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public interface SeqIOListener
Notification interface for objects which listen to a sequence stream
parser.
More functionality is offered by the
RichSeqIOListener
.
RichSeqIOListener
Method Summary | |
---|---|
void |
addFeatureProperty(java.lang.Object key,
java.lang.Object value)
Notify the listener of a feature property. |
void |
addSequenceProperty(java.lang.Object key,
java.lang.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. |
void |
setName(java.lang.String name)
Notify the listener that the current sequence is generally known by a particular name. |
void |
setURI(java.lang.String uri)
Notify the listener of a URI identifying the current sequence. |
void |
startFeature(Feature.Template templ)
Notify the listener that a new feature object is starting. |
void |
startSequence()
Start the processing of a sequence. |
Method Detail |
---|
void startSequence() throws ParseException
ParseException
void endSequence() throws ParseException
ParseException
void setName(java.lang.String name) throws ParseException
name
- the String that should be returned by getName for the sequence
being parsed
ParseException
void setURI(java.lang.String uri) throws ParseException
ParseException
void addSymbols(Alphabet alpha, Symbol[] syms, int start, int length) throws IllegalAlphabetException
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 array
IllegalAlphabetException
- if we can't cope with this
alphabet.void addSequenceProperty(java.lang.Object key, java.lang.Object value) throws ParseException
ParseException
void startFeature(Feature.Template templ) throws ParseException
ParseException
void endFeature() throws ParseException
ParseException
void addFeatureProperty(java.lang.Object key, java.lang.Object value) throws ParseException
ParseException
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