public interface Sequence extends SymbolList, FeatureHolder, Annotatable
A biological sequence.
Sequence myDNA = DNATools.createDNASequence("ATTATTCGTG", "mySeq");
Sequence myFasta = SeqIOTools.readFastaProtein("mySeq.fa");
Sequence myGenbank = SeqIOTools.readGenbank("mySeq.gb");
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);
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.
TheRichSequence interface
offers considerably more functionality and better persitence to BioSQL than
it's super interface Sequence. We would recommend using it wherever possible.RichSequenceFeatureHolder.EmptyFeatureHolderAnnotatable.AnnotationForwarderEDIT, EMPTY_LISTEMPTY_FEATURE_HOLDER, FEATURES, SCHEMAANNOTATION| Modifier and Type | Method and Description |
|---|---|
String |
getName()
The name of this sequence.
|
String |
getURN()
A Uniform
Resource Identifier (URI) which identifies the sequence
represented by this object.
|
edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toListcontainsFeature, countFeatures, createFeature, features, filter, filter, getSchema, removeFeaturegetAnnotationaddChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListenerString getURN()
urn:sequence/embl:AL121903It 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
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