## 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
`Indexer2(File file, IndexStore indexStore, Index2Model model)` Build a new Indexer.

Method Summary
`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