Package com.biomatters.geneious.publicapi.documents.sequence

Class SequenceBuilder

  • public class SequenceBuilder
extends java.lang.Object
    Provides methods for creating CharSequences for use as biological sequences.

    • Constructor Detail

      • SequenceBuilder

        public SequenceBuilder()

    • Method Detail

      • isCompactCharSequence

        public static boolean isCompactCharSequence​(java.lang.CharSequence charSequence)
        Returns:
        true if this charSequence is a compact sequence produced by one of the methods in this class (e.g. createCompactCharSequence(CharSequence))
        Since:
        API 4.900 (Geneious 9.0.0)

      • createCompactCharSequence

        public static SequenceCharSequence createCompactCharSequence​(java.lang.CharSequence charSequence)
        Equivalent to createCompactCharSequence(charSequence, false)
        Parameters:
        charSequence - the charSequence to create a compact version of
        Returns:
        a memory compacted char sequence, or the original char sequence wrapped in a SequenceCharSequence if it can not be compacted

      • createCompactCharSequence

        public static SequenceCharSequence createCompactCharSequence​(java.lang.CharSequence charSequence,
                                                             boolean removeGaps)
        Creates a charSequence which uses a minimal amount of memory to represent the given charSequence by analyzing the contents and returning an appropriate CharSequence implementation. (e.g. a charSequence backed by 2-bit sequence characters for sequences only containing ACGT)
        Parameters:
        charSequence - the charSequence to return a memory compacted version of.
        removeGaps - if the original sequence contained gaps, removes them in the returned sequence.
        Returns:
        a memory compacted char sequence, or the original char sequence wrapped in a SequenceCharSequence if it can not be compacted
        Since:
        API 4.40 (Geneious 5.4.0)