Package org.biojava.nbio.aaproperties.profeat

Interface IProfeatProperties

    • Method Detail

      • getComposition

        double getComposition​(ProteinSequence sequence,
                      IProfeatProperties.ATTRIBUTE attribute,
                      IProfeatProperties.GROUPING group)
               throws java.lang.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:
        java.lang.Exception - throws Exception if attribute or group are unknown

      • getTransition

        double getTransition​(ProteinSequence sequence,
                     IProfeatProperties.ATTRIBUTE attribute,
                     IProfeatProperties.TRANSITION transition)
              throws java.lang.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:
        java.lang.Exception - throws Exception if attribute or group are unknown

      • getDistributionPosition

        double getDistributionPosition​(ProteinSequence sequence,
                               IProfeatProperties.ATTRIBUTE attribute,
                               IProfeatProperties.GROUPING group,
                               IProfeatProperties.DISTRIBUTION distribution)
                        throws java.lang.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:
        java.lang.Exception - throws Exception if attribute or group are unknown