X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fuk%2Fac%2Fvamsas%2Fobjects%2Fcore%2Fdescriptors%2FSequenceDescriptor.java;h=d67e4e8e747b6f6db4e3eff413b78cc7ac57798e;hb=844ccad5a3fcbedec17b2af66d460f31abc7cff1;hp=d18b8c122dcc0749fad5e049d079103952e6bf60;hpb=6f33f705957d674dc2ab6c994a6ea87f7a91f40f;p=vamsas.git
diff --git a/src/uk/ac/vamsas/objects/core/descriptors/SequenceDescriptor.java b/src/uk/ac/vamsas/objects/core/descriptors/SequenceDescriptor.java
index d18b8c1..d67e4e8 100644
--- a/src/uk/ac/vamsas/objects/core/descriptors/SequenceDescriptor.java
+++ b/src/uk/ac/vamsas/objects/core/descriptors/SequenceDescriptor.java
@@ -1,14 +1,28 @@
/*
- * This class was automatically generated with
- * Castor 1.1, using an XML
- * Schema.
- * $Id$
+ * This file is part of the Vamsas Client version 0.1.
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite,
+ * Andrew Waterhouse and Dominik Lindner.
+ *
+ * Earlier versions have also been incorporated into Jalview version 2.4
+ * since 2008, and TOPALi version 2 since 2007.
+ *
+ * The Vamsas Client is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Lesser General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * The Vamsas Client is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with the Vamsas Client. If not, see .
*/
-
package uk.ac.vamsas.objects.core.descriptors;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
//---------------------------------/
import uk.ac.vamsas.objects.core.Sequence;
@@ -18,303 +32,302 @@ import uk.ac.vamsas.objects.core.Sequence;
*
* @version $Revision$ $Date$
*/
-public class SequenceDescriptor extends uk.ac.vamsas.objects.core.descriptors.SequenceTypeDescriptor {
-
-
- //--------------------------/
- //- 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 SequenceDescriptor() {
- super();
- setExtendsWithoutFlatten(new uk.ac.vamsas.objects.core.descriptors.SequenceTypeDescriptor());
- _nsURI = "http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes";
- _xmlName = "Sequence";
- _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
-
- //-- _id
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
- super.setIdentity(desc);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Sequence target = (Sequence) object;
- return target.getId();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Sequence target = (Sequence) object;
- target.setId( (java.lang.String) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new java.lang.String();
- }
- };
- desc.setHandler(handler);
- desc.setMultivalued(false);
- addFieldDescriptor(desc);
-
- //-- validation code for: _id
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- { //-- local scope
- org.exolab.castor.xml.validators.IdValidator typeValidator;
- typeValidator = new org.exolab.castor.xml.validators.IdValidator();
- fieldValidator.setValidator(typeValidator);
+public class SequenceDescriptor extends
+ uk.ac.vamsas.objects.core.descriptors.SequenceTypeDescriptor {
+
+ // --------------------------/
+ // - 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 SequenceDescriptor() {
+ super();
+ setExtendsWithoutFlatten(new uk.ac.vamsas.objects.core.descriptors.SequenceTypeDescriptor());
+ _nsURI = "http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes";
+ _xmlName = "Sequence";
+ _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
+
+ // -- _id
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_id", "id",
+ org.exolab.castor.xml.NodeType.Attribute);
+ super.setIdentity(desc);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException {
+ Sequence target = (Sequence) object;
+ return target.getId();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException {
+ try {
+ Sequence target = (Sequence) object;
+ target.setId((java.lang.String) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _dictionary
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dictionary", "dictionary", 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
- {
- Sequence target = (Sequence) object;
- return target.getDictionary();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Sequence target = (Sequence) object;
- target.setDictionary( (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: _dictionary
- 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");
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return new java.lang.String();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setMultivalued(false);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _id
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ { // -- local scope
+ org.exolab.castor.xml.validators.IdValidator typeValidator;
+ typeValidator = new org.exolab.castor.xml.validators.IdValidator();
+ fieldValidator.setValidator(typeValidator);
+ }
+ desc.setValidator(fieldValidator);
+ // -- _dictionary
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ java.lang.String.class, "_dictionary", "dictionary",
+ 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 {
+ Sequence target = (Sequence) object;
+ return target.getDictionary();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException {
+ try {
+ Sequence target = (Sequence) object;
+ target.setDictionary((java.lang.String) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- initialize element descriptors
-
- //-- _dbRefList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(uk.ac.vamsas.objects.core.DbRef.class, "_dbRefList", "dbRef", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Sequence target = (Sequence) object;
- return target.getDbRef();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Sequence target = (Sequence) object;
- target.addDbRef( (uk.ac.vamsas.objects.core.DbRef) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- Sequence target = (Sequence) object;
- target.removeAllDbRef();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new uk.ac.vamsas.objects.core.DbRef();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _dbRefList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ }
+
+ 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: _dictionary
+ 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
+
+ // -- _dbRefList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ uk.ac.vamsas.objects.core.DbRef.class, "_dbRefList", "dbRef",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException {
+ Sequence target = (Sequence) object;
+ return target.getDbRef();
+ }
+
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException {
+ try {
+ Sequence target = (Sequence) object;
+ target.addDbRef((uk.ac.vamsas.objects.core.DbRef) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
- //-- _vxrefList
- desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(uk.ac.vamsas.objects.core.Vxref.class, "_vxrefList", "vxref", org.exolab.castor.xml.NodeType.Element);
- handler = new org.exolab.castor.xml.XMLFieldHandler() {
- public java.lang.Object getValue( java.lang.Object object )
- throws IllegalStateException
- {
- Sequence target = (Sequence) object;
- return target.getVxref();
- }
- public void setValue( java.lang.Object object, java.lang.Object value)
- throws IllegalStateException, IllegalArgumentException
- {
- try {
- Sequence target = (Sequence) object;
- target.addVxref( (uk.ac.vamsas.objects.core.Vxref) value);
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {
- try {
- Sequence target = (Sequence) object;
- target.removeAllVxref();
- } catch (java.lang.Exception ex) {
- throw new IllegalStateException(ex.toString());
- }
- }
- public java.lang.Object newInstance(java.lang.Object parent) {
- return new uk.ac.vamsas.objects.core.Vxref();
- }
- };
- desc.setHandler(handler);
- desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
- desc.setMultivalued(true);
- addFieldDescriptor(desc);
-
- //-- validation code for: _vxrefList
- fieldValidator = new org.exolab.castor.xml.FieldValidator();
- fieldValidator.setMinOccurs(0);
- { //-- local scope
+ }
+
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException {
+ try {
+ Sequence target = (Sequence) object;
+ target.removeAllDbRef();
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
}
- desc.setValidator(fieldValidator);
+ }
+
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return new uk.ac.vamsas.objects.core.DbRef();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
+
+ // -- validation code for: _dbRefList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ // -- _vxrefList
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+ uk.ac.vamsas.objects.core.Vxref.class, "_vxrefList", "vxref",
+ org.exolab.castor.xml.NodeType.Element);
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {
+ public java.lang.Object getValue(java.lang.Object object)
+ throws IllegalStateException {
+ Sequence target = (Sequence) object;
+ return target.getVxref();
+ }
+ public void setValue(java.lang.Object object, java.lang.Object value)
+ throws IllegalStateException, IllegalArgumentException {
+ try {
+ Sequence target = (Sequence) object;
+ target.addVxref((uk.ac.vamsas.objects.core.Vxref) value);
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- //-----------/
- //- Methods -/
- //-----------/
+ public void resetValue(Object object) throws IllegalStateException,
+ IllegalArgumentException {
+ try {
+ Sequence target = (Sequence) object;
+ target.removeAllVxref();
+ } catch (java.lang.Exception ex) {
+ throw new IllegalStateException(ex.toString());
+ }
+ }
- /**
- * Method getAccessMode.
- *
- * @return the access mode specified for this class.
- */
- public org.exolab.castor.mapping.AccessMode getAccessMode(
- ) {
- return null;
- }
+ public java.lang.Object newInstance(java.lang.Object parent) {
+ return new uk.ac.vamsas.objects.core.Vxref();
+ }
+ };
+ desc.setHandler(handler);
+ desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");
+ desc.setMultivalued(true);
+ addFieldDescriptor(desc);
- /**
- * Method getIdentity.
- *
- * @return the identity field, null if this class has no
- * identity.
- */
- public org.exolab.castor.mapping.FieldDescriptor getIdentity(
- ) {
- return super.getIdentity();
+ // -- validation code for: _vxrefList
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();
+ fieldValidator.setMinOccurs(0);
+ { // -- local scope
}
+ desc.setValidator(fieldValidator);
+ }
- /**
- * Method getJavaClass.
- *
- * @return the Java class represented by this descriptor.
- */
- public java.lang.Class getJavaClass(
- ) {
- return uk.ac.vamsas.objects.core.Sequence.class;
- }
+ // -----------/
+ // - Methods -/
+ // -----------/
- /**
- * Method getNameSpacePrefix.
- *
- * @return the namespace prefix to use when marshaling as XML.
- */
- public java.lang.String getNameSpacePrefix(
- ) {
- return _nsPrefix;
- }
+ /**
+ * Method getAccessMode.
+ *
+ * @return the access mode specified for this class.
+ */
+ public org.exolab.castor.mapping.AccessMode getAccessMode() {
+ return null;
+ }
- /**
- * Method getNameSpaceURI.
- *
- * @return the namespace URI used when marshaling and
- * unmarshaling as XML.
- */
- public java.lang.String getNameSpaceURI(
- ) {
- return _nsURI;
- }
+ /**
+ * Method getIdentity.
+ *
+ * @return the identity field, null if this class has no identity.
+ */
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity() {
+ return super.getIdentity();
+ }
- /**
- * Method getValidator.
- *
- * @return a specific validator for the class described by this
- * ClassDescriptor.
- */
- public org.exolab.castor.xml.TypeValidator getValidator(
- ) {
- return this;
- }
+ /**
+ * Method getJavaClass.
+ *
+ * @return the Java class represented by this descriptor.
+ */
+ public java.lang.Class getJavaClass() {
+ return uk.ac.vamsas.objects.core.Sequence.class;
+ }
- /**
- * Method getXMLName.
- *
- * @return the XML Name for the Class being described.
- */
- public java.lang.String getXMLName(
- ) {
- return _xmlName;
- }
+ /**
+ * Method getNameSpacePrefix.
+ *
+ * @return the namespace prefix to use when marshaling as XML.
+ */
+ public java.lang.String getNameSpacePrefix() {
+ return _nsPrefix;
+ }
- /**
- * 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;
- }
+ /**
+ * 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;
+ }
}