ambit2.rest.model.predictor

Class ModelPredictor<Predictor,NativeTypeItem>

java.lang.Object

net.idea.modbcum.p.DefaultAmbitProcessor<Target,Result>

net.idea.modbcum.p.AbstractDBProcessor<NativeTypeItem,IStructureRecord>

ambit2.rest.model.predictor.ModelPredictor<Predictor,NativeTypeItem>

Type Parameters:

NativeTypeItem -

All Implemented Interfaces:

IStructureDiagramDepiction<BufferedImage>, IStructureDiagramHighlights, Serializable, net.idea.modbcum.i.IDBProcessor<NativeTypeItem,IStructureRecord>, net.idea.modbcum.i.processors.IProcessor<NativeTypeItem,IStructureRecord>

Direct Known Subclasses:

AbstractStructureProcessor, CoveragePredictor, DescriptorPredictor, ExpertModelpredictor, ExternalModelPredictor, FilteredWekaPredictor, WekaPredictor

public abstract class ModelPredictor<Predictor,NativeTypeItem>
extends net.idea.modbcum.p.AbstractDBProcessor<NativeTypeItem,IStructureRecord>
implements IStructureDiagramHighlights

Abstract class for all predictive models TODO - refactor to avoid weka dependence! weka models should be subclassed

Author:

nina

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
protected org.restlet.data.Reference	applicationRootReference
protected int	classIndex
protected weka.filters.Filter	filter
protected weka.core.Instances	header
protected Dimension	imageSize
protected ModelQueryResults	model
protected ModelURIReporter	modelReporter
protected PropertyURIReporter	propertyReporter
protected IStructureRecord	record
protected boolean	structureRequired
protected String[]	targetURI
protected boolean	valuesRequired

Fields inherited from class net.idea.modbcum.p.AbstractDBProcessor

closeConnection, connection

Fields inherited from class net.idea.modbcum.p.DefaultAmbitProcessor

enabled, logger, propertyChangeSupport

Constructor Summary

Constructors

Constructor and Description
ModelPredictor(org.restlet.data.Reference applicationRootReference, ModelQueryResults model, ModelURIReporter modelReporter, PropertyURIReporter propertyReporter, String[] targetURI)

Method Summary

Modifier and Type	Method and Description
void	assignResults(IStructureRecord record, Object value)
Predictor	createPredictor(ModelQueryResults model)
String	createResultReference()
protected void	extractRecordID(NativeTypeItem target, String url, IStructureRecord record)
protected int	getClassIndex(org.restlet.data.Form form)
abstract String	getCompoundURL(NativeTypeItem target)
protected weka.core.Instances	getHeader(org.restlet.data.Form form)
BufferedImage	getImage(org.openscience.cdk.interfaces.IAtomContainer mol)
BufferedImage	getImage(org.openscience.cdk.interfaces.IAtomContainer mol, String ruleID, int width, int height, boolean atomnumbers)
Dimension	getImageSize()
BufferedImage	getLegend(int width, int height)
ModelQueryResults	getModel()
ModelURIReporter	getModelReporter()
Predictor	getPredictor()
PropertyURIReporter	getPropertyReporter()
boolean	isStructureRequired()
protected boolean	isSupported(Object predictor)
boolean	isValuesRequired()
void	open()
abstract Object	predict(NativeTypeItem target)
IStructureRecord	process(NativeTypeItem target)
void	setImageSize(Dimension imageSize)
void	setModelReporter(ModelURIReporter modelReporter)
void	setPropertyReporter(PropertyURIReporter propertyReporter)
void	setStructureRequired(boolean structureRequired)
void	setValuesRequired(boolean valuesRequired)
String	toString()
protected BufferedImage	writeMessages(String[] msg, int width, int height)

Methods inherited from class net.idea.modbcum.p.AbstractDBProcessor

close, getConnection, isCloseConnection, isEnabled, setCloseConnection, setConnection

Methods inherited from class net.idea.modbcum.p.DefaultAmbitProcessor

addPropertyChangeListener, addPropertyChangeListener, getID, removePropertyChangeListener, removePropertyChangeListener, setEnabled

Methods inherited from class java.lang.Object

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

Methods inherited from interface net.idea.modbcum.i.processors.IProcessor

getID, setEnabled

Field Detail

model

protected ModelQueryResults model

imageSize

protected Dimension imageSize

structureRequired

protected boolean structureRequired

valuesRequired

protected boolean valuesRequired

classIndex

protected int classIndex

header

protected weka.core.Instances header

filter

protected weka.filters.Filter filter

targetURI

protected String[] targetURI

modelReporter

protected ModelURIReporter modelReporter

propertyReporter

protected PropertyURIReporter propertyReporter

applicationRootReference

protected org.restlet.data.Reference applicationRootReference

record

protected IStructureRecord record

Constructor Detail

ModelPredictor

public ModelPredictor(org.restlet.data.Reference applicationRootReference,
                      ModelQueryResults model,
                      ModelURIReporter modelReporter,
                      PropertyURIReporter propertyReporter,
                      String[] targetURI)
               throws org.restlet.resource.ResourceException

Throws:

org.restlet.resource.ResourceException

Method Detail

getImageSize

public Dimension getImageSize()

Specified by:

getImageSize in interface IStructureDiagramDepiction<BufferedImage>

setImageSize

public void setImageSize(Dimension imageSize)

Specified by:

setImageSize in interface IStructureDiagramDepiction<BufferedImage>

getModel

public ModelQueryResults getModel()

isValuesRequired

public boolean isValuesRequired()

setValuesRequired

public void setValuesRequired(boolean valuesRequired)

isStructureRequired

public boolean isStructureRequired()

setStructureRequired

public void setStructureRequired(boolean structureRequired)

getPredictor

public Predictor getPredictor()

getPropertyReporter

public PropertyURIReporter getPropertyReporter()

setPropertyReporter

public void setPropertyReporter(PropertyURIReporter propertyReporter)

getModelReporter

public ModelURIReporter getModelReporter()

setModelReporter

public void setModelReporter(ModelURIReporter modelReporter)

getHeader

protected weka.core.Instances getHeader(org.restlet.data.Form form)
                                 throws IOException

Throws:

IOException

getClassIndex

protected int getClassIndex(org.restlet.data.Form form)
                     throws Exception

Throws:

Exception

isSupported

protected boolean isSupported(Object predictor)
                       throws org.restlet.resource.ResourceException

Parameters:

predictor -

Returns:

true if this is the expected object type,

Throws:

org.restlet.resource.ResourceException

extractRecordID

protected void extractRecordID(NativeTypeItem target,
                               String url,
                               IStructureRecord record)
                        throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException

createPredictor

public Predictor createPredictor(ModelQueryResults model)
                          throws org.restlet.resource.ResourceException

Throws:

org.restlet.resource.ResourceException

getCompoundURL

public abstract String getCompoundURL(NativeTypeItem target)
                               throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException

predict

public abstract Object predict(NativeTypeItem target)
                        throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException

process

public IStructureRecord process(NativeTypeItem target)
                         throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

process in interface net.idea.modbcum.i.processors.IProcessor<NativeTypeItem,IStructureRecord>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

assignResults

public void assignResults(IStructureRecord record,
                          Object value)
                   throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException

open

public void open()
          throws net.idea.modbcum.i.exceptions.DbAmbitException

Specified by:

open in interface net.idea.modbcum.i.processors.IProcessor<NativeTypeItem,IStructureRecord>

Overrides:

open in class net.idea.modbcum.p.DefaultAmbitProcessor<NativeTypeItem,IStructureRecord>

Throws:

net.idea.modbcum.i.exceptions.DbAmbitException

createResultReference

public String createResultReference()
                             throws Exception

Throws:

Exception

getImage

public BufferedImage getImage(org.openscience.cdk.interfaces.IAtomContainer mol)
                       throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

getImage in interface IStructureDiagramDepiction<BufferedImage>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

getImage

public BufferedImage getImage(org.openscience.cdk.interfaces.IAtomContainer mol,
                              String ruleID,
                              int width,
                              int height,
                              boolean atomnumbers)
                       throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

getImage in interface IStructureDiagramDepiction<BufferedImage>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

toString

public String toString()

Overrides:

toString in class net.idea.modbcum.p.DefaultAmbitProcessor<NativeTypeItem,IStructureRecord>

getLegend

public BufferedImage getLegend(int width,
                               int height)
                        throws net.idea.modbcum.i.exceptions.AmbitException

Specified by:

getLegend in interface IStructureDiagramDepiction<BufferedImage>

Throws:

net.idea.modbcum.i.exceptions.AmbitException

writeMessages

protected BufferedImage writeMessages(String[] msg,
                                      int width,
                                      int height)
                               throws net.idea.modbcum.i.exceptions.AmbitException

Throws:

net.idea.modbcum.i.exceptions.AmbitException