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
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.
TheRichSequence
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:
-
Nested Class Summary
Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable
Annotatable.AnnotationForwarder
Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolder
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Field Summary
Fields inherited from interface org.biojava.bio.Annotatable
ANNOTATION
Fields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA
Fields inherited from interface org.biojava.bio.symbol.SymbolList
EDIT, EMPTY_LIST
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Method Summary
Modifier and TypeMethodDescriptiongetName()
The name of this sequence.getURN()
A Uniform Resource Identifier (URI) which identifies the sequence represented by this object.Methods inherited from interface org.biojava.bio.Annotatable
getAnnotation
Methods inherited from interface org.biojava.utils.Changeable
addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener
Methods inherited from interface org.biojava.bio.seq.FeatureHolder
containsFeature, countFeatures, createFeature, features, filter, filter, getSchema, removeFeature
Methods inherited from interface org.biojava.bio.symbol.SymbolList
edit, getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList
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Method Details
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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 networkfile:///home/thomas/myseq.fa|seq22 http://www.mysequences.net/chr22.seq
- Returns:
- the URI as a String
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getName
The name of this sequence.The name may contain spaces or odd characters.
- Returns:
- the name as a String
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