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.