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java.lang.Objectorg.biojava.bio.seq.ragbag.RagbagIdleSequenceBuilder
A breakfast cereal of a SequenceBuilder, jes' sits there soakin' up all those events and doin' absolutely nuffin'.
Constructor Summary | |
RagbagIdleSequenceBuilder()
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Method Summary | |
void |
addFeatureProperty(java.lang.Object key,
java.lang.Object value)
Notify the listener of a feature property. |
void |
addProperty(Annotation ann,
java.lang.Object key,
java.lang.Object value)
|
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 pos,
int len)
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. |
Sequence |
makeSequence()
Return the Sequence object which has been constructed by this builder. |
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. |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
public RagbagIdleSequenceBuilder()
Method Detail |
public void startSequence()
SeqIOListener
startSequence
in interface SeqIOListener
public void endSequence()
SeqIOListener
endSequence
in interface SeqIOListener
public void setName(java.lang.String name)
SeqIOListener
setName
in interface SeqIOListener
public void setURI(java.lang.String uri)
SeqIOListener
setURI
in interface SeqIOListener
public void addSymbols(Alphabet alpha, Symbol[] syms, int pos, int len) throws IllegalAlphabetException
SeqIOListener
addSymbols
in interface SeqIOListener
alpha
- The alphabet of the symbol datasyms
- An array containing symbolspos
- The start offset of valid data within the arraylen
- The number of valid symbols in the array
IllegalAlphabetException
- if we can't cope with this
alphabet.public void addSequenceProperty(java.lang.Object key, java.lang.Object value)
SeqIOListener
addSequenceProperty
in interface SeqIOListener
public void startFeature(Feature.Template templ)
SeqIOListener
startFeature
in interface SeqIOListener
public void addFeatureProperty(java.lang.Object key, java.lang.Object value) throws ParseException
SeqIOListener
addFeatureProperty
in interface SeqIOListener
ParseException
public void endFeature()
SeqIOListener
endFeature
in interface SeqIOListener
public Sequence makeSequence()
SequenceBuilder
makeSequence
in interface SequenceBuilder
public void addProperty(Annotation ann, java.lang.Object key, java.lang.Object value)
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