Package org.biojava.nbio.core.sequence.template

Class SequenceMixin

java.lang.Object
org.biojava.nbio.core.sequence.template.SequenceMixin
public class SequenceMixin extends Object
Provides a set of static methods to be used as static imports when needed across multiple Sequence implementations but inheritance gets in the way. It also provides a place to put utility methods whose application can be to a single class of Sequence e.g. NucleotideCompound Sequence; or to any Sequence e.g. looking for the getComposition(Sequence) or getDistribution(Sequence) for any type of Sequence. All of these methods assume that you can use the Iterable interface offered by the implementations of Sequence to provide all the compounds that implementation allows you to see. Since sequence should know nothing about its backing stores (apart from calling out to it) this should be true.
Author:
ayates

  • Constructor Details

    • SequenceMixin

      public SequenceMixin()

  • Method Details

    • countCompounds

      public static <C extends Compound> int countCompounds(Sequence<C> sequence, C... compounds)
      For the given vargs of compounds this method counts the number of times those compounds appear in the given sequence
      Type Parameters:
      C - The type of compound we are looking for
      Parameters:
      sequence - The Sequence to perform the count on
      compounds - The compounds to look for
      Returns:
      The number of times the given compounds appear in this Sequence

    • countGC

      public static int countGC(Sequence<NucleotideCompound> sequence)
      Returns the count of GC in the given sequence
      Parameters:
      sequence - The NucleotideCompound Sequence to perform the GC analysis on
      Returns:
      The number of GC compounds in the sequence

    • countAT

      public static int countAT(Sequence<NucleotideCompound> sequence)
      Returns the count of AT in the given sequence
      Parameters:
      sequence - The NucleotideCompound Sequence to perform the AT analysis on
      Returns:
      The number of AT compounds in the sequence

    • getDistribution

      public static <C extends Compound> Map<C,Double> getDistribution(Sequence<C> sequence)
      Analogous to getComposition(Sequence) but returns the distribution of that Compound over the given sequence.
      Type Parameters:
      C - The type of compound to look for
      Parameters:
      sequence - The type of sequence to look over
      Returns:
      Returns the decimal fraction of the compounds in the given sequence. Any compound not in the Map will return a fraction of 0.

    • getComposition

      public static <C extends Compound> Map<C,Integer> getComposition(Sequence<C> sequence)
      Does a linear scan over the given Sequence and records the number of times each base appears. The returned map will return 0 if a compound is asked for and the Map has no record of it.
      Type Parameters:
      C - The type of compound to look for
      Parameters:
      sequence - The type of sequence to look over
      Returns:
      Counts for the instances of all compounds in the sequence

    • write

      public static <C extends Compound> void write(Appendable appendable, Sequence<C> sequence) throws IOException
      Used as a way of sending a Sequence to a writer without the cost of converting to a full length String and then writing the data out
      Type Parameters:
      C - Type of compound
      Parameters:
      writer - The writer to send data to
      sequence - The sequence to write out
      Throws:
      IOException - Thrown if we encounter a problem

    • toStringBuilder

      public static <C extends Compound> StringBuilder toStringBuilder(Sequence<C> sequence)
      For the given Sequence this will return a StringBuilder object filled with the results of Compound#toString(). Does not used write(java.lang.Appendable, org.biojava.nbio.core.sequence.template.Sequence) because of its IOException signature.

    • toString

      public static <C extends Compound> String toString(Sequence<C> sequence)
      Shortcut to toStringBuilder(org.biojava.nbio.core.sequence.template.Sequence) which calls toString() on the resulting object.

    • toList

      public static <C extends Compound> List<C> toList(Sequence<C> sequence)
      For the given Sequence this will return a List filled with the Compounds of that Sequence.

    • indexOf

      public static <C extends Compound> int indexOf(Sequence<C> sequence, C compound)
      Performs a linear search of the given Sequence for the given compound. Once we find the compound we return the position.

    • lastIndexOf

      public static <C extends Compound> int lastIndexOf(Sequence<C> sequence, C compound)
      Performs a reversed linear search of the given Sequence by wrapping it in a ReversedSequenceView and passing it into indexOf(Sequence, Compound). We then inverse the index coming out of it.

    • createIterator

      public static <C extends Compound> Iterator<C> createIterator(Sequence<C> sequence)
      Creates a simple sequence iterator which moves through a sequence going from 1 to the length of the Sequence. Modification of the Sequence is not allowed.

    • createSubSequence

      public static <C extends Compound> SequenceView<C> createSubSequence(Sequence<C> sequence, int start, int end)
      Creates a simple sub sequence view delimited by the given start and end.

    • shuffle

      public static <C extends Compound> Sequence<C> shuffle(Sequence<C> sequence)
      Implements sequence shuffling by first materializing the given Sequence into a List, applying Collections.shuffle(List) and then returning the shuffled elements in a new instance of SequenceBackingStore which behaves as a Sequence.

    • checksum

      public static <C extends Compound> String checksum(Sequence<C> sequence)
      Performs a simple CRC64 checksum on any given sequence.

    • nonOverlappingKmers

      public static <C extends Compound> List<SequenceView<C>> nonOverlappingKmers(Sequence<C> sequence, int kmer)
      Produces kmers of the specified size e.g. ATGTGA returns two views which have ATG TGA
      Type Parameters:
      C - Compound to use
      Parameters:
      sequence - Sequence to build from
      kmer - Kmer size
      Returns:
      The list of non-overlapping K-mers

    • overlappingKmers

      public static <C extends Compound> List<SequenceView<C>> overlappingKmers(Sequence<C> sequence, int kmer)
      Used to generate overlapping k-mers such i.e. ATGTA will give rise to ATG, TGT & GTA
      Type Parameters:
      C - Compound to use
      Parameters:
      sequence - Sequence to build from
      kmer - Kmer size
      Returns:
      The list of overlapping K-mers

    • inverse

      public static <C extends Compound> SequenceView<C> inverse(Sequence<C> sequence)
      A method which attempts to do the right thing when is comes to a reverse/reverse complement
      Type Parameters:
      C - The type of compound
      Parameters:
      sequence - The input sequence
      Returns:
      The inverted sequence which is optionally complemented

    • sequenceEqualityIgnoreCase

      public static <C extends Compound> boolean sequenceEqualityIgnoreCase(Sequence<C> source, Sequence<C> target)
      A case-insensitive manner of comparing two sequence objects together. We will throw out any compounds which fail to match on their sequence length & compound sets used. The code will also bail out the moment we find something is wrong with a Sequence. Cost to run is linear to the length of the Sequence.
      Type Parameters:
      C - The type of compound
      Parameters:
      source - Source sequence to assess
      target - Target sequence to assess
      Returns:
      Boolean indicating if the sequences matched ignoring case

    • sequenceEquality

      public static <C extends Compound> boolean sequenceEquality(Sequence<C> source, Sequence<C> target)
      A case-sensitive manner of comparing two sequence objects together. We will throw out any compounds which fail to match on their sequence length & compound sets used. The code will also bail out the moment we find something is wrong with a Sequence. Cost to run is linear to the length of the Sequence.
      Type Parameters:
      C - The type of compound
      Parameters:
      source - Source sequence to assess
      target - Target sequence to assess
      Returns:
      Boolean indicating if the sequences matched