uk.ac.ed.morphml_handler
Class MorphologyData

java.lang.Object
  extended by org.virtualratbrain.namespace.impl.MorphologyDataImpl
      extended by uk.ac.ed.morphml_handler.MorphologyData
All Implemented Interfaces:
com.sun.xml.bind.JAXBObject, org.virtualratbrain.namespace.impl.runtime.UnmarshallableObject, org.virtualratbrain.namespace.impl.runtime.ValidatableObject, org.virtualratbrain.namespace.impl.runtime.XMLSerializable, org.virtualratbrain.namespace.MorphologyData, MorphMLEntity

public class MorphologyData
extends org.virtualratbrain.namespace.impl.MorphologyDataImpl
implements MorphMLEntity


Nested Class Summary
static class MorphologyData.MorphologyDataAdapter
           
static class MorphologyData.MorphologyDataEvent
           
static interface MorphologyData.MorphologyDataListener
           
 
Nested classes/interfaces inherited from class org.virtualratbrain.namespace.impl.MorphologyDataImpl
org.virtualratbrain.namespace.impl.MorphologyDataImpl.Unmarshaller
 
Nested classes/interfaces inherited from interface uk.ac.ed.morphml_handler.MorphMLEntity
MorphMLEntity.MorphMLEntityListener
 
Field Summary
static String DATA_ACQUISITION_SYSTEM_ACCUSTAGE
           
static String DATA_ACQUISITION_SYSTEM_NEUROLUCIDA
           
protected  ArrayList morphology_data_listeners
           
protected  MorphologyList morphology_list
           
protected  String name
           
protected  Morphology raw_data_file
           
protected  URI uri
           
protected  boolean visible
           
static String WARP_ALGORITHM_AFFLINE
           
protected  Morphology warped_data_file
           
 
Fields inherited from class org.virtualratbrain.namespace.impl.MorphologyDataImpl
_AnatomicalTracers, _BlockingOrientation, _BlockingSymmetry, _CellTypes, _Content, _ContributedBy, _ContributedDate, _CuttingInstrument, _DataAcquisitionSystem, _DataAnalysisSystem, _HistologicalProcessing, _ImageFile, _InjectionSite, _IsReferenceBrain, _NeuronStructure, _RawDataFile, _Strain, _Thickness, _Tracing, _UniqueId, _WarpAlgorithmType, _WarpData, _WarpedDataFile, _Weight, has_IsReferenceBrain, has_Thickness, has_Weight, version
 
Constructor Summary
MorphologyData()
           
 
Method Summary
 void addMorphologyDataListener(MorphologyData.MorphologyDataListener listener)
           
 boolean canHide()
           
 boolean canShow()
           
 boolean canWarp()
           
protected  void fireHidden()
           
protected  void fireRawMorphologyChanged(Morphology new_morphology, Morphology old_morphology)
           
protected  void fireShown()
           
protected  void fireWarpDataChanged()
           
protected  void fireWarpedMorphologyChanged(Morphology new_morphology, Morphology old_morphology)
           
 MorphologyList getMorphologyList()
           
 String getName()
           
 MorphMLEntity getParentEntity()
           
 URI getRawDataURI()
           
 URL getRawDataURL()
           
 Morphology getRawMorphology()
           
 URI getURI()
           
 URL getURL()
           
 URI getWarpedDataURI()
           
 Morphology getWarpedMorphology()
           
 void hide()
           
 boolean isVisible()
           
 void removeMorphologyDataListener(MorphologyData.MorphologyDataListener listener)
           
 DatabaseHandler.UploadResult saveData(String username, String password)
           
 void setMorphologyList(MorphologyList morphology_list)
           
 void setName(String name)
           
 void setRawDataFile(URI uri)
           
 void setRawMorphology(Morphology morphology)
           
 void setURI(URI uri)
           
protected  void setVisible(boolean visible)
           
protected  void setVisibleDown(boolean visible)
           
protected  void setVisibleUp(boolean visible)
           
 void setWarpData(org.virtualratbrain.namespace.WarpDataStructure warp_data)
           
 void setWarpedDataFile(URI uri)
           
 void setWarpedMorphology(Morphology morphology)
           
 void show()
           
 String toString()
           
 void validate()
           
 void warp()
           
 
Methods inherited from class org.virtualratbrain.namespace.impl.MorphologyDataImpl
createRawValidator, createUnmarshaller, getAnatomicalTracers, getBlockingOrientation, getBlockingSymmetry, getCellTypes, getContent, getContributedBy, getContributedDate, getCuttingInstrument, getDataAcquisitionSystem, getDataAnalysisSystem, getHistologicalProcessing, getImageFile, getInjectionSite, getNeuronStructure, getPrimaryInterface, getRawDataFile, getStrain, getThickness, getTracing, getUniqueId, getWarpAlgorithmType, getWarpData, getWarpedDataFile, getWeight, isIsReferenceBrain, serializeAttributes, serializeBody, serializeURIs, setAnatomicalTracers, setBlockingOrientation, setBlockingSymmetry, setCellTypes, setContent, setContributedBy, setContributedDate, setCuttingInstrument, setDataAcquisitionSystem, setDataAnalysisSystem, setHistologicalProcessing, setImageFile, setInjectionSite, setIsReferenceBrain, setNeuronStructure, setRawDataFile, setStrain, setThickness, setTracing, setUniqueId, setWarpAlgorithmType, setWarpedDataFile, setWeight
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

WARP_ALGORITHM_AFFLINE

public static final String WARP_ALGORITHM_AFFLINE
See Also:
Constant Field Values

DATA_ACQUISITION_SYSTEM_NEUROLUCIDA

public static final String DATA_ACQUISITION_SYSTEM_NEUROLUCIDA
See Also:
Constant Field Values

DATA_ACQUISITION_SYSTEM_ACCUSTAGE

public static final String DATA_ACQUISITION_SYSTEM_ACCUSTAGE
See Also:
Constant Field Values

visible

protected boolean visible

morphology_list

protected MorphologyList morphology_list

uri

protected URI uri

name

protected String name

warped_data_file

protected Morphology warped_data_file

raw_data_file

protected Morphology raw_data_file

morphology_data_listeners

protected ArrayList morphology_data_listeners
Constructor Detail

MorphologyData

public MorphologyData()
Method Detail

isVisible

public boolean isVisible()
Specified by:
isVisible in interface MorphMLEntity

canShow

public boolean canShow()
Specified by:
canShow in interface MorphMLEntity

canHide

public boolean canHide()
Specified by:
canHide in interface MorphMLEntity

show

public void show()
Specified by:
show in interface MorphMLEntity

hide

public void hide()
Specified by:
hide in interface MorphMLEntity

setVisible

protected void setVisible(boolean visible)

setVisibleUp

protected void setVisibleUp(boolean visible)

setVisibleDown

protected void setVisibleDown(boolean visible)

validate

public void validate()
Specified by:
validate in interface MorphMLEntity

getParentEntity

public MorphMLEntity getParentEntity()
Specified by:
getParentEntity in interface MorphMLEntity

getMorphologyList

public MorphologyList getMorphologyList()

getURI

public URI getURI()

getURL

public URL getURL()

setURI

public void setURI(URI uri)

getName

public String getName()

setName

public void setName(String name)

setMorphologyList

public void setMorphologyList(MorphologyList morphology_list)

setRawDataFile

public void setRawDataFile(URI uri)

getRawDataURI

public URI getRawDataURI()

getRawDataURL

public URL getRawDataURL()

setRawMorphology

public void setRawMorphology(Morphology morphology)

setWarpedDataFile

public void setWarpedDataFile(URI uri)

getWarpedDataURI

public URI getWarpedDataURI()

setWarpedMorphology

public void setWarpedMorphology(Morphology morphology)

getRawMorphology

public Morphology getRawMorphology()

saveData

public DatabaseHandler.UploadResult saveData(String username,
                                             String password)

setWarpData

public void setWarpData(org.virtualratbrain.namespace.WarpDataStructure warp_data)
Specified by:
setWarpData in interface org.virtualratbrain.namespace.MorphologyData
Overrides:
setWarpData in class org.virtualratbrain.namespace.impl.MorphologyDataImpl

canWarp

public boolean canWarp()

warp

public void warp()

getWarpedMorphology

public Morphology getWarpedMorphology()

addMorphologyDataListener

public void addMorphologyDataListener(MorphologyData.MorphologyDataListener listener)

removeMorphologyDataListener

public void removeMorphologyDataListener(MorphologyData.MorphologyDataListener listener)

toString

public String toString()
Overrides:
toString in class Object

fireShown

protected void fireShown()

fireHidden

protected void fireHidden()

fireRawMorphologyChanged

protected void fireRawMorphologyChanged(Morphology new_morphology,
                                        Morphology old_morphology)

fireWarpedMorphologyChanged

protected void fireWarpedMorphologyChanged(Morphology new_morphology,
                                           Morphology old_morphology)

fireWarpDataChanged

protected void fireWarpDataChanged()