Package org.biojava.nbio.core.util

Class SequenceTools

  • public class SequenceTools
extends java.lang.Object

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected static java.lang.String NUCLEOTIDE_LETTERS  

    • Constructor Summary

      Constructors 
      Constructor Description
      SequenceTools()  

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      static boolean equalLengthSequences​(ProteinSequence[] sequences)
      A method to check whether an array of sequences contains at least two sequences having an equal length.
      Sequence<?> getSequenceFromString​(java.lang.String sequence)
      Attempts to parse String as a DNA sequence first.
      If this fails it tries to parse as a ProteinSequence.
      static boolean isNucleotideSequence​(java.lang.String sequence)  
      static int percentNucleotideSequence​(java.lang.String sequence)  
      static java.lang.String permuteCyclic​(java.lang.String string, int n)
      Cyclically permute the characters in string forward by n elements.
      static <T> void permuteCyclic​(T[] array, T[] fill, int n)
      Cyclically permute array forward by n elements.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • NUCLEOTIDE_LETTERS

        protected static final java.lang.String NUCLEOTIDE_LETTERS
        See Also:
        Constant Field Values

    • Constructor Detail

      • SequenceTools

        public SequenceTools()

    • Method Detail

      • permuteCyclic

        public static java.lang.String permuteCyclic​(java.lang.String string,
                                             int n)
        Cyclically permute the characters in string forward by n elements.
        Parameters:
        string - The string to permute
        n - The number of characters to permute by; can be positive or negative; values greater than the length of the array are acceptable

      • permuteCyclic

        public static <T> void permuteCyclic​(T[] array,
                                     T[] fill,
                                     int n)
        Cyclically permute array forward by n elements.
        Parameters:
        array - The original result; will not be changed
        fill - The permuted result will be filled into this array
        n - The number of elements to permute by; can be positive or negative; values greater than the length of the array are acceptable

      • percentNucleotideSequence

        public static int percentNucleotideSequence​(java.lang.String sequence)

      • isNucleotideSequence

        public static boolean isNucleotideSequence​(java.lang.String sequence)

      • getSequenceFromString

        public Sequence<?> getSequenceFromString​(java.lang.String sequence)
                                  throws CompoundNotFoundException
        Attempts to parse String as a DNA sequence first.
        If this fails it tries to parse as a ProteinSequence.
        This method does not attempt to create an RNASequence.

        Also, a sequence such as 'ATCGTA' which is both a peptide sequence and a DNA sequence, will always be returned as a DNA sequence.

        An empty string argument returns a ProteinSequence of length 0. A null argument throws a NullPointerException

        Parameters:
        sequence -
        Returns:
        Either a DNASequence or a ProteinSequence
        Throws:
        CompoundNotFoundException

      • equalLengthSequences

        public static boolean equalLengthSequences​(ProteinSequence[] sequences)
        A method to check whether an array of sequences contains at least two sequences having an equal length.
        Parameters:
        sequences - the array of ProteinSequence sequences
        Returns:
        true if any two sequences are of an equal length