X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2Fdescriptors%2FSequenceSetDescriptor.java;h=cd74c6e61ace466d14fc0ec881aa1c11a2137a0c;hb=382f5ff058a4c2fed1e9874bb712b40f16ec1a4e;hp=2801940f03c43d56d2c87701045891e139a03f14;hpb=09ee1649c4427f534331aa2017a890529f0932f5;p=jalview.git diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java index 2801940..cd74c6e 100644 --- a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java @@ -1,330 +1,472 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.schemabinding.version2.descriptors; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import jalview.schemabinding.version2.SequenceSet; - -/** - * Class SequenceSetDescriptor. - * - * @version $Revision$ $Date$ - */ -public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - /** - * Field _identity. - */ - private org.exolab.castor.xml.XMLFieldDescriptor _identity; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceSetDescriptor() { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "SequenceSet"; - _elementDefinition = true; - - //-- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - //-- initialize attribute descriptors - - //-- _gapChar - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getGapChar(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSet target = (SequenceSet) object; - target.setGapChar( (java.lang.String) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - //-- validation code for: _gapChar - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { //-- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - //-- initialize element descriptors - - //-- _sequenceList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getSequence(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSet target = (SequenceSet) object; - target.addSequence( (jalview.schemabinding.version2.Sequence) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - SequenceSet target = (SequenceSet) object; - target.removeAllSequence(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.Sequence(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _sequenceList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _annotationList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotationList", "Annotation", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getAnnotation(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSet target = (SequenceSet) object; - target.addAnnotation( (jalview.schemabinding.version2.Annotation) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - SequenceSet target = (SequenceSet) object; - target.removeAllAnnotation(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.Annotation(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _annotationList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - //-- _sequenceSetPropertiesList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSetProperties.class, "_sequenceSetPropertiesList", "sequenceSetProperties", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() { - public java.lang.Object getValue( java.lang.Object object ) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getSequenceSetProperties(); - } - public void setValue( java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try { - SequenceSet target = (SequenceSet) object; - target.addSequenceSetProperties( (jalview.schemabinding.version2.SequenceSetProperties) value); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { - try { - SequenceSet target = (SequenceSet) object; - target.removeAllSequenceSetProperties(); - } catch (java.lang.Exception ex) { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) { - return new jalview.schemabinding.version2.SequenceSetProperties(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - //-- validation code for: _sequenceSetPropertiesList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { //-- local scope - } - desc.setValidator(fieldValidator); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode( - ) { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no - * identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity( - ) { - return _identity; - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass( - ) { - return jalview.schemabinding.version2.SequenceSet.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix( - ) { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and - * unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI( - ) { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator( - ) { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName( - ) { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that - * of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition( - ) { - return _elementDefinition; - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.SequenceSet; + +/** + * Class SequenceSetDescriptor. + * + * @version $Revision$ $Date$ + */ +public class SequenceSetDescriptor extends + org.exolab.castor.xml.util.XMLClassDescriptorImpl +{ + + // --------------------------/ + // - Class/Member Variables -/ + // --------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + // ----------------/ + // - Constructors -/ + // ----------------/ + + public SequenceSetDescriptor() + { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "SequenceSet"; + _elementDefinition = true; + + // -- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + // -- initialize attribute descriptors + + // -- _gapChar + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( + java.lang.String.class, "_gapChar", "gapChar", + org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() + { + public java.lang.Object getValue(java.lang.Object object) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getGapChar(); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + SequenceSet target = (SequenceSet) object; + target.setGapChar((java.lang.String) value); + } catch (java.lang.Exception ex) + { + throw new IllegalStateException(ex.toString()); + } + } + + public java.lang.Object newInstance(java.lang.Object parent) + { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + // -- validation code for: _gapChar + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { // -- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + // -- _datasetId + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( + java.lang.String.class, "_datasetId", "datasetId", + org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() + { + public java.lang.Object getValue(java.lang.Object object) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getDatasetId(); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + SequenceSet target = (SequenceSet) object; + target.setDatasetId((java.lang.String) value); + } catch (java.lang.Exception ex) + { + throw new IllegalStateException(ex.toString()); + } + } + + public java.lang.Object newInstance(java.lang.Object parent) + { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + // -- validation code for: _datasetId + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { // -- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + // -- initialize element descriptors + + // -- _sequenceList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( + jalview.schemabinding.version2.Sequence.class, "_sequenceList", + "Sequence", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() + { + public java.lang.Object getValue(java.lang.Object object) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getSequence(); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + SequenceSet target = (SequenceSet) object; + target.addSequence((jalview.schemabinding.version2.Sequence) value); + } catch (java.lang.Exception ex) + { + throw new IllegalStateException(ex.toString()); + } + } + + public void resetValue(Object object) throws IllegalStateException, + IllegalArgumentException + { + try + { + SequenceSet target = (SequenceSet) object; + target.removeAllSequence(); + } catch (java.lang.Exception ex) + { + throw new IllegalStateException(ex.toString()); + } + } + + public java.lang.Object newInstance(java.lang.Object parent) + { + return new jalview.schemabinding.version2.Sequence(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + // -- validation code for: _sequenceList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { // -- local scope + } + desc.setValidator(fieldValidator); + // -- _annotationList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( + jalview.schemabinding.version2.Annotation.class, + "_annotationList", "Annotation", + org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() + { + public java.lang.Object getValue(java.lang.Object object) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getAnnotation(); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + SequenceSet target = (SequenceSet) object; + target.addAnnotation((jalview.schemabinding.version2.Annotation) value); + } catch (java.lang.Exception ex) + { + throw new IllegalStateException(ex.toString()); + } + } + + public void resetValue(Object object) throws IllegalStateException, + IllegalArgumentException + { + try + { + SequenceSet target = (SequenceSet) object; + target.removeAllAnnotation(); + } catch (java.lang.Exception ex) + { + throw new IllegalStateException(ex.toString()); + } + } + + public java.lang.Object newInstance(java.lang.Object parent) + { + return new jalview.schemabinding.version2.Annotation(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + // -- validation code for: _annotationList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { // -- local scope + } + desc.setValidator(fieldValidator); + // -- _sequenceSetPropertiesList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( + jalview.schemabinding.version2.SequenceSetProperties.class, + "_sequenceSetPropertiesList", "sequenceSetProperties", + org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() + { + public java.lang.Object getValue(java.lang.Object object) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getSequenceSetProperties(); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + SequenceSet target = (SequenceSet) object; + target.addSequenceSetProperties((jalview.schemabinding.version2.SequenceSetProperties) value); + } catch (java.lang.Exception ex) + { + throw new IllegalStateException(ex.toString()); + } + } + + public void resetValue(Object object) throws IllegalStateException, + IllegalArgumentException + { + try + { + SequenceSet target = (SequenceSet) object; + target.removeAllSequenceSetProperties(); + } catch (java.lang.Exception ex) + { + throw new IllegalStateException(ex.toString()); + } + } + + public java.lang.Object newInstance(java.lang.Object parent) + { + return new jalview.schemabinding.version2.SequenceSetProperties(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + // -- validation code for: _sequenceSetPropertiesList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { // -- local scope + } + desc.setValidator(fieldValidator); + // -- _alcodonFrameList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( + jalview.schemabinding.version2.AlcodonFrame.class, + "_alcodonFrameList", "AlcodonFrame", + org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() + { + public java.lang.Object getValue(java.lang.Object object) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getAlcodonFrame(); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + SequenceSet target = (SequenceSet) object; + target.addAlcodonFrame((jalview.schemabinding.version2.AlcodonFrame) value); + } catch (java.lang.Exception ex) + { + throw new IllegalStateException(ex.toString()); + } + } + + public void resetValue(Object object) throws IllegalStateException, + IllegalArgumentException + { + try + { + SequenceSet target = (SequenceSet) object; + target.removeAllAlcodonFrame(); + } catch (java.lang.Exception ex) + { + throw new IllegalStateException(ex.toString()); + } + } + + public java.lang.Object newInstance(java.lang.Object parent) + { + return new jalview.schemabinding.version2.AlcodonFrame(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + // -- validation code for: _alcodonFrameList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { // -- local scope + } + desc.setValidator(fieldValidator); + } + + // -----------/ + // - Methods -/ + // -----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode() + { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity() + { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass() + { + return jalview.schemabinding.version2.SequenceSet.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix() + { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI() + { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator() + { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName() + { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition() + { + return _elementDefinition; + } + +}