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java.lang.Objectorg.biojava.bio.seq.io.SequenceBuilderBase
Basic SequenceBuilder implementation which accumulates all notified information. Subclass this to implement specific Sequence implementations.
Field Summary | |
protected Annotation |
annotation
|
static java.lang.Object |
ERROR_FEATURES_PROPERTY
|
protected java.lang.String |
name
|
protected Sequence |
seq
|
protected java.lang.String |
uri
|
Constructor Summary | |
SequenceBuilderBase()
|
Method Summary | |
void |
addFeatureProperty(java.lang.Object key,
java.lang.Object value)
Add an annotation-bundle entry to the feature. |
protected void |
addProperty(Annotation ann,
java.lang.Object key,
java.lang.Object value)
|
void |
addSequenceProperty(java.lang.Object key,
java.lang.Object value)
Add an annotation-bundle entry to the sequence. |
abstract 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 |
Field Detail |
public static java.lang.Object ERROR_FEATURES_PROPERTY
protected java.lang.String name
protected java.lang.String uri
protected Annotation annotation
protected Sequence seq
Constructor Detail |
public SequenceBuilderBase()
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 abstract 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)
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
addFeatureProperty
in interface SeqIOListener
ParseException
public void endFeature()
SeqIOListener
endFeature
in interface SeqIOListener
public Sequence makeSequence()
SequenceBuilder
makeSequence
in interface SequenceBuilder
protected void addProperty(Annotation ann, java.lang.Object key, java.lang.Object value)
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