Package org.biojava.nbio.aaproperties.profeat

Interface IProfeatProperties

All Known Implementing Classes:

ProfeatPropertiesImpl

public interface IProfeatProperties

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	IProfeatProperties.ATTRIBUTE	Enumeration of the seven different attributes
static class	IProfeatProperties.DISTRIBUTION	Enumeration of the distribution for the first, first 25%, first 50%, first 75% and 100% of the grouping
static class	IProfeatProperties.GROUPING	Enumeration of the three different groupings for each attributes
static class	IProfeatProperties.TRANSITION	Enumeration of the transition between groupA and groupB

Method Summary

Modifier and Type	Method	Description
Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Double>>	getComposition(org.biojava.nbio.core.sequence.ProteinSequence sequence)
Map<IProfeatProperties.GROUPING,Double>	getComposition(org.biojava.nbio.core.sequence.ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
double	getComposition(org.biojava.nbio.core.sequence.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(org.biojava.nbio.core.sequence.ProteinSequence sequence)
Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>	getDistributionPosition(org.biojava.nbio.core.sequence.ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
Map<IProfeatProperties.DISTRIBUTION,Double>	getDistributionPosition(org.biojava.nbio.core.sequence.ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute, IProfeatProperties.GROUPING group)
double	getDistributionPosition(org.biojava.nbio.core.sequence.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(org.biojava.nbio.core.sequence.ProteinSequence sequence)
Map<IProfeatProperties.TRANSITION,Double>	getTransition(org.biojava.nbio.core.sequence.ProteinSequence sequence, IProfeatProperties.ATTRIBUTE attribute)
double	getTransition(org.biojava.nbio.core.sequence.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.

Method Detail

getComposition

double getComposition(org.biojava.nbio.core.sequence.ProteinSequence sequence,
                      IProfeatProperties.ATTRIBUTE attribute,
                      IProfeatProperties.GROUPING group)
               throws Exception

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

Map<IProfeatProperties.GROUPING,Double> getComposition(org.biojava.nbio.core.sequence.ProteinSequence sequence,
                                                             IProfeatProperties.ATTRIBUTE attribute)
                                                      throws Exception

Throws:

Exception

getComposition

Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Double>> getComposition(org.biojava.nbio.core.sequence.ProteinSequence sequence)
                                                                                              throws Exception

Throws:

Exception

getTransition

double getTransition(org.biojava.nbio.core.sequence.ProteinSequence sequence,
                     IProfeatProperties.ATTRIBUTE attribute,
                     IProfeatProperties.TRANSITION transition)
              throws Exception

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

Map<IProfeatProperties.TRANSITION,Double> getTransition(org.biojava.nbio.core.sequence.ProteinSequence sequence,
                                                              IProfeatProperties.ATTRIBUTE attribute)
                                                       throws Exception

Throws:

Exception

getTransition

Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.TRANSITION,Double>> getTransition(org.biojava.nbio.core.sequence.ProteinSequence sequence)
                                                                                               throws Exception

Throws:

Exception

getDistributionPosition

double getDistributionPosition(org.biojava.nbio.core.sequence.ProteinSequence sequence,
                               IProfeatProperties.ATTRIBUTE attribute,
                               IProfeatProperties.GROUPING group,
                               IProfeatProperties.DISTRIBUTION distribution)
                        throws Exception

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

Map<IProfeatProperties.DISTRIBUTION,Double> getDistributionPosition(org.biojava.nbio.core.sequence.ProteinSequence sequence,
                                                                          IProfeatProperties.ATTRIBUTE attribute,
                                                                          IProfeatProperties.GROUPING group)
                                                                   throws Exception

Throws:

Exception

getDistributionPosition

Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>> getDistributionPosition(org.biojava.nbio.core.sequence.ProteinSequence sequence,
                                                                                                                 IProfeatProperties.ATTRIBUTE attribute)
                                                                                                          throws Exception

Throws:

Exception

getDistributionPosition

Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>> getDistributionPosition(org.biojava.nbio.core.sequence.ProteinSequence sequence)
                                                                                                                                                  throws Exception

Throws:

Exception