org.biojava.bio.seq
Interface Sequence

All Known Implementing Classes:
AceSequence, SimpleSequence, ViewSequence, SequenceAdapter

public interface Sequence
extends SymbolList, FeatureHolder, Annotatable

A sequence.

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 mathematicaly, and turns it into a biologicaly useful object.

Author:
Matthew Pocock, Thomas Down

Inner classes inherited from class org.biojava.bio.symbol.SymbolList
SymbolList.EmptySymbolList
 
Inner classes inherited from class org.biojava.bio.seq.FeatureHolder
FeatureHolder.EmptyFeatureHolder
 
Fields inherited from interface org.biojava.bio.symbol.SymbolList
EMPTY_LIST
 
Fields inherited from interface org.biojava.bio.seq.FeatureHolder
EMPTY_FEATURE_HOLDER
 
Method Summary
 java.lang.String getName()
          The name of this sequence.
 java.lang.String getURN()
          The URN for this sequence.
 
Methods inherited from interface org.biojava.bio.symbol.SymbolList
getAlphabet, iterator, length, seqString, subList, subStr, symbolAt, toList
 
Methods inherited from interface org.biojava.bio.seq.FeatureHolder
countFeatures, createFeature, features, filter, removeFeature
 
Methods inherited from interface org.biojava.bio.Annotatable
getAnnotation
 

Method Detail

getURN

public java.lang.String getURN()
The URN for this sequence. This will be something like urn:sequence/embl:U32766 or urn:sequence/fasta:sequences.fasta|hox3.
Returns:
the urn 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