Class RichSequence.Tools

java.lang.Object
org.biojavax.bio.seq.RichSequence.Tools
Enclosing interface:
RichSequence

public static class RichSequence.Tools extends Object
Some useful tools for working with RichSequence objects.
Since:
1.5
  • Method Details

    • createRichSequence

      public static RichSequence createRichSequence(String name, String seqString, Alphabet alpha) throws BioException
      Create a new RichSequence in the default namespace.
      Parameters:
      name - The name for the sequence. Will also be used for the accession.
      seqString - The sequence string
      alpha - The Alphabet for the sequence
      Returns:
      A new RichSequence. All versions are 1 or 1.0
      Throws:
      BioException - If the symbols in seqString are not valid in alpha
    • createRichSequence

      public static RichSequence createRichSequence(String namespace, String name, String seqString, Alphabet alpha) throws BioException
      Create a new RichSequence in the specified namespace.
      Parameters:
      namespace - the namespace to create the sequence in. A singleton Namespace will be created or retrieved as appropriate.
      name - The name for the sequence. Will also be used for the accession.
      seqString - The sequence string
      alpha - The Alphabet for the sequence
      Returns:
      A new RichSequence. All versions are 1 or 1.0
      Throws:
      BioException - If the symbols in seqString are not valid in alpha
    • createRichSequence

      public static RichSequence createRichSequence(Namespace ns, String name, String seqString, Alphabet alpha) throws BioException
      Create a new RichSequence in the specified namespace.
      Parameters:
      ns - The namespace to create the sequence in.
      name - The name for the sequence. Will also be used for the accession.
      seqString - The sequence string
      alpha - The Alphabet for the sequence
      Returns:
      A new RichSequence. All versions are 1 or 1.0
      Throws:
      BioException - If the symbols in seqString are not valid in alpha
    • createRichSequence

      public static RichSequence createRichSequence(String name, SymbolList syms)
      Create a new RichSequence in the default namespace.
      Parameters:
      name - The name for the sequence. Will also be used for the accession.
      syms - The symbols to add to the sequence.
      Returns:
      A new RichSequence. All versions are 1 or 1.0
    • createRichSequence

      public static RichSequence createRichSequence(Namespace ns, String name, SymbolList syms)
      Create a new RichSequence in the specified namespace.
      Parameters:
      ns - the namespace to create the sequence in.
      name - The name for the sequence. Will also be used for the accession.
      syms - The symbols to add to the sequence.
      Returns:
      A new RichSequence. All versions are 1 or 1.0
    • enrich

      public static RichSequence enrich(Sequence s) throws ChangeVetoException
      Boldly attempts to convert a Sequence into a RichSequence. Sequences will be assigned to the default namespace. The accession will be assumed to be the name of the old sequence. The version of the sequence will be set to 0 and the seqversion set to 0.0. Features are converted to RichFeatures. The old Annotation bundle is converted to a RichAnnotation
      Parameters:
      s - The Sequence to enrich
      Returns:
      a new RichSequence
      Throws:
      ChangeVetoException - if s is locked or the conversion fails.
    • subSequence

      public static RichSequence subSequence(RichSequence s, int from, int to, Namespace newNamespace, String newName, String newAccession, String newIdentifier, int newVersion, Double seqVersion) throws IndexOutOfBoundsException

      Creates a new sequence from a subregion of another sequence. The sequence is not a view. The sequence can be given a new Namespace, Accession, Name, Identifier etc. or you can copy over the old values. For unique identification in databases we recommend you change at least the name and identifier.

      The new sequence will retain all features that are fully contained by the new subsequence, the note set (annotation), Taxon, and description, modified to reflect the subsequence as follows:

       seq.setDescription("subsequence (" + from + ":" + to + ") of "
                      + s.getDescription());
       
      No other properties are copied.
      Parameters:
      s - the original RichSequence.
      from - the 1st subsequence coordinate (inclusive)
      to - the last subsequence coordinate (inclusive)
      newNamespace - the new Namespace
      newName - the new name
      newAccession - the new accession number
      newIdentifier - the new identifier
      newVersion - the new version number
      seqVersion - the new sequence version
      Returns:
      A new RichSequence
      Throws:
      IndexOutOfBoundsException - if from or to lie outside of the bounds of s.