Transformation (LibSBML Java API)

java.lang.Object
- org.sbml.libsbml.SBase
- - org.sbml.libsbml.Transformation

Direct Known Subclasses:

Transformation2D
```
public class Transformation
extends SBase
```
render Implementation of a 3D transformation matrix.
The Transformation class represents a 3D transformation which normally is a 4x4 matrix. Since the last row is always 0 0 0 1 for affine transformations, we leave out those values and store the matrix as an array of 4x3 columns

Constructor Summary

Constructors
Constructor and Description
`Transformation()` Creates a new `Transformation` using the given SBML Level, Version and “render” package version.
`Transformation(long level)` Creates a new `Transformation` using the given SBML Level, Version and “render” package version.
`Transformation(long level, long version)` Creates a new `Transformation` using the given SBML Level, Version and “render” package version.
`Transformation(long level, long version, long pkgVersion)` Creates a new `Transformation` using the given SBML Level, Version and “render” package version.
`Transformation(RenderPkgNamespaces renderns)` Creates a new `Transformation` using the given `RenderPkgNamespaces` object.
`Transformation(Transformation orig)` Copy constructor for `Transformation`.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`SBase`	`cloneObject()` Creates and returns a deep copy of this `Transformation` object.
`void`	`delete()` Explicitly deletes the underlying native object.
`java.lang.String`	`getElementName()` Returns the XML element name of this `Transformation` object.
`static SWIGTYPE_p_double`	`getIdentityMatrix()` Returns a 3D identity matrix.
`SWIGTYPE_p_double`	`getMatrix()` Returns the value of the 'transform' attribute of this `Transformation`.
`java.lang.String`	`getName()` Returns the value of the 'name' attribute of this `Transformation`.
`void`	`getTransform(SWIGTYPE_p_double outArray)` Returns the value of the 'transform' attribute of this `Transformation`.
`int`	`getTypeCode()` Returns the libSBML type code for this `Transformation` object.
`boolean`	`isEllipse()` Predicate returning `true` if this abstract `Transformation` is of type `Ellipse`
`boolean`	`isImage()` Predicate returning `true` if this abstract `Transformation` is of type `Image`
`boolean`	`isLineEnding()` Predicate returning `true` if this abstract `Transformation` is of type `LineEnding`
`boolean`	`isPolygon()` Predicate returning `true` if this abstract `Transformation` is of type `Polygon`
`boolean`	`isRectangle()` Predicate returning `true` if this abstract `Transformation` is of type `Rectangle`
`boolean`	`isRenderCurve()` Predicate returning `true` if this abstract `Transformation` is of type `RenderCurve`
`boolean`	`isRenderGroup()` Predicate returning `true` if this abstract `Transformation` is of type `RenderGroup`
`boolean`	`isSetMatrix()` Returns `true` if the matrix has been set or `false` otherwise.
`boolean`	`isSetName()` Predicate returning `true` if this `Transformation`'s 'name' attribute is set.
`boolean`	`isSetTransform()` Predicate returning `true` if this `Transformation`'s 'transform' attribute is set.
`boolean`	`isText()` Predicate returning `true` if this abstract `Transformation` is of type `Text`
`void`	`setMatrix(SWIGTYPE_p_double m)` Sets the matrix to the values given in the array.
`int`	`setName(java.lang.String name)` Sets the value of the 'name' attribute of this `Transformation`.
`int`	`setTransform(SWIGTYPE_p_double inArray)` Sets the value of the 'transform' attribute of this `Transformation`.
`int`	`unsetMatrix()` Unsets the value of the 'transform' attribute of this `Transformation`.
`int`	`unsetName()` Unsets the value of the 'name' attribute of this `Transformation`.
`int`	`unsetTransform()` Unsets the value of the 'transform' attribute of this `Transformation`.

Methods inherited from class org.sbml.libsbml.SBase
addCVTerm, addCVTerm, appendAnnotation, appendAnnotation, appendNotes, appendNotes, connectToChild, deleteDisabledPlugins, deleteDisabledPlugins, disablePackage, enablePackage, equals, getAncestorOfType, getAncestorOfType, getAnnotation, getAnnotationString, getColumn, getCVTerm, getCVTerms, getDisabledPlugin, getElementByMetaId, getElementBySId, getId, getIdAttribute, getLevel, getLine, getListOfAllElements, getListOfAllElements, getListOfAllElementsFromPlugins, getListOfAllElementsFromPlugins, getMetaId, getModel, getModelHistory, getNamespaces, getNotes, getNotesString, getNumCVTerms, getNumDisabledPlugins, getNumPlugins, getPackageCoreVersion, getPackageName, getPackageVersion, getParentSBMLObject, getPlugin, getPlugin, getPrefix, getResourceBiologicalQualifier, getResourceModelQualifier, getSBMLDocument, getSBOTerm, getSBOTermAsURL, getSBOTermID, getURI, getVersion, hashCode, hasValidLevelVersionNamespaceCombination, isPackageEnabled, isPackageURIEnabled, isPkgEnabled, isPkgURIEnabled, isSetAnnotation, isSetId, isSetIdAttribute, isSetMetaId, isSetModelHistory, isSetNotes, isSetSBOTerm, isSetUserData, matchesRequiredSBMLNamespacesForAddition, matchesSBMLNamespaces, removeFromParentAndDelete, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, removeTopLevelAnnotationElement, renameMetaIdRefs, renameSIdRefs, renameUnitSIdRefs, replaceTopLevelAnnotationElement, replaceTopLevelAnnotationElement, setAnnotation, setAnnotation, setId, setIdAttribute, setMetaId, setModelHistory, setNamespaces, setNotes, setNotes, setNotes, setSBOTerm, setSBOTerm, toSBML, toXMLNode, unsetAnnotation, unsetCVTerms, unsetId, unsetIdAttribute, unsetMetaId, unsetModelHistory, unsetNotes, unsetSBOTerm, unsetUserData

Methods inherited from class java.lang.Object
getClass, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - Transformation
```
public Transformation(long level,
                      long version,
                      long pkgVersion)
```
    Creates a new Transformation using the given SBML Level, Version and “render” package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this Transformation.
    
    version - a long integer, the SBML Version to assign to this Transformation.
    
    pkgVersion - a long integer, the SBML Render Version to assign to this Transformation.
    
    Note:
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - Transformation
```
public Transformation(long level,
                      long version)
```
    Creates a new Transformation using the given SBML Level, Version and “render” package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this Transformation.
    
    version - a long integer, the SBML Version to assign to this Transformation.
    
    pkgVersion - a long integer, the SBML Render Version to assign to this Transformation.
    
    Note:
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - Transformation
```
public Transformation(long level)
```
    Creates a new Transformation using the given SBML Level, Version and “render” package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this Transformation.
    
    version - a long integer, the SBML Version to assign to this Transformation.
    
    pkgVersion - a long integer, the SBML Render Version to assign to this Transformation.
    
    Note:
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - Transformation
```
public Transformation()
```
    Creates a new Transformation using the given SBML Level, Version and “render” package version.
    
    Parameters:
    
    level - a long integer, the SBML Level to assign to this Transformation.
    
    version - a long integer, the SBML Version to assign to this Transformation.
    
    pkgVersion - a long integer, the SBML Render Version to assign to this Transformation.
    
    Note:
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - Transformation
```
public Transformation(RenderPkgNamespaces renderns)
```
    Creates a new Transformation using the given RenderPkgNamespaces object.
    
    The package namespaces object used in this constructor is derived from a SBMLNamespaces object, which encapsulates SBML Level/Version/namespaces information. It is used to communicate the SBML Level, Version, and package version and name information used in addition to SBML Level 3 Core. A common approach to using libSBML's SBMLNamespaces facilities is to create an package namespace object somewhere in a program once, then hand that object as needed to object constructors of that package that accept it as and argument, such as this one.
    
    Parameters:
    
    renderns - the RenderPkgNamespaces object.
    
    Note:
    
    Attempting to add an object to an SBMLDocument having a different combination of SBML Level, Version and XML namespaces than the object itself will result in an error at the time a caller attempts to make the addition. A parent object must have compatible Level, Version and XML namespaces. (Strictly speaking, a parent may also have more XML namespaces than a child, but the reverse is not permitted.) The restriction is necessary to ensure that an SBML model has a consistent overall structure. This requires callers to manage their objects carefully, but the benefit is increased flexibility in how models can be created by permitting callers to create objects bottom-up if desired. In situations where objects are not yet attached to parents (e.g., SBMLDocument), knowledge of the intented SBML Level and Version help libSBML determine such things as whether it is valid to assign a particular value to an attribute. For packages, this means that the parent object to which this package element is being added must have been created with the package namespace, or that the package namespace was added to it, even if that parent is not a package object itself.
  - Transformation
```
public Transformation(Transformation orig)
```
    Copy constructor for Transformation.
    
    Parameters:
    
    orig - the Transformation instance to copy.
- Method Detail
  - delete
```
public void delete()
```
    Explicitly deletes the underlying native object.
    In general, application software will not need to call this method directly. The Java language binding for libSBML is implemented as a language wrapper that provides a Java interface to libSBML's underlying C++/C code. Some of the Java methods return objects that are linked to objects created not by Java code, but by C++ code. The Java objects wrapped around them will be deleted when the garbage collector invokes the corresponding C++ finalize() methods for the objects. The finalize() methods in turn call the Transformation.delete() method on the libSBML object.
    This method is exposed in case calling programs want to ensure that the underlying object is freed immediately, and not at some arbitrary time determined by the Java garbage collector. In normal usage, callers do not need to invoke Transformation.delete() themselves.
    
    Overrides:
    
    delete in class SBase
  - cloneObject
```
public SBase cloneObject()
```
    Creates and returns a deep copy of this Transformation object.
    
    Overrides:
    
    cloneObject in class SBase
    
    Returns:
    
    a (deep) copy of this Transformation object.
  - getTransform
```
public void getTransform(SWIGTYPE_p_double outArray)
```
    Returns the value of the 'transform' attribute of this Transformation.
    
    Parameters:
    
    outArray - double* array that will be used to return the value of the 'transform' attribute of this Transformation.
    
    Note:
    
    the value of the 'transform' attribute of this Transformation is returned in the argument array.
  - getName
```
public java.lang.String getName()
```
    Returns the value of the 'name' attribute of this Transformation.
    
    Overrides:
    
    getName in class SBase
    
    Returns:
    
    the value of the 'name' attribute of this Transformation as a string.
    
    See Also:
    
    SBase.getIdAttribute(), SBase.isSetName(), SBase.setName(String sid), SBase.unsetName()
  - getMatrix
```
public SWIGTYPE_p_double getMatrix()
```
    Returns the value of the 'transform' attribute of this Transformation. which is an array of double values of length 12.
    
    Returns:
    
    a pointer to the array of numbers for the transformation.
  - getIdentityMatrix
```
public static SWIGTYPE_p_double getIdentityMatrix()
```
    Returns a 3D identity matrix. The matrix contains 12 double values.
  - isSetTransform
```
public boolean isSetTransform()
```
    Predicate returning true if this Transformation's 'transform' attribute is set.
    
    Returns:
    
    true if this Transformation's 'transform' attribute has been set, otherwise false is returned.
  - isSetName
```
public boolean isSetName()
```
    Predicate returning true if this Transformation's 'name' attribute is set.
    
    Overrides:
    
    isSetName in class SBase
    
    Returns:
    
    true if this Transformation's 'name' attribute has been set, otherwise false is returned.
    
    See Also:
    
    SBase.getName(), SBase.setName(String sid), SBase.unsetName()
  - isSetMatrix
```
public boolean isSetMatrix()
```
    Returns true if the matrix has been set or false otherwise. The matrix is considered as set if none of the values in the matrix is NaN.
    
    Returns:
    
    true or false depending on whether a NaN was found.
  - setTransform
```
public int setTransform(SWIGTYPE_p_double inArray)
```
    Sets the value of the 'transform' attribute of this Transformation.
    Parameters:
    
    inArray - double* array value of the 'transform' attribute to be set.
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_INVALID_ATTRIBUTE_VALUE
  - setName
```
public int setName(java.lang.String name)
```
    Sets the value of the 'name' attribute of this Transformation.
    Overrides:
    
    setName in class SBase
    
    Parameters:
    
    name - String& value of the 'name' attribute to be set.
    
    Returns:
    integer value indicating success/failure of the function. This particular function only does one thing irrespective of user input or object state, and thus will only return a single value:
    
    LIBSBML_OPERATION_SUCCESS
    
    Calling this function with name = null or an empty string is equivalent to calling unsetName().
  - setMatrix
```
public void setMatrix(SWIGTYPE_p_double m)
```
    Sets the matrix to the values given in the array.
    
    Parameters:
    
    m - array with new values to be set for this Transformation object.
  - unsetTransform
```
public int unsetTransform()
```
    Unsets the value of the 'transform' attribute of this Transformation.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - unsetName
```
public int unsetName()
```
    Unsets the value of the 'name' attribute of this Transformation.
    Overrides:
    
    unsetName in class SBase
    
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
    See Also:
    
    SBase.getName(), SBase.setName(String sid), SBase.isSetName()
  - unsetMatrix
```
public int unsetMatrix()
```
    Unsets the value of the 'transform' attribute of this Transformation.
    Returns:
    integer value indicating success/failure of the function. The possible values returned by this function are:
    
    LIBSBML_OPERATION_SUCCESS
    LIBSBML_OPERATION_FAILED
  - isImage
```
public boolean isImage()
```
    Predicate returning true if this abstract Transformation is of type Image
    
    Returns:
    
    true if this abstract Transformation is of type Image, false otherwise
  - isEllipse
```
public boolean isEllipse()
```
    Predicate returning true if this abstract Transformation is of type Ellipse
    
    Returns:
    
    true if this abstract Transformation is of type Ellipse, false otherwise
  - isRectangle
```
public boolean isRectangle()
```
    Predicate returning true if this abstract Transformation is of type Rectangle
    
    Returns:
    
    true if this abstract Transformation is of type Rectangle, false otherwise
  - isPolygon
```
public boolean isPolygon()
```
    Predicate returning true if this abstract Transformation is of type Polygon
    
    Returns:
    
    true if this abstract Transformation is of type Polygon, false otherwise
  - isRenderGroup
```
public boolean isRenderGroup()
```
    Predicate returning true if this abstract Transformation is of type RenderGroup
    
    Returns:
    
    true if this abstract Transformation is of type RenderGroup, false otherwise
  - isLineEnding
```
public boolean isLineEnding()
```
    Predicate returning true if this abstract Transformation is of type LineEnding
    
    Returns:
    
    true if this abstract Transformation is of type LineEnding, false otherwise
  - isText
```
public boolean isText()
```
    Predicate returning true if this abstract Transformation is of type Text
    
    Returns:
    
    true if this abstract Transformation is of type Text, false otherwise
  - isRenderCurve
```
public boolean isRenderCurve()
```
    Predicate returning true if this abstract Transformation is of type RenderCurve
    
    Returns:
    
    true if this abstract Transformation is of type RenderCurve, false otherwise
  - getElementName
```
public java.lang.String getElementName()
```
    Returns the XML element name of this Transformation object.
    For Transformation, the XML element name is always 'transformation'.
    
    Overrides:
    
    getElementName in class SBase
    
    Returns:
    
    the name of this element, i.e. 'transformation'.
  - getTypeCode
```
public int getTypeCode()
```
    Returns the libSBML type code for this Transformation object.
    
    LibSBML attaches an identifying code to every kind of SBML object. These are integer constants known as SBML type codes. The names of all the codes begin with the characters SBML_. In the Java language interface for libSBML, the type codes are defined as static integer constants in the interface class libsbmlConstants. Note that different Level 3 package plug-ins may use overlapping type codes; to identify the package to which a given object belongs, call the SBase.getPackageName() method on the object.
    The exception to this is lists: all SBML-style list elements have the type SBML_LIST_OF, regardless of what package they are from.
    
    Overrides:
    
    getTypeCode in class SBase
    
    Returns:
    
    the SBML type code for this object: SBML_RENDER_TRANSFORMATION.
    
    See Also:
    
    Transformation.getElementName(), SBase.getPackageName()
    
    Warning:
    
    The specific integer values of the possible type codes may be reused by different libSBML plug-ins for SBML Level 3. packages, To fully identify the correct code, it is necessary to invoke both getPackageName() and getTypeCode() (or ListOf.getItemTypeCode()).

Class Transformation

Constructor Summary

Method Summary

Methods inherited from class org.sbml.libsbml.SBase

Methods inherited from class java.lang.Object

Constructor Detail

Transformation

Transformation

Transformation

Transformation

Transformation

Transformation

Method Detail

delete

cloneObject

getTransform

getName

getMatrix

getIdentityMatrix

isSetTransform

isSetName

isSetMatrix

setTransform

setName

setMatrix

unsetTransform

unsetName

unsetMatrix

isImage

isEllipse

isRectangle

isPolygon

isRenderGroup

isLineEnding

isText

isRenderCurve

getElementName

getTypeCode