Package org.biojava.nbio.aaproperties

Class Utils

  • public class Utils
extends Object
    This is a utility class that contains utility methods which will facilitates the coding of other methods
    Since:
    3.0.2
    Version:
    2011.08.22
    Author:
    kohchuanhock

    • Constructor Detail

    • Method Detail

      • roundToDecimals

        public static final double roundToDecimals​(double d,
                                           int c)
        Returns a value with the desired number of decimal places.
        Parameters:
        d - value to round
        c - number of decimal places desired. Must be greater or equal to zero, otherwise, the given value d would be returned without any modification.
        Returns:
        a value with the given number of decimal places.

      • doesSequenceContainInvalidChar

        public static final boolean doesSequenceContainInvalidChar​(String sequence,
                                                           Set<Character> cSet)
        Checks if given sequence contains invalid characters. Returns true if invalid characters are found, else return false. Note that any characters are deemed as valid only if it is found in cSet.
        Parameters:
        sequence - protein sequence to be check.
        cSet - the set of characters that are deemed valid.
        Returns:
        true if invalid characters are found, else return false.

      • getNumberOfInvalidChar

        public static final int getNumberOfInvalidChar​(String sequence,
                                               Set<Character> cSet,
                                               boolean ignoreCase)
        Return the number of invalid characters in sequence.
        Parameters:
        sequence - protein sequence to count for invalid characters.
        cSet - the set of characters that are deemed valid.
        ignoreCase - indicates if cases should be ignored
        Returns:
        the number of invalid characters in sequence.

      • cleanSequence

        public static final String cleanSequence​(String sequence,
                                         Set<Character> cSet)
        Returns a new sequence with all invalid characters being replaced by '-'. Note that any character outside of the 20 standard protein amino acid codes are considered as invalid.
        Parameters:
        sequence - protein sequence to be clean
        cSet - user defined characters that are valid. Can be null. If null, then 20 standard protein amino acid codes will be considered as valid.
        Returns:
        a new sequence with all invalid characters being replaced by '-'.

      • checkSequence

        public static final String checkSequence​(String sequence)
        Checks if the sequence contains invalid characters. Note that any character outside of the 20 standard protein amino acid codes are considered as invalid. If yes, it will return a new sequence where invalid characters are replaced with '-'. If no, it will simply return the input sequence.
        Parameters:
        sequence - protein sequence to be check for invalid characters.
        Returns:
        a sequence with no invalid characters.

      • checkSequence

        public static final String checkSequence​(String sequence,
                                         Set<Character> cSet)
        Checks if the sequence contains invalid characters. Note that any character outside of the 20 standard protein amino acid codes are considered as invalid. If yes, it will return a new sequence where invalid characters are replaced with '-'. If no, it will simply return the input sequence.
        Parameters:
        sequence - protein sequence to be check for invalid characters.
        cSet - character set which define the valid characters.
        Returns:
        a sequence with no invalid characters.