net.obsearch.index.utils
Class AbstractCommandLine<O extends OB,I extends Index<O>,A extends Ambient<O,I>>

java.lang.Object
  net.obsearch.index.utils.AbstractCommandLine<O,I,A>

All Implemented Interfaces:

org.opt4j.core.problem.Evaluator<org.opt4j.benchmark.DoubleString>

Direct Known Subclasses:

AbstractNewLineCommandLine

public abstract class AbstractCommandLine<O extends OB,I extends Index<O>,A extends Ambient<O,I>>
extends Object
implements org.opt4j.core.problem.Evaluator<org.opt4j.benchmark.DoubleString>

Nested Class Summary

protected static class

AbstractCommandLine.Mode

Field Summary

protected double	approxEvalEp
protected double	approxEvalRecall
protected boolean	bulkMode
protected String	experimentName
protected String	experimentResultFileName
protected String	experimentSet
protected int	iterations Options related to opt4j optimization
protected int	k
protected int	maxQueries
protected AbstractCommandLine.Mode	mode
protected int	optNumChildren
protected int	optNumParents
protected int	optPopulationSize
protected int	pivots
protected Properties	props Properties that modify the behavior of this application.
protected int	queries Number of queries executed.
protected double	r
protected long	time Total ellapsed time during each query.
protected boolean	validate

Constructor Summary

AbstractCommandLine()

Method Summary

protected void	add()
protected abstract void	addObjects(I index, File load) Adds objects to the index.
protected void	closeAll(FileWriter[] files)
protected void	create()
org.opt4j.core.Objectives	evaluate(org.opt4j.benchmark.DoubleString config)
protected abstract String	expDetails()
protected String	expName()
protected abstract org.opt4j.core.problem.Creator<org.opt4j.benchmark.DoubleString>	getCreator() Returns the creator used to generate new configurations for this index.
protected I	getIndex()
Collection<org.opt4j.core.Objective>	getObjectives()
protected abstract AbstractCommandLine	getReference() Return the "this" reference, used to access all the command line options.
void	initProperties()
protected abstract A	instantiateAmbient(File dbFolder)
protected abstract A	instantiateNewAmbient(File dbFolder)
protected boolean	isApproxMode()
void	processUserCommands(String[] args) This method must be called by the children of this class.
protected void	search() Perform one search for a given k and r.
protected Pair<Statistics,Statistics>	searchAux()
protected abstract void	searchObjects(I index, File query, Statistics other) Opens a query file and queries the index storing all the results there.
protected abstract void	updateIndexConfig(org.opt4j.benchmark.DoubleString phenotype) Updates the configuration of the index with the given phenotype.
protected abstract void	updateParams() Updates the underlying index based on different parameters
protected void	writeAll(FileWriter[] files, String str)

Methods inherited from class java.lang.Object

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

Field Detail

props

protected Properties props

Properties that modify the behavior of this application.

pivots

protected int pivots

k

protected int k

mode

protected AbstractCommandLine.Mode mode

maxQueries

protected int maxQueries

experimentName

protected String experimentName

experimentResultFileName

protected String experimentResultFileName

bulkMode

protected boolean bulkMode

experimentSet

protected String experimentSet

r

protected double r

approxEvalEp

protected double approxEvalEp

approxEvalRecall

protected double approxEvalRecall

iterations

protected int iterations

Options related to opt4j optimization

optPopulationSize

protected int optPopulationSize

optNumParents

protected int optNumParents

optNumChildren

protected int optNumChildren

validate

protected boolean validate

queries

protected int queries

Number of queries executed.

time

protected long time

Total ellapsed time during each query.

Constructor Detail

AbstractCommandLine

public AbstractCommandLine()

Method Detail

initProperties

public void initProperties()
                    throws IOException

Throws:

IOException

getReference

protected abstract AbstractCommandLine getReference()

Return the "this" reference, used to access all the command line options.

Returns:

The reference of the bottommost class that contains parameters.

getIndex

protected I getIndex()

processUserCommands

public void processUserCommands(String[] args)

This method must be called by the children of this class.

Parameters:

thisReference - this reference of the subclass.

args - Arguments sent to the application.

instantiateNewAmbient

protected abstract A instantiateNewAmbient(File dbFolder)
                                                         throws OBStorageException,
                                                                OBException,
                                                                FileNotFoundException,
                                                                IllegalAccessException,
                                                                InstantiationException,
                                                                IOException

Throws:

OBStorageException

OBException

FileNotFoundException

IllegalAccessException

InstantiationException

IOException

instantiateAmbient

protected abstract A instantiateAmbient(File dbFolder)
                                                      throws OBStorageException,
                                                             OBException,
                                                             FileNotFoundException,
                                                             IllegalAccessException,
                                                             InstantiationException,
                                                             IOException

Throws:

OBStorageException

OBException

FileNotFoundException

IllegalAccessException

InstantiationException

IOException

addObjects

protected abstract void addObjects(I index,
                                   File load)
                            throws FileNotFoundException,
                                   IOException,
                                   OBStorageException,
                                   OBException,
                                   IllegalAccessException,
                                   InstantiationException

Adds objects to the index. Loads the objects from File.

Parameters:

index - Index to load the objects into.

load - File to load.

Throws:

FileNotFoundException

IOException

OBStorageException

OBException

IllegalAccessException

InstantiationException

searchObjects

protected abstract void searchObjects(I index,
                                      File query,
                                      Statistics other)
                               throws IOException,
                                      OBException,
                                      InstantiationException,
                                      IllegalAccessException

Opens a query file and queries the index storing all the results there.

Parameters:

index - The index to query.

query - The query to load.

Throws:

IOException

OBException

InstantiationException

IllegalAccessException

create

protected void create()
               throws IOException,
                      OBStorageException,
                      OBException,
                      com.sleepycat.je.DatabaseException,
                      InstantiationException,
                      IllegalAccessException,
                      PivotsUnavailableException

Throws:

IOException

OBStorageException

OBException

com.sleepycat.je.DatabaseException

InstantiationException

IllegalAccessException

PivotsUnavailableException

add

protected void add()
            throws IOException,
                   OBStorageException,
                   OBException,
                   com.sleepycat.je.DatabaseException,
                   InstantiationException,
                   IllegalAccessException

Throws:

IOException

OBStorageException

OBException

com.sleepycat.je.DatabaseException

InstantiationException

IllegalAccessException

getObjectives

public Collection<org.opt4j.core.Objective> getObjectives()

Specified by:

getObjectives in interface org.opt4j.core.problem.Evaluator<org.opt4j.benchmark.DoubleString>

getCreator

protected abstract org.opt4j.core.problem.Creator<org.opt4j.benchmark.DoubleString> getCreator()
                                                                                        throws OBException

Returns the creator used to generate new configurations for this index.

Returns:

a new creator

Throws:

OBException

evaluate

public org.opt4j.core.Objectives evaluate(org.opt4j.benchmark.DoubleString config)

Specified by:

evaluate in interface org.opt4j.core.problem.Evaluator<org.opt4j.benchmark.DoubleString>

updateIndexConfig

protected abstract void updateIndexConfig(org.opt4j.benchmark.DoubleString phenotype)

Updates the configuration of the index with the given phenotype.

Parameters:

phenotype -

expName

protected String expName()

writeAll

protected void writeAll(FileWriter[] files,
                        String str)
                 throws IOException

Throws:

IOException

closeAll

protected void closeAll(FileWriter[] files)
                 throws IOException

Throws:

IOException

updateParams

protected abstract void updateParams()

Updates the underlying index based on different parameters

searchAux

protected Pair<Statistics,Statistics> searchAux()
                                         throws IOException,
                                                OBStorageException,
                                                OBException,
                                                com.sleepycat.je.DatabaseException,
                                                InstantiationException,
                                                IllegalAccessException

Throws:

IOException

OBStorageException

OBException

com.sleepycat.je.DatabaseException

InstantiationException

IllegalAccessException

isApproxMode

protected boolean isApproxMode()

expDetails

protected abstract String expDetails()

search

protected void search()
               throws IOException,
                      OBStorageException,
                      OBException,
                      com.sleepycat.je.DatabaseException,
                      InstantiationException,
                      IllegalAccessException

Perform one search for a given k and r.

Throws:

IOException

OBStorageException

OBException

com.sleepycat.je.DatabaseException

InstantiationException

IllegalAccessException