public interface SeqIOListener
RichSeqIOListener
.RichSeqIOListener
Modifier and Type | Method and Description |
---|---|
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.
|
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 parsedParseException
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 arrayIllegalAlphabetException
- 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