de.lmu.ifi.dbs.elki.database.connection
Class AbstractDatabaseConnection<O extends DatabaseObject>

java.lang.Object
  de.lmu.ifi.dbs.elki.logging.AbstractLoggable
      de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizable
          de.lmu.ifi.dbs.elki.database.connection.AbstractDatabaseConnection<O>

Type Parameters:

O - the type of DatabaseObject to be provided by the implementing class as element of the supplied database

All Implemented Interfaces:

DatabaseConnection<O>, Parameterizable

Direct Known Subclasses:

InputStreamDatabaseConnection, MultipleFileBasedDatabaseConnection

public abstract class AbstractDatabaseConnection<O extends DatabaseObject>
extends AbstractParameterizable
implements DatabaseConnection<O>

Abstract super class for all database connections. AbstractDatabaseConnection already provides the setting of the database according to parameters.

Author:

Elke Achtert

Field Summary

static OptionID	CLASS_LABEL_CLASS_ID OptionID for CLASS_LABEL_CLASS_PARAM
private ClassParameter<ClassLabel>	CLASS_LABEL_CLASS_PARAM Parameter to specify the association of occurring class labels, must extend ClassLabel.
static OptionID	CLASS_LABEL_INDEX_ID OptionID for CLASS_LABEL_INDEX_PARAM
private IntParameter	CLASS_LABEL_INDEX_PARAM Optional parameter that specifies the index of the label to be used as class label, must be an integer equal to or greater than 0.
private String	classLabelClass Holds the value of CLASS_LABEL_CLASS_PARAM.
protected Integer	classLabelIndex Holds the value of CLASS_LABEL_INDEX_PARAM, null if no class label is specified.
(package private) Database<O>	database Holds the instance of the database specified by DATABASE_PARAM.
static OptionID	DATABASE_ID OptionID for DATABASE_PARAM
private ClassParameter<Database<O>>	DATABASE_PARAM Parameter to specify the database to be provided by the parse method, must extend Database.
static OptionID	EXTERNAL_ID_INDEX_ID OptionID for EXTERNAL_ID_INDEX_PARAM
private IntParameter	EXTERNAL_ID_INDEX_PARAM Optional parameter that specifies the index of the label to be used as an external id, must be an integer equal to or greater than 0.
private Integer	externalIDIndex Holds the value of EXTERNAL_ID_INDEX_PARAM.
(package private) boolean	forceExternalID True, if an external label needs to be set.
static String	LABEL_CONCATENATION A sign to separate components of a label.

Fields inherited from class de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizable

optionHandler

Fields inherited from class de.lmu.ifi.dbs.elki.logging.AbstractLoggable

debug, logger

Constructor Summary

protected

AbstractDatabaseConnection() Adds parameters DATABASE_PARAM, CLASS_LABEL_INDEX_PARAM, CLASS_LABEL_CLASS_PARAM, and EXTERNAL_ID_INDEX_PARAM, to the option handler additionally to parameters of super class.

Method Summary

protected List<Pair<O,Associations>>	normalizeAndTransformLabels(List<Pair<O,List<String>>> objectAndLabelsList, Normalization<O> normalization) Normalizes and transforms the specified list of objects and their labels into a list of objects and their associations.
List<String>	setParameters(List<String> args) Calls the super method and sets additionally the value of the parameters CLASS_LABEL_INDEX_PARAM, CLASS_LABEL_CLASS_PARAM, and EXTERNAL_ID_INDEX_PARAM and instantiates database according to the value of parameter DATABASE_PARAM.
private List<Pair<O,Associations>>	transformLabels(List<Pair<O,List<String>>> objectAndLabelsList) Transforms the specified list of objects and their labels into a list of objects and their associations.

Methods inherited from class de.lmu.ifi.dbs.elki.utilities.optionhandling.AbstractParameterizable

addOption, addParameterizable, addParameterizable, checkGlobalParameterConstraints, collectOptions, getAttributeSettings, getParameters, rememberParametersExcept, removeOption, removeParameterizable, shortDescription

Methods inherited from class de.lmu.ifi.dbs.elki.logging.AbstractLoggable

debugFine, debugFiner, debugFinest, exception, progress, verbose, warning

Methods inherited from class java.lang.Object

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

Methods inherited from interface de.lmu.ifi.dbs.elki.database.connection.DatabaseConnection

getDatabase

Methods inherited from interface de.lmu.ifi.dbs.elki.utilities.optionhandling.Parameterizable

checkGlobalParameterConstraints, collectOptions, getParameters, shortDescription

Field Detail

LABEL_CONCATENATION

public static final String LABEL_CONCATENATION

A sign to separate components of a label.

See Also:

Constant Field Values

DATABASE_ID

public static final OptionID DATABASE_ID

OptionID for DATABASE_PARAM

DATABASE_PARAM

private final ClassParameter<Database<O extends DatabaseObject>> DATABASE_PARAM

Parameter to specify the database to be provided by the parse method, must extend Database.

Default value: SequentialDatabase

Key: -dbc.database

database

Database<O extends DatabaseObject> database

Holds the instance of the database specified by DATABASE_PARAM.

CLASS_LABEL_INDEX_ID

public static final OptionID CLASS_LABEL_INDEX_ID

OptionID for CLASS_LABEL_INDEX_PARAM

CLASS_LABEL_INDEX_PARAM

private final IntParameter CLASS_LABEL_INDEX_PARAM

Optional parameter that specifies the index of the label to be used as class label, must be an integer equal to or greater than 0.

Key: -dbc.classLabelIndex

classLabelIndex

protected Integer classLabelIndex

Holds the value of CLASS_LABEL_INDEX_PARAM, null if no class label is specified.

CLASS_LABEL_CLASS_ID

public static final OptionID CLASS_LABEL_CLASS_ID

OptionID for CLASS_LABEL_CLASS_PARAM

CLASS_LABEL_CLASS_PARAM

private final ClassParameter<ClassLabel> CLASS_LABEL_CLASS_PARAM

Parameter to specify the association of occurring class labels, must extend ClassLabel.

Default value: SimpleClassLabel

Key: -dbc.classLabelClass

classLabelClass

private String classLabelClass

Holds the value of CLASS_LABEL_CLASS_PARAM.

EXTERNAL_ID_INDEX_ID

public static final OptionID EXTERNAL_ID_INDEX_ID

OptionID for EXTERNAL_ID_INDEX_PARAM

EXTERNAL_ID_INDEX_PARAM

private final IntParameter EXTERNAL_ID_INDEX_PARAM

Optional parameter that specifies the index of the label to be used as an external id, must be an integer equal to or greater than 0.

Key: -dbc.externalIDIndex

externalIDIndex

private Integer externalIDIndex

Holds the value of EXTERNAL_ID_INDEX_PARAM.

forceExternalID

boolean forceExternalID

True, if an external label needs to be set. Default is false.

Constructor Detail

AbstractDatabaseConnection

protected AbstractDatabaseConnection()

Adds parameters DATABASE_PARAM, CLASS_LABEL_INDEX_PARAM, CLASS_LABEL_CLASS_PARAM, and EXTERNAL_ID_INDEX_PARAM, to the option handler additionally to parameters of super class.

Method Detail

setParameters

public List<String> setParameters(List<String> args)
                           throws ParameterException

Calls the super method and sets additionally the value of the parameters CLASS_LABEL_INDEX_PARAM, CLASS_LABEL_CLASS_PARAM, and EXTERNAL_ID_INDEX_PARAM and instantiates database according to the value of parameter DATABASE_PARAM. The remaining parameters are passed to the database.

Specified by:

setParameters in interface Parameterizable

Overrides:

setParameters in class AbstractParameterizable

Parameters:

args - parameters to set the attributes accordingly to

Returns:

a list containing the unused parameters

Throws:

ParameterException - in case of wrong parameter-setting

normalizeAndTransformLabels

protected List<Pair<O,Associations>> normalizeAndTransformLabels(List<Pair<O,List<String>>> objectAndLabelsList,
                                                                 Normalization<O> normalization)
                                                                                 throws NonNumericFeaturesException

Normalizes and transforms the specified list of objects and their labels into a list of objects and their associations.

Parameters:

objectAndLabelsList - the list of object and their labels to be transformed

normalization - the normalization to be applied

Returns:

a list of normalized objects and their associations

Throws:

NonNumericFeaturesException - if any exception occurs during normalization

transformLabels

private List<Pair<O,Associations>> transformLabels(List<Pair<O,List<String>>> objectAndLabelsList)

Transforms the specified list of objects and their labels into a list of objects and their associations.

Parameters:

objectAndLabelsList - the list of object and their labels to be transformed

Returns:

a list of objects and their associations