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 |
Enzyme.getParserListener(TagValueListener listener) |
ParserListener |
Ligand.Enzyme.getParserListener(TagValueListener listener) |
ParserListener |
Ligand.Reaction.getParserListener(TagValueListener listener) |
ParserListener |
Ligand.Compound.getParserListener(TagValueListener listener) |
ParserListener |
Swissprot.getParserListener(TagValueListener listener) |
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.
|
Modifier and Type | Interface and Description |
---|---|
interface |
TagValueWrapper
Interface for TagValueListeners that wrap other TagValueListeners
Implementations will tend to intercept the tags or values as they stream
through and modify them in some manner before forwarding them to the delegate
listener.
|
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 |
SimpleTagValueWrapper.getDelegate() |
TagValueListener |
TagValueWrapper.getDelegate()
get listener to which all calls will be delegated
|
TagValueListener |
AbstractWrapper.getDelegate() |
TagValueListener |
StateMachine.getDelegate() |
TagValueListener |
ParserListener.getListener()
getListener returns the listener of the pair. |
TagValueListener |
StateMachine.State.getListener() |
TagValueListener |
StateMachine.BasicState.getListener()
return the TagValueListener assigned to this State.
|
TagValueListener |
TagDelegator.getListener(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(BufferedReader reader,
TagValueParser parser,
TagValueListener listener) |
void |
SimpleTagValueWrapper.setDelegate(TagValueListener delegate) |
void |
TagValueWrapper.setDelegate(TagValueListener delegate)
set listener to which all calls will be delegated
|
void |
AbstractWrapper.setDelegate(TagValueListener delegate) |
void |
StateMachine.setDelegate(TagValueListener delegate)
TagValueWrapper interface
|
void |
TagDelegator.setListener(Object tag,
TagValueListener listener) |
void |
StateMachine.BasicState.setListener(TagValueListener listener)
set a TagValueListener for this State.
|
void |
TagDelegator.setParserListener(Object tag,
TagValueParser parser,
TagValueListener listener) |
Constructor and Description |
---|
Aggregator(TagValueListener listener,
BoundaryFinder observer,
String joiner) |
BasicState(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,
Pattern pattern,
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.
|
Copyright © 2020 BioJava. All rights reserved.