public class SpatialSBMLExporter extends Object
Constructor and Description |
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SpatialSBMLExporter()
Instantiates a new spatial SBML exporter.
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SpatialSBMLExporter(SpatialImage spImg)
Instantiates a new spatial SBML exporter with given SpatialImage.
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Modifier and Type | Method and Description |
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void |
addAdjacentDomains()
Adds the adjacent domains.
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void |
addCoordinates()
Adds the coordinates to the Geometry object.
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void |
addCoordinates(HashMap<String,org.scijava.vecmath.Point3d> hashBound)
Adds the coordinates to the Geometry object.
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void |
addCoordParameter()
Adds the global Parameter to each CoordinateComponent.
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void |
addDomains()
Adds domains to corresponding domaintypes.
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void |
addDomainTypes()
Adds the domain types to the Geometry object.
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void |
addGeometryDefinitions()
Adds the geometry definitions.
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void |
addParaGeoDefinitions(HashMap<String,List<org.scijava.vecmath.Point3d>> hashVertices,
HashMap<String,org.scijava.vecmath.Point3d> hashBound)
Adds the parametric geometry definitions.
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void |
addUniqueVertices(org.sbml.jsbml.ext.spatial.SpatialPoints sp,
ArrayList<org.scijava.vecmath.Point3d> uniquePointSet)
Adds the unique vertices to the SpatialPoints object.
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void |
addUnits()
Adds the units (length, area and volume) to the model.
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int[] |
byteArrayToIntArray(byte[] compressed)
Convert byte array to int array.
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byte[] |
compressRawData(byte[] raw)
Compress raw data of spatial image in 1D array.
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void |
createGeometryElements()
Creates the geometry elements.
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void |
createParametric(HashMap<String,List<org.scijava.vecmath.Point3d>> hashVertices,
HashMap<String,org.scijava.vecmath.Point3d> hathBound)
Creates the ParametricGeometry.
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org.sbml.jsbml.SBMLDocument |
getDocument()
Gets the SBML document.
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org.sbml.jsbml.ext.spatial.SpatialNamedSBase |
getFromSpatialList(org.sbml.jsbml.ListOf<?> list,
String id)
Returns SpatialNamedSBase object which has SpatialId "id" from given list of Objects.
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org.sbml.jsbml.Model |
getModel()
Gets the SBML model.
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void |
setCoordinateBoundary(org.sbml.jsbml.ext.spatial.CoordinateComponent coordinateComponent,
String spId,
double min,
double max,
double delta)
Sets the minimum and maximum values of the coordinate axis (boundary) to
a CoordinateComponent object which explicitly defines a coordinate component of
the coordinate axes.
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void |
setPointIndex(org.sbml.jsbml.ext.spatial.ParametricObject po,
List<org.scijava.vecmath.Point3d> list,
ArrayList<org.scijava.vecmath.Point3d> uniquePointSet)
Sets the index of unique vertices to the SpatialPoints object.
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public SpatialSBMLExporter()
public SpatialSBMLExporter(SpatialImage spImg)
spImg
- the SpatialImage
public void createGeometryElements()
public void addGeometryDefinitions()
public byte[] compressRawData(byte[] raw)
raw
- the raw data of spatial image in 1D arraypublic int[] byteArrayToIntArray(byte[] compressed)
compressed
- the compressed 1D byte arraypublic void addAdjacentDomains()
public void addDomains()
public org.sbml.jsbml.ext.spatial.SpatialNamedSBase getFromSpatialList(org.sbml.jsbml.ListOf<?> list, String id)
list
- list of objects (ex. SpatialNamedSbase)id
- SpatialIdpublic void addDomainTypes()
public void addCoordinates()
public void setCoordinateBoundary(org.sbml.jsbml.ext.spatial.CoordinateComponent coordinateComponent, String spId, double min, double max, double delta)
coordinateComponent
- the CoordinateComponent objectspId
- the spatialId as Stringmin
- the minimum value of the coordinate axismax
- the maximum value of the coordinate axisdelta
- the deltapublic void addCoordParameter()
public org.sbml.jsbml.Model getModel()
public org.sbml.jsbml.SBMLDocument getDocument()
public void addUnits()
public void createParametric(HashMap<String,List<org.scijava.vecmath.Point3d>> hashVertices, HashMap<String,org.scijava.vecmath.Point3d> hathBound)
hashVertices
- the hashmap of verticeshathBound
- the hashmap of boundarypublic void addCoordinates(HashMap<String,org.scijava.vecmath.Point3d> hashBound)
hashBound
- the hashmap of boundarypublic void addParaGeoDefinitions(HashMap<String,List<org.scijava.vecmath.Point3d>> hashVertices, HashMap<String,org.scijava.vecmath.Point3d> hashBound)
hashVertices
- the hashmap of verticeshashBound
- the hashmap of boundarypublic void addUniqueVertices(org.sbml.jsbml.ext.spatial.SpatialPoints sp, ArrayList<org.scijava.vecmath.Point3d> uniquePointSet)
sp
- the SpatialPoints of the ParametricGeometryuniquePointSet
- the ArrayList of Point3d (unique point set)public void setPointIndex(org.sbml.jsbml.ext.spatial.ParametricObject po, List<org.scijava.vecmath.Point3d> list, ArrayList<org.scijava.vecmath.Point3d> uniquePointSet)
po
- the ParametricObjectlist
- the list of Point3duniquePointSet
- the ArrayList of Point3d (unique point set)Copyright © 2017–2019 Funahashi Lab.. All rights reserved.