AbstractEventReader

java.lang.Object
- info.bioinfweb.jphyloio.AbstractEventReader<P>

All Implemented Interfaces:

JPhyloIOEventReader, JPhyloIOFormatSpecificObject, ReadWriteConstants

Direct Known Subclasses:

AbstractTextEventReader, AbstractXMLEventReader
```
public abstract class AbstractEventReader<P extends ReaderStreamDataProvider<? extends AbstractEventReader<P>>>
extends java.lang.Object
implements JPhyloIOEventReader, ReadWriteConstants
```
Basic implementation for event readers in PhyloIO.

Author:

Ben Stöver

Field Summary
- Fields inherited from interface info.bioinfweb.jphyloio.ReadWriteConstants
  ATTRIBUTE_STRING_KEY, ATTRIBUTES_NAMESPACE_FOLDER, DATA_TYPE_NAMESPACE_FOLDER, DATA_TYPE_SIMPLE_VALUE_LIST, DEFAULT_CHAR_SET_ID_PREFIX, DEFAULT_CHARACTER_DEFINITION_ID_PREFIX, DEFAULT_EDGE_ID_PREFIX, DEFAULT_GENERAL_ID_PREFIX, DEFAULT_MATRIX_ID_PREFIX, DEFAULT_MAX_COMMENT_LENGTH, DEFAULT_MAX_TOKENS_TO_READ, DEFAULT_META_ID_PREFIX, DEFAULT_NETWORK_ID_PREFIX, DEFAULT_NODE_EDGE_SET_ID_PREFIX, DEFAULT_NODE_ID_PREFIX, DEFAULT_OTU_ID_PREFIX, DEFAULT_OTU_LIST_ID_PREFIX, DEFAULT_OTU_SET_ID_PREFIX, DEFAULT_SEQUENCE_ID_PREFIX, DEFAULT_SEQUENCE_SET_ID_PREFIX, DEFAULT_TOKEN_DEFINITION_ID_PREFIX, DEFAULT_TOKEN_SET_ID_PREFIX, DEFAULT_TREE_ID_PREFIX, DEFAULT_TREE_NETWORK_GROUP_ID_PREFIX, DEFAULT_TREE_NETWORK_SET_ID_PREFIX, JPHYLOIO_ATTRIBUTES_NAMESPACE, JPHYLOIO_ATTRIBUTES_PREFIX, JPHYLOIO_DATA_TYPE_NAMESPACE, JPHYLOIO_DATA_TYPE_PREFIX, JPHYLOIO_FORMATS_NAMESPACE_PREFIX, JPHYLOIO_GENERAL_NAMESPACE, JPHYLOIO_NAMESPACE_PREFIX, JPHYLOIO_PREDICATE_NAMESPACE, JPHYLOIO_PREDICATE_PREFIX, PREDICATE_CHARACTER_COUNT, PREDICATE_EDGE_LENGTH, PREDICATE_EDGE_SOURCE_NODE, PREDICATE_EDGE_TARGET_NODE, PREDICATE_HAS_CUSTOM_XML, PREDICATE_HAS_LITERAL_METADATA, PREDICATE_HAS_RESOURCE_METADATA, PREDICATE_IS_CROSSLINK, PREDICATE_NAMESPACE_FOLDER, PREDICATE_PART_SEPERATOR, PREDICATE_SEQUENCE_COUNT, RESERVED_ID_PREFIX

Constructor Summary

Constructors
Constructor and Description

AbstractEventReader(ReadWriteParameterMap parameters, java.lang.String matchToken)

Constructors
Constructor and Description
`AbstractEventReader(ReadWriteParameterMap parameters, java.lang.String matchToken)`

Method Summary

All Methods Instance Methods Abstract Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addEventListener(JPhyloIOEventListener listener)` Adds a `JPhyloIOEventListener` to the reader that will be informed on all events generated by this reader (e.g.
`void`	`close()` Closes the underlying document source (usually a stream).
`protected P`	`createStreamDataProvider()` This method is called in the constructor of `AbstractEventReader` to initialize the stream data provider that will be returned by `getStreamDataProvider()`.
`protected void`	`fireEvent(JPhyloIOEvent event)`
`protected java.util.Collection<JPhyloIOEvent>`	`getCurrentEventCollection()` Returns the event collection that is currently used to take up new events.
`protected LongIDManager`	`getIDManager()`
`JPhyloIOEvent`	`getLastNonCommentEvent()` Returns the last event that has been returned by previous calls of `readNextEvent()` that was not a comment event.
`protected ReadWriteParameterMap`	`getParameters()`
`ParentEventInformation`	`getParentInformation()` The returned object provides information on the start events fired by this reader until now.
`JPhyloIOEvent`	`getPreviousEvent()` Returns the event that has been returned by the previous call of `readNextEvent()`.
`protected SequenceTokensEventManager`	`getSequenceTokensEventManager()` Returns the manager object used by this instance to create `SequenceTokensEvent`s.
`protected P`	`getStreamDataProvider()`
`protected java.util.Queue<JPhyloIOEvent>`	`getUpcomingEvents()` Returns the queue to store events in, that shall be returned by upcoming calls of `next()`.
`boolean`	`hasNextEvent()` Checks if another event could be parsed from the underlying document.
`protected boolean`	`hasSpecialEventCollection()` Determines whether the current event collection is different from the queue of upcoming events.
`protected boolean`	`isBeforeFirstAccess()` Indicates whether there have been any previous calls of `readNextEvent()` since the last call of `#reset()`.
`JPhyloIOEvent`	`next()` Returns the next event from the underlying document and moves one step forward.
`JPhyloIOEvent`	`nextOfType(java.util.Set<EventType> types)` Reads elements from the underlying stream until one of the specified is found or the end of the document is reached.
`JPhyloIOEvent`	`peek()` Returns the event from the underlying document that will be returned in the next call of `JPhyloIOEventReader.next()` without moving forward.
`protected abstract void`	`readNextEvent()` Method to be implemented be inherited classes that adds at least one additional event (determined from the underlying data source) to the event queue.
`void`	`removeEventListener(JPhyloIOEventListener listener)` Removes a `JPhyloIOEventListener` from the reader.
`protected java.util.Collection<JPhyloIOEvent>`	`resetCurrentEventCollection()` Removes the event collection at the top of the eventCollections stack and returns it.
`protected java.util.Collection<JPhyloIOEvent>`	`setCurrentEventCollection(java.util.Collection<JPhyloIOEvent> newCollection)` Adds a new current event collection to the stack.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface info.bioinfweb.jphyloio.JPhyloIOFormatSpecificObject
getFormatID

- Constructor Detail
  - AbstractEventReader
```
public AbstractEventReader(ReadWriteParameterMap parameters,
                           java.lang.String matchToken)
```
- Method Detail
  - getParentInformation
```
public ParentEventInformation getParentInformation()
```
    The returned object provides information on the start events fired by this reader until now. It allows applications to determine information on the nesting of the current event.
    
    Specified by:
    
    getParentInformation in interface JPhyloIOEventReader
    
    Returns:
    
    the parent information object
  - createStreamDataProvider
```
protected P createStreamDataProvider()
```
    This method is called in the constructor of AbstractEventReader to initialize the stream data provider that will be returned by getStreamDataProvider(). Inherit classes that use their own stream data provider implementation should overwrite this method.
    This default implementation creates a new instance of ReaderStreamDataProvider.
    
    Returns:
    
    the stream data provider to be used with this instance
  - getStreamDataProvider
```
protected P getStreamDataProvider()
```
  - getParameters
```
protected ReadWriteParameterMap getParameters()
```
  - resetCurrentEventCollection
```
protected java.util.Collection<JPhyloIOEvent> resetCurrentEventCollection()
```
    Removes the event collection at the top of the eventCollections stack and returns it.
    
    Returns:
    
    the removed event collection
  - setCurrentEventCollection
```
protected java.util.Collection<JPhyloIOEvent> setCurrentEventCollection(java.util.Collection<JPhyloIOEvent> newCollection)
```
    Adds a new current event collection to the stack.
    
    Parameters:
    
    newCollection - the new collection to take up new events from now on
    
    Returns:
    
    the event collection that was previously at the top of the stack
    
    Throws:
    
    java.lang.NullPointerException - if newCollection is null
  - getCurrentEventCollection
```
protected java.util.Collection<JPhyloIOEvent> getCurrentEventCollection()
```
    Returns the event collection that is currently used to take up new events.
    
    Returns:
    
    the current event collection
  - hasSpecialEventCollection
```
protected boolean hasSpecialEventCollection()
```
    Determines whether the current event collection is different from the queue of upcoming events.
    
    Returns:
    
    false if getCurrentEventCollection() returns the same instance as getUpcomingEvents() or true otherwise
  - getUpcomingEvents
```
protected java.util.Queue<JPhyloIOEvent> getUpcomingEvents()
```
    Returns the queue to store events in, that shall be returned by upcoming calls of next().
    Note that new events should generally be added to getCurrentEventCollection() instead.
    
    Returns:
    
    the queue of upcoming events
  - getIDManager
```
protected LongIDManager getIDManager()
```
  - getSequenceTokensEventManager
```
protected SequenceTokensEventManager getSequenceTokensEventManager()
```
    Returns the manager object used by this instance to create SequenceTokensEvents. Such events should always be created using the returned object by inherited classes and never directly.
    
    Returns:
    
    the character event manager used by this instance (never null)
  - fireEvent
```
protected void fireEvent(JPhyloIOEvent event)
                  throws java.io.IOException
```
    Throws:
    
    java.io.IOException
  - getPreviousEvent
```
public JPhyloIOEvent getPreviousEvent()
```
    Returns the event that has been returned by the previous call of readNextEvent().
    
    Specified by:
    
    getPreviousEvent in interface JPhyloIOEventReader
    
    Returns:
    
    the previous event or null if there was no previous call of readNextEvent()
    
    See Also:
    
    JPhyloIOEventReader.getLastNonCommentEvent()
  - getLastNonCommentEvent
```
public JPhyloIOEvent getLastNonCommentEvent()
```
    Returns the last event that has been returned by previous calls of readNextEvent() that was not a comment event.
    
    Specified by:
    
    getLastNonCommentEvent in interface JPhyloIOEventReader
    
    Returns:
    
    the last non-comment event or null if no non-comment event was returned until now
    
    See Also:
    
    JPhyloIOEventReader.getPreviousEvent()
  - isBeforeFirstAccess
```
protected boolean isBeforeFirstAccess()
```
    Indicates whether there have been any previous calls of readNextEvent() since the last call of #reset().
    This method in meant for internal use in readNextEvent().
    
    Returns:
    
    true if there were no previous calls, false otherwise
  - hasNextEvent
```
public boolean hasNextEvent()
                     throws java.io.IOException
```
    Description copied from interface: JPhyloIOEventReader
    
    Checks if another event could be parsed from the underlying document.
    
    Specified by:
    
    hasNextEvent in interface JPhyloIOEventReader
    
    Returns:
    
    true if another event is waiting, false if the end of the underlying document was reached
    
    Throws:
    
    java.io.IOException
  - next
```
public JPhyloIOEvent next()
                   throws java.io.IOException
```
    Description copied from interface: JPhyloIOEventReader
    
    Returns the next event from the underlying document and moves one step forward.
    
    Specified by:
    
    next in interface JPhyloIOEventReader
    
    Returns:
    
    the next event object
    
    Throws:
    
    java.io.IOException - Implementing classes might throw additional exceptions
  - nextOfType
```
public JPhyloIOEvent nextOfType(java.util.Set<EventType> types)
                         throws java.io.IOException
```
    Description copied from interface: JPhyloIOEventReader
    
    Reads elements from the underlying stream until one of the specified is found or the end of the document is reached. All elements of other types are consumed and ignored.
    
    Specified by:
    
    nextOfType in interface JPhyloIOEventReader
    
    Parameters:
    
    types - a set of valid types to be returned
    
    Returns:
    
    the next element of the specified type or null if end of the file was reached before an according element was found
    
    Throws:
    
    java.io.IOException - Implementing classes might throw additional exceptions
  - peek
```
public JPhyloIOEvent peek()
                   throws java.io.IOException
```
    Description copied from interface: JPhyloIOEventReader
    
    Returns the event from the underlying document that will be returned in the next call of JPhyloIOEventReader.next() without moving forward.
    
    Specified by:
    
    peek in interface JPhyloIOEventReader
    
    Returns:
    
    the next event object
    
    Throws:
    
    java.io.IOException - Implementing classes might throw additional exceptions
  - addEventListener
```
public void addEventListener(JPhyloIOEventListener listener)
```
    Description copied from interface: JPhyloIOEventReader
    
    Adds a JPhyloIOEventListener to the reader that will be informed on all events generated by this reader (e.g. when its #next() method is called).
    Registering listeners here allows to combine pull- and push-parsing in a single implementation. Note that EventForwarder will usually be more useful for sole push-parsing implementations.
    Internal tool classes may also use this method to listen to events.
    
    Specified by:
    
    addEventListener in interface JPhyloIOEventReader
    
    Parameters:
    
    listener - the listener that shall be added
  - removeEventListener
```
public void removeEventListener(JPhyloIOEventListener listener)
```
    Description copied from interface: JPhyloIOEventReader
    
    Removes a JPhyloIOEventListener from the reader.
    
    Specified by:
    
    removeEventListener in interface JPhyloIOEventReader
    
    Parameters:
    
    listener - the listener that shall be removed
  - readNextEvent
```
protected abstract void readNextEvent()
                               throws java.io.IOException
```
    Method to be implemented be inherited classes that adds at least one additional event (determined from the underlying data source) to the event queue.
    
    Throws:
    
    java.io.IOException
  - close
```
public void close()
           throws java.io.IOException
```
    Description copied from interface: JPhyloIOEventReader
    
    Closes the underlying document source (usually a stream).
    
    Specified by:
    
    close in interface JPhyloIOEventReader
    
    Throws:
    
    java.io.IOException - Implementing classes might throw different types of exceptions if the stream cannot be closed properly

Class AbstractEventReader<P extends ReaderStreamDataProvider<? extends AbstractEventReader<P>>>

Field Summary

Fields inherited from interface info.bioinfweb.jphyloio.ReadWriteConstants

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface info.bioinfweb.jphyloio.JPhyloIOFormatSpecificObject

Constructor Detail

AbstractEventReader

Method Detail

getParentInformation

createStreamDataProvider

getStreamDataProvider

getParameters

resetCurrentEventCollection

setCurrentEventCollection

getCurrentEventCollection

hasSpecialEventCollection

getUpcomingEvents

getIDManager

getSequenceTokensEventManager

fireEvent

getPreviousEvent

getLastNonCommentEvent

isBeforeFirstAccess

hasNextEvent

next

nextOfType

peek

addEventListener

removeEventListener

readNextEvent

close