org.biojava3.aaproperties.profeat
Interface IProfeatProperties

All Known Implementing Classes:
ProfeatPropertiesImpl

public interface IProfeatProperties


Nested Class Summary
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
 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.
 

Method Detail

getComposition

double getComposition(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(ProteinSequence sequence,
                                                       IProfeatProperties.ATTRIBUTE attribute)
                                                       throws Exception
Throws:
Exception

getComposition

Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Double>> getComposition(ProteinSequence sequence)
                                                                                         throws Exception
Throws:
Exception

getTransition

double getTransition(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(ProteinSequence sequence,
                                                        IProfeatProperties.ATTRIBUTE attribute)
                                                        throws Exception
Throws:
Exception

getTransition

Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.TRANSITION,Double>> getTransition(ProteinSequence sequence)
                                                                                          throws Exception
Throws:
Exception

getDistributionPosition

double getDistributionPosition(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(ProteinSequence sequence,
                                                                    IProfeatProperties.ATTRIBUTE attribute,
                                                                    IProfeatProperties.GROUPING group)
                                                                    throws Exception
Throws:
Exception

getDistributionPosition

Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>> getDistributionPosition(ProteinSequence sequence,
                                                                                                     IProfeatProperties.ATTRIBUTE attribute)
                                                                                                     throws Exception
Throws:
Exception

getDistributionPosition

Map<IProfeatProperties.ATTRIBUTE,Map<IProfeatProperties.GROUPING,Map<IProfeatProperties.DISTRIBUTION,Double>>> getDistributionPosition(ProteinSequence sequence)
                                                                                                                                       throws Exception
Throws:
Exception