
  public static Map<IProfeatProperties.GROUPING,Double> getComposition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws Exception
  
  Throws:
  
  Exception
- getComposition
  
  public static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Double>> getComposition(ProteinSequence sequence) throws Exception
  
  Throws:
  
  Exception
- getComposition
  
  public static double getComposition(String sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws Exception
  
  Throws:
  
  Exception
- getComposition
  
  public static Map<IProfeatProperties.GROUPING,Double> getComposition(String sequence, IProfeatProperties.ATTRIBUTE attribute) throws Exception
  
  Throws:
  
  Exception
- getComposition
  
  public static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Double>> getComposition(String sequence) throws Exception
  
  Throws:
  
  Exception
- getTransition
  
  public static double getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.TRANSITION transition) throws Exception
  
  An adaptor method which returns the number of transition between the specified groups for the given attribute with respect to the length of sequence.
  
  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
- getTransition
  
  public static Map<IProfeatProperties.TRANSITION,Double> getTransition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws Exception
  
  Throws:
  
  Exception
- getTransition
  
  public static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.TRANSITION,Double>> getTransition(ProteinSequence sequence) throws Exception
  
  Throws:
  
  Exception
- getTransition
  
  public static double getTransition(String sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.TRANSITION transition) throws Exception
  
  Throws:
  
  Exception
- getTransition
  
  public static Map<IProfeatProperties.TRANSITION,Double> getTransition(String sequence, IProfeatProperties.ATTRIBUTE attribute) throws Exception
  
  Throws:
  
  Exception
- getTransition
  
  public static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.TRANSITION,Double>> getTransition(String sequence) throws Exception
  
  Throws:
  
  Exception
- getDistributionPosition
  
  public static double getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group, IProfeatProperties.DISTRIBUTION distribution) throws Exception
  
  An adaptor method which 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)
  
  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
- getDistributionPosition
  
  public static Map<IProfeatProperties.DISTRIBUTION,Double> getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws Exception
  
  Throws:
  
  Exception
- getDistributionPosition
  
  public static Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>> getDistributionPosition(ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute) throws Exception
  
  Throws:
  
  Exception
- getDistributionPosition
  
  public static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>> getDistributionPosition(ProteinSequence sequence) throws Exception
  
  Throws:
  
  Exception
- getDistributionPosition
  
  public static double getDistributionPosition(String sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group, IProfeatProperties.DISTRIBUTION distribution) throws Exception
  
  Throws:
  
  Exception
- getDistributionPosition
  
  public static Map<IProfeatProperties.DISTRIBUTION,Double> getDistributionPosition(String sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group) throws Exception
  
  Throws:
  
  Exception
- getDistributionPosition
  
  public static Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>> getDistributionPosition(String sequence, IProfeatProperties.ATTRIBUTE attribute) throws Exception
  
  Throws:
  
  Exception
- getDistributionPosition
  
  public static Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>> getDistributionPosition(String sequence) throws Exception
  
  Throws:
  
  Exception

Class ProfeatProperties

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Details

ProfeatProperties

Method Details

getComposition

getComposition

getComposition

getComposition

getComposition

getComposition

getTransition

getTransition

getTransition

getTransition

getTransition

getTransition

getDistributionPosition

getDistributionPosition

getDistributionPosition

getDistributionPosition

getDistributionPosition

getDistributionPosition

getDistributionPosition

getDistributionPosition