info.bioinfweb.jphyloio.formats.text

Class TextSequenceContentReceiver<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>>

java.lang.Object

info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver<P>

info.bioinfweb.jphyloio.dataadapters.implementations.receivers.AbstractSequenceContentReceiver<P>

info.bioinfweb.jphyloio.formats.text.TextSequenceContentReceiver<P>

All Implemented Interfaces:

JPhyloIOEventReceiver

public class TextSequenceContentReceiver<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>>
extends AbstractSequenceContentReceiver<P>

Receiver that writes all encountered sequence tokens and comments to the current line and ignores all metadata. Comments can also be ignored, of null is specified as the comment start token.

It will log an according warning, if comments need to be edited (e.g. because they contain character that are reserved in the target format).

Since:

0.0.0

Author:

Ben Stöver

Constructor Summary

Constructors

Constructor and Description
TextSequenceContentReceiver(P streamDataProvider, ReadWriteParameterMap parameterMap, boolean longTokens, java.lang.String commentStart, java.lang.String commentEnd)

Method Summary

Modifier and Type	Method and Description
protected void	handleComment(CommentEvent event)
protected void	handleToken(java.lang.String token, java.lang.String label) Creates a new instance of this class.

Methods inherited from class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.AbstractSequenceContentReceiver

doAdd, isLongTokens

Methods inherited from class info.bioinfweb.jphyloio.dataadapters.implementations.receivers.BasicEventReceiver

add, addIgnoredComments, addIgnoredLiteralMetadata, addIgnoredResourceMetadata, addIgnoreLogMessage, didIgnoreComments, didIgnoreLiteralMetadata, didIgnoreMetadata, didIgnoreResourceMetadata, getIgnoredComments, getIgnoredLiteralMetadata, getIgnoredMetadata, getIgnoredResourceMetadata, getLogger, getParameterMap, getParentEvent, getParentEvents, getStreamDataProvider, handleLiteralContentMeta, handleLiteralMetaStart, handleMetaEndEvent, handleResourceMetaStart, isInComment

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

TextSequenceContentReceiver

public TextSequenceContentReceiver(P streamDataProvider,
                                   ReadWriteParameterMap parameterMap,
                                   boolean longTokens,
                                   java.lang.String commentStart,
                                   java.lang.String commentEnd)

Method Detail

handleToken

protected void handleToken(java.lang.String token,
                           java.lang.String label)
                    throws java.io.IOException

Creates a new instance of this class.

Specified by:

handleToken in class AbstractSequenceContentReceiver<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>>

Parameters:

writer - the writer to write the sequence to

parameterMap - the parameter map specified to the calling event writer

commentStart - a comment start token or null, if this writer shall ignore comment events

commentEnd - a comment end token or null, if this writer shall ignore comment events

longTokens - Specify true here if sequence tokens shall be separated by spaces (if one token may be longer than one character) or false otherwise.

Throws:

java.io.IOException

handleComment

protected void handleComment(CommentEvent event)
                      throws java.io.IOException,
                             javax.xml.stream.XMLStreamException

Overrides:

handleComment in class BasicEventReceiver<P extends TextWriterStreamDataProvider<? extends AbstractTextEventWriter<P>>>

Throws:

java.io.IOException

javax.xml.stream.XMLStreamException