Package org.biojava.bio.seq

Interface Sequence

  • All Superinterfaces:
    Annotatable, Changeable, FeatureHolder, SymbolList
    All Known Subinterfaces:
    GappedSequence, RichSequence
    All Known Implementing Classes:
    CircularView, DummySequence, NewSimpleAssembly, PhredSequence, RevCompSequence, SimpleAssembly, SimpleGappedSequence, SimpleRichSequence, SimpleSequence, SubSequence, ThinRichSequence, ViewSequence
    public interface Sequence
extends SymbolList, FeatureHolder, Annotatable

    A biological sequence.

    Instantiation

     Sequence myDNA = DNATools.createDNASequence("ATTATTCGTG", "mySeq");
 Sequence myFasta = SeqIOTools.readFastaProtein("mySeq.fa");
 Sequence myGenbank = SeqIOTools.readGenbank("mySeq.gb");

    Common operations

     System.out.println("Length: " + myGenbank.length());
 System.out.println("Features: " + myGenbank.countFeatures());
 for(Iterator fi = myGenbank.features(); fi.hasNext(); ) {
   Feature f = (Feature) fi.next();
   System.out.println(f.getType() + "\t" + f.getLocation());
 }

 // create a new feature on a sequence
 StrandedFeature.Template ft = new StrandedFeature.Template();
 ft.type = "span";
 ft.location = new RangeLocation(230, 450);
 ft.source = "hand_made";
 ft.strand = StrandedFeature.NEGATIVE;

 StrandedFeature newSpan = (StrandedFeature) mySeq.createFeature(ft);

    Description

    This interface is a symbol list, so it contains symbols. It is annotatable so that you can add annotation to it, and it is a FeatureHolder so that you can add information about specific regions.

    It is expected that there may be several implementations of this interface, each of which may be fairly heavy-weight. It takes the SymbolList interface that is nice mathematically, and turns it into a biologically useful object.

    The RichSequence interface offers considerably more functionality and better persitence to BioSQL than it's super interface Sequence. We would recommend using it wherever possible.
    Author:
    Matthew Pocock, Thomas Down
    See Also:
    RichSequence

    • Method Detail

      • getURN

        String getURN()
        A Uniform Resource Identifier (URI) which identifies the sequence represented by this object. For sequences in well-known database, this may be a URN, e.g. 
         urn:sequence/embl:AL121903
        It may also be a URL identifying a specific resource, either locally or over the network 
         file:///home/thomas/myseq.fa|seq22
 http://www.mysequences.net/chr22.seq
        Returns:
        the URI as a String

      • getName

        String getName()
        The name of this sequence.

        The name may contain spaces or odd characters.

        Returns:
        the name as a String