Class Indexer
- java.lang.Object
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- org.biojava.bio.program.tagvalue.Indexer
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- 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
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Constructor Summary
Constructors Constructor Description Indexer(File file, IndexStore indexStore)
Build a new Indexer.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addSecondaryKey(String secKeyName)
Add a secondary key.void
endRecord()
The current record has ended.void
endTag()
End the current tag.String
getPrimaryKeyName()
Retrieve the tag currently used as primary key.CountedBufferedReader
getReader()
Retrieve the reader that can be safely used to index this file.void
removeSecondaryKey(String secKeyName)
Remove a secondary key.void
setPrimaryKeyName(String primaryKeyName)
Set the tag to use as a primary key in the index.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.
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Constructor Detail
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Indexer
public Indexer(File file, IndexStore indexStore) throws FileNotFoundException
Build a new Indexer.- Parameters:
file
- the file to be processedindexStore
- the IndexStore to write to- Throws:
FileNotFoundException
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Method Detail
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getReader
public CountedBufferedReader getReader()
Retrieve the reader that can be safely used to index this file.- Returns:
- the CountedBufferedReader that should be processed
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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
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getPrimaryKeyName
public String getPrimaryKeyName()
Retrieve the tag currently used as primary key.- Returns:
- a String representing the primary key name
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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
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removeSecondaryKey
public void removeSecondaryKey(String secKeyName)
Remove a secondary key.- Parameters:
secKeyName
- the name of the secondary key to remove
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startRecord
public void startRecord()
Description copied from interface:TagValueListener
A new record is about to start.- Specified by:
startRecord
in interfaceTagValueListener
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startTag
public void startTag(Object tag)
Description copied from interface:TagValueListener
Start a new tag.- Specified by:
startTag
in interfaceTagValueListener
- Parameters:
tag
- the Object representing the new tag
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value
public void value(TagValueContext ctxt, Object value)
Description copied from interface:TagValueListener
A value has been seen.- Specified by:
value
in interfaceTagValueListener
- Parameters:
ctxt
- a TagValueContext that could be used to push a sub-documentvalue
- the value Object observed
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endTag
public void endTag()
Description copied from interface:TagValueListener
End the current tag.- Specified by:
endTag
in interfaceTagValueListener
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endRecord
public void endRecord() throws ParserException
Description copied from interface:TagValueListener
The current record has ended.- Specified by:
endRecord
in interfaceTagValueListener
- Throws:
ParserException
- if the record can not be ended
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