Package org.biojava.nbio.core.util

Class SequenceTools

java.lang.Object
org.biojava.nbio.core.util.SequenceTools
public class SequenceTools extends Object

  • Field Details

  • Constructor Details

    • SequenceTools

      public SequenceTools()

  • Method Details

    • permuteCyclic

      public static String permuteCyclic(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(String sequence)

    • isNucleotideSequence

      public static boolean isNucleotideSequence(String sequence)

    • getSequenceFromString

      public Sequence<?> getSequenceFromString(String sequence) throws CompoundNotFoundException
      Throws:
      CompoundNotFoundException