--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class DBRef.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class DBRef implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _source\r
+ */\r
+ private java.lang.String _source;\r
+\r
+ /**\r
+ * Field _version\r
+ */\r
+ private java.lang.String _version;\r
+\r
+ /**\r
+ * Field _accessionId\r
+ */\r
+ private java.lang.String _accessionId;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public DBRef() {\r
+ super();\r
+ } //-- jalview.schemabinding.version2.DBRef()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Returns the value of field 'accessionId'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'accessionId'.\r
+ */\r
+ public java.lang.String getAccessionId()\r
+ {\r
+ return this._accessionId;\r
+ } //-- java.lang.String getAccessionId() \r
+\r
+ /**\r
+ * Returns the value of field 'source'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'source'.\r
+ */\r
+ public java.lang.String getSource()\r
+ {\r
+ return this._source;\r
+ } //-- java.lang.String getSource() \r
+\r
+ /**\r
+ * Returns the value of field 'version'.\r
+ * \r
+ * @return String\r
+ * @return the value of field 'version'.\r
+ */\r
+ public java.lang.String getVersion()\r
+ {\r
+ return this._version;\r
+ } //-- java.lang.String getVersion() \r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ } //-- boolean isValid() \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param out\r
+ */\r
+ public void marshal(java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, out);\r
+ } //-- void marshal(java.io.Writer) \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param handler\r
+ */\r
+ public void marshal(org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Sets the value of field 'accessionId'.\r
+ * \r
+ * @param accessionId the value of field 'accessionId'.\r
+ */\r
+ public void setAccessionId(java.lang.String accessionId)\r
+ {\r
+ this._accessionId = accessionId;\r
+ } //-- void setAccessionId(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'source'.\r
+ * \r
+ * @param source the value of field 'source'.\r
+ */\r
+ public void setSource(java.lang.String source)\r
+ {\r
+ this._source = source;\r
+ } //-- void setSource(java.lang.String) \r
+\r
+ /**\r
+ * Sets the value of field 'version'.\r
+ * \r
+ * @param version the value of field 'version'.\r
+ */\r
+ public void setVersion(java.lang.String version)\r
+ {\r
+ this._version = version;\r
+ } //-- void setVersion(java.lang.String) \r
+\r
+ /**\r
+ * Method unmarshal\r
+ * \r
+ * \r
+ * \r
+ * @param reader\r
+ * @return Object\r
+ */\r
+ public static java.lang.Object unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal(jalview.schemabinding.version2.DBRef.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+ /**\r
+ * Method validate\r
+ * \r
+ */\r
+ public void validate()\r
+ throws org.exolab.castor.xml.ValidationException\r
+ {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
+import org.exolab.castor.xml.validators.*;\r
+\r
+/**\r
+ * Class DBRefDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class DBRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field nsPrefix\r
+ */\r
+ private java.lang.String nsPrefix;\r
+\r
+ /**\r
+ * Field nsURI\r
+ */\r
+ private java.lang.String nsURI;\r
+\r
+ /**\r
+ * Field xmlName\r
+ */\r
+ private java.lang.String xmlName;\r
+\r
+ /**\r
+ * Field identity\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public DBRefDescriptor() {\r
+ super();\r
+ nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ xmlName = "DBRef";\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.xml.XMLFieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _source\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ DBRef target = (DBRef) object;\r
+ return target.getSource();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ DBRef target = (DBRef) object;\r
+ target.setSource( (java.lang.String) value);\r
+ }\r
+ catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance( java.lang.Object parent ) {\r
+ return null;\r
+ }\r
+ } );\r
+ desc.setHandler(handler);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _source\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ StringValidator typeValidator = new StringValidator();\r
+ typeValidator.setWhiteSpace("preserve");\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _version\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ DBRef target = (DBRef) object;\r
+ return target.getVersion();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ DBRef target = (DBRef) object;\r
+ target.setVersion( (java.lang.String) value);\r
+ }\r
+ catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance( java.lang.Object parent ) {\r
+ return null;\r
+ }\r
+ } );\r
+ desc.setHandler(handler);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _version\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ StringValidator typeValidator = new StringValidator();\r
+ typeValidator.setWhiteSpace("preserve");\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _accessionId\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ DBRef target = (DBRef) object;\r
+ return target.getAccessionId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ DBRef target = (DBRef) object;\r
+ target.setAccessionId( (java.lang.String) value);\r
+ }\r
+ catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance( java.lang.Object parent ) {\r
+ return null;\r
+ }\r
+ } );\r
+ desc.setHandler(handler);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _accessionId\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ StringValidator typeValidator = new StringValidator();\r
+ typeValidator.setWhiteSpace("preserve");\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ } //-- jalview.schemabinding.version2.DBRefDescriptor()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode\r
+ * \r
+ * \r
+ * \r
+ * @return AccessMode\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+ {\r
+ return null;\r
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+ /**\r
+ * Method getExtends\r
+ * \r
+ * \r
+ * \r
+ * @return ClassDescriptor\r
+ */\r
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
+ {\r
+ return null;\r
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+ /**\r
+ * Method getIdentity\r
+ * \r
+ * \r
+ * \r
+ * @return FieldDescriptor\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+ {\r
+ return identity;\r
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+ /**\r
+ * Method getJavaClass\r
+ * \r
+ * \r
+ * \r
+ * @return Class\r
+ */\r
+ public java.lang.Class getJavaClass()\r
+ {\r
+ return jalview.schemabinding.version2.DBRef.class;\r
+ } //-- java.lang.Class getJavaClass() \r
+\r
+ /**\r
+ * Method getNameSpacePrefix\r
+ * \r
+ * \r
+ * \r
+ * @return String\r
+ */\r
+ public java.lang.String getNameSpacePrefix()\r
+ {\r
+ return nsPrefix;\r
+ } //-- java.lang.String getNameSpacePrefix() \r
+\r
+ /**\r
+ * Method getNameSpaceURI\r
+ * \r
+ * \r
+ * \r
+ * @return String\r
+ */\r
+ public java.lang.String getNameSpaceURI()\r
+ {\r
+ return nsURI;\r
+ } //-- java.lang.String getNameSpaceURI() \r
+\r
+ /**\r
+ * Method getValidator\r
+ * \r
+ * \r
+ * \r
+ * @return TypeValidator\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator()\r
+ {\r
+ return this;\r
+ } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+ /**\r
+ * Method getXMLName\r
+ * \r
+ * \r
+ * \r
+ * @return String\r
+ */\r
+ public java.lang.String getXMLName()\r
+ {\r
+ return xmlName;\r
+ } //-- java.lang.String getXMLName() \r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class HiddenColumns.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class HiddenColumns implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _start\r
+ */\r
+ private int _start;\r
+\r
+ /**\r
+ * keeps track of state for field: _start\r
+ */\r
+ private boolean _has_start;\r
+\r
+ /**\r
+ * Field _end\r
+ */\r
+ private int _end;\r
+\r
+ /**\r
+ * keeps track of state for field: _end\r
+ */\r
+ private boolean _has_end;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public HiddenColumns() {\r
+ super();\r
+ } //-- jalview.schemabinding.version2.HiddenColumns()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method deleteEnd\r
+ * \r
+ */\r
+ public void deleteEnd()\r
+ {\r
+ this._has_end= false;\r
+ } //-- void deleteEnd() \r
+\r
+ /**\r
+ * Method deleteStart\r
+ * \r
+ */\r
+ public void deleteStart()\r
+ {\r
+ this._has_start= false;\r
+ } //-- void deleteStart() \r
+\r
+ /**\r
+ * Returns the value of field 'end'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'end'.\r
+ */\r
+ public int getEnd()\r
+ {\r
+ return this._end;\r
+ } //-- int getEnd() \r
+\r
+ /**\r
+ * Returns the value of field 'start'.\r
+ * \r
+ * @return int\r
+ * @return the value of field 'start'.\r
+ */\r
+ public int getStart()\r
+ {\r
+ return this._start;\r
+ } //-- int getStart() \r
+\r
+ /**\r
+ * Method hasEnd\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasEnd()\r
+ {\r
+ return this._has_end;\r
+ } //-- boolean hasEnd() \r
+\r
+ /**\r
+ * Method hasStart\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasStart()\r
+ {\r
+ return this._has_start;\r
+ } //-- boolean hasStart() \r
+\r
+ /**\r
+ * Method isValid\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean isValid()\r
+ {\r
+ try {\r
+ validate();\r
+ }\r
+ catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ } //-- boolean isValid() \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param out\r
+ */\r
+ public void marshal(java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, out);\r
+ } //-- void marshal(java.io.Writer) \r
+\r
+ /**\r
+ * Method marshal\r
+ * \r
+ * \r
+ * \r
+ * @param handler\r
+ */\r
+ public void marshal(org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ \r
+ Marshaller.marshal(this, handler);\r
+ } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+ /**\r
+ * Sets the value of field 'end'.\r
+ * \r
+ * @param end the value of field 'end'.\r
+ */\r
+ public void setEnd(int end)\r
+ {\r
+ this._end = end;\r
+ this._has_end = true;\r
+ } //-- void setEnd(int) \r
+\r
+ /**\r
+ * Sets the value of field 'start'.\r
+ * \r
+ * @param start the value of field 'start'.\r
+ */\r
+ public void setStart(int start)\r
+ {\r
+ this._start = start;\r
+ this._has_start = true;\r
+ } //-- void setStart(int) \r
+\r
+ /**\r
+ * Method unmarshal\r
+ * \r
+ * \r
+ * \r
+ * @param reader\r
+ * @return Object\r
+ */\r
+ public static java.lang.Object unmarshal(java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+ {\r
+ return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller.unmarshal(jalview.schemabinding.version2.HiddenColumns.class, reader);\r
+ } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+ /**\r
+ * Method validate\r
+ * \r
+ */\r
+ public void validate()\r
+ throws org.exolab.castor.xml.ValidationException\r
+ {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ } //-- void validate() \r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
+import org.exolab.castor.xml.validators.*;\r
+\r
+/**\r
+ * Class HiddenColumnsDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class HiddenColumnsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field nsPrefix\r
+ */\r
+ private java.lang.String nsPrefix;\r
+\r
+ /**\r
+ * Field nsURI\r
+ */\r
+ private java.lang.String nsURI;\r
+\r
+ /**\r
+ * Field xmlName\r
+ */\r
+ private java.lang.String xmlName;\r
+\r
+ /**\r
+ * Field identity\r
+ */\r
+ private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public HiddenColumnsDescriptor() {\r
+ super();\r
+ nsURI = "www.jalview.org";\r
+ xmlName = "hiddenColumns";\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.xml.XMLFieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _start\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ HiddenColumns target = (HiddenColumns) object;\r
+ if(!target.hasStart())\r
+ return null;\r
+ return new java.lang.Integer(target.getStart());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ HiddenColumns target = (HiddenColumns) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteStart();\r
+ return;\r
+ }\r
+ target.setStart( ((java.lang.Integer)value).intValue());\r
+ }\r
+ catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance( java.lang.Object parent ) {\r
+ return null;\r
+ }\r
+ } );\r
+ desc.setHandler(handler);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _start\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ IntegerValidator typeValidator= new IntegerValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _end\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ HiddenColumns target = (HiddenColumns) object;\r
+ if(!target.hasEnd())\r
+ return null;\r
+ return new java.lang.Integer(target.getEnd());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ HiddenColumns target = (HiddenColumns) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteEnd();\r
+ return;\r
+ }\r
+ target.setEnd( ((java.lang.Integer)value).intValue());\r
+ }\r
+ catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance( java.lang.Object parent ) {\r
+ return null;\r
+ }\r
+ } );\r
+ desc.setHandler(handler);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _end\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ IntegerValidator typeValidator= new IntegerValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ } //-- jalview.schemabinding.version2.HiddenColumnsDescriptor()\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode\r
+ * \r
+ * \r
+ * \r
+ * @return AccessMode\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+ {\r
+ return null;\r
+ } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+ /**\r
+ * Method getExtends\r
+ * \r
+ * \r
+ * \r
+ * @return ClassDescriptor\r
+ */\r
+ public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
+ {\r
+ return null;\r
+ } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+ /**\r
+ * Method getIdentity\r
+ * \r
+ * \r
+ * \r
+ * @return FieldDescriptor\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+ {\r
+ return identity;\r
+ } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+ /**\r
+ * Method getJavaClass\r
+ * \r
+ * \r
+ * \r
+ * @return Class\r
+ */\r
+ public java.lang.Class getJavaClass()\r
+ {\r
+ return jalview.schemabinding.version2.HiddenColumns.class;\r
+ } //-- java.lang.Class getJavaClass() \r
+\r
+ /**\r
+ * Method getNameSpacePrefix\r
+ * \r
+ * \r
+ * \r
+ * @return String\r
+ */\r
+ public java.lang.String getNameSpacePrefix()\r
+ {\r
+ return nsPrefix;\r
+ } //-- java.lang.String getNameSpacePrefix() \r
+\r
+ /**\r
+ * Method getNameSpaceURI\r
+ * \r
+ * \r
+ * \r
+ * @return String\r
+ */\r
+ public java.lang.String getNameSpaceURI()\r
+ {\r
+ return nsURI;\r
+ } //-- java.lang.String getNameSpaceURI() \r
+\r
+ /**\r
+ * Method getValidator\r
+ * \r
+ * \r
+ * \r
+ * @return TypeValidator\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator()\r
+ {\r
+ return this;\r
+ } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+ /**\r
+ * Method getXMLName\r
+ * \r
+ * \r
+ * \r
+ * @return String\r
+ */\r
+ public java.lang.String getXMLName()\r
+ {\r
+ return xmlName;\r
+ } //-- java.lang.String getXMLName() \r
+\r
+}\r
private boolean _has_id;\r
\r
/**\r
+ * Field _hidden\r
+ */\r
+ private boolean _hidden;\r
+\r
+ /**\r
+ * keeps track of state for field: _hidden\r
+ */\r
+ private boolean _has_hidden;\r
+\r
+ /**\r
* Field _featuresList\r
*/\r
private java.util.Vector _featuresList;\r
*/\r
private java.util.Vector _pdbidsList;\r
\r
+ /**\r
+ * Field _hiddenSequencesList\r
+ */\r
+ private java.util.Vector _hiddenSequencesList;\r
+\r
\r
//----------------/\r
//- Constructors -/\r
super();\r
_featuresList = new Vector();\r
_pdbidsList = new Vector();\r
+ _hiddenSequencesList = new Vector();\r
} //-- jalview.schemabinding.version2.JSeq()\r
\r
\r
} //-- void addFeatures(int, jalview.schemabinding.version2.Features) \r
\r
/**\r
+ * Method addHiddenSequences\r
+ * \r
+ * \r
+ * \r
+ * @param vHiddenSequences\r
+ */\r
+ public void addHiddenSequences(int vHiddenSequences)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));\r
+ } //-- void addHiddenSequences(int) \r
+\r
+ /**\r
+ * Method addHiddenSequences\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vHiddenSequences\r
+ */\r
+ public void addHiddenSequences(int index, int vHiddenSequences)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _hiddenSequencesList.insertElementAt(new java.lang.Integer(vHiddenSequences), index);\r
+ } //-- void addHiddenSequences(int, int) \r
+\r
+ /**\r
* Method addPdbids\r
* \r
* \r
} //-- void deleteEnd() \r
\r
/**\r
+ * Method deleteHidden\r
+ * \r
+ */\r
+ public void deleteHidden()\r
+ {\r
+ this._has_hidden= false;\r
+ } //-- void deleteHidden() \r
+\r
+ /**\r
* Method deleteId\r
* \r
*/\r
} //-- java.util.Enumeration enumerateFeatures() \r
\r
/**\r
+ * Method enumerateHiddenSequences\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateHiddenSequences()\r
+ {\r
+ return _hiddenSequencesList.elements();\r
+ } //-- java.util.Enumeration enumerateHiddenSequences() \r
+\r
+ /**\r
* Method enumeratePdbids\r
* \r
* \r
} //-- int getFeaturesCount() \r
\r
/**\r
+ * Returns the value of field 'hidden'.\r
+ * \r
+ * @return boolean\r
+ * @return the value of field 'hidden'.\r
+ */\r
+ public boolean getHidden()\r
+ {\r
+ return this._hidden;\r
+ } //-- boolean getHidden() \r
+\r
+ /**\r
+ * Method getHiddenSequences\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return int\r
+ */\r
+ public int getHiddenSequences(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _hiddenSequencesList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).intValue();\r
+ } //-- int getHiddenSequences(int) \r
+\r
+ /**\r
+ * Method getHiddenSequences\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int[] getHiddenSequences()\r
+ {\r
+ int size = _hiddenSequencesList.size();\r
+ int[] mArray = new int[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).intValue();\r
+ }\r
+ return mArray;\r
+ } //-- int[] getHiddenSequences() \r
+\r
+ /**\r
+ * Method getHiddenSequencesCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getHiddenSequencesCount()\r
+ {\r
+ return _hiddenSequencesList.size();\r
+ } //-- int getHiddenSequencesCount() \r
+\r
+ /**\r
* Returns the value of field 'id'.\r
* \r
* @return int\r
} //-- boolean hasEnd() \r
\r
/**\r
+ * Method hasHidden\r
+ * \r
+ * \r
+ * \r
+ * @return boolean\r
+ */\r
+ public boolean hasHidden()\r
+ {\r
+ return this._has_hidden;\r
+ } //-- boolean hasHidden() \r
+\r
+ /**\r
* Method hasId\r
* \r
* \r
} //-- void removeAllFeatures() \r
\r
/**\r
+ * Method removeAllHiddenSequences\r
+ * \r
+ */\r
+ public void removeAllHiddenSequences()\r
+ {\r
+ _hiddenSequencesList.removeAllElements();\r
+ } //-- void removeAllHiddenSequences() \r
+\r
+ /**\r
* Method removeAllPdbids\r
* \r
*/\r
} //-- jalview.schemabinding.version2.Features removeFeatures(int) \r
\r
/**\r
+ * Method removeHiddenSequences\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return int\r
+ */\r
+ public int removeHiddenSequences(int index)\r
+ {\r
+ java.lang.Object obj = _hiddenSequencesList.elementAt(index);\r
+ _hiddenSequencesList.removeElementAt(index);\r
+ return ((java.lang.Integer)obj).intValue();\r
+ } //-- int removeHiddenSequences(int) \r
+\r
+ /**\r
* Method removePdbids\r
* \r
* \r
} //-- void setFeatures(jalview.schemabinding.version2.Features) \r
\r
/**\r
+ * Sets the value of field 'hidden'.\r
+ * \r
+ * @param hidden the value of field 'hidden'.\r
+ */\r
+ public void setHidden(boolean hidden)\r
+ {\r
+ this._hidden = hidden;\r
+ this._has_hidden = true;\r
+ } //-- void setHidden(boolean) \r
+\r
+ /**\r
+ * Method setHiddenSequences\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vHiddenSequences\r
+ */\r
+ public void setHiddenSequences(int index, int vHiddenSequences)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _hiddenSequencesList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _hiddenSequencesList.setElementAt(new java.lang.Integer(vHiddenSequences), index);\r
+ } //-- void setHiddenSequences(int, int) \r
+\r
+ /**\r
+ * Method setHiddenSequences\r
+ * \r
+ * \r
+ * \r
+ * @param hiddenSequencesArray\r
+ */\r
+ public void setHiddenSequences(int[] hiddenSequencesArray)\r
+ {\r
+ //-- copy array\r
+ _hiddenSequencesList.removeAllElements();\r
+ for (int i = 0; i < hiddenSequencesArray.length; i++) {\r
+ _hiddenSequencesList.addElement(new java.lang.Integer(hiddenSequencesArray[i]));\r
+ }\r
+ } //-- void setHiddenSequences(int) \r
+\r
+ /**\r
* Sets the value of field 'id'.\r
* \r
* @param id the value of field 'id'.\r
fieldValidator.setValidator(typeValidator);\r
}\r
desc.setValidator(fieldValidator);\r
+ //-- _hidden\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_hidden", "hidden", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JSeq target = (JSeq) object;\r
+ if(!target.hasHidden())\r
+ return null;\r
+ return (target.getHidden() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deleteHidden();\r
+ return;\r
+ }\r
+ target.setHidden( ((java.lang.Boolean)value).booleanValue());\r
+ }\r
+ catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance( java.lang.Object parent ) {\r
+ return null;\r
+ }\r
+ } );\r
+ desc.setHandler(handler);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _hidden\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ BooleanValidator typeValidator = new BooleanValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
//-- initialize element descriptors\r
\r
//-- _featuresList\r
{ //-- local scope\r
}\r
desc.setValidator(fieldValidator);\r
+ //-- _hiddenSequencesList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_hiddenSequencesList", "hiddenSequences", org.exolab.castor.xml.NodeType.Element);\r
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ JSeq target = (JSeq) object;\r
+ return target.getHiddenSequences();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ JSeq target = (JSeq) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) return;\r
+ \r
+ target.addHiddenSequences( ((java.lang.Integer)value).intValue());\r
+ }\r
+ catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance( java.lang.Object parent ) {\r
+ return null;\r
+ }\r
+ } );\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _hiddenSequencesList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ IntegerValidator typeValidator= new IntegerValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
} //-- jalview.schemabinding.version2.JSeqDescriptor()\r
\r
\r
import java.io.Reader;\r
import java.io.Serializable;\r
import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class Sequence extends SequenceType \r
+public class Sequence extends jalview.schemabinding.version2.SequenceType \r
implements java.io.Serializable\r
{\r
\r
\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _DBRefList\r
+ */\r
+ private java.util.Vector _DBRefList;\r
+\r
+\r
//----------------/\r
//- Constructors -/\r
//----------------/\r
\r
public Sequence() {\r
super();\r
+ _DBRefList = new Vector();\r
} //-- jalview.schemabinding.version2.Sequence()\r
\r
\r
//-----------/\r
\r
/**\r
+ * Method addDBRef\r
+ * \r
+ * \r
+ * \r
+ * @param vDBRef\r
+ */\r
+ public void addDBRef(jalview.schemabinding.version2.DBRef vDBRef)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _DBRefList.addElement(vDBRef);\r
+ } //-- void addDBRef(jalview.schemabinding.version2.DBRef) \r
+\r
+ /**\r
+ * Method addDBRef\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vDBRef\r
+ */\r
+ public void addDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _DBRefList.insertElementAt(vDBRef, index);\r
+ } //-- void addDBRef(int, jalview.schemabinding.version2.DBRef) \r
+\r
+ /**\r
+ * Method enumerateDBRef\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateDBRef()\r
+ {\r
+ return _DBRefList.elements();\r
+ } //-- java.util.Enumeration enumerateDBRef() \r
+\r
+ /**\r
+ * Method getDBRef\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return DBRef\r
+ */\r
+ public jalview.schemabinding.version2.DBRef getDBRef(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _DBRefList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);\r
+ } //-- jalview.schemabinding.version2.DBRef getDBRef(int) \r
+\r
+ /**\r
+ * Method getDBRef\r
+ * \r
+ * \r
+ * \r
+ * @return DBRef\r
+ */\r
+ public jalview.schemabinding.version2.DBRef[] getDBRef()\r
+ {\r
+ int size = _DBRefList.size();\r
+ jalview.schemabinding.version2.DBRef[] mArray = new jalview.schemabinding.version2.DBRef[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.schemabinding.version2.DBRef[] getDBRef() \r
+\r
+ /**\r
+ * Method getDBRefCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getDBRefCount()\r
+ {\r
+ return _DBRefList.size();\r
+ } //-- int getDBRefCount() \r
+\r
+ /**\r
* Method isValid\r
* \r
* \r
} //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
+ * Method removeAllDBRef\r
+ * \r
+ */\r
+ public void removeAllDBRef()\r
+ {\r
+ _DBRefList.removeAllElements();\r
+ } //-- void removeAllDBRef() \r
+\r
+ /**\r
+ * Method removeDBRef\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return DBRef\r
+ */\r
+ public jalview.schemabinding.version2.DBRef removeDBRef(int index)\r
+ {\r
+ java.lang.Object obj = _DBRefList.elementAt(index);\r
+ _DBRefList.removeElementAt(index);\r
+ return (jalview.schemabinding.version2.DBRef) obj;\r
+ } //-- jalview.schemabinding.version2.DBRef removeDBRef(int) \r
+\r
+ /**\r
+ * Method setDBRef\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vDBRef\r
+ */\r
+ public void setDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _DBRefList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _DBRefList.setElementAt(vDBRef, index);\r
+ } //-- void setDBRef(int, jalview.schemabinding.version2.DBRef) \r
+\r
+ /**\r
+ * Method setDBRef\r
+ * \r
+ * \r
+ * \r
+ * @param DBRefArray\r
+ */\r
+ public void setDBRef(jalview.schemabinding.version2.DBRef[] DBRefArray)\r
+ {\r
+ //-- copy array\r
+ _DBRefList.removeAllElements();\r
+ for (int i = 0; i < DBRefArray.length; i++) {\r
+ _DBRefList.addElement(DBRefArray[i]);\r
+ }\r
+ } //-- void setDBRef(jalview.schemabinding.version2.DBRef) \r
+\r
+ /**\r
* Method unmarshal\r
* \r
* \r
* \r
* @version $Revision$ $Date$\r
*/\r
-public class SequenceDescriptor extends SequenceTypeDescriptor {\r
+public class SequenceDescriptor extends jalview.schemabinding.version2.SequenceTypeDescriptor {\r
\r
\r
//--------------------------/\r
\r
public SequenceDescriptor() {\r
super();\r
- setExtendsWithoutFlatten(new SequenceTypeDescriptor());\r
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.SequenceTypeDescriptor());\r
nsURI = "www.vamsas.ac.uk/jalview/version2";\r
xmlName = "Sequence";\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.xml.XMLFieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _DBRefList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.DBRef.class, "_DBRefList", "DBRef", org.exolab.castor.xml.NodeType.Element);\r
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Sequence target = (Sequence) object;\r
+ return target.getDBRef();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Sequence target = (Sequence) object;\r
+ target.addDBRef( (jalview.schemabinding.version2.DBRef) value);\r
+ }\r
+ catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance( java.lang.Object parent ) {\r
+ return new jalview.schemabinding.version2.DBRef();\r
+ }\r
+ } );\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _DBRefList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
} //-- jalview.schemabinding.version2.SequenceDescriptor()\r
\r
\r
import java.io.Reader;\r
import java.io.Serializable;\r
import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
import org.exolab.castor.xml.MarshalException;\r
import org.exolab.castor.xml.Marshaller;\r
import org.exolab.castor.xml.Unmarshaller;\r
*/\r
private jalview.schemabinding.version2.AnnotationColours _annotationColours;\r
\r
+ /**\r
+ * Field _hiddenColumnsList\r
+ */\r
+ private java.util.Vector _hiddenColumnsList;\r
+\r
\r
//----------------/\r
//- Constructors -/\r
\r
public Viewport() {\r
super();\r
+ _hiddenColumnsList = new Vector();\r
} //-- jalview.schemabinding.version2.Viewport()\r
\r
\r
//-----------/\r
\r
/**\r
+ * Method addHiddenColumns\r
+ * \r
+ * \r
+ * \r
+ * @param vHiddenColumns\r
+ */\r
+ public void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _hiddenColumnsList.addElement(vHiddenColumns);\r
+ } //-- void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns) \r
+\r
+ /**\r
+ * Method addHiddenColumns\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vHiddenColumns\r
+ */\r
+ public void addHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ _hiddenColumnsList.insertElementAt(vHiddenColumns, index);\r
+ } //-- void addHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) \r
+\r
+ /**\r
* Method deleteConsThreshold\r
* \r
*/\r
} //-- void deleteYpos() \r
\r
/**\r
+ * Method enumerateHiddenColumns\r
+ * \r
+ * \r
+ * \r
+ * @return Enumeration\r
+ */\r
+ public java.util.Enumeration enumerateHiddenColumns()\r
+ {\r
+ return _hiddenColumnsList.elements();\r
+ } //-- java.util.Enumeration enumerateHiddenColumns() \r
+\r
+ /**\r
* Returns the value of field 'annotationColours'.\r
* \r
* @return AnnotationColours\r
} //-- int getHeight() \r
\r
/**\r
+ * Method getHiddenColumns\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return HiddenColumns\r
+ */\r
+ public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int index)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _hiddenColumnsList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);\r
+ } //-- jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int) \r
+\r
+ /**\r
+ * Method getHiddenColumns\r
+ * \r
+ * \r
+ * \r
+ * @return HiddenColumns\r
+ */\r
+ public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()\r
+ {\r
+ int size = _hiddenColumnsList.size();\r
+ jalview.schemabinding.version2.HiddenColumns[] mArray = new jalview.schemabinding.version2.HiddenColumns[size];\r
+ for (int index = 0; index < size; index++) {\r
+ mArray[index] = (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);\r
+ }\r
+ return mArray;\r
+ } //-- jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns() \r
+\r
+ /**\r
+ * Method getHiddenColumnsCount\r
+ * \r
+ * \r
+ * \r
+ * @return int\r
+ */\r
+ public int getHiddenColumnsCount()\r
+ {\r
+ return _hiddenColumnsList.size();\r
+ } //-- int getHiddenColumnsCount() \r
+\r
+ /**\r
* Returns the value of field 'pidSelected'.\r
* \r
* @return boolean\r
} //-- void marshal(org.xml.sax.ContentHandler) \r
\r
/**\r
+ * Method removeAllHiddenColumns\r
+ * \r
+ */\r
+ public void removeAllHiddenColumns()\r
+ {\r
+ _hiddenColumnsList.removeAllElements();\r
+ } //-- void removeAllHiddenColumns() \r
+\r
+ /**\r
+ * Method removeHiddenColumns\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @return HiddenColumns\r
+ */\r
+ public jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int index)\r
+ {\r
+ java.lang.Object obj = _hiddenColumnsList.elementAt(index);\r
+ _hiddenColumnsList.removeElementAt(index);\r
+ return (jalview.schemabinding.version2.HiddenColumns) obj;\r
+ } //-- jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int) \r
+\r
+ /**\r
* Sets the value of field 'annotationColours'.\r
* \r
* @param annotationColours the value of field\r
} //-- void setHeight(int) \r
\r
/**\r
+ * Method setHiddenColumns\r
+ * \r
+ * \r
+ * \r
+ * @param index\r
+ * @param vHiddenColumns\r
+ */\r
+ public void setHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+ throws java.lang.IndexOutOfBoundsException\r
+ {\r
+ //-- check bounds for index\r
+ if ((index < 0) || (index > _hiddenColumnsList.size())) {\r
+ throw new IndexOutOfBoundsException();\r
+ }\r
+ _hiddenColumnsList.setElementAt(vHiddenColumns, index);\r
+ } //-- void setHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) \r
+\r
+ /**\r
+ * Method setHiddenColumns\r
+ * \r
+ * \r
+ * \r
+ * @param hiddenColumnsArray\r
+ */\r
+ public void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns[] hiddenColumnsArray)\r
+ {\r
+ //-- copy array\r
+ _hiddenColumnsList.removeAllElements();\r
+ for (int i = 0; i < hiddenColumnsArray.length; i++) {\r
+ _hiddenColumnsList.addElement(hiddenColumnsArray[i]);\r
+ }\r
+ } //-- void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns) \r
+\r
+ /**\r
* Sets the value of field 'pidSelected'.\r
* \r
* @param pidSelected the value of field 'pidSelected'.\r
{ //-- local scope\r
}\r
desc.setValidator(fieldValidator);\r
+ //-- _hiddenColumnsList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.HiddenColumns.class, "_hiddenColumnsList", "hiddenColumns", org.exolab.castor.xml.NodeType.Element);\r
+ handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Viewport target = (Viewport) object;\r
+ return target.getHiddenColumns();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Viewport target = (Viewport) object;\r
+ target.addHiddenColumns( (jalview.schemabinding.version2.HiddenColumns) value);\r
+ }\r
+ catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance( java.lang.Object parent ) {\r
+ return new jalview.schemabinding.version2.HiddenColumns();\r
+ }\r
+ } );\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.jalview.org");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _hiddenColumnsList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
} //-- jalview.schemabinding.version2.ViewportDescriptor()\r
\r
\r