org.biojava.bio.seq.io
Class SimpleAssemblyBuilder

java.lang.Object
  extended byorg.biojava.bio.seq.io.SequenceBuilderBase
      extended byorg.biojava.bio.seq.io.SimpleAssemblyBuilder
All Implemented Interfaces:
SeqIOListener, SequenceBuilder

public class SimpleAssemblyBuilder
extends SequenceBuilderBase

Basic SequenceBuilder implementation which accumulates all notified information and creates a SimpleAssembly.

Version:
1.2
Author:
David Huen

Field Summary
static SequenceBuilderFactory FACTORY
           
 
Fields inherited from class org.biojava.bio.seq.io.SequenceBuilderBase
ERROR_FEATURES_PROPERTY, seq
 
Constructor Summary
SimpleAssemblyBuilder()
           
 
Method Summary
 ComponentFeature addComponentSequence(ComponentFeature.Template cft)
           
 void addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len)
          Notify the listener of symbol data.
 Sequence makeSequence()
          Return the Sequence object which has been constructed by this builder.
 
Methods inherited from class org.biojava.bio.seq.io.SequenceBuilderBase
addFeatureProperty, addProperty, addSequenceProperty, endFeature, endSequence, setName, setURI, startFeature, startSequence
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

FACTORY

public static final SequenceBuilderFactory FACTORY
Constructor Detail

SimpleAssemblyBuilder

public SimpleAssemblyBuilder()
Method Detail

addSymbols

public void addSymbols(Alphabet alpha,
                       Symbol[] syms,
                       int pos,
                       int len)
                throws IllegalAlphabetException
Description copied from interface: SeqIOListener
Notify the listener of symbol data. All symbols passed to this method are guarenteed to be contained within the specified alphabet. Generally all calls to a given Listener should have the same alphabet -- if not, the listener implementation is likely to throw an exception

Specified by:
addSymbols in interface SeqIOListener
Specified by:
addSymbols in class SequenceBuilderBase
Throws:
IllegalAlphabetException

addComponentSequence

public ComponentFeature addComponentSequence(ComponentFeature.Template cft)
                                      throws BioException,
                                             ChangeVetoException
Throws:
BioException
ChangeVetoException

makeSequence

public Sequence makeSequence()
Description copied from interface: SequenceBuilder
Return the Sequence object which has been constructed by this builder. This method is only expected to succeed after the endSequence() notifier has been called.

Specified by:
makeSequence in interface SequenceBuilder
Overrides:
makeSequence in class SequenceBuilderBase