org.biojava.nbio.aaproperties.profeat

Class ProfeatPropertiesImpl

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 and Description
ProfeatPropertiesImpl()

Method Summary

Methods

Modifier and Type	Method and 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 Detail

ProfeatPropertiesImpl

public ProfeatPropertiesImpl()

Method Detail

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