org.biojava.bio.program.tagvalue

Class Indexer2

java.lang.Object

org.biojava.bio.program.tagvalue.Indexer2

All Implemented Interfaces:

TagValueListener

public class Indexer2
extends Object
implements TagValueListener

Listens to tag-value events and passes on indexing events to an IndexStore. This is an update to Indexer that understands that indexed properties may not be at the top level.

This class is provided to allow the indexing of arbitrary record-based text files. Indexer objects are built for a single file and the indexes are written to a single index store. To keep all of the reader offsets in sync with one another, you will almost certainly wish to use the getReader() method to retrieve a CountedBufferedReader instance if you want to read the byte-offset between calls to Parser.read(). Below is an example of how to index a file.

 File fileToIndex; // get this from somewhere

 // don't forget to register all the apropreate keys to the factory first.
 BioIndexStore indexStore = bioIndxStrFact.createBioStore();

 Indexer indexer = new Indexer(fileToIndex, indexStore);
 indexer.setPrimaryKeyName("foo", new String[] { "foo" });
 indexer.addSecondaryKey("bar", new String[] { "x", "y", "bar"});
 indexer.addSecondaryKey("baz", new String[] { "z" });

 TagValueParser tvParser; // make this appropriate for your format
 TagValueListener listener; // make this appropriate for your format
                            // and forward all events to indexer
 
 Parser parser = new Parser();
 while(
   parser.read(indexer.getReader(), tvParser, listener)
 ) {
   System.out.print(".");
 }
 

Since:

1.2

Author:

Matthew Pocock

Constructor Summary

Constructors

Constructor and Description
Indexer2(File file, IndexStore indexStore, Index2Model model) Build a new Indexer.

Method Summary

Methods

Modifier and Type	Method and Description
void	endRecord() The current record has ended.
void	endTag() End the current tag.
CountedBufferedReader	getReader() Retrieve the reader that can be safely used to index this file.
void	startRecord() A new record is about to start.
void	startTag(Object tag) Start a new tag.
void	value(TagValueContext ctxt, Object value) A value has been seen.

Methods inherited from class java.lang.Object

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

Constructor Detail

Indexer2

public Indexer2(File file,
        IndexStore indexStore,
        Index2Model model)
         throws FileNotFoundException

Build a new Indexer.

Parameters:

file - the file to be processed

indexStore - the IndexStore to write to

Throws:

FileNotFoundException

Method Detail

getReader

public CountedBufferedReader getReader()

Retrieve the reader that can be safely used to index this file.

Returns:

the CountedBufferedReader that should be processed

startRecord

public void startRecord()

Description copied from interface: TagValueListener

A new record is about to start.

Specified by:

startRecord in interface TagValueListener

startTag

public void startTag(Object tag)

Description copied from interface: TagValueListener

Start a new tag.

Specified by:

startTag in interface TagValueListener

Parameters:

tag - the Object representing the new tag

value

public void value(TagValueContext ctxt,
         Object value)

Description copied from interface: TagValueListener

A value has been seen.

Specified by:

value in interface TagValueListener

Parameters:

ctxt - a TagValueContext that could be used to push a sub-document

value - the value Object observed

endTag

public void endTag()

Description copied from interface: TagValueListener

End the current tag.

Specified by:

endTag in interface TagValueListener

endRecord

public void endRecord()
               throws ParserException

Description copied from interface: TagValueListener

The current record has ended.

Specified by:

endRecord in interface TagValueListener

Throws:

ParserException - if the record can not be ended