org.biojava.bio.seq.io
Class SimpleAssemblyBuilder
java.lang.Object
org.biojava.bio.seq.io.SequenceBuilderBase
org.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
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
FACTORY
public static final SequenceBuilderFactory FACTORY
SimpleAssemblyBuilder
public SimpleAssemblyBuilder()
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