org.biojava3.aaproperties.profeat
Class ProfeatProperties

java.lang.Object
  extended by org.biojava3.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:
IProfeatProperties, ProfeatPropertiesImpl

Constructor Summary
ProfeatProperties()
           
 
Method Summary
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,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,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.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.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.
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)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

ProfeatProperties

public ProfeatProperties()
Method Detail

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