Package | Description |
---|---|
org.biojava.bio.annodb |
Databases of generic structured data (annotation) objects.
|
org.biojava.bio.program.formats |
Experimental parsers using the tagvalue framework.
|
org.biojava.bio.program.tagvalue |
Process files as streams of records, each with tags with values.
|
org.biojava.bio.program.unigene |
Objects for representing Unigene clusters.
|
Modifier and Type | Method and Description |
---|---|
ParserListener |
IndexedAnnotationDB.ParserListenerFactory.getParserListener(TagValueListener listener)
Get the ParserListener for a TagValueListener.
|
ParserListener |
IndexedAnnotationDB.StaticMethodRPFactory.getParserListener(TagValueListener tvl) |
Modifier and Type | Method and Description |
---|---|
ParserListener |
Embl.getParserListener(TagValueListener listener) |
ParserListener |
Format.getParserListener(TagValueListener listener)
Retrieve a ParserListener pair for the format that will pass all events
on to a listener.
|
ParserListener |
Enzyme.getParserListener(TagValueListener listener) |
ParserListener |
Swissprot.getParserListener(TagValueListener listener) |
ParserListener |
Ligand.Enzyme.getParserListener(TagValueListener listener) |
ParserListener |
Ligand.Reaction.getParserListener(TagValueListener listener) |
ParserListener |
Ligand.Compound.getParserListener(TagValueListener listener) |
Modifier and Type | Interface and Description |
---|---|
interface |
TagValueWrapper
Interface for TagValueListeners that wrap other TagValueListeners
|
Modifier and Type | Class and Description |
---|---|
class |
AbstractWrapper
An abstract TagValueWrapper that does nothing!
|
class |
Aggregator
Joins multipel values into single values.
|
class |
AnnotationBuilder
Builds an Annotation tree from TagValue events using an AnnotationType to
work out which fields are of what type.
|
class |
Echo
A simple listener that just echoes events back to the console.
|
class |
Indexer
Listens to tag-value events and passes on indexing events to an IndexStore.
|
class |
Indexer2
Listens to tag-value events and passes on indexing events to an IndexStore.
|
class |
MultiTagger
Partician multiple values for a tag into their own tag groups.
|
class |
RegexFieldFinder |
class |
SimpleTagValueWrapper
Helper class to wrap one TagValueListener inside another one.
|
class |
StateMachine
This class implements a state machine for parsing events from
the Parser class.
|
class |
StateMachine.SimpleStateListener
a basic listener for a State.
|
class |
TagDelegator
Pushes a new parser and listener, or delegate to a listener depending on the
tag.
|
class |
TagDropper
Silently drop all tags except those specified, and pass the rest onto a
delegate.
|
class |
TagRenamer
Rename tags using a TagMapper.
|
class |
ValueChanger
Intercept the values associated with some tags and change them
systematically.
|
Modifier and Type | Field and Description |
---|---|
protected TagValueListener |
StateMachine.delegate |
Modifier and Type | Method and Description |
---|---|
TagValueListener |
StateMachine.getDelegate() |
TagValueListener |
AbstractWrapper.getDelegate() |
TagValueListener |
SimpleTagValueWrapper.getDelegate() |
TagValueListener |
TagValueWrapper.getDelegate()
get listener to which all calls will be delegated
|
TagValueListener |
StateMachine.State.getListener() |
TagValueListener |
StateMachine.BasicState.getListener()
return the TagValueListener assigned to this State.
|
TagValueListener |
ParserListener.getListener()
getListener returns the listener of the pair. |
TagValueListener |
TagDelegator.getListener(java.lang.Object tag) |
Modifier and Type | Method and Description |
---|---|
static ParserListener |
Formats.createEmblParserListener(TagValueListener listener) |
static ParserListener |
Formats.createSwissprotParserListener(TagValueListener listener) |
void |
TagValueContext.pushParser(TagValueParser subParser,
TagValueListener subListener)
Push a parser and listener pair onto the parser stack.
|
boolean |
Parser.read(java.io.BufferedReader reader,
TagValueParser parser,
TagValueListener listener) |
void |
StateMachine.setDelegate(TagValueListener delegate)
TagValueWrapper interface
|
void |
AbstractWrapper.setDelegate(TagValueListener delegate) |
void |
SimpleTagValueWrapper.setDelegate(TagValueListener delegate) |
void |
TagValueWrapper.setDelegate(TagValueListener delegate)
set listener to which all calls will be delegated
|
void |
TagDelegator.setListener(java.lang.Object tag,
TagValueListener listener) |
void |
StateMachine.BasicState.setListener(TagValueListener listener)
set a TagValueListener for this State.
|
void |
TagDelegator.setParserListener(java.lang.Object tag,
TagValueParser parser,
TagValueListener listener) |
Constructor and Description |
---|
Aggregator(TagValueListener listener,
BoundaryFinder observer,
java.lang.String joiner) |
BasicState(java.lang.String label,
TagValueListener listener)
when this constructor is used, a fixed listener
is used with this state.
|
MultiTagger(TagValueListener listener,
BoundaryFinder observer) |
ParserListener(TagValueParser parser,
TagValueListener listener)
Creates a new
ParserListener instance. |
RegexFieldFinder(TagValueListener delegate,
java.util.regex.Pattern pattern,
java.lang.String[] tags,
boolean inLine)
Creates a new RegexFiledFinder.
|
SimpleTagValueWrapper(TagValueListener delegate)
Build a SimpleTagValueWrapper that will forward everything to a delegate.
|
TagDelegator(TagValueListener delegate) |
TagDropper(TagValueListener tvl)
Create a new TagDropper that will pass on all retained tags and values to
tvl.
|
TagRenamer(TagValueListener delegate,
PropertyChanger mapper)
Build a new TagRenamer with a delegate and mapper.
|
ValueChanger(TagValueListener delegate) |
ValueChanger(TagValueListener delegate,
ChangeTable changeTable)
Create a new changer that will pass the modified event stream to a
delegate.
|
Modifier and Type | Method and Description |
---|---|
static ParserListener |
UnigeneTools.buildDataParser(TagValueListener listener)
Generate a tag-value parser for unigene data files that will pass all
parsing events on to your listener.
|
static ParserListener |
UnigeneTools.buildLibInfoParser(TagValueListener listener)
Generate a tag-value parser for the library info unigene files.
|