public class SequenceBuilderFilter extends Object implements SequenceBuilder
RichSeqIOAdapter
Constructor and Description |
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SequenceBuilderFilter(SequenceBuilder delegate)
Create a new SeqIOFilter that will forward events on to another listener.
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Modifier and Type | Method and Description |
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void |
addFeatureProperty(Object key,
Object value)
Notify the listener of a feature property.
|
void |
addSequenceProperty(Object key,
Object value)
Notify the listener of a sequence-wide property.
|
void |
addSymbols(Alphabet alpha,
Symbol[] syms,
int start,
int length)
Notify the listener of symbol data.
|
void |
endFeature()
Mark the end of data associated with one specific feature.
|
void |
endSequence()
Notify the listener that processing of the sequence is complete.
|
SequenceBuilder |
getDelegate()
Retrieve the delegate that is wrapped.
|
Sequence |
makeSequence()
Return the Sequence object which has been constructed
by this builder.
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void |
setName(String name)
Notify the listener that the current sequence is generally known
by a particular name.
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void |
setURI(String uri)
Notify the listener of a URI identifying the current sequence.
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void |
startFeature(Feature.Template templ)
Notify the listener that a new feature object is starting.
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void |
startSequence()
Start the processing of a sequence.
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public SequenceBuilderFilter(SequenceBuilder delegate)
delegate
- the SequenceBuilder to wrappublic SequenceBuilder getDelegate()
public void startSequence() throws ParseException
SeqIOListener
startSequence
in interface SeqIOListener
ParseException
public void endSequence() throws ParseException
SeqIOListener
endSequence
in interface SeqIOListener
ParseException
public void setName(String name) throws ParseException
SeqIOListener
setName
in interface SeqIOListener
name
- the String that should be returned by getName for the sequence
being parsedParseException
public void setURI(String uri) throws ParseException
SeqIOListener
setURI
in interface SeqIOListener
ParseException
public void addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) throws IllegalAlphabetException
SeqIOListener
addSymbols
in interface SeqIOListener
alpha
- The alphabet of the symbol datasyms
- An array containing symbolsstart
- The start offset of valid data within the arraylength
- The number of valid symbols in the arrayIllegalAlphabetException
- if we can't cope with this
alphabet.public void addSequenceProperty(Object key, Object value) throws ParseException
SeqIOListener
addSequenceProperty
in interface SeqIOListener
ParseException
public void startFeature(Feature.Template templ) throws ParseException
SeqIOListener
startFeature
in interface SeqIOListener
ParseException
public void endFeature() throws ParseException
SeqIOListener
endFeature
in interface SeqIOListener
ParseException
public void addFeatureProperty(Object key, Object value) throws ParseException
SeqIOListener
addFeatureProperty
in interface SeqIOListener
ParseException
public Sequence makeSequence() throws BioException
SequenceBuilder
makeSequence
in interface SequenceBuilder
BioException
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