A B C D E F G H I J L M N O P R S T U V W X

A

accustage_handler - Static variable in class uk.ac.ed.morphml_handler.MorphMLHandler

AccustageHandler - Class in uk.ac.ed.morphml_handler.accustage

AccustageHandler() - Constructor for class uk.ac.ed.morphml_handler.accustage.AccustageHandler

addAffineWarpDataListener(AffineWarpDataStructure.AffineWarpDataListener) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

addAffineWarpPointListener(AffineWarpPoint.AffineWarpPointListener) - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint

addBranch(NeurolucidaObject, MorphMLHandler, Morphology, Cell, Segment) - Method in class uk.ac.ed.morphml_handler.neurolucida.NeurolucidaHandler

addBranch(NeurolucidaObject, MorphMLHandler, Morphology, Cell, Segment, String) - Method in class uk.ac.ed.morphml_handler.neurolucida.NeurolucidaHandler

addCell(Cell) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

addCell(Cell, int) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

addCell(Cell) - Method in class uk.ac.ed.morphml_handler.MorphMLTree

addCell(Cell, MorphMLTree.MorphMLTreeNode) - Method in class uk.ac.ed.morphml_handler.MorphMLTree

addCell(Cell) - Method in class uk.ac.ed.morphml_handler.Morphology

addCellBody(CellBody) - Method in class uk.ac.ed.morphml_handler.Cell

addCellBodyPolygon(Polygon) - Method in class uk.ac.ed.morphml_handler.Cell

addCellListener(Cell.CellListener) - Method in class uk.ac.ed.morphml_handler.Cell

addEditorListener(Editor.EditorListener) - Method in class uk.ac.ed.morphml_handler.Editor

addErrorMessage(String) - Method in class uk.ac.ed.morphml_handler.DatabaseHandler.UploadResult

addFeature(Feature) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

addFeature(Feature, int) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

addFeature(Feature) - Method in class uk.ac.ed.morphml_handler.MorphMLTree

addFeature(Feature, MorphMLTree.MorphMLTreeNode) - Method in class uk.ac.ed.morphml_handler.MorphMLTree

addFeature(Feature) - Method in class uk.ac.ed.morphml_handler.Morphology

addFeatureListener(Feature.FeatureListener) - Method in class uk.ac.ed.morphml_handler.Feature

addFreePoints(FreePoints) - Method in class uk.ac.ed.morphml_handler.Feature

addFreePoints(NeurolucidaObject, MorphMLHandler, Morphology, FreePoints) - Method in class uk.ac.ed.morphml_handler.neurolucida.NeurolucidaHandler

addListeners(AffineWarpDataStructure) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable.TableModel

addListeners(AffineWarpPoint) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable.TableModel

addLocalPoint(AffineWarpPoint) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

addLocalPoint(AffineWarpPoint, int) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

addLocalWarpPoint(AffineWarpPoint) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

addMorphMLHandlerListener(MorphMLHandler.MorphMLHandlerListener) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

addMorphology(Morphology) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

addMorphology(Morphology, int) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

addMorphology(Morphology) - Method in class uk.ac.ed.morphml_handler.MorphMLTree

addMorphology(Morphology, MorphMLTree.MorphMLTreeNode) - Method in class uk.ac.ed.morphml_handler.MorphMLTree

addMorphologyData(MorphologyData) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

addMorphologyData(MorphologyData, int) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

addMorphologyData(MorphologyData) - Method in class uk.ac.ed.morphml_handler.MorphMLTree

addMorphologyData(MorphologyData, MorphMLTree.MorphMLTreeNode) - Method in class uk.ac.ed.morphml_handler.MorphMLTree

addMorphologyData(MorphologyData) - Method in class uk.ac.ed.morphml_handler.MorphologyList

addMorphologyDataListener(MorphologyData.MorphologyDataListener) - Method in class uk.ac.ed.morphml_handler.MorphologyData

addMorphologyList(MorphologyList) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

addMorphologyList(MorphologyList) - Method in class uk.ac.ed.morphml_handler.MorphMLTree

addMorphologyList(MorphologyList, MorphMLTree.MorphMLTreeNode) - Method in class uk.ac.ed.morphml_handler.MorphMLTree

addMorphologyListener(Morphology.MorphologyListener) - Method in class uk.ac.ed.morphml_handler.Morphology

addMorphologyListListener(MorphologyList.MorphologyListListener) - Method in class uk.ac.ed.morphml_handler.MorphologyList

addPoint(Point) - Method in class uk.ac.ed.morphml_handler.Morphology

addPolygon(Polygon) - Method in class uk.ac.ed.morphml_handler.Feature

addPolygon(NeurolucidaObject, MorphMLHandler, Morphology, Polygon) - Method in class uk.ac.ed.morphml_handler.neurolucida.NeurolucidaHandler

addProperties(NeurolucidaObject, MorphMLHandler, Morphology, Properties) - Method in class uk.ac.ed.morphml_handler.neurolucida.NeurolucidaHandler

addPropertiesListener(Properties.PropertiesListener) - Method in class uk.ac.ed.morphml_handler.Properties

addProperty(Properties, Property) - Method in class uk.ac.ed.morphml_handler.neurolucida.NeurolucidaHandler

addProperty(Property) - Method in class uk.ac.ed.morphml_handler.Properties

addResponseMessage(String) - Method in class uk.ac.ed.morphml_handler.DatabaseHandler.UploadResult

addSegment(Segment) - Method in class uk.ac.ed.morphml_handler.Cell

addWorldPoint(AffineWarpPoint) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

addWorldPoint(AffineWarpPoint, int) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

addWorldWarpPoint(AffineWarpPoint) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

affine_warp_data - Variable in class uk.ac.ed.morphml_handler.AffineWarpPoint

AffineTransformation - Class in uk.ac.ed.morphml_handler.warp

AffineTransformation(Matrix4d) - Constructor for class uk.ac.ed.morphml_handler.warp.AffineTransformation

AffineWarp - Class in uk.ac.ed.morphml_handler.warp

AffineWarp() - Constructor for class uk.ac.ed.morphml_handler.warp.AffineWarp

Creates a new instance of AffineWarp

AffineWarpDataStructure - Class in uk.ac.ed.morphml_handler

AffineWarpDataStructure() - Constructor for class uk.ac.ed.morphml_handler.AffineWarpDataStructure

AffineWarpDataStructure.AffineWarpDataAdapter - Class in uk.ac.ed.morphml_handler

AffineWarpDataStructure.AffineWarpDataAdapter() - Constructor for class uk.ac.ed.morphml_handler.AffineWarpDataStructure.AffineWarpDataAdapter

AffineWarpDataStructure.AffineWarpDataEvent - Class in uk.ac.ed.morphml_handler

AffineWarpDataStructure.AffineWarpDataEvent(Object, AffineWarpPoint) - Constructor for class uk.ac.ed.morphml_handler.AffineWarpDataStructure.AffineWarpDataEvent

AffineWarpDataStructure.AffineWarpDataListener - Interface in uk.ac.ed.morphml_handler

AffineWarpDataStructure.Pair - Class in uk.ac.ed.morphml_handler

AffineWarpDataStructure.Pair(AffineWarpPoint, AffineWarpPoint) - Constructor for class uk.ac.ed.morphml_handler.AffineWarpDataStructure.Pair

AffineWarpDataTable - Class in uk.ac.ed.morphml_handler

AffineWarpDataTable() - Constructor for class uk.ac.ed.morphml_handler.AffineWarpDataTable

AffineWarpDataTable.CellEditor - Class in uk.ac.ed.morphml_handler

AffineWarpDataTable.CellEditor() - Constructor for class uk.ac.ed.morphml_handler.AffineWarpDataTable.CellEditor

AffineWarpDataTable.CellRenderer - Class in uk.ac.ed.morphml_handler

AffineWarpDataTable.CellRenderer() - Constructor for class uk.ac.ed.morphml_handler.AffineWarpDataTable.CellRenderer

AffineWarpDataTable.TableModel - Class in uk.ac.ed.morphml_handler

AffineWarpDataTable.TableModel() - Constructor for class uk.ac.ed.morphml_handler.AffineWarpDataTable.TableModel

AffineWarpPoint - Class in uk.ac.ed.morphml_handler

AffineWarpPoint() - Constructor for class uk.ac.ed.morphml_handler.AffineWarpPoint

AffineWarpPoint.AffineWarpPointAdapter - Class in uk.ac.ed.morphml_handler

AffineWarpPoint.AffineWarpPointAdapter() - Constructor for class uk.ac.ed.morphml_handler.AffineWarpPoint.AffineWarpPointAdapter

AffineWarpPoint.AffineWarpPointListener - Interface in uk.ac.ed.morphml_handler

B

blank_panel - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

C

canHide() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

canHide() - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint

canHide() - Method in class uk.ac.ed.morphml_handler.Cell

canHide() - Method in class uk.ac.ed.morphml_handler.Feature

canHide() - Method in interface uk.ac.ed.morphml_handler.MorphMLEntity

canHide() - Method in class uk.ac.ed.morphml_handler.Morphology

canHide() - Method in class uk.ac.ed.morphml_handler.MorphologyData

canHide() - Method in class uk.ac.ed.morphml_handler.MorphologyList

canShow() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

canShow() - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint

canShow() - Method in class uk.ac.ed.morphml_handler.Cell

canShow() - Method in class uk.ac.ed.morphml_handler.Feature

canShow() - Method in interface uk.ac.ed.morphml_handler.MorphMLEntity

canShow() - Method in class uk.ac.ed.morphml_handler.Morphology

canShow() - Method in class uk.ac.ed.morphml_handler.MorphologyData

canShow() - Method in class uk.ac.ed.morphml_handler.MorphologyList

canWarp() - Method in class uk.ac.ed.morphml_handler.MorphologyData

cards - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

Cell - Class in uk.ac.ed.morphml_handler

Cell() - Constructor for class uk.ac.ed.morphml_handler.Cell

cell - Variable in class uk.ac.ed.morphml_handler.Morphology.MorphologyEvent

Cell.CellAdapter - Class in uk.ac.ed.morphml_handler

Cell.CellAdapter() - Constructor for class uk.ac.ed.morphml_handler.Cell.CellAdapter

Cell.CellEvent - Class in uk.ac.ed.morphml_handler

Cell.CellEvent(Object) - Constructor for class uk.ac.ed.morphml_handler.Cell.CellEvent

Cell.CellListener - Interface in uk.ac.ed.morphml_handler

cell_listeners - Variable in class uk.ac.ed.morphml_handler.Cell

cell_panel - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

cell_properties_table - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

cellAdded(Morphology.MorphologyEvent) - Method in class uk.ac.ed.morphml_handler.Morphology.MorphologyAdapter

cellAdded(Morphology.MorphologyEvent) - Method in interface uk.ac.ed.morphml_handler.Morphology.MorphologyListener

cellRemoved(Morphology.MorphologyEvent) - Method in class uk.ac.ed.morphml_handler.Morphology.MorphologyAdapter

cellRemoved(Morphology.MorphologyEvent) - Method in interface uk.ac.ed.morphml_handler.Morphology.MorphologyListener

changed(EventObject) - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint.AffineWarpPointAdapter

changed(EventObject) - Method in interface uk.ac.ed.morphml_handler.AffineWarpPoint.AffineWarpPointListener

changeProperty(Property) - Method in class uk.ac.ed.morphml_handler.Properties

clear() - Method in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

cloneSegments(Segment[]) - Static method in class uk.ac.ed.morphml_handler.MorphMLCompressor

close() - Method in class uk.ac.ed.morphml_handler.http.MultiPartFormOutputStream

Closes the stream.

component - Variable in class uk.ac.ed.morphml_handler.Editor

compressPolygons(Polygon[], boolean, boolean, Hashtable) - Static method in class uk.ac.ed.morphml_handler.MorphMLCompressor

compressSegments(Segment[], Hashtable) - Static method in class uk.ac.ed.morphml_handler.MorphMLCompressor

compressSurface(Point3d[][], double) - Static method in class uk.ac.ed.morphml_handler.MorphMLCompressor

controller - Variable in class uk.ac.ed.morphml_handler.MorphMLTree.PopupMenu

createBoundary() - Static method in class uk.ac.ed.morphml_handler.http.MultiPartFormOutputStream

Creates a multipart boundary string by concatenating 20 hyphens (-) and the hexadecimal (base-16) representation of the current time in milliseconds.

createConnection(URL) - Static method in class uk.ac.ed.morphml_handler.http.MultiPartFormOutputStream

Creates a new java.net.URLConnection object from the specified java.net.URL.

createNode() - Method in class uk.ac.ed.morphml_handler.MorphMLTree

createRenderer() - Method in class uk.ac.ed.morphml_handler.MorphMLTree

D

DATA_ACQUISITION_SYSTEM_ACCUSTAGE - Static variable in class uk.ac.ed.morphml_handler.MorphologyData

DATA_ACQUISITION_SYSTEM_NEUROLUCIDA - Static variable in class uk.ac.ed.morphml_handler.MorphologyData

database_handler - Static variable in class uk.ac.ed.morphml_handler.MorphMLHandler

DATABASE_MORPHOLOGY_LIST_URL - Static variable in class uk.ac.ed.morphml_handler.DatabaseHandler

DATABASE_POST_URL - Static variable in class uk.ac.ed.morphml_handler.DatabaseHandler

DatabaseHandler - Class in uk.ac.ed.morphml_handler

DatabaseHandler() - Constructor for class uk.ac.ed.morphml_handler.DatabaseHandler

Creates a new instance of DatabaseHandler

DatabaseHandler.UploadResult - Class in uk.ac.ed.morphml_handler

DatabaseHandler.UploadResult() - Constructor for class uk.ac.ed.morphml_handler.DatabaseHandler.UploadResult

Creates a new instance of DataFormError

detault_color - Static variable in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

E

edit(Object) - Method in class uk.ac.ed.morphml_handler.Editor

editCancelled() - Method in class uk.ac.ed.morphml_handler.Editor

editCancelled(EventObject) - Method in class uk.ac.ed.morphml_handler.Editor.EditorAdapter

editCancelled(EventObject) - Method in interface uk.ac.ed.morphml_handler.Editor.EditorListener

editCompleted() - Method in class uk.ac.ed.morphml_handler.Editor

editCompleted(EventObject) - Method in class uk.ac.ed.morphml_handler.Editor.EditorAdapter

editCompleted(EventObject) - Method in interface uk.ac.ed.morphml_handler.Editor.EditorListener

edited_object - Variable in class uk.ac.ed.morphml_handler.Editor

Editor - Class in uk.ac.ed.morphml_handler

Editor() - Constructor for class uk.ac.ed.morphml_handler.Editor

Editor.EditorAdapter - Class in uk.ac.ed.morphml_handler

Editor.EditorAdapter() - Constructor for class uk.ac.ed.morphml_handler.Editor.EditorAdapter

Editor.EditorEvent - Class in uk.ac.ed.morphml_handler

Editor.EditorEvent(Object) - Constructor for class uk.ac.ed.morphml_handler.Editor.EditorEvent

Editor.EditorListener - Interface in uk.ac.ed.morphml_handler

editor_listeners - Variable in class uk.ac.ed.morphml_handler.Editor

editStarted(EventObject) - Method in class uk.ac.ed.morphml_handler.Editor.EditorAdapter

editStarted(EventObject) - Method in interface uk.ac.ed.morphml_handler.Editor.EditorListener

entity - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

entityHidden(EventObject) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure.AffineWarpDataAdapter

entityHidden(EventObject) - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint.AffineWarpPointAdapter

entityHidden(EventObject) - Method in class uk.ac.ed.morphml_handler.Cell.CellAdapter

entityHidden(EventObject) - Method in class uk.ac.ed.morphml_handler.Feature.FeatureAdapter

entityHidden(EventObject) - Method in interface uk.ac.ed.morphml_handler.MorphMLEntity.MorphMLEntityListener

entityHidden(EventObject) - Method in class uk.ac.ed.morphml_handler.Morphology.MorphologyAdapter

entityHidden(EventObject) - Method in class uk.ac.ed.morphml_handler.MorphologyData.MorphologyDataAdapter

entityHidden(EventObject) - Method in class uk.ac.ed.morphml_handler.MorphologyList.MorphologyListAdapter

entityShown(EventObject) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure.AffineWarpDataAdapter

entityShown(EventObject) - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint.AffineWarpPointAdapter

entityShown(EventObject) - Method in class uk.ac.ed.morphml_handler.Cell.CellAdapter

entityShown(EventObject) - Method in class uk.ac.ed.morphml_handler.Feature.FeatureAdapter

entityShown(EventObject) - Method in interface uk.ac.ed.morphml_handler.MorphMLEntity.MorphMLEntityListener

entityShown(EventObject) - Method in class uk.ac.ed.morphml_handler.Morphology.MorphologyAdapter

entityShown(EventObject) - Method in class uk.ac.ed.morphml_handler.MorphologyData.MorphologyDataAdapter

entityShown(EventObject) - Method in class uk.ac.ed.morphml_handler.MorphologyList.MorphologyListAdapter

ext - Static variable in class uk.ac.ed.morphml_handler.accustage.AccustageHandler

ext - Static variable in class uk.ac.ed.morphml_handler.neurolucida.NeurolucidaHandler

F

Feature - Class in uk.ac.ed.morphml_handler

Feature() - Constructor for class uk.ac.ed.morphml_handler.Feature

feature - Variable in class uk.ac.ed.morphml_handler.Morphology.MorphologyEvent

Feature.FeatureAdapter - Class in uk.ac.ed.morphml_handler

Feature.FeatureAdapter() - Constructor for class uk.ac.ed.morphml_handler.Feature.FeatureAdapter

Feature.FeatureEvent - Class in uk.ac.ed.morphml_handler

Feature.FeatureEvent(Object) - Constructor for class uk.ac.ed.morphml_handler.Feature.FeatureEvent

Feature.FeatureListener - Interface in uk.ac.ed.morphml_handler

feature_listeners - Variable in class uk.ac.ed.morphml_handler.Feature

feature_panel - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

feature_properties_table - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

featureAdded(Morphology.MorphologyEvent) - Method in class uk.ac.ed.morphml_handler.Morphology.MorphologyAdapter

featureAdded(Morphology.MorphologyEvent) - Method in interface uk.ac.ed.morphml_handler.Morphology.MorphologyListener

featureRemoved(Morphology.MorphologyEvent) - Method in class uk.ac.ed.morphml_handler.Morphology.MorphologyAdapter

featureRemoved(Morphology.MorphologyEvent) - Method in interface uk.ac.ed.morphml_handler.Morphology.MorphologyListener

fireCellAdded(Cell) - Method in class uk.ac.ed.morphml_handler.Morphology

fireCellRemoved(Cell) - Method in class uk.ac.ed.morphml_handler.Morphology

fireEditCancelled() - Method in class uk.ac.ed.morphml_handler.Editor

fireEditCompleted() - Method in class uk.ac.ed.morphml_handler.Editor

fireEditStarted() - Method in class uk.ac.ed.morphml_handler.Editor

fireFeatureAdded(Feature) - Method in class uk.ac.ed.morphml_handler.Morphology

fireFeatureRemoved(Feature) - Method in class uk.ac.ed.morphml_handler.Morphology

fireHidden() - Method in class uk.ac.ed.morphml_handler.MorphologyData

fireMorphologDataRemoved(MorphologyData) - Method in class uk.ac.ed.morphml_handler.MorphologyList

fireMorphologListRemoved(MorphologyList) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

fireMorphologyDataAdded(MorphologyData) - Method in class uk.ac.ed.morphml_handler.MorphologyList

fireMorphologyListAdded(MorphologyList) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

firePropertyAdded(Property) - Method in class uk.ac.ed.morphml_handler.Properties

firePropertyChanged(Property) - Method in class uk.ac.ed.morphml_handler.Properties

firePropertyRemoved(Property) - Method in class uk.ac.ed.morphml_handler.Properties

fireRawMorphologyChanged(Morphology, Morphology) - Method in class uk.ac.ed.morphml_handler.MorphologyData

fireShown() - Method in class uk.ac.ed.morphml_handler.MorphologyData

fireWarpDataChanged() - Method in class uk.ac.ed.morphml_handler.MorphologyData

fireWarpedMorphologyChanged(Morphology, Morphology) - Method in class uk.ac.ed.morphml_handler.MorphologyData

flush() - Method in class uk.ac.ed.morphml_handler.http.MultiPartFormOutputStream

Flushes the stream.

G

gauss(double[][]) - Static method in class uk.ac.ed.morphml_handler.warp.WarpMath

generateAppearance(Properties, int) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

generateSelectedAppearance(Properties, int) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

getAccustageHandler() - Static method in class uk.ac.ed.morphml_handler.MorphMLHandler

getAffineWarpData() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable.TableModel

getAffineWarpData() - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint

getAffineWarpPointEditor() - Static method in class uk.ac.ed.morphml_handler.Editor

getAnnotationEditor() - Static method in class uk.ac.ed.morphml_handler.Editor

getBoundary() - Method in class uk.ac.ed.morphml_handler.http.MultiPartFormOutputStream

Gets the multipart boundary string being used by this stream.

getCell() - Method in class uk.ac.ed.morphml_handler.Morphology.MorphologyEvent

getCellEditorValue() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable.CellEditor

getCellEditorValue() - Method in class uk.ac.ed.morphml_handler.PropertiesTable.CellEditor

getColor(String) - Method in class uk.ac.ed.morphml_handler.neurolucida.NeurolucidaHandler

getColourEditor() - Static method in class uk.ac.ed.morphml_handler.Editor

getColumnClass(int) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable.TableModel

getColumnClass(int) - Method in class uk.ac.ed.morphml_handler.PropertiesTable.TableModel

getColumnCount() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable.TableModel

getColumnCount() - Method in class uk.ac.ed.morphml_handler.PropertiesTable.TableModel

getColumnName(int) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable.TableModel

getColumnName(int) - Method in class uk.ac.ed.morphml_handler.PropertiesTable.TableModel

getComponent() - Method in class uk.ac.ed.morphml_handler.Editor

getContentType(String) - Static method in class uk.ac.ed.morphml_handler.http.MultiPartFormOutputStream

Gets the content type string suitable for the java.net.URLConnection which includes the multipart boundary string.

getDatabaseHandler() - Static method in class uk.ac.ed.morphml_handler.MorphMLHandler

getDefaultMorphologyList() - Method in class uk.ac.ed.morphml_handler.DatabaseHandler

getErrorMessages() - Method in class uk.ac.ed.morphml_handler.DatabaseHandler.UploadResult

getFeature() - Method in class uk.ac.ed.morphml_handler.Morphology.MorphologyEvent

getFileFilter() - Static method in class uk.ac.ed.morphml_handler.accustage.AccustageHandler

getFileFilter() - Static method in class uk.ac.ed.morphml_handler.MorphMLHandler

getFileFilter() - Static method in class uk.ac.ed.morphml_handler.neurolucida.NeurolucidaHandler

getLocalPoint() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure.Pair

getMorphMLHandler() - Static method in class uk.ac.ed.morphml_handler.MorphMLHandler

getMorphology() - Method in class uk.ac.ed.morphml_handler.Cell

getMorphology() - Method in class uk.ac.ed.morphml_handler.Feature

getMorphologyData() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

getMorphologyData() - Method in class uk.ac.ed.morphml_handler.Morphology

getMorphologyData() - Method in class uk.ac.ed.morphml_handler.MorphologyList.MorphologyListEvent

getMorphologyList() - Method in class uk.ac.ed.morphml_handler.MorphMLHandler.MorphMLHandlerEvent

getMorphologyList() - Method in class uk.ac.ed.morphml_handler.MorphologyData

getMorphologyLists() - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

getName() - Method in class uk.ac.ed.morphml_handler.MorphologyData

getName() - Method in class uk.ac.ed.morphml_handler.MorphologyList

getNeurolucidaHandler() - Static method in class uk.ac.ed.morphml_handler.MorphMLHandler

getNewMorphology() - Method in class uk.ac.ed.morphml_handler.MorphologyData.MorphologyDataEvent

getNode(Object) - Method in class uk.ac.ed.morphml_handler.MorphMLTree

getNumberOfPointPairs() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

getObject() - Method in class uk.ac.ed.morphml_handler.Editor

getOldMorphology() - Method in class uk.ac.ed.morphml_handler.MorphologyData.MorphologyDataEvent

getParent() - Method in class uk.ac.ed.morphml_handler.Properties

getParentEntity() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

getParentEntity() - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint

getParentEntity() - Method in class uk.ac.ed.morphml_handler.Cell

getParentEntity() - Method in class uk.ac.ed.morphml_handler.Feature

getParentEntity() - Method in interface uk.ac.ed.morphml_handler.MorphMLEntity

getParentEntity() - Method in class uk.ac.ed.morphml_handler.Morphology

getParentEntity() - Method in class uk.ac.ed.morphml_handler.MorphologyData

getParentEntity() - Method in class uk.ac.ed.morphml_handler.MorphologyList

getPoint(String) - Method in class uk.ac.ed.morphml_handler.Morphology

getPointPairs() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

getPointTale() - Method in class uk.ac.ed.morphml_handler.Morphology

getProperty(String) - Method in class uk.ac.ed.morphml_handler.Cell

getProperty(String) - Method in class uk.ac.ed.morphml_handler.Feature

getProperty(String) - Method in class uk.ac.ed.morphml_handler.Morphology

getProperty(Properties, String) - Method in class uk.ac.ed.morphml_handler.neurolucida.NeurolucidaHandler

getProperty(String) - Method in class uk.ac.ed.morphml_handler.Properties

getProperty() - Method in class uk.ac.ed.morphml_handler.Properties.PropertiesEvent

getRawDataURI() - Method in class uk.ac.ed.morphml_handler.MorphologyData

getRawDataURL() - Method in class uk.ac.ed.morphml_handler.MorphologyData

getRawMorphology() - Method in class uk.ac.ed.morphml_handler.MorphologyData

getRowCount() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable.TableModel

getRowCount() - Method in class uk.ac.ed.morphml_handler.PropertiesTable.TableModel

getSelectedReferencePoint() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable.TableModel

getStringEditor() - Static method in class uk.ac.ed.morphml_handler.Editor

getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable.CellEditor

getTableCellEditorComponent(JTable, Object, boolean, int, int) - Method in class uk.ac.ed.morphml_handler.PropertiesTable.CellEditor

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable.CellRenderer

getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class uk.ac.ed.morphml_handler.PropertiesTable.CellRenderer

getTreeCellRendererComponent(JTree, Object, boolean, boolean, boolean, int, boolean) - Method in class uk.ac.ed.morphml_handler.MorphMLTree.MorphMLTreeRenderer

getURI() - Method in class uk.ac.ed.morphml_handler.Morphology

getURI() - Method in class uk.ac.ed.morphml_handler.MorphologyData

getURI() - Method in class uk.ac.ed.morphml_handler.MorphologyList

getURL() - Method in class uk.ac.ed.morphml_handler.Morphology

getURL() - Method in class uk.ac.ed.morphml_handler.MorphologyData

getURL() - Method in class uk.ac.ed.morphml_handler.MorphologyList

getValueAt(int, int) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable.TableModel

getValueAt(int, int) - Method in class uk.ac.ed.morphml_handler.PropertiesTable.TableModel

getWarpedDataURI() - Method in class uk.ac.ed.morphml_handler.MorphologyData

getWarpedMorphology() - Method in class uk.ac.ed.morphml_handler.MorphologyData

getWarpMatrix() - Method in class uk.ac.ed.morphml_handler.MorphologyData.MorphologyDataEvent

getWarpPoint() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure.AffineWarpDataEvent

getWorldPoint() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure.Pair

H

handler - Static variable in class uk.ac.ed.morphml_handler.MorphMLHandler

hide() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

hide() - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint

hide() - Method in class uk.ac.ed.morphml_handler.Cell

hide() - Method in class uk.ac.ed.morphml_handler.Feature

hide() - Method in interface uk.ac.ed.morphml_handler.MorphMLEntity

hide() - Method in class uk.ac.ed.morphml_handler.Morphology

hide() - Method in class uk.ac.ed.morphml_handler.MorphologyData

hide() - Method in class uk.ac.ed.morphml_handler.MorphologyList

I

initBlankPanel() - Method in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

initCards() - Method in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

initCellPanel() - Method in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

initComponent() - Method in class uk.ac.ed.morphml_handler.Editor

initFeaturePanel() - Method in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

initJAXBContext() - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

initListener() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable.TableModel

initMenu(Object) - Method in class uk.ac.ed.morphml_handler.MorphMLTree.PopupMenu

initMorphologyDataPanel() - Method in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

initMorphologyListPanel() - Method in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

initMorphologyPanel() - Method in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

initPopupMenu() - Method in class uk.ac.ed.morphml_handler.MorphMLTree

initPropertiesListener() - Method in class uk.ac.ed.morphml_handler.PropertiesTable.TableModel

initScrollPane() - Method in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

initToolbarEventHandlers(Object) - Method in class uk.ac.ed.morphml_handler.MorphMLTree.PopupMenuController

initTree() - Method in class uk.ac.ed.morphml_handler.MorphMLTree

isAccustageFile(File) - Static method in class uk.ac.ed.morphml_handler.accustage.AccustageHandler

isAccustageFileName(String) - Static method in class uk.ac.ed.morphml_handler.accustage.AccustageHandler

isCellEditable(int, int) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable.TableModel

isCellEditable(int, int) - Method in class uk.ac.ed.morphml_handler.PropertiesTable.TableModel

isClientSideValid() - Method in class uk.ac.ed.morphml_handler.DatabaseHandler.UploadResult

isMorphmlFile(File) - Static method in class uk.ac.ed.morphml_handler.MorphMLHandler

isMorphmlFileName(String) - Static method in class uk.ac.ed.morphml_handler.MorphMLHandler

isNeurolucidaFile(File) - Static method in class uk.ac.ed.morphml_handler.neurolucida.NeurolucidaHandler

isNeurolucidaFileName(String) - Static method in class uk.ac.ed.morphml_handler.neurolucida.NeurolucidaHandler

isSucceed() - Method in class uk.ac.ed.morphml_handler.DatabaseHandler.UploadResult

isVisible() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

isVisible() - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint

isVisible() - Method in class uk.ac.ed.morphml_handler.Cell

isVisible() - Method in class uk.ac.ed.morphml_handler.Feature

isVisible() - Method in interface uk.ac.ed.morphml_handler.MorphMLEntity

isVisible() - Method in class uk.ac.ed.morphml_handler.Morphology

isVisible() - Method in class uk.ac.ed.morphml_handler.MorphologyData

isVisible() - Method in class uk.ac.ed.morphml_handler.MorphologyList

J

jc - Variable in class uk.ac.ed.morphml_handler.MorphMLHandler

L

local_point - Variable in class uk.ac.ed.morphml_handler.AffineWarpDataStructure.Pair

localWarpPointAdded(AffineWarpDataStructure.AffineWarpDataEvent) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure.AffineWarpDataAdapter

localWarpPointAdded(AffineWarpDataStructure.AffineWarpDataEvent) - Method in interface uk.ac.ed.morphml_handler.AffineWarpDataStructure.AffineWarpDataListener

localWarpPointRemoved(AffineWarpDataStructure.AffineWarpDataEvent) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure.AffineWarpDataAdapter

localWarpPointRemoved(AffineWarpDataStructure.AffineWarpDataEvent) - Method in interface uk.ac.ed.morphml_handler.AffineWarpDataStructure.AffineWarpDataListener

M

mergeShortSegments(Segment[], double, Hashtable, ArrayList) - Static method in class uk.ac.ed.morphml_handler.MorphMLCompressor

mergeStraightSegments(Segment[], double, Hashtable, ArrayList) - Static method in class uk.ac.ed.morphml_handler.MorphMLCompressor

morphml - Static variable in class uk.ac.ed.morphml_handler.MorphMLHandler

morphml_handler_listeners - Variable in class uk.ac.ed.morphml_handler.MorphMLHandler

MorphMLCompressor - Class in uk.ac.ed.morphml_handler

MorphMLCompressor() - Constructor for class uk.ac.ed.morphml_handler.MorphMLCompressor

MorphMLEntity - Interface in uk.ac.ed.morphml_handler

MorphMLEntity.MorphMLEntityListener - Interface in uk.ac.ed.morphml_handler

MorphMLHandler - Class in uk.ac.ed.morphml_handler

MorphMLHandler() - Constructor for class uk.ac.ed.morphml_handler.MorphMLHandler

MorphMLHandler.MorphMLHandlerAdapter - Class in uk.ac.ed.morphml_handler

MorphMLHandler.MorphMLHandlerAdapter() - Constructor for class uk.ac.ed.morphml_handler.MorphMLHandler.MorphMLHandlerAdapter

MorphMLHandler.MorphMLHandlerEvent - Class in uk.ac.ed.morphml_handler

MorphMLHandler.MorphMLHandlerEvent(Object, MorphologyList) - Constructor for class uk.ac.ed.morphml_handler.MorphMLHandler.MorphMLHandlerEvent

MorphMLHandler.MorphMLHandlerListener - Interface in uk.ac.ed.morphml_handler

MorphMLJava3DPanel - Class in uk.ac.ed.morphml_handler

MorphMLJava3DPanel(double) - Constructor for class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

MorphMLJava3DPanel(Java3DHandler) - Constructor for class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

MorphMLPropertiesPanel - Class in uk.ac.ed.morphml_handler

MorphMLPropertiesPanel() - Constructor for class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

MorphMLTree - Class in uk.ac.ed.morphml_handler

MorphMLTree() - Constructor for class uk.ac.ed.morphml_handler.MorphMLTree

MorphMLTree.MorphMLTreeNode - Class in uk.ac.ed.morphml_handler

MorphMLTree.MorphMLTreeNode() - Constructor for class uk.ac.ed.morphml_handler.MorphMLTree.MorphMLTreeNode

MorphMLTree.MorphMLTreeRenderer - Class in uk.ac.ed.morphml_handler

MorphMLTree.MorphMLTreeRenderer() - Constructor for class uk.ac.ed.morphml_handler.MorphMLTree.MorphMLTreeRenderer

MorphMLTree.PopupMenu - Class in uk.ac.ed.morphml_handler

MorphMLTree.PopupMenu(Object) - Constructor for class uk.ac.ed.morphml_handler.MorphMLTree.PopupMenu

MorphMLTree.PopupMenuController - Class in uk.ac.ed.morphml_handler

MorphMLTree.PopupMenuController(MorphMLTree.PopupMenu, Object) - Constructor for class uk.ac.ed.morphml_handler.MorphMLTree.PopupMenuController

morphology - Variable in class uk.ac.ed.morphml_handler.Cell

morphology - Variable in class uk.ac.ed.morphml_handler.Feature

Morphology - Class in uk.ac.ed.morphml_handler

Morphology() - Constructor for class uk.ac.ed.morphml_handler.Morphology

Morphology.MorphologyAdapter - Class in uk.ac.ed.morphml_handler

Morphology.MorphologyAdapter() - Constructor for class uk.ac.ed.morphml_handler.Morphology.MorphologyAdapter

Morphology.MorphologyEvent - Class in uk.ac.ed.morphml_handler

Morphology.MorphologyEvent(Object) - Constructor for class uk.ac.ed.morphml_handler.Morphology.MorphologyEvent

Morphology.MorphologyEvent(Object, Cell) - Constructor for class uk.ac.ed.morphml_handler.Morphology.MorphologyEvent

Morphology.MorphologyEvent(Object, Feature) - Constructor for class uk.ac.ed.morphml_handler.Morphology.MorphologyEvent

Morphology.MorphologyListener - Interface in uk.ac.ed.morphml_handler

morphology_data - Variable in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

morphology_data - Variable in class uk.ac.ed.morphml_handler.Morphology

morphology_data - Variable in class uk.ac.ed.morphml_handler.MorphologyList.MorphologyListEvent

morphology_data_algorithm_type - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

morphology_data_contributed_by - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

morphology_data_contributed_date - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

morphology_data_listeners - Variable in class uk.ac.ed.morphml_handler.MorphologyData

morphology_data_morphml_file - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

morphology_data_neurolucida_file - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

morphology_data_panel - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

morphology_data_warp_button - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

morphology_list - Variable in class uk.ac.ed.morphml_handler.MorphMLHandler.MorphMLHandlerEvent

morphology_list - Variable in class uk.ac.ed.morphml_handler.MorphologyData

morphology_list_listeners - Variable in class uk.ac.ed.morphml_handler.MorphologyList

morphology_list_panel - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

morphology_listeners - Variable in class uk.ac.ed.morphml_handler.Morphology

morphology_lists - Variable in class uk.ac.ed.morphml_handler.MorphMLHandler

morphology_panel - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

morphology_properties_table - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

MorphologyData - Class in uk.ac.ed.morphml_handler

MorphologyData() - Constructor for class uk.ac.ed.morphml_handler.MorphologyData

MorphologyData.MorphologyDataAdapter - Class in uk.ac.ed.morphml_handler

MorphologyData.MorphologyDataAdapter() - Constructor for class uk.ac.ed.morphml_handler.MorphologyData.MorphologyDataAdapter

MorphologyData.MorphologyDataEvent - Class in uk.ac.ed.morphml_handler

MorphologyData.MorphologyDataEvent(Object) - Constructor for class uk.ac.ed.morphml_handler.MorphologyData.MorphologyDataEvent

MorphologyData.MorphologyDataEvent(Object, Matrix4d) - Constructor for class uk.ac.ed.morphml_handler.MorphologyData.MorphologyDataEvent

MorphologyData.MorphologyDataEvent(Object, Morphology, Morphology) - Constructor for class uk.ac.ed.morphml_handler.MorphologyData.MorphologyDataEvent

MorphologyData.MorphologyDataListener - Interface in uk.ac.ed.morphml_handler

morphologyDataAdded(MorphologyList.MorphologyListEvent) - Method in class uk.ac.ed.morphml_handler.MorphologyList.MorphologyListAdapter

morphologyDataAdded(MorphologyList.MorphologyListEvent) - Method in interface uk.ac.ed.morphml_handler.MorphologyList.MorphologyListListener

morphologyDataRemoved(MorphologyList.MorphologyListEvent) - Method in class uk.ac.ed.morphml_handler.MorphologyList.MorphologyListAdapter

morphologyDataRemoved(MorphologyList.MorphologyListEvent) - Method in interface uk.ac.ed.morphml_handler.MorphologyList.MorphologyListListener

MorphologyList - Class in uk.ac.ed.morphml_handler

MorphologyList() - Constructor for class uk.ac.ed.morphml_handler.MorphologyList

MorphologyList.MorphologyListAdapter - Class in uk.ac.ed.morphml_handler

MorphologyList.MorphologyListAdapter() - Constructor for class uk.ac.ed.morphml_handler.MorphologyList.MorphologyListAdapter

MorphologyList.MorphologyListEvent - Class in uk.ac.ed.morphml_handler

MorphologyList.MorphologyListEvent(Object) - Constructor for class uk.ac.ed.morphml_handler.MorphologyList.MorphologyListEvent

MorphologyList.MorphologyListEvent(Object, MorphologyData) - Constructor for class uk.ac.ed.morphml_handler.MorphologyList.MorphologyListEvent

MorphologyList.MorphologyListListener - Interface in uk.ac.ed.morphml_handler

morphologyListAdded(MorphMLHandler.MorphMLHandlerEvent) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler.MorphMLHandlerAdapter

morphologyListAdded(MorphMLHandler.MorphMLHandlerEvent) - Method in interface uk.ac.ed.morphml_handler.MorphMLHandler.MorphMLHandlerListener

morphologyListRemoved(MorphMLHandler.MorphMLHandlerEvent) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler.MorphMLHandlerAdapter

morphologyListRemoved(MorphMLHandler.MorphMLHandlerEvent) - Method in interface uk.ac.ed.morphml_handler.MorphMLHandler.MorphMLHandlerListener

MultiPartFormOutputStream - Class in uk.ac.ed.morphml_handler.http

MultiPartFormOutputStream is used to write "multipart/form-data" to a java.net.URLConnection for POSTing.

MultiPartFormOutputStream(OutputStream, String) - Constructor for class uk.ac.ed.morphml_handler.http.MultiPartFormOutputStream

Creates a new MultiPartFormOutputStream object using the specified output stream and boundary.

N

name - Variable in class uk.ac.ed.morphml_handler.MorphologyData

name - Variable in class uk.ac.ed.morphml_handler.MorphologyList

neurolucida_handler - Static variable in class uk.ac.ed.morphml_handler.MorphMLHandler

NeurolucidaHandler - Class in uk.ac.ed.morphml_handler.neurolucida

NeurolucidaHandler() - Constructor for class uk.ac.ed.morphml_handler.neurolucida.NeurolucidaHandler

new_morphology - Variable in class uk.ac.ed.morphml_handler.MorphologyData.MorphologyDataEvent

newAffineWarpData() - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

newAffineWarpPoint(int) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

newCell(String) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

newCellBody() - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

newFeature(String) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

newFreePoints() - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

newMorphology() - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

newMorphologyData() - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

newMorphologyList() - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

newPoint(Point) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

newPoint(int, double, double, double, double) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

newPolygon() - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

newProperties() - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

newProperty(String, String) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

newSegment(Segment) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

newSegment(int, int, int, int, String) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

newSegment(int, int, int, int) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

newSegment(int, int, int, String) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

newSegment(int, int, int) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

O

old_morphology - Variable in class uk.ac.ed.morphml_handler.MorphologyData.MorphologyDataEvent

open_file_chooser - Static variable in class uk.ac.ed.morphml_handler.MorphMLHandler

openAccustageURI(URI) - Static method in class uk.ac.ed.morphml_handler.MorphMLHandler

openMorphologyDateURI(URI) - Static method in class uk.ac.ed.morphml_handler.MorphMLHandler

openMorphologyListURI(URI) - Static method in class uk.ac.ed.morphml_handler.MorphMLHandler

openMorphologyURI(URI) - Static method in class uk.ac.ed.morphml_handler.MorphMLHandler

openNeurolucidaURI(URI) - Static method in class uk.ac.ed.morphml_handler.MorphMLHandler

openZippedInputStream(URL) - Static method in class uk.ac.ed.morphml_handler.DatabaseHandler

P

points_table - Variable in class uk.ac.ed.morphml_handler.Morphology

Properties - Class in uk.ac.ed.morphml_handler

Properties() - Constructor for class uk.ac.ed.morphml_handler.Properties

Properties(Cell) - Constructor for class uk.ac.ed.morphml_handler.Properties

Properties(Feature) - Constructor for class uk.ac.ed.morphml_handler.Properties

Properties.PropertiesAdapter - Class in uk.ac.ed.morphml_handler

Properties.PropertiesAdapter() - Constructor for class uk.ac.ed.morphml_handler.Properties.PropertiesAdapter

Properties.PropertiesEvent - Class in uk.ac.ed.morphml_handler

Properties.PropertiesEvent(Object, Property) - Constructor for class uk.ac.ed.morphml_handler.Properties.PropertiesEvent

Properties.PropertiesListener - Interface in uk.ac.ed.morphml_handler

properties_listeners - Variable in class uk.ac.ed.morphml_handler.Properties

PropertiesTable - Class in uk.ac.ed.morphml_handler

PropertiesTable() - Constructor for class uk.ac.ed.morphml_handler.PropertiesTable

PropertiesTable.CellEditor - Class in uk.ac.ed.morphml_handler

PropertiesTable.CellEditor() - Constructor for class uk.ac.ed.morphml_handler.PropertiesTable.CellEditor

PropertiesTable.CellRenderer - Class in uk.ac.ed.morphml_handler

PropertiesTable.CellRenderer() - Constructor for class uk.ac.ed.morphml_handler.PropertiesTable.CellRenderer

PropertiesTable.TableModel - Class in uk.ac.ed.morphml_handler

PropertiesTable.TableModel() - Constructor for class uk.ac.ed.morphml_handler.PropertiesTable.TableModel

propertyAdded(Properties.PropertiesEvent) - Method in class uk.ac.ed.morphml_handler.Properties.PropertiesAdapter

propertyAdded(Properties.PropertiesEvent) - Method in interface uk.ac.ed.morphml_handler.Properties.PropertiesListener

propertyChanged(Properties.PropertiesEvent) - Method in class uk.ac.ed.morphml_handler.Properties.PropertiesAdapter

propertyChanged(Properties.PropertiesEvent) - Method in interface uk.ac.ed.morphml_handler.Properties.PropertiesListener

propertyRemoved(Properties.PropertiesEvent) - Method in class uk.ac.ed.morphml_handler.Properties.PropertiesAdapter

propertyRemoved(Properties.PropertiesEvent) - Method in interface uk.ac.ed.morphml_handler.Properties.PropertiesListener

R

raw_data_file - Variable in class uk.ac.ed.morphml_handler.MorphologyData

rawMorphologyChanged(MorphologyData.MorphologyDataEvent) - Method in class uk.ac.ed.morphml_handler.MorphologyData.MorphologyDataAdapter

rawMorphologyChanged(MorphologyData.MorphologyDataEvent) - Method in interface uk.ac.ed.morphml_handler.MorphologyData.MorphologyDataListener

readMorphMLStream(InputStream) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

readStream(MorphMLHandler, InputStream) - Method in class uk.ac.ed.morphml_handler.accustage.AccustageHandler

readStream(MorphMLHandler, InputStream) - Method in class uk.ac.ed.morphml_handler.neurolucida.NeurolucidaHandler

removeAffineWarpDataListener(AffineWarpDataStructure.AffineWarpDataListener) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

removeAffineWarpPointListener(AffineWarpPoint.AffineWarpPointListener) - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint

removeCell(Cell) - Method in class uk.ac.ed.morphml_handler.MorphMLTree

removeCell(Cell) - Method in class uk.ac.ed.morphml_handler.Morphology

removeCellListener(Cell.CellListener) - Method in class uk.ac.ed.morphml_handler.Cell

removeEditorListener(Editor.EditorListener) - Method in class uk.ac.ed.morphml_handler.Editor

removeFeature(Feature) - Method in class uk.ac.ed.morphml_handler.MorphMLTree

removeFeature(Feature) - Method in class uk.ac.ed.morphml_handler.Morphology

removeFeatureListener(Feature.FeatureListener) - Method in class uk.ac.ed.morphml_handler.Feature

removeListeners(AffineWarpDataStructure) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable.TableModel

removeListeners(AffineWarpPoint) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable.TableModel

removeLocalWarpPoint(AffineWarpPoint) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

removeMorphMLHandlerListener(MorphMLHandler.MorphMLHandlerListener) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

removeMorphology(Morphology) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

removeMorphology(Morphology) - Method in class uk.ac.ed.morphml_handler.MorphMLTree

removeMorphologyData(MorphologyData) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

removeMorphologyData(MorphologyData) - Method in class uk.ac.ed.morphml_handler.MorphMLTree

removeMorphologyData(MorphologyData) - Method in class uk.ac.ed.morphml_handler.MorphologyList

removeMorphologyDataListener(MorphologyData.MorphologyDataListener) - Method in class uk.ac.ed.morphml_handler.MorphologyData

removeMorphologyList(MorphologyList) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

removeMorphologyList(MorphologyList) - Method in class uk.ac.ed.morphml_handler.MorphMLTree

removeMorphologyListener(Morphology.MorphologyListener) - Method in class uk.ac.ed.morphml_handler.Morphology

removeMorphologyListListener(MorphologyList.MorphologyListListener) - Method in class uk.ac.ed.morphml_handler.MorphologyList

removePoint(AffineWarpPoint) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

removePropertiesListener(Properties.PropertiesListener) - Method in class uk.ac.ed.morphml_handler.Properties

removeProperty(Property) - Method in class uk.ac.ed.morphml_handler.Properties

removeWorldWarpPoint(AffineWarpPoint) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

renderCell(Cell, int) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

renderClosedPolygonsSolid(Polygon[], Hashtable) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

renderClosedPolygonWireframe(Polygon, Hashtable) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

renderColouredClosedPolygonWireframe(Polygon, Hashtable) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

renderCrosshairWireframe() - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

renderFeature(Feature, int) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

renderFreePointsSolid(FreePoints, Hashtable) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

renderFreePointsWireframe(FreePoints, Hashtable) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

renderLocalPoint(AffineWarpPoint, int) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

renderMorphology(Morphology, int) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

renderOpenPolygonsSolid(Polygon[], Hashtable) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

renderOpenPolygonWireframe(Polygon, Hashtable) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

renderPointSolid() - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

renderPolygonSolid(Polygon, Hashtable) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

renderSegmentsSolid(Segment[], Hashtable) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

renderSegmentsWireframe(Segment[], Hashtable) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

renderSegmentWireframe(Segment, Hashtable) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

renderSurface(Point3d[][]) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

renderWorldPoint(AffineWarpPoint, int) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

S

saveData(String, String) - Method in class uk.ac.ed.morphml_handler.MorphologyData

savefile_chooser - Static variable in class uk.ac.ed.morphml_handler.MorphMLHandler

saveMorphology(Morphology) - Static method in class uk.ac.ed.morphml_handler.MorphMLHandler

saveMorphologyData(MorphologyData) - Static method in class uk.ac.ed.morphml_handler.MorphMLHandler

saveMorphologyList(MorphologyList) - Static method in class uk.ac.ed.morphml_handler.MorphMLHandler

SCALE - Static variable in class uk.ac.ed.morphml_handler.accustage.AccustageHandler

SCALE - Static variable in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

SCALE - Static variable in class uk.ac.ed.morphml_handler.neurolucida.NeurolucidaHandler

scroll_pane - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

select(Object) - Method in class uk.ac.ed.morphml_handler.MorphMLTree

selectFileToOpen() - Static method in class uk.ac.ed.morphml_handler.MorphMLHandler

selectFileToSave() - Static method in class uk.ac.ed.morphml_handler.MorphMLHandler

set(Vector3d) - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint

set(double, double, double) - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint

set(AffineWarpPoint) - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint

setAffineWarpData(AffineWarpDataStructure) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable

setAffineWarpData(AffineWarpDataStructure) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable.TableModel

setAfflineWarpData(AffineWarpDataStructure) - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint

setMorphology(Morphology) - Method in class uk.ac.ed.morphml_handler.Cell

setMorphology(Morphology) - Method in class uk.ac.ed.morphml_handler.Feature

setMorphologyData(MorphologyData) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

setMorphologyData(MorphologyData) - Method in class uk.ac.ed.morphml_handler.Morphology

setMorphologyList(MorphologyList) - Method in class uk.ac.ed.morphml_handler.MorphologyData

setMorplMLEntity(MorphMLEntity) - Method in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

setMorplMLEntity(MorphologyList) - Method in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

setMorplMLEntity(MorphologyData) - Method in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

setMorplMLEntity(Morphology) - Method in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

setMorplMLEntity(Cell) - Method in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

setMorplMLEntity(Feature) - Method in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

setName(String) - Method in class uk.ac.ed.morphml_handler.MorphologyData

setName(String) - Method in class uk.ac.ed.morphml_handler.MorphologyList

setParent(Object) - Method in class uk.ac.ed.morphml_handler.Properties

setProperties(Properties) - Method in class uk.ac.ed.morphml_handler.Cell

setProperties(Properties) - Method in class uk.ac.ed.morphml_handler.Feature

setProperties(Properties) - Method in class uk.ac.ed.morphml_handler.Morphology

setProperties(Properties) - Method in class uk.ac.ed.morphml_handler.PropertiesTable

setProperties(Properties) - Method in class uk.ac.ed.morphml_handler.PropertiesTable.TableModel

setRawDataFile(URI) - Method in class uk.ac.ed.morphml_handler.MorphologyData

setRawMorphology(Morphology) - Method in class uk.ac.ed.morphml_handler.MorphologyData

setURI(URI) - Method in class uk.ac.ed.morphml_handler.Morphology

setURI(URI) - Method in class uk.ac.ed.morphml_handler.MorphologyData

setURI(URI) - Method in class uk.ac.ed.morphml_handler.MorphologyList

setValueAt(Object, int, int) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataTable.TableModel

setValueAt(Object, int, int) - Method in class uk.ac.ed.morphml_handler.PropertiesTable.TableModel

setVisible(boolean) - Method in class uk.ac.ed.morphml_handler.Cell

setVisible(boolean) - Method in class uk.ac.ed.morphml_handler.Feature

setVisible(boolean) - Method in class uk.ac.ed.morphml_handler.Morphology

setVisible(boolean) - Method in class uk.ac.ed.morphml_handler.MorphologyData

setVisible(boolean) - Method in class uk.ac.ed.morphml_handler.MorphologyList

setVisibleDown(boolean) - Method in class uk.ac.ed.morphml_handler.Morphology

setVisibleDown(boolean) - Method in class uk.ac.ed.morphml_handler.MorphologyData

setVisibleDown(boolean) - Method in class uk.ac.ed.morphml_handler.MorphologyList

setVisibleUp(boolean) - Method in class uk.ac.ed.morphml_handler.Cell

setVisibleUp(boolean) - Method in class uk.ac.ed.morphml_handler.Feature

setVisibleUp(boolean) - Method in class uk.ac.ed.morphml_handler.Morphology

setVisibleUp(boolean) - Method in class uk.ac.ed.morphml_handler.MorphologyData

setWarpData(WarpDataStructure) - Method in class uk.ac.ed.morphml_handler.MorphologyData

setWarpedDataFile(URI) - Method in class uk.ac.ed.morphml_handler.MorphologyData

setWarpedMorphology(Morphology) - Method in class uk.ac.ed.morphml_handler.MorphologyData

setX(double) - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint

setY(double) - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint

setZ(double) - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint

show() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

show() - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint

show() - Method in class uk.ac.ed.morphml_handler.Cell

show() - Method in class uk.ac.ed.morphml_handler.Feature

show() - Method in interface uk.ac.ed.morphml_handler.MorphMLEntity

show() - Method in class uk.ac.ed.morphml_handler.Morphology

show() - Method in class uk.ac.ed.morphml_handler.MorphologyData

show() - Method in class uk.ac.ed.morphml_handler.MorphologyList

SOLID - Static variable in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

surfaceSmoother(Point3d[][]) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

T

toString() - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint

toString() - Method in class uk.ac.ed.morphml_handler.Morphology

toString() - Method in class uk.ac.ed.morphml_handler.MorphologyData

toString() - Method in class uk.ac.ed.morphml_handler.MorphologyList

transform(Point) - Method in class uk.ac.ed.morphml_handler.warp.AffineTransformation

transform(Point) - Method in interface uk.ac.ed.morphml_handler.warp.WarpingTransformation

transformMorphology(Morphology, Matrix4d) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

transformPoint(AffineWarpPoint, Matrix4d) - Method in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

U

uk.ac.ed.morphml_handler - package uk.ac.ed.morphml_handler

uk.ac.ed.morphml_handler.accustage - package uk.ac.ed.morphml_handler.accustage

uk.ac.ed.morphml_handler.http - package uk.ac.ed.morphml_handler.http

uk.ac.ed.morphml_handler.neurolucida - package uk.ac.ed.morphml_handler.neurolucida

uk.ac.ed.morphml_handler.warp - package uk.ac.ed.morphml_handler.warp

uk.ac.ed.morphml_handler.warp.exception - package uk.ac.ed.morphml_handler.warp.exception

uploadMorphMLFile(MorphologyData, String, String) - Method in class uk.ac.ed.morphml_handler.DatabaseHandler

uploadMorphologyDataFile(MorphologyData) - Method in class uk.ac.ed.morphml_handler.DatabaseHandler

uri - Variable in class uk.ac.ed.morphml_handler.Morphology

uri - Variable in class uk.ac.ed.morphml_handler.MorphologyData

uri - Variable in class uk.ac.ed.morphml_handler.MorphologyList

V

validate() - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

validate() - Method in class uk.ac.ed.morphml_handler.AffineWarpPoint

validate() - Method in class uk.ac.ed.morphml_handler.Cell

validate() - Method in class uk.ac.ed.morphml_handler.Feature

validate() - Method in interface uk.ac.ed.morphml_handler.MorphMLEntity

validate() - Method in class uk.ac.ed.morphml_handler.Morphology

validate() - Method in class uk.ac.ed.morphml_handler.MorphologyData

validate() - Method in class uk.ac.ed.morphml_handler.MorphologyList

view - Variable in class uk.ac.ed.morphml_handler.MorphMLTree.PopupMenuController

visible - Variable in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

visible - Variable in class uk.ac.ed.morphml_handler.AffineWarpPoint

visible - Variable in class uk.ac.ed.morphml_handler.Cell

visible - Variable in class uk.ac.ed.morphml_handler.Feature

visible - Variable in class uk.ac.ed.morphml_handler.Morphology

visible - Variable in class uk.ac.ed.morphml_handler.MorphologyData

visible - Variable in class uk.ac.ed.morphml_handler.MorphologyList

W

warp() - Method in class uk.ac.ed.morphml_handler.MorphologyData

warp(Object) - Method in class uk.ac.ed.morphml_handler.warp.AffineWarp

warp(Object) - Method in interface uk.ac.ed.morphml_handler.warp.WarpingMethod

WARP_ALGORITHM_AFFLINE - Static variable in class uk.ac.ed.morphml_handler.MorphologyData

warp_matrix - Variable in class uk.ac.ed.morphml_handler.MorphologyData.MorphologyDataEvent

warp_point_listeners - Variable in class uk.ac.ed.morphml_handler.AffineWarpPoint

warp_points_listeners - Variable in class uk.ac.ed.morphml_handler.AffineWarpDataStructure

warp_points_table - Variable in class uk.ac.ed.morphml_handler.MorphMLPropertiesPanel

warpDataChanged(MorphologyData.MorphologyDataEvent) - Method in class uk.ac.ed.morphml_handler.MorphologyData.MorphologyDataAdapter

warpDataChanged(MorphologyData.MorphologyDataEvent) - Method in interface uk.ac.ed.morphml_handler.MorphologyData.MorphologyDataListener

warped_data_file - Variable in class uk.ac.ed.morphml_handler.MorphologyData

warpedMorphologyChanged(MorphologyData.MorphologyDataEvent) - Method in class uk.ac.ed.morphml_handler.MorphologyData.MorphologyDataAdapter

warpedMorphologyChanged(MorphologyData.MorphologyDataEvent) - Method in interface uk.ac.ed.morphml_handler.MorphologyData.MorphologyDataListener

WarpingException - Class in uk.ac.ed.morphml_handler.warp.exception

WarpingException(String) - Constructor for class uk.ac.ed.morphml_handler.warp.exception.WarpingException

Creates a new instance of WarpingException

WarpingMethod - Interface in uk.ac.ed.morphml_handler.warp

WarpingTransformation - Interface in uk.ac.ed.morphml_handler.warp

WarpMath - Class in uk.ac.ed.morphml_handler.warp

WarpMath() - Constructor for class uk.ac.ed.morphml_handler.warp.WarpMath

Creates a new instance of WarpMath

WIREFRAME - Static variable in class uk.ac.ed.morphml_handler.MorphMLJava3DPanel

world_point - Variable in class uk.ac.ed.morphml_handler.AffineWarpDataStructure.Pair

worldWarpPointAdded(AffineWarpDataStructure.AffineWarpDataEvent) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure.AffineWarpDataAdapter

worldWarpPointAdded(AffineWarpDataStructure.AffineWarpDataEvent) - Method in interface uk.ac.ed.morphml_handler.AffineWarpDataStructure.AffineWarpDataListener

worldWarpPointRemoved(AffineWarpDataStructure.AffineWarpDataEvent) - Method in class uk.ac.ed.morphml_handler.AffineWarpDataStructure.AffineWarpDataAdapter

worldWarpPointRemoved(AffineWarpDataStructure.AffineWarpDataEvent) - Method in interface uk.ac.ed.morphml_handler.AffineWarpDataStructure.AffineWarpDataListener

writeField(String, boolean) - Method in class uk.ac.ed.morphml_handler.http.MultiPartFormOutputStream

Writes an boolean field value.

writeField(String, double) - Method in class uk.ac.ed.morphml_handler.http.MultiPartFormOutputStream

Writes an double field value.

writeField(String, float) - Method in class uk.ac.ed.morphml_handler.http.MultiPartFormOutputStream

Writes an float field value.

writeField(String, long) - Method in class uk.ac.ed.morphml_handler.http.MultiPartFormOutputStream

Writes an long field value.

writeField(String, int) - Method in class uk.ac.ed.morphml_handler.http.MultiPartFormOutputStream

Writes an int field value.

writeField(String, short) - Method in class uk.ac.ed.morphml_handler.http.MultiPartFormOutputStream

Writes an short field value.

writeField(String, char) - Method in class uk.ac.ed.morphml_handler.http.MultiPartFormOutputStream

Writes an char field value.

writeField(String, String) - Method in class uk.ac.ed.morphml_handler.http.MultiPartFormOutputStream

Writes an string field value.

writeFile(String, String, File) - Method in class uk.ac.ed.morphml_handler.http.MultiPartFormOutputStream

Writes a file's contents.

writeFile(String, String, String, InputStream) - Method in class uk.ac.ed.morphml_handler.http.MultiPartFormOutputStream

Writes a input stream's contents.

writeFile(String, String, String, byte[]) - Method in class uk.ac.ed.morphml_handler.http.MultiPartFormOutputStream

Writes the given bytes.

writeMorphMLStream(MorphMLEntity, OutputStream) - Method in class uk.ac.ed.morphml_handler.MorphMLHandler

X

xml - Static variable in class uk.ac.ed.morphml_handler.MorphMLHandler

A B C D E F G H I J L M N O P R S T U V W X