org.biojava.bio.seq
Interface Sequence
- All Superinterfaces:
- Annotatable, Changeable, FeatureHolder, SymbolList
- All Known Subinterfaces:
- GappedSequence
- All Known Implementing Classes:
- DummySequence, org.biojava.bio.seq.ragbag.RagbagAbstractSequence, SimpleAssembly, SimpleGappedSequence, SimpleSequence, SubSequence, 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.
- Author:
- Matthew Pocock, Thomas Down
getURN
public java.lang.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
public java.lang.String getName()
- The name of this sequence.
The name may contain spaces or odd characters.
- Returns:
- the name as a String