uk.ac.ed.morphml_handler
Class MorphMLHandler
java.lang.Object
javax.xml.bind.JAXBContext
org.virtualratbrain.namespace.impl.runtime.DefaultJAXBContextImpl
org.virtualratbrain.namespace.ObjectFactory
uk.ac.ed.morphml_handler.MorphMLHandler
public class MorphMLHandler
- extends org.virtualratbrain.namespace.ObjectFactory
| Fields inherited from class org.virtualratbrain.namespace.ObjectFactory |
grammarInfo, version |
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Method Summary |
void |
addMorphMLHandlerListener(MorphMLHandler.MorphMLHandlerListener listener)
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void |
addMorphologyList(MorphologyList morphology_list)
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protected void |
fireMorphologListRemoved(MorphologyList morphology_list)
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protected void |
fireMorphologyListAdded(MorphologyList morphology_list)
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static AccustageHandler |
getAccustageHandler()
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static DatabaseHandler |
getDatabaseHandler()
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static FileFilter |
getFileFilter()
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static MorphMLHandler |
getMorphMLHandler()
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MorphologyList[] |
getMorphologyLists()
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static NeurolucidaHandler |
getNeurolucidaHandler()
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protected void |
initJAXBContext()
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static boolean |
isMorphmlFile(File file)
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static boolean |
isMorphmlFileName(String file_name)
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AffineWarpDataStructure |
newAffineWarpData()
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AffineWarpPoint |
newAffineWarpPoint(int id)
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Cell |
newCell(String name)
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org.virtualratbrain.namespace.CellBody |
newCellBody()
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Feature |
newFeature(String name)
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org.virtualratbrain.namespace.FreePoints |
newFreePoints()
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Morphology |
newMorphology()
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MorphologyData |
newMorphologyData()
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MorphologyList |
newMorphologyList()
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org.virtualratbrain.namespace.Point |
newPoint(int id,
double x,
double y,
double z,
double diam)
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org.virtualratbrain.namespace.Point |
newPoint(org.virtualratbrain.namespace.Point point)
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org.virtualratbrain.namespace.Polygon |
newPolygon()
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Properties |
newProperties()
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org.virtualratbrain.namespace.Property |
newProperty(String name,
String value)
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org.virtualratbrain.namespace.Segment |
newSegment(int segment_id,
int proximal_point_id,
int distal_point_id)
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org.virtualratbrain.namespace.Segment |
newSegment(int segment_id,
int proximal_point_id,
int distal_point_id,
int parent_segment_id)
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org.virtualratbrain.namespace.Segment |
newSegment(int segment_id,
int proximal_point_id,
int distal_point_id,
int parent_segment_id,
String group_name)
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org.virtualratbrain.namespace.Segment |
newSegment(int segment_id,
int proximal_point_id,
int distal_point_id,
String group_name)
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org.virtualratbrain.namespace.Segment |
newSegment(org.virtualratbrain.namespace.Segment segment)
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static Morphology |
openAccustageURI(URI uri)
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static MorphologyData |
openMorphologyDateURI(URI uri)
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static MorphologyList |
openMorphologyListURI(URI uri)
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static Morphology |
openMorphologyURI(URI uri)
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static Morphology |
openNeurolucidaURI(URI uri)
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protected MorphMLEntity |
readMorphMLStream(InputStream stream)
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void |
removeMorphMLHandlerListener(MorphMLHandler.MorphMLHandlerListener listener)
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void |
removeMorphologyList(MorphologyList morphology_list)
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static void |
saveMorphology(Morphology morphology)
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static void |
saveMorphologyData(MorphologyData morphology_data)
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static void |
saveMorphologyList(MorphologyList morphology_list)
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static File |
selectFileToOpen()
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static File |
selectFileToSave()
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protected void |
writeMorphMLStream(MorphMLEntity entity,
OutputStream stream)
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| Methods inherited from class org.virtualratbrain.namespace.ObjectFactory |
createAffineWarpData, createAffineWarpDataStructure, createAffineWarpPoint, createCell, createCellBody, createCellSegmentsType, createCellSpinesType, createDendritic, createFeature, createFreePoints, createManifold, createMorphology, createMorphologyCellsType, createMorphologyData, createMorphologyFeaturesType, createMorphologyList, createMorphologyPointsType, createPath, createPoint, createPointIds, createPolygon, createPolyhedron, createPolyhedronPolygonsType, createProperties, createProperty, createRootMorphology, createRootMorphologyData, createRootMorphologyList, createSegment, createSphere, createSpine, createWarpData, createWarpDataStructure, getProperty, newInstance, setProperty |
| Methods inherited from class org.virtualratbrain.namespace.impl.runtime.DefaultJAXBContextImpl |
createMarshaller, createUnmarshaller, createValidator, getGrammar, getGrammarInfo |
| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
xml
public static final String xml
- See Also:
- Constant Field Values
morphml
public static final String morphml
- See Also:
- Constant Field Values
handler
protected static MorphMLHandler handler
database_handler
protected static DatabaseHandler database_handler
neurolucida_handler
protected static NeurolucidaHandler neurolucida_handler
accustage_handler
protected static AccustageHandler accustage_handler
open_file_chooser
protected static JFileChooser open_file_chooser
savefile_chooser
protected static JFileChooser savefile_chooser
jc
protected JAXBContext jc
morphology_lists
protected ArrayList morphology_lists
morphml_handler_listeners
protected ArrayList morphml_handler_listeners
MorphMLHandler
protected MorphMLHandler()
isMorphmlFile
public static boolean isMorphmlFile(File file)
isMorphmlFileName
public static boolean isMorphmlFileName(String file_name)
selectFileToOpen
public static File selectFileToOpen()
selectFileToSave
public static File selectFileToSave()
getFileFilter
public static FileFilter getFileFilter()
openMorphologyURI
public static Morphology openMorphologyURI(URI uri)
openNeurolucidaURI
public static Morphology openNeurolucidaURI(URI uri)
openAccustageURI
public static Morphology openAccustageURI(URI uri)
openMorphologyListURI
public static MorphologyList openMorphologyListURI(URI uri)
openMorphologyDateURI
public static MorphologyData openMorphologyDateURI(URI uri)
saveMorphology
public static void saveMorphology(Morphology morphology)
saveMorphologyData
public static void saveMorphologyData(MorphologyData morphology_data)
saveMorphologyList
public static void saveMorphologyList(MorphologyList morphology_list)
getMorphMLHandler
public static MorphMLHandler getMorphMLHandler()
getDatabaseHandler
public static DatabaseHandler getDatabaseHandler()
getNeurolucidaHandler
public static NeurolucidaHandler getNeurolucidaHandler()
getAccustageHandler
public static AccustageHandler getAccustageHandler()
newMorphologyList
public MorphologyList newMorphologyList()
newMorphologyData
public MorphologyData newMorphologyData()
newAffineWarpData
public AffineWarpDataStructure newAffineWarpData()
newAffineWarpPoint
public AffineWarpPoint newAffineWarpPoint(int id)
addMorphologyList
public void addMorphologyList(MorphologyList morphology_list)
removeMorphologyList
public void removeMorphologyList(MorphologyList morphology_list)
getMorphologyLists
public MorphologyList[] getMorphologyLists()
addMorphMLHandlerListener
public void addMorphMLHandlerListener(MorphMLHandler.MorphMLHandlerListener listener)
removeMorphMLHandlerListener
public void removeMorphMLHandlerListener(MorphMLHandler.MorphMLHandlerListener listener)
readMorphMLStream
protected MorphMLEntity readMorphMLStream(InputStream stream)
writeMorphMLStream
protected void writeMorphMLStream(MorphMLEntity entity,
OutputStream stream)
fireMorphologyListAdded
protected void fireMorphologyListAdded(MorphologyList morphology_list)
fireMorphologListRemoved
protected void fireMorphologListRemoved(MorphologyList morphology_list)
newMorphology
public Morphology newMorphology()
newProperty
public org.virtualratbrain.namespace.Property newProperty(String name,
String value)
newCell
public Cell newCell(String name)
newPoint
public org.virtualratbrain.namespace.Point newPoint(org.virtualratbrain.namespace.Point point)
newPoint
public org.virtualratbrain.namespace.Point newPoint(int id,
double x,
double y,
double z,
double diam)
newFeature
public Feature newFeature(String name)
newProperties
public Properties newProperties()
newPolygon
public org.virtualratbrain.namespace.Polygon newPolygon()
newFreePoints
public org.virtualratbrain.namespace.FreePoints newFreePoints()
newCellBody
public org.virtualratbrain.namespace.CellBody newCellBody()
newSegment
public org.virtualratbrain.namespace.Segment newSegment(org.virtualratbrain.namespace.Segment segment)
newSegment
public org.virtualratbrain.namespace.Segment newSegment(int segment_id,
int proximal_point_id,
int distal_point_id,
int parent_segment_id,
String group_name)
newSegment
public org.virtualratbrain.namespace.Segment newSegment(int segment_id,
int proximal_point_id,
int distal_point_id,
int parent_segment_id)
newSegment
public org.virtualratbrain.namespace.Segment newSegment(int segment_id,
int proximal_point_id,
int distal_point_id,
String group_name)
newSegment
public org.virtualratbrain.namespace.Segment newSegment(int segment_id,
int proximal_point_id,
int distal_point_id)
initJAXBContext
protected void initJAXBContext()