Package org.biojava.bio.program.tagvalue

Class Indexer

  • All Implemented Interfaces:
    TagValueListener
    public class Indexer
extends Object
implements TagValueListener

    Listens to tag-value events and passes on indexing events to an IndexStore.

    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.

    Note: It is very important to configure the BioStoreFactory instance with all the right keys before hand.

     File fileToIndex; // get this from somewhere
 BioStore store = bsf.createBioStore();
 Indexer indexer = new Indexer(fileToIndex, store);
 indexer.setPrimaryKeyName("foo");
 indexer.addSecondaryKey("bar");
 indexer.addSecondaryKey("baz");

 TagValueParser tvParser; // make this appropriate for your format
 TagValueListener listener; // make this appropriate for your format
                            // and forward all events to changer
 
 Parser parser = new Parser();
 while(
   parser.read(indexer.getReader(), tvParser, listener)
 ) {
   System.out.print(".");
 }
    Since:
    1.2
    Author:
    Matthew Pocock

    • 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

      • setPrimaryKeyName

        public void setPrimaryKeyName​(String primaryKeyName)

        Set the tag to use as a primary key in the index.

        Whenever a value for the primary key tag is seen, this is passed to the indexer as the primary key for indexing.

        Primary keys must be unique between entries, and each entry must provide exactly one primary key value.

        Parameters:
        primaryKeyName - the tag to use as primary key

      • getPrimaryKeyName

        public String getPrimaryKeyName()
        Retrieve the tag currently used as primary key.
        Returns:
        a String representing the primary key name

      • addSecondaryKey

        public void addSecondaryKey​(String secKeyName)

        Add a secondary key.

        Secondary keys are potentially non-unique properties of the entries being indexed. Multiple records can use the same secondary key values, and a single record can have multiple values for a secondary key.

        Parameters:
        secKeyName - the name of the secondary key to add

      • removeSecondaryKey

        public void removeSecondaryKey​(String secKeyName)
        Remove a secondary key.
        Parameters:
        secKeyName - the name of the secondary key to remove