verbose="true"
properties="${schemaDir}/jalview.properties"
+ />
+ <!--
+ now build the jalview.binding package with the old schema set
+ -->
+ <delete>
+ <fileset dir="${sourceDir}/jalview/binding/">
+ <include name="**"/>
+ </fileset>
+ </delete>
+ <castor-srcgen file="${schemaDir}/vamsasJvV1.xsd"
+ todir="${sourceDir}"
+ package="jalview.binding"
+ warnings="false"
+ nodesc="true"
+ verbose="true"
+ properties="${schemaDir}/jalview.nodesc.properties"
+ />
+ <castor-srcgen file="${schemaDir}/JalviewUserColours.xsd"
+ todir="${sourceDir}"
+ package="jalview.binding"
+ warnings="false"
+ nodesc="true"
+ verbose="true"
+ properties="${schemaDir}/jalview.nodesc.properties"
+ />
+ <castor-srcgen file="${schemaDir}/jalviewJvV1.xsd"
+ todir="${sourceDir}"
+ package="jalview.binding"
+ warnings="false"
+ nodesc="true"
+ verbose="true"
+ properties="${schemaDir}/jalview.nodesc.properties"
/>
</target>
</project>
--- /dev/null
+#\r
+# Property file for SourceCodeGenerator for jalview project XML for parsing without descriptors\r
+#\r
+\r
+#org.exolab.castor.builder.superclass=com.xyz.BaseObject\r
+\r
+# XML namespace mapping to Java packages\r
+#\r
+org.exolab.castor.builder.nspackages=\\r
+ www.vamsas.ac.uk/jalview/version2=jalview.binding,\\r
+ www.jalview.org/colours=jalview.binding,\\r
+ www.jalview.org=jalview.binding\r
+\r
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>\r
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"\r
+ xmlns:vamsas="www.vamsas.org"\r
+ xmlns:jalview="www.jalview.org/colours"\r
+ xmlns:jv="www.jalview.org" \r
+ targetNamespace="www.jalview.org" elementFormDefault="qualified" attributeFormDefault="unqualified">\r
+ \r
+ <xs:import schemaLocation="vamsasJvV1.xsd" namespace="www.vamsas.org"/>\r
+ <xs:import schemaLocation="jalviewUserColours.xsd" namespace="www.jalview.org/colours"/>\r
+ <xs:complexType name="JalviewModel">\r
+ <xs:sequence>\r
+ <xs:element name="creationDate" type="xs:dateTime"/>\r
+ <xs:element name="version" type="xs:string"/>\r
+ <xs:element name="vamsasModel" type="vamsas:VAMSAS"/>\r
+ <xs:sequence>\r
+ <xs:element name="JSeq" maxOccurs="unbounded">\r
+ <xs:complexType>\r
+ <xs:sequence>\r
+ <xs:element name="features" type="jv:feature" minOccurs="0" maxOccurs="unbounded"/>\r
+ <xs:element name="pdbids" type="jv:pdbentry" minOccurs="0" maxOccurs="unbounded"/>\r
+ </xs:sequence>\r
+ \r
+ <xs:attribute name="colour" type="xs:int" use="optional"/>\r
+ <xs:attribute name="start" type="xs:int" use="required"/>\r
+ <xs:attribute name="end" type="xs:int" use="required"/>\r
+ <xs:attribute name="id" type="xs:int" use="required"/>\r
+ </xs:complexType>\r
+ </xs:element>\r
+ <xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">\r
+ <xs:complexType>\r
+ <xs:sequence minOccurs="1">\r
+ <xs:element name="seq" maxOccurs="unbounded" type="xs:int"/>\r
+ </xs:sequence>\r
+ <xs:attribute name="start" type="xs:int"/>\r
+ <xs:attribute name="end" type="xs:int"/>\r
+ <xs:attribute name="name" type="xs:string"/>\r
+ <xs:attribute name="colour" type="xs:string"/>\r
+ <xs:attribute name="consThreshold" type="xs:int"/>\r
+ <xs:attribute name="pidThreshold" type="xs:int"/>\r
+ <xs:attribute name="outlineColour" type="xs:int"/>\r
+ <xs:attribute name="displayBoxes" type="xs:boolean"/>\r
+ <xs:attribute name="displayText" type="xs:boolean"/>\r
+ <xs:attribute name="colourText" type="xs:boolean"/>\r
+ </xs:complexType>\r
+ </xs:element>\r
+ <xs:element name="Viewport" maxOccurs="unbounded">\r
+ <xs:complexType>\r
+ <xs:attribute name="conservationSelected" type="xs:boolean"/>\r
+ <xs:attribute name="pidSelected" type="xs:boolean"/>\r
+ <xs:attribute name="bgColour" type="xs:string"/>\r
+ <xs:attribute name="consThreshold" type="xs:int"/>\r
+ <xs:attribute name="pidThreshold" type="xs:int"/>\r
+ <xs:attribute name="title" type="xs:string"/>\r
+ <xs:attribute name="showFullId" type="xs:boolean"/>\r
+ <xs:attribute name="showText" type="xs:boolean"/>\r
+ <xs:attribute name="showColourText" type="xs:boolean"/>\r
+ <xs:attribute name="showBoxes" type="xs:boolean"/>\r
+ <xs:attribute name="wrapAlignment" type="xs:boolean"/>\r
+ <xs:attribute name="renderGaps" type="xs:boolean"/>\r
+ <xs:attribute name="showSequenceFeatures" type="xs:boolean"/>\r
+ <xs:attribute name="showAnnotation" type="xs:boolean"/>\r
+ <xs:attribute name="showConservation" type="xs:boolean"/>\r
+ <xs:attribute name="showQuality" type="xs:boolean"/>\r
+ <xs:attribute name="showIdentity" type="xs:boolean"/>\r
+ <xs:attribute name="xpos" type="xs:int"/>\r
+ <xs:attribute name="ypos" type="xs:int"/>\r
+ <xs:attribute name="width" type="xs:int"/>\r
+ <xs:attribute name="height" type="xs:int"/>\r
+ <xs:attribute name="startRes" type="xs:int"/>\r
+ <xs:attribute name="startSeq" type="xs:int"/>\r
+ <xs:attribute name="fontName" type="xs:string"/>\r
+ <xs:attribute name="fontSize" type="xs:int"/>\r
+ <xs:attribute name="fontStyle" type="xs:int"/>\r
+ </xs:complexType>\r
+ </xs:element>\r
+ <xs:element name="UserColours" minOccurs="0" maxOccurs="unbounded">\r
+ <xs:complexType>\r
+ <xs:sequence minOccurs="1">\r
+ <xs:element name="UserColourScheme" type="jalview:JalviewUserColours"/>\r
+ </xs:sequence>\r
+ <xs:attribute name="id" type="xs:string"/>\r
+ </xs:complexType>\r
+ </xs:element>\r
+ <xs:element name="tree" minOccurs="0" maxOccurs="unbounded">\r
+ <xs:complexType>\r
+ <xs:sequence minOccurs="0" maxOccurs="1">\r
+ <xs:element name="title" type="xs:string"/>\r
+ <xs:element name="newick" type="xs:string"/>\r
+ </xs:sequence>\r
+ <xs:attribute name="width" type="xs:int"/>\r
+ <xs:attribute name="height" type="xs:int"/>\r
+ <xs:attribute name="xpos" type="xs:int"/>\r
+ <xs:attribute name="ypos" type="xs:int"/>\r
+ <xs:attribute name="fontName" type="xs:string"/>\r
+ <xs:attribute name="fontSize" type="xs:int"/>\r
+ <xs:attribute name="fontStyle" type="xs:int"/>\r
+ <xs:attribute name="threshold" type="xs:float"/>\r
+ <xs:attribute name="showBootstrap" type="xs:boolean"/>\r
+ <xs:attribute name="showDistances" type="xs:boolean"/>\r
+ <xs:attribute name="markUnlinked" type="xs:boolean"/>\r
+ <xs:attribute name="fitToWindow" type="xs:boolean"/>\r
+ <xs:attribute name="currentTree" type="xs:boolean"/>\r
+ </xs:complexType>\r
+ </xs:element>\r
+ \r
+ <xs:element name="FeatureSettings" minOccurs="0" maxOccurs="1">\r
+ <xs:complexType>\r
+ <xs:sequence>\r
+ <xs:element name="setting" minOccurs="0" maxOccurs="unbounded">\r
+ <xs:complexType>\r
+ <xs:attribute name="type" type="xs:string" use="required"/>\r
+ <xs:attribute name="colour" type="xs:int" use="required"/>\r
+ <xs:attribute name="display" type="xs:boolean" use="required"/>\r
+ </xs:complexType>\r
+ </xs:element>\r
+ </xs:sequence>\r
+ </xs:complexType>\r
+ </xs:element>\r
+ \r
+ </xs:sequence>\r
+ </xs:sequence>\r
+ </xs:complexType>\r
+ \r
+ <xs:complexType name="feature">\r
+ <xs:attribute name="begin" type="xs:int" use="required"/>\r
+ <xs:attribute name="end" type="xs:int" use="required"/>\r
+ <xs:attribute name="type" type="xs:string" use="required"/>\r
+ <xs:attribute name="description" type="xs:string" use="optional"/>\r
+ <xs:attribute name="status" type="xs:string" use="optional"/>\r
+ </xs:complexType>\r
+ \r
+ <xs:complexType name="pdbentry">\r
+ <xs:sequence minOccurs="0" maxOccurs="unbounded">\r
+ <xs:element name="property" minOccurs="0" maxOccurs="unbounded">\r
+ <xs:complexType>\r
+ <xs:attribute name="name" type="xs:string" use="required"/>\r
+ <xs:attribute name="value" type="xs:string" use="required"/>\r
+ </xs:complexType>\r
+ </xs:element>\r
+ </xs:sequence>\r
+ <xs:attribute name="id" type="xs:string" use="required"/>\r
+ <xs:attribute name="type" type="xs:string" use="optional"/>\r
+ </xs:complexType>\r
+ \r
+</xs:schema>\r
--- /dev/null
+<?xml version="1.0" encoding="UTF-8"?>\r
+<!-- edited with XMLSpy v2006 sp1 U (http://www.altova.com) by ioh[ (o[ih[oh) -->\r
+<xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:vamsas="www.vamsas.org" targetNamespace="www.vamsas.org" elementFormDefault="qualified" attributeFormDefault="unqualified">\r
+ <xs:complexType name="VAMSAS">\r
+ <xs:sequence>\r
+ <xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">\r
+ <xs:complexType>\r
+ <xs:sequence>\r
+ <xs:element name="Annotation" minOccurs="0">\r
+ <xs:complexType>\r
+ <xs:sequence>\r
+ <xs:element ref="vamsas:annotationElement" maxOccurs="unbounded"/>\r
+ <xs:element name="label" type="xs:string"/>\r
+ <xs:element name="description" type="xs:string"/>\r
+ </xs:sequence>\r
+ <xs:attribute name="graph" type="xs:boolean" use="required"/>\r
+ <xs:attribute name="graphType" type="xs:int" use="optional"/>\r
+ </xs:complexType>\r
+ </xs:element>\r
+ <xs:element ref="vamsas:SequenceSet"/>\r
+ </xs:sequence>\r
+ </xs:complexType>\r
+ </xs:element>\r
+ <xs:element name="Tree" type="xs:string" minOccurs="0" maxOccurs="unbounded"/>\r
+ <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>\r
+ </xs:sequence>\r
+ </xs:complexType>\r
+ <xs:element name="SequenceSet">\r
+ <xs:complexType>\r
+ <xs:sequence>\r
+ <xs:element name="Sequence" type="vamsas:SequenceType" maxOccurs="unbounded"/>\r
+ <xs:element name="Annotation" minOccurs="0" maxOccurs="unbounded">\r
+ <xs:complexType>\r
+ <xs:sequence>\r
+ <xs:element name="description" type="xs:string" minOccurs="0"/>\r
+ <xs:element name="status" type="xs:string" minOccurs="0"/>\r
+ <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>\r
+ </xs:sequence>\r
+ <xs:attribute name="type" type="xs:string" use="required"/>\r
+ <xs:attribute name="end" type="xs:string" use="required"/>\r
+ <xs:attribute name="begin" type="xs:string" use="required"/>\r
+ <xs:attribute name="seqRef" type="xs:string" use="required"/>\r
+ </xs:complexType>\r
+ </xs:element>\r
+ </xs:sequence>\r
+ <xs:attribute name="gapChar" type="xs:string" use="required"/>\r
+ <xs:attribute name="aligned" type="xs:boolean" use="optional"/>\r
+ </xs:complexType>\r
+ </xs:element>\r
+ <xs:element name="annotationElement">\r
+ <xs:complexType>\r
+ <xs:sequence>\r
+ <xs:element name="displayCharacter" type="xs:string"/>\r
+ <xs:element name="description" type="xs:string"/>\r
+ <xs:element name="secondaryStructure">\r
+ <xs:simpleType>\r
+ <xs:restriction base="xs:string">\r
+ <xs:length value="1"/>\r
+ </xs:restriction>\r
+ </xs:simpleType>\r
+ </xs:element>\r
+ <xs:element name="value" type="xs:float"/>\r
+ </xs:sequence>\r
+ <xs:attribute name="position" type="xs:int" use="required"/>\r
+ </xs:complexType>\r
+ </xs:element>\r
+ <xs:complexType name="SequenceType">\r
+ <xs:sequence>\r
+ <xs:element name="sequence" type="xs:string"/>\r
+ <xs:element name="name" type="xs:string"/>\r
+ </xs:sequence>\r
+ <xs:attribute name="id" type="xs:string"/>\r
+ </xs:complexType>\r
+</xs:schema>\r
-/*\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.binding;\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 Alignment.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Alignment implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _annotation\r
- */\r
- private jalview.binding.Annotation _annotation;\r
-\r
- /**\r
- * Field _sequenceSet\r
- */\r
- private jalview.binding.SequenceSet _sequenceSet;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Alignment() {\r
- super();\r
- } //-- jalview.binding.Alignment()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Returns the value of field 'annotation'.\r
- * \r
- * @return Annotation\r
- * @return the value of field 'annotation'.\r
- */\r
- public jalview.binding.Annotation getAnnotation()\r
- {\r
- return this._annotation;\r
- } //-- jalview.binding.Annotation getAnnotation() \r
-\r
- /**\r
- * Returns the value of field 'sequenceSet'.\r
- * \r
- * @return SequenceSet\r
- * @return the value of field 'sequenceSet'.\r
- */\r
- public jalview.binding.SequenceSet getSequenceSet()\r
- {\r
- return this._sequenceSet;\r
- } //-- jalview.binding.SequenceSet getSequenceSet() \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 'annotation'.\r
- * \r
- * @param annotation the value of field 'annotation'.\r
- */\r
- public void setAnnotation(jalview.binding.Annotation annotation)\r
- {\r
- this._annotation = annotation;\r
- } //-- void setAnnotation(jalview.binding.Annotation) \r
-\r
- /**\r
- * Sets the value of field 'sequenceSet'.\r
- * \r
- * @param sequenceSet the value of field 'sequenceSet'.\r
- */\r
- public void setSequenceSet(jalview.binding.SequenceSet sequenceSet)\r
- {\r
- this._sequenceSet = sequenceSet;\r
- } //-- void setSequenceSet(jalview.binding.SequenceSet) \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.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Alignment.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Alignment implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _annotation.
+ */
+ private jalview.binding.Annotation _annotation;
+
+ /**
+ * Field _sequenceSet.
+ */
+ private jalview.binding.SequenceSet _sequenceSet;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Alignment() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Returns the value of field 'annotation'.
+ *
+ * @return the value of field 'Annotation'.
+ */
+ public jalview.binding.Annotation getAnnotation(
+ ) {
+ return this._annotation;
+ }
+
+ /**
+ * Returns the value of field 'sequenceSet'.
+ *
+ * @return the value of field 'SequenceSet'.
+ */
+ public jalview.binding.SequenceSet getSequenceSet(
+ ) {
+ return this._sequenceSet;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'annotation'.
+ *
+ * @param annotation the value of field 'annotation'.
+ */
+ public void setAnnotation(
+ final jalview.binding.Annotation annotation) {
+ this._annotation = annotation;
+ }
+
+ /**
+ * Sets the value of field 'sequenceSet'.
+ *
+ * @param sequenceSet the value of field 'sequenceSet'.
+ */
+ public void setSequenceSet(
+ final jalview.binding.SequenceSet sequenceSet) {
+ this._sequenceSet = sequenceSet;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Alignment
+ */
+ public static jalview.binding.Alignment unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 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
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Annotation.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Annotation implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _graph\r
- */\r
- private boolean _graph;\r
-\r
- /**\r
- * keeps track of state for field: _graph\r
- */\r
- private boolean _has_graph;\r
-\r
- /**\r
- * Field _graphType\r
- */\r
- private int _graphType;\r
-\r
- /**\r
- * keeps track of state for field: _graphType\r
- */\r
- private boolean _has_graphType;\r
-\r
- /**\r
- * Field _annotationElementList\r
- */\r
- private java.util.Vector _annotationElementList;\r
-\r
- /**\r
- * Field _label\r
- */\r
- private java.lang.String _label;\r
-\r
- /**\r
- * Field _description\r
- */\r
- private java.lang.String _description;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Annotation() {\r
- super();\r
- _annotationElementList = new Vector();\r
- } //-- jalview.binding.Annotation()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addAnnotationElement\r
- * \r
- * \r
- * \r
- * @param vAnnotationElement\r
- */\r
- public void addAnnotationElement(jalview.binding.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationElementList.addElement(vAnnotationElement);\r
- } //-- void addAnnotationElement(jalview.binding.AnnotationElement) \r
-\r
- /**\r
- * Method addAnnotationElement\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vAnnotationElement\r
- */\r
- public void addAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationElementList.insertElementAt(vAnnotationElement, index);\r
- } //-- void addAnnotationElement(int, jalview.binding.AnnotationElement) \r
-\r
- /**\r
- * Method deleteGraph\r
- * \r
- */\r
- public void deleteGraph()\r
- {\r
- this._has_graph= false;\r
- } //-- void deleteGraph() \r
-\r
- /**\r
- * Method deleteGraphType\r
- * \r
- */\r
- public void deleteGraphType()\r
- {\r
- this._has_graphType= false;\r
- } //-- void deleteGraphType() \r
-\r
- /**\r
- * Method enumerateAnnotationElement\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateAnnotationElement()\r
- {\r
- return _annotationElementList.elements();\r
- } //-- java.util.Enumeration enumerateAnnotationElement() \r
-\r
- /**\r
- * Method getAnnotationElement\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return AnnotationElement\r
- */\r
- public jalview.binding.AnnotationElement getAnnotationElement(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _annotationElementList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index);\r
- } //-- jalview.binding.AnnotationElement getAnnotationElement(int) \r
-\r
- /**\r
- * Method getAnnotationElement\r
- * \r
- * \r
- * \r
- * @return AnnotationElement\r
- */\r
- public jalview.binding.AnnotationElement[] getAnnotationElement()\r
- {\r
- int size = _annotationElementList.size();\r
- jalview.binding.AnnotationElement[] mArray = new jalview.binding.AnnotationElement[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.AnnotationElement[] getAnnotationElement() \r
-\r
- /**\r
- * Method getAnnotationElementCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getAnnotationElementCount()\r
- {\r
- return _annotationElementList.size();\r
- } //-- int getAnnotationElementCount() \r
-\r
- /**\r
- * Returns the value of field 'description'.\r
- * \r
- * @return String\r
- * @return the value of field 'description'.\r
- */\r
- public java.lang.String getDescription()\r
- {\r
- return this._description;\r
- } //-- java.lang.String getDescription() \r
-\r
- /**\r
- * Returns the value of field 'graph'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'graph'.\r
- */\r
- public boolean getGraph()\r
- {\r
- return this._graph;\r
- } //-- boolean getGraph() \r
-\r
- /**\r
- * Returns the value of field 'graphType'.\r
- * \r
- * @return int\r
- * @return the value of field 'graphType'.\r
- */\r
- public int getGraphType()\r
- {\r
- return this._graphType;\r
- } //-- int getGraphType() \r
-\r
- /**\r
- * Returns the value of field 'label'.\r
- * \r
- * @return String\r
- * @return the value of field 'label'.\r
- */\r
- public java.lang.String getLabel()\r
- {\r
- return this._label;\r
- } //-- java.lang.String getLabel() \r
-\r
- /**\r
- * Method hasGraph\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasGraph()\r
- {\r
- return this._has_graph;\r
- } //-- boolean hasGraph() \r
-\r
- /**\r
- * Method hasGraphType\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasGraphType()\r
- {\r
- return this._has_graphType;\r
- } //-- boolean hasGraphType() \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
- * Method removeAllAnnotationElement\r
- * \r
- */\r
- public void removeAllAnnotationElement()\r
- {\r
- _annotationElementList.removeAllElements();\r
- } //-- void removeAllAnnotationElement() \r
-\r
- /**\r
- * Method removeAnnotationElement\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return AnnotationElement\r
- */\r
- public jalview.binding.AnnotationElement removeAnnotationElement(int index)\r
- {\r
- java.lang.Object obj = _annotationElementList.elementAt(index);\r
- _annotationElementList.removeElementAt(index);\r
- return (jalview.binding.AnnotationElement) obj;\r
- } //-- jalview.binding.AnnotationElement removeAnnotationElement(int) \r
-\r
- /**\r
- * Method setAnnotationElement\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vAnnotationElement\r
- */\r
- public void setAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _annotationElementList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _annotationElementList.setElementAt(vAnnotationElement, index);\r
- } //-- void setAnnotationElement(int, jalview.binding.AnnotationElement) \r
-\r
- /**\r
- * Method setAnnotationElement\r
- * \r
- * \r
- * \r
- * @param annotationElementArray\r
- */\r
- public void setAnnotationElement(jalview.binding.AnnotationElement[] annotationElementArray)\r
- {\r
- //-- copy array\r
- _annotationElementList.removeAllElements();\r
- for (int i = 0; i < annotationElementArray.length; i++) {\r
- _annotationElementList.addElement(annotationElementArray[i]);\r
- }\r
- } //-- void setAnnotationElement(jalview.binding.AnnotationElement) \r
-\r
- /**\r
- * Sets the value of field 'description'.\r
- * \r
- * @param description the value of field 'description'.\r
- */\r
- public void setDescription(java.lang.String description)\r
- {\r
- this._description = description;\r
- } //-- void setDescription(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'graph'.\r
- * \r
- * @param graph the value of field 'graph'.\r
- */\r
- public void setGraph(boolean graph)\r
- {\r
- this._graph = graph;\r
- this._has_graph = true;\r
- } //-- void setGraph(boolean) \r
-\r
- /**\r
- * Sets the value of field 'graphType'.\r
- * \r
- * @param graphType the value of field 'graphType'.\r
- */\r
- public void setGraphType(int graphType)\r
- {\r
- this._graphType = graphType;\r
- this._has_graphType = true;\r
- } //-- void setGraphType(int) \r
-\r
- /**\r
- * Sets the value of field 'label'.\r
- * \r
- * @param label the value of field 'label'.\r
- */\r
- public void setLabel(java.lang.String label)\r
- {\r
- this._label = label;\r
- } //-- void setLabel(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.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Annotation.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Annotation implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _graph.
+ */
+ private boolean _graph;
+
+ /**
+ * keeps track of state for field: _graph
+ */
+ private boolean _has_graph;
+
+ /**
+ * Field _graphType.
+ */
+ private int _graphType;
+
+ /**
+ * keeps track of state for field: _graphType
+ */
+ private boolean _has_graphType;
+
+ /**
+ * Field _annotationElementList.
+ */
+ private java.util.Vector _annotationElementList;
+
+ /**
+ * Field _label.
+ */
+ private java.lang.String _label;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Annotation() {
+ super();
+ this._annotationElementList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAnnotationElement(
+ final jalview.binding.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException {
+ this._annotationElementList.addElement(vAnnotationElement);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAnnotationElement(
+ final int index,
+ final jalview.binding.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException {
+ this._annotationElementList.add(index, vAnnotationElement);
+ }
+
+ /**
+ */
+ public void deleteGraph(
+ ) {
+ this._has_graph= false;
+ }
+
+ /**
+ */
+ public void deleteGraphType(
+ ) {
+ this._has_graphType= false;
+ }
+
+ /**
+ * Method enumerateAnnotationElement.
+ *
+ * @return an Enumeration over all
+ * jalview.binding.AnnotationElement elements
+ */
+ public java.util.Enumeration enumerateAnnotationElement(
+ ) {
+ return this._annotationElementList.elements();
+ }
+
+ /**
+ * Method getAnnotationElement.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.AnnotationElement
+ * at the given index
+ */
+ public jalview.binding.AnnotationElement getAnnotationElement(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationElementList.size()) {
+ throw new IndexOutOfBoundsException("getAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.AnnotationElement) _annotationElementList.get(index);
+ }
+
+ /**
+ * Method getAnnotationElement.Returns the contents of the
+ * collection in an Array. <p>Note: Just in case the
+ * collection contents are changing in another thread, we pass
+ * a 0-length Array of the correct type into the API call.
+ * This way we <i>know</i> that the Array returned is of
+ * exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.AnnotationElement[] getAnnotationElement(
+ ) {
+ jalview.binding.AnnotationElement[] array = new jalview.binding.AnnotationElement[0];
+ return (jalview.binding.AnnotationElement[]) this._annotationElementList.toArray(array);
+ }
+
+ /**
+ * Method getAnnotationElementCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAnnotationElementCount(
+ ) {
+ return this._annotationElementList.size();
+ }
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription(
+ ) {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'graph'.
+ *
+ * @return the value of field 'Graph'.
+ */
+ public boolean getGraph(
+ ) {
+ return this._graph;
+ }
+
+ /**
+ * Returns the value of field 'graphType'.
+ *
+ * @return the value of field 'GraphType'.
+ */
+ public int getGraphType(
+ ) {
+ return this._graphType;
+ }
+
+ /**
+ * Returns the value of field 'label'.
+ *
+ * @return the value of field 'Label'.
+ */
+ public java.lang.String getLabel(
+ ) {
+ return this._label;
+ }
+
+ /**
+ * Method hasGraph.
+ *
+ * @return true if at least one Graph has been added
+ */
+ public boolean hasGraph(
+ ) {
+ return this._has_graph;
+ }
+
+ /**
+ * Method hasGraphType.
+ *
+ * @return true if at least one GraphType has been added
+ */
+ public boolean hasGraphType(
+ ) {
+ return this._has_graphType;
+ }
+
+ /**
+ * Returns the value of field 'graph'.
+ *
+ * @return the value of field 'Graph'.
+ */
+ public boolean isGraph(
+ ) {
+ return this._graph;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllAnnotationElement(
+ ) {
+ this._annotationElementList.clear();
+ }
+
+ /**
+ * Method removeAnnotationElement.
+ *
+ * @param vAnnotationElement
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAnnotationElement(
+ final jalview.binding.AnnotationElement vAnnotationElement) {
+ boolean removed = _annotationElementList.remove(vAnnotationElement);
+ return removed;
+ }
+
+ /**
+ * Method removeAnnotationElementAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.AnnotationElement removeAnnotationElementAt(
+ final int index) {
+ java.lang.Object obj = this._annotationElementList.remove(index);
+ return (jalview.binding.AnnotationElement) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setAnnotationElement(
+ final int index,
+ final jalview.binding.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationElementList.size()) {
+ throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
+ }
+
+ this._annotationElementList.set(index, vAnnotationElement);
+ }
+
+ /**
+ *
+ *
+ * @param vAnnotationElementArray
+ */
+ public void setAnnotationElement(
+ final jalview.binding.AnnotationElement[] vAnnotationElementArray) {
+ //-- copy array
+ _annotationElementList.clear();
+
+ for (int i = 0; i < vAnnotationElementArray.length; i++) {
+ this._annotationElementList.add(vAnnotationElementArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description the value of field 'description'.
+ */
+ public void setDescription(
+ final java.lang.String description) {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'graph'.
+ *
+ * @param graph the value of field 'graph'.
+ */
+ public void setGraph(
+ final boolean graph) {
+ this._graph = graph;
+ this._has_graph = true;
+ }
+
+ /**
+ * Sets the value of field 'graphType'.
+ *
+ * @param graphType the value of field 'graphType'.
+ */
+ public void setGraphType(
+ final int graphType) {
+ this._graphType = graphType;
+ this._has_graphType = true;
+ }
+
+ /**
+ * Sets the value of field 'label'.
+ *
+ * @param label the value of field 'label'.
+ */
+ public void setLabel(
+ final java.lang.String label) {
+ this._label = label;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Annotation
+ */
+ public static jalview.binding.Annotation unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 AnnotationElement.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AnnotationElement implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _position\r
- */\r
- private int _position;\r
-\r
- /**\r
- * keeps track of state for field: _position\r
- */\r
- private boolean _has_position;\r
-\r
- /**\r
- * Field _displayCharacter\r
- */\r
- private java.lang.String _displayCharacter;\r
-\r
- /**\r
- * Field _description\r
- */\r
- private java.lang.String _description;\r
-\r
- /**\r
- * Field _secondaryStructure\r
- */\r
- private java.lang.String _secondaryStructure;\r
-\r
- /**\r
- * Field _value\r
- */\r
- private float _value;\r
-\r
- /**\r
- * keeps track of state for field: _value\r
- */\r
- private boolean _has_value;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public AnnotationElement() {\r
- super();\r
- } //-- jalview.binding.AnnotationElement()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deletePosition\r
- * \r
- */\r
- public void deletePosition()\r
- {\r
- this._has_position= false;\r
- } //-- void deletePosition() \r
-\r
- /**\r
- * Method deleteValue\r
- * \r
- */\r
- public void deleteValue()\r
- {\r
- this._has_value= false;\r
- } //-- void deleteValue() \r
-\r
- /**\r
- * Returns the value of field 'description'.\r
- * \r
- * @return String\r
- * @return the value of field 'description'.\r
- */\r
- public java.lang.String getDescription()\r
- {\r
- return this._description;\r
- } //-- java.lang.String getDescription() \r
-\r
- /**\r
- * Returns the value of field 'displayCharacter'.\r
- * \r
- * @return String\r
- * @return the value of field 'displayCharacter'.\r
- */\r
- public java.lang.String getDisplayCharacter()\r
- {\r
- return this._displayCharacter;\r
- } //-- java.lang.String getDisplayCharacter() \r
-\r
- /**\r
- * Returns the value of field 'position'.\r
- * \r
- * @return int\r
- * @return the value of field 'position'.\r
- */\r
- public int getPosition()\r
- {\r
- return this._position;\r
- } //-- int getPosition() \r
-\r
- /**\r
- * Returns the value of field 'secondaryStructure'.\r
- * \r
- * @return String\r
- * @return the value of field 'secondaryStructure'.\r
- */\r
- public java.lang.String getSecondaryStructure()\r
- {\r
- return this._secondaryStructure;\r
- } //-- java.lang.String getSecondaryStructure() \r
-\r
- /**\r
- * Returns the value of field 'value'.\r
- * \r
- * @return float\r
- * @return the value of field 'value'.\r
- */\r
- public float getValue()\r
- {\r
- return this._value;\r
- } //-- float getValue() \r
-\r
- /**\r
- * Method hasPosition\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasPosition()\r
- {\r
- return this._has_position;\r
- } //-- boolean hasPosition() \r
-\r
- /**\r
- * Method hasValue\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasValue()\r
- {\r
- return this._has_value;\r
- } //-- boolean hasValue() \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 'description'.\r
- * \r
- * @param description the value of field 'description'.\r
- */\r
- public void setDescription(java.lang.String description)\r
- {\r
- this._description = description;\r
- } //-- void setDescription(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'displayCharacter'.\r
- * \r
- * @param displayCharacter the value of field 'displayCharacter'\r
- */\r
- public void setDisplayCharacter(java.lang.String displayCharacter)\r
- {\r
- this._displayCharacter = displayCharacter;\r
- } //-- void setDisplayCharacter(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'position'.\r
- * \r
- * @param position the value of field 'position'.\r
- */\r
- public void setPosition(int position)\r
- {\r
- this._position = position;\r
- this._has_position = true;\r
- } //-- void setPosition(int) \r
-\r
- /**\r
- * Sets the value of field 'secondaryStructure'.\r
- * \r
- * @param secondaryStructure the value of field\r
- * 'secondaryStructure'.\r
- */\r
- public void setSecondaryStructure(java.lang.String secondaryStructure)\r
- {\r
- this._secondaryStructure = secondaryStructure;\r
- } //-- void setSecondaryStructure(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'value'.\r
- * \r
- * @param value the value of field 'value'.\r
- */\r
- public void setValue(float value)\r
- {\r
- this._value = value;\r
- this._has_value = true;\r
- } //-- void setValue(float) \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.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class AnnotationElement.
+ *
+ * @version $Revision$ $Date$
+ */
+public class AnnotationElement implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _position.
+ */
+ private int _position;
+
+ /**
+ * keeps track of state for field: _position
+ */
+ private boolean _has_position;
+
+ /**
+ * Field _displayCharacter.
+ */
+ private java.lang.String _displayCharacter;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+ /**
+ * Field _secondaryStructure.
+ */
+ private java.lang.String _secondaryStructure;
+
+ /**
+ * Field _value.
+ */
+ private float _value;
+
+ /**
+ * keeps track of state for field: _value
+ */
+ private boolean _has_value;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public AnnotationElement() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deletePosition(
+ ) {
+ this._has_position= false;
+ }
+
+ /**
+ */
+ public void deleteValue(
+ ) {
+ this._has_value= false;
+ }
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription(
+ ) {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'displayCharacter'.
+ *
+ * @return the value of field 'DisplayCharacter'.
+ */
+ public java.lang.String getDisplayCharacter(
+ ) {
+ return this._displayCharacter;
+ }
+
+ /**
+ * Returns the value of field 'position'.
+ *
+ * @return the value of field 'Position'.
+ */
+ public int getPosition(
+ ) {
+ return this._position;
+ }
+
+ /**
+ * Returns the value of field 'secondaryStructure'.
+ *
+ * @return the value of field 'SecondaryStructure'.
+ */
+ public java.lang.String getSecondaryStructure(
+ ) {
+ return this._secondaryStructure;
+ }
+
+ /**
+ * Returns the value of field 'value'.
+ *
+ * @return the value of field 'Value'.
+ */
+ public float getValue(
+ ) {
+ return this._value;
+ }
+
+ /**
+ * Method hasPosition.
+ *
+ * @return true if at least one Position has been added
+ */
+ public boolean hasPosition(
+ ) {
+ return this._has_position;
+ }
+
+ /**
+ * Method hasValue.
+ *
+ * @return true if at least one Value has been added
+ */
+ public boolean hasValue(
+ ) {
+ return this._has_value;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description the value of field 'description'.
+ */
+ public void setDescription(
+ final java.lang.String description) {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'displayCharacter'.
+ *
+ * @param displayCharacter the value of field 'displayCharacter'
+ */
+ public void setDisplayCharacter(
+ final java.lang.String displayCharacter) {
+ this._displayCharacter = displayCharacter;
+ }
+
+ /**
+ * Sets the value of field 'position'.
+ *
+ * @param position the value of field 'position'.
+ */
+ public void setPosition(
+ final int position) {
+ this._position = position;
+ this._has_position = true;
+ }
+
+ /**
+ * Sets the value of field 'secondaryStructure'.
+ *
+ * @param secondaryStructure the value of field
+ * 'secondaryStructure'.
+ */
+ public void setSecondaryStructure(
+ final java.lang.String secondaryStructure) {
+ this._secondaryStructure = secondaryStructure;
+ }
+
+ /**
+ * Sets the value of field 'value'.
+ *
+ * @param value the value of field 'value'.
+ */
+ public void setValue(
+ final float value) {
+ this._value = value;
+ this._has_value = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.AnnotationElement
+ */
+ public static jalview.binding.AnnotationElement unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 Colour.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Colour implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _name\r
- */\r
- private java.lang.String _name;\r
-\r
- /**\r
- * Field _RGB\r
- */\r
- private java.lang.String _RGB;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Colour() {\r
- super();\r
- } //-- jalview.binding.Colour()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Returns the value of field 'name'.\r
- * \r
- * @return String\r
- * @return the value of field 'name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- } //-- java.lang.String getName() \r
-\r
- /**\r
- * Returns the value of field 'RGB'.\r
- * \r
- * @return String\r
- * @return the value of field 'RGB'.\r
- */\r
- public java.lang.String getRGB()\r
- {\r
- return this._RGB;\r
- } //-- java.lang.String getRGB() \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 'name'.\r
- * \r
- * @param name the value of field 'name'.\r
- */\r
- public void setName(java.lang.String name)\r
- {\r
- this._name = name;\r
- } //-- void setName(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'RGB'.\r
- * \r
- * @param RGB the value of field 'RGB'.\r
- */\r
- public void setRGB(java.lang.String RGB)\r
- {\r
- this._RGB = RGB;\r
- } //-- void setRGB(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.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Colour.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Colour implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _RGB.
+ */
+ private java.lang.String _RGB;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Colour() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName(
+ ) {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'RGB'.
+ *
+ * @return the value of field 'RGB'.
+ */
+ public java.lang.String getRGB(
+ ) {
+ return this._RGB;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name the value of field 'name'.
+ */
+ public void setName(
+ final java.lang.String name) {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'RGB'.
+ *
+ * @param RGB the value of field 'RGB'.
+ */
+ public void setRGB(
+ final java.lang.String RGB) {
+ this._RGB = RGB;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Colour
+ */
+ public static jalview.binding.Colour unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 Feature.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Feature implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _begin\r
- */\r
- private int _begin;\r
-\r
- /**\r
- * keeps track of state for field: _begin\r
- */\r
- private boolean _has_begin;\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
- * Field _type\r
- */\r
- private java.lang.String _type;\r
-\r
- /**\r
- * Field _description\r
- */\r
- private java.lang.String _description;\r
-\r
- /**\r
- * Field _status\r
- */\r
- private java.lang.String _status;\r
-\r
- /**\r
- * Field _featureGroup\r
- */\r
- private java.lang.String _featureGroup;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Feature() {\r
- super();\r
- } //-- jalview.binding.Feature()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteBegin\r
- * \r
- */\r
- public void deleteBegin()\r
- {\r
- this._has_begin= false;\r
- } //-- void deleteBegin() \r
-\r
- /**\r
- * Method deleteEnd\r
- * \r
- */\r
- public void deleteEnd()\r
- {\r
- this._has_end= false;\r
- } //-- void deleteEnd() \r
-\r
- /**\r
- * Returns the value of field 'begin'.\r
- * \r
- * @return int\r
- * @return the value of field 'begin'.\r
- */\r
- public int getBegin()\r
- {\r
- return this._begin;\r
- } //-- int getBegin() \r
-\r
- /**\r
- * Returns the value of field 'description'.\r
- * \r
- * @return String\r
- * @return the value of field 'description'.\r
- */\r
- public java.lang.String getDescription()\r
- {\r
- return this._description;\r
- } //-- java.lang.String getDescription() \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 'featureGroup'.\r
- * \r
- * @return String\r
- * @return the value of field 'featureGroup'.\r
- */\r
- public java.lang.String getFeatureGroup()\r
- {\r
- return this._featureGroup;\r
- } //-- java.lang.String getFeatureGroup() \r
-\r
- /**\r
- * Returns the value of field 'status'.\r
- * \r
- * @return String\r
- * @return the value of field 'status'.\r
- */\r
- public java.lang.String getStatus()\r
- {\r
- return this._status;\r
- } //-- java.lang.String getStatus() \r
-\r
- /**\r
- * Returns the value of field 'type'.\r
- * \r
- * @return String\r
- * @return the value of field 'type'.\r
- */\r
- public java.lang.String getType()\r
- {\r
- return this._type;\r
- } //-- java.lang.String getType() \r
-\r
- /**\r
- * Method hasBegin\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasBegin()\r
- {\r
- return this._has_begin;\r
- } //-- boolean hasBegin() \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 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 'begin'.\r
- * \r
- * @param begin the value of field 'begin'.\r
- */\r
- public void setBegin(int begin)\r
- {\r
- this._begin = begin;\r
- this._has_begin = true;\r
- } //-- void setBegin(int) \r
-\r
- /**\r
- * Sets the value of field 'description'.\r
- * \r
- * @param description the value of field 'description'.\r
- */\r
- public void setDescription(java.lang.String description)\r
- {\r
- this._description = description;\r
- } //-- void setDescription(java.lang.String) \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 'featureGroup'.\r
- * \r
- * @param featureGroup the value of field 'featureGroup'.\r
- */\r
- public void setFeatureGroup(java.lang.String featureGroup)\r
- {\r
- this._featureGroup = featureGroup;\r
- } //-- void setFeatureGroup(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'status'.\r
- * \r
- * @param status the value of field 'status'.\r
- */\r
- public void setStatus(java.lang.String status)\r
- {\r
- this._status = status;\r
- } //-- void setStatus(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'type'.\r
- * \r
- * @param type the value of field 'type'.\r
- */\r
- public void setType(java.lang.String type)\r
- {\r
- this._type = type;\r
- } //-- void setType(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.binding.Feature) Unmarshaller.unmarshal(jalview.binding.Feature.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Feature.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Feature implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _begin.
+ */
+ private int _begin;
+
+ /**
+ * keeps track of state for field: _begin
+ */
+ private boolean _has_begin;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _type.
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+ /**
+ * Field _status.
+ */
+ private java.lang.String _status;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Feature() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteBegin(
+ ) {
+ this._has_begin= false;
+ }
+
+ /**
+ */
+ public void deleteEnd(
+ ) {
+ this._has_end= false;
+ }
+
+ /**
+ * Returns the value of field 'begin'.
+ *
+ * @return the value of field 'Begin'.
+ */
+ public int getBegin(
+ ) {
+ return this._begin;
+ }
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription(
+ ) {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd(
+ ) {
+ return this._end;
+ }
+
+ /**
+ * Returns the value of field 'status'.
+ *
+ * @return the value of field 'Status'.
+ */
+ public java.lang.String getStatus(
+ ) {
+ return this._status;
+ }
+
+ /**
+ * Returns the value of field 'type'.
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType(
+ ) {
+ return this._type;
+ }
+
+ /**
+ * Method hasBegin.
+ *
+ * @return true if at least one Begin has been added
+ */
+ public boolean hasBegin(
+ ) {
+ return this._has_begin;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd(
+ ) {
+ return this._has_end;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'begin'.
+ *
+ * @param begin the value of field 'begin'.
+ */
+ public void setBegin(
+ final int begin) {
+ this._begin = begin;
+ this._has_begin = true;
+ }
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description the value of field 'description'.
+ */
+ public void setDescription(
+ final java.lang.String description) {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end the value of field 'end'.
+ */
+ public void setEnd(
+ final int end) {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ * Sets the value of field 'status'.
+ *
+ * @param status the value of field 'status'.
+ */
+ public void setStatus(
+ final java.lang.String status) {
+ this._status = status;
+ }
+
+ /**
+ * Sets the value of field 'type'.
+ *
+ * @param type the value of field 'type'.
+ */
+ public void setType(
+ final java.lang.String type) {
+ this._type = type;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Feature
+ */
+ public static jalview.binding.Feature unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Feature) Unmarshaller.unmarshal(jalview.binding.Feature.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 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
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class FeatureSettings.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class FeatureSettings implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _settingList\r
- */\r
- private java.util.Vector _settingList;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public FeatureSettings() {\r
- super();\r
- _settingList = new Vector();\r
- } //-- jalview.binding.FeatureSettings()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addSetting\r
- * \r
- * \r
- * \r
- * @param vSetting\r
- */\r
- public void addSetting(jalview.binding.Setting vSetting)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _settingList.addElement(vSetting);\r
- } //-- void addSetting(jalview.binding.Setting) \r
-\r
- /**\r
- * Method addSetting\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vSetting\r
- */\r
- public void addSetting(int index, jalview.binding.Setting vSetting)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _settingList.insertElementAt(vSetting, index);\r
- } //-- void addSetting(int, jalview.binding.Setting) \r
-\r
- /**\r
- * Method enumerateSetting\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateSetting()\r
- {\r
- return _settingList.elements();\r
- } //-- java.util.Enumeration enumerateSetting() \r
-\r
- /**\r
- * Method getSetting\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Setting\r
- */\r
- public jalview.binding.Setting getSetting(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _settingList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.binding.Setting) _settingList.elementAt(index);\r
- } //-- jalview.binding.Setting getSetting(int) \r
-\r
- /**\r
- * Method getSetting\r
- * \r
- * \r
- * \r
- * @return Setting\r
- */\r
- public jalview.binding.Setting[] getSetting()\r
- {\r
- int size = _settingList.size();\r
- jalview.binding.Setting[] mArray = new jalview.binding.Setting[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.Setting) _settingList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.Setting[] getSetting() \r
-\r
- /**\r
- * Method getSettingCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getSettingCount()\r
- {\r
- return _settingList.size();\r
- } //-- int getSettingCount() \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
- * Method removeAllSetting\r
- * \r
- */\r
- public void removeAllSetting()\r
- {\r
- _settingList.removeAllElements();\r
- } //-- void removeAllSetting() \r
-\r
- /**\r
- * Method removeSetting\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Setting\r
- */\r
- public jalview.binding.Setting removeSetting(int index)\r
- {\r
- java.lang.Object obj = _settingList.elementAt(index);\r
- _settingList.removeElementAt(index);\r
- return (jalview.binding.Setting) obj;\r
- } //-- jalview.binding.Setting removeSetting(int) \r
-\r
- /**\r
- * Method setSetting\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vSetting\r
- */\r
- public void setSetting(int index, jalview.binding.Setting vSetting)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _settingList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _settingList.setElementAt(vSetting, index);\r
- } //-- void setSetting(int, jalview.binding.Setting) \r
-\r
- /**\r
- * Method setSetting\r
- * \r
- * \r
- * \r
- * @param settingArray\r
- */\r
- public void setSetting(jalview.binding.Setting[] settingArray)\r
- {\r
- //-- copy array\r
- _settingList.removeAllElements();\r
- for (int i = 0; i < settingArray.length; i++) {\r
- _settingList.addElement(settingArray[i]);\r
- }\r
- } //-- void setSetting(jalview.binding.Setting) \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.binding.FeatureSettings) Unmarshaller.unmarshal(jalview.binding.FeatureSettings.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class FeatureSettings.
+ *
+ * @version $Revision$ $Date$
+ */
+public class FeatureSettings implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _settingList.
+ */
+ private java.util.Vector _settingList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public FeatureSettings() {
+ super();
+ this._settingList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vSetting
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSetting(
+ final jalview.binding.Setting vSetting)
+ throws java.lang.IndexOutOfBoundsException {
+ this._settingList.addElement(vSetting);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSetting
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSetting(
+ final int index,
+ final jalview.binding.Setting vSetting)
+ throws java.lang.IndexOutOfBoundsException {
+ this._settingList.add(index, vSetting);
+ }
+
+ /**
+ * Method enumerateSetting.
+ *
+ * @return an Enumeration over all jalview.binding.Setting
+ * elements
+ */
+ public java.util.Enumeration enumerateSetting(
+ ) {
+ return this._settingList.elements();
+ }
+
+ /**
+ * Method getSetting.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Setting at the
+ * given index
+ */
+ public jalview.binding.Setting getSetting(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._settingList.size()) {
+ throw new IndexOutOfBoundsException("getSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Setting) _settingList.get(index);
+ }
+
+ /**
+ * Method getSetting.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Setting[] getSetting(
+ ) {
+ jalview.binding.Setting[] array = new jalview.binding.Setting[0];
+ return (jalview.binding.Setting[]) this._settingList.toArray(array);
+ }
+
+ /**
+ * Method getSettingCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSettingCount(
+ ) {
+ return this._settingList.size();
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllSetting(
+ ) {
+ this._settingList.clear();
+ }
+
+ /**
+ * Method removeSetting.
+ *
+ * @param vSetting
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSetting(
+ final jalview.binding.Setting vSetting) {
+ boolean removed = _settingList.remove(vSetting);
+ return removed;
+ }
+
+ /**
+ * Method removeSettingAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Setting removeSettingAt(
+ final int index) {
+ java.lang.Object obj = this._settingList.remove(index);
+ return (jalview.binding.Setting) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSetting
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setSetting(
+ final int index,
+ final jalview.binding.Setting vSetting)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._settingList.size()) {
+ throw new IndexOutOfBoundsException("setSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
+ }
+
+ this._settingList.set(index, vSetting);
+ }
+
+ /**
+ *
+ *
+ * @param vSettingArray
+ */
+ public void setSetting(
+ final jalview.binding.Setting[] vSettingArray) {
+ //-- copy array
+ _settingList.clear();
+
+ for (int i = 0; i < vSettingArray.length; i++) {
+ this._settingList.add(vSettingArray[i]);
+ }
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.FeatureSettings
+ */
+ public static jalview.binding.FeatureSettings unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(jalview.binding.FeatureSettings.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 Features.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Features extends Feature \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Features() {\r
- super();\r
- } //-- jalview.binding.Features()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\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
- * 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.binding.Features) Unmarshaller.unmarshal(jalview.binding.Features.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Features.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Features extends Feature
+implements java.io.Serializable
+{
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Features() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Feature
+ */
+ public static jalview.binding.Feature unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Feature) Unmarshaller.unmarshal(jalview.binding.Features.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 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
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class JGroup.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class JGroup 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
- * Field _name\r
- */\r
- private java.lang.String _name;\r
-\r
- /**\r
- * Field _colour\r
- */\r
- private java.lang.String _colour;\r
-\r
- /**\r
- * Field _consThreshold\r
- */\r
- private int _consThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _consThreshold\r
- */\r
- private boolean _has_consThreshold;\r
-\r
- /**\r
- * Field _pidThreshold\r
- */\r
- private int _pidThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _pidThreshold\r
- */\r
- private boolean _has_pidThreshold;\r
-\r
- /**\r
- * Field _outlineColour\r
- */\r
- private int _outlineColour;\r
-\r
- /**\r
- * keeps track of state for field: _outlineColour\r
- */\r
- private boolean _has_outlineColour;\r
-\r
- /**\r
- * Field _displayBoxes\r
- */\r
- private boolean _displayBoxes;\r
-\r
- /**\r
- * keeps track of state for field: _displayBoxes\r
- */\r
- private boolean _has_displayBoxes;\r
-\r
- /**\r
- * Field _displayText\r
- */\r
- private boolean _displayText;\r
-\r
- /**\r
- * keeps track of state for field: _displayText\r
- */\r
- private boolean _has_displayText;\r
-\r
- /**\r
- * Field _colourText\r
- */\r
- private boolean _colourText;\r
-\r
- /**\r
- * keeps track of state for field: _colourText\r
- */\r
- private boolean _has_colourText;\r
-\r
- /**\r
- * Field _seqList\r
- */\r
- private java.util.Vector _seqList;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public JGroup() {\r
- super();\r
- _seqList = new Vector();\r
- } //-- jalview.binding.JGroup()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addSeq\r
- * \r
- * \r
- * \r
- * @param vSeq\r
- */\r
- public void addSeq(int vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _seqList.addElement(new java.lang.Integer(vSeq));\r
- } //-- void addSeq(int) \r
-\r
- /**\r
- * Method addSeq\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vSeq\r
- */\r
- public void addSeq(int index, int vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _seqList.insertElementAt(new java.lang.Integer(vSeq), index);\r
- } //-- void addSeq(int, int) \r
-\r
- /**\r
- * Method deleteColourText\r
- * \r
- */\r
- public void deleteColourText()\r
- {\r
- this._has_colourText= false;\r
- } //-- void deleteColourText() \r
-\r
- /**\r
- * Method deleteConsThreshold\r
- * \r
- */\r
- public void deleteConsThreshold()\r
- {\r
- this._has_consThreshold= false;\r
- } //-- void deleteConsThreshold() \r
-\r
- /**\r
- * Method deleteDisplayBoxes\r
- * \r
- */\r
- public void deleteDisplayBoxes()\r
- {\r
- this._has_displayBoxes= false;\r
- } //-- void deleteDisplayBoxes() \r
-\r
- /**\r
- * Method deleteDisplayText\r
- * \r
- */\r
- public void deleteDisplayText()\r
- {\r
- this._has_displayText= false;\r
- } //-- void deleteDisplayText() \r
-\r
- /**\r
- * Method deleteEnd\r
- * \r
- */\r
- public void deleteEnd()\r
- {\r
- this._has_end= false;\r
- } //-- void deleteEnd() \r
-\r
- /**\r
- * Method deleteOutlineColour\r
- * \r
- */\r
- public void deleteOutlineColour()\r
- {\r
- this._has_outlineColour= false;\r
- } //-- void deleteOutlineColour() \r
-\r
- /**\r
- * Method deletePidThreshold\r
- * \r
- */\r
- public void deletePidThreshold()\r
- {\r
- this._has_pidThreshold= false;\r
- } //-- void deletePidThreshold() \r
-\r
- /**\r
- * Method deleteStart\r
- * \r
- */\r
- public void deleteStart()\r
- {\r
- this._has_start= false;\r
- } //-- void deleteStart() \r
-\r
- /**\r
- * Method enumerateSeq\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateSeq()\r
- {\r
- return _seqList.elements();\r
- } //-- java.util.Enumeration enumerateSeq() \r
-\r
- /**\r
- * Returns the value of field 'colour'.\r
- * \r
- * @return String\r
- * @return the value of field 'colour'.\r
- */\r
- public java.lang.String getColour()\r
- {\r
- return this._colour;\r
- } //-- java.lang.String getColour() \r
-\r
- /**\r
- * Returns the value of field 'colourText'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'colourText'.\r
- */\r
- public boolean getColourText()\r
- {\r
- return this._colourText;\r
- } //-- boolean getColourText() \r
-\r
- /**\r
- * Returns the value of field 'consThreshold'.\r
- * \r
- * @return int\r
- * @return the value of field 'consThreshold'.\r
- */\r
- public int getConsThreshold()\r
- {\r
- return this._consThreshold;\r
- } //-- int getConsThreshold() \r
-\r
- /**\r
- * Returns the value of field 'displayBoxes'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'displayBoxes'.\r
- */\r
- public boolean getDisplayBoxes()\r
- {\r
- return this._displayBoxes;\r
- } //-- boolean getDisplayBoxes() \r
-\r
- /**\r
- * Returns the value of field 'displayText'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'displayText'.\r
- */\r
- public boolean getDisplayText()\r
- {\r
- return this._displayText;\r
- } //-- boolean getDisplayText() \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 'name'.\r
- * \r
- * @return String\r
- * @return the value of field 'name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- } //-- java.lang.String getName() \r
-\r
- /**\r
- * Returns the value of field 'outlineColour'.\r
- * \r
- * @return int\r
- * @return the value of field 'outlineColour'.\r
- */\r
- public int getOutlineColour()\r
- {\r
- return this._outlineColour;\r
- } //-- int getOutlineColour() \r
-\r
- /**\r
- * Returns the value of field 'pidThreshold'.\r
- * \r
- * @return int\r
- * @return the value of field 'pidThreshold'.\r
- */\r
- public int getPidThreshold()\r
- {\r
- return this._pidThreshold;\r
- } //-- int getPidThreshold() \r
-\r
- /**\r
- * Method getSeq\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return int\r
- */\r
- public int getSeq(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _seqList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return ((java.lang.Integer)_seqList.elementAt(index)).intValue();\r
- } //-- int getSeq(int) \r
-\r
- /**\r
- * Method getSeq\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int[] getSeq()\r
- {\r
- int size = _seqList.size();\r
- int[] mArray = new int[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue();\r
- }\r
- return mArray;\r
- } //-- int[] getSeq() \r
-\r
- /**\r
- * Method getSeqCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getSeqCount()\r
- {\r
- return _seqList.size();\r
- } //-- int getSeqCount() \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 hasColourText\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasColourText()\r
- {\r
- return this._has_colourText;\r
- } //-- boolean hasColourText() \r
-\r
- /**\r
- * Method hasConsThreshold\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasConsThreshold()\r
- {\r
- return this._has_consThreshold;\r
- } //-- boolean hasConsThreshold() \r
-\r
- /**\r
- * Method hasDisplayBoxes\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasDisplayBoxes()\r
- {\r
- return this._has_displayBoxes;\r
- } //-- boolean hasDisplayBoxes() \r
-\r
- /**\r
- * Method hasDisplayText\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasDisplayText()\r
- {\r
- return this._has_displayText;\r
- } //-- boolean hasDisplayText() \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 hasOutlineColour\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasOutlineColour()\r
- {\r
- return this._has_outlineColour;\r
- } //-- boolean hasOutlineColour() \r
-\r
- /**\r
- * Method hasPidThreshold\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasPidThreshold()\r
- {\r
- return this._has_pidThreshold;\r
- } //-- boolean hasPidThreshold() \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
- * Method removeAllSeq\r
- * \r
- */\r
- public void removeAllSeq()\r
- {\r
- _seqList.removeAllElements();\r
- } //-- void removeAllSeq() \r
-\r
- /**\r
- * Method removeSeq\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return int\r
- */\r
- public int removeSeq(int index)\r
- {\r
- java.lang.Object obj = _seqList.elementAt(index);\r
- _seqList.removeElementAt(index);\r
- return ((java.lang.Integer)obj).intValue();\r
- } //-- int removeSeq(int) \r
-\r
- /**\r
- * Sets the value of field 'colour'.\r
- * \r
- * @param colour the value of field 'colour'.\r
- */\r
- public void setColour(java.lang.String colour)\r
- {\r
- this._colour = colour;\r
- } //-- void setColour(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'colourText'.\r
- * \r
- * @param colourText the value of field 'colourText'.\r
- */\r
- public void setColourText(boolean colourText)\r
- {\r
- this._colourText = colourText;\r
- this._has_colourText = true;\r
- } //-- void setColourText(boolean) \r
-\r
- /**\r
- * Sets the value of field 'consThreshold'.\r
- * \r
- * @param consThreshold the value of field 'consThreshold'.\r
- */\r
- public void setConsThreshold(int consThreshold)\r
- {\r
- this._consThreshold = consThreshold;\r
- this._has_consThreshold = true;\r
- } //-- void setConsThreshold(int) \r
-\r
- /**\r
- * Sets the value of field 'displayBoxes'.\r
- * \r
- * @param displayBoxes the value of field 'displayBoxes'.\r
- */\r
- public void setDisplayBoxes(boolean displayBoxes)\r
- {\r
- this._displayBoxes = displayBoxes;\r
- this._has_displayBoxes = true;\r
- } //-- void setDisplayBoxes(boolean) \r
-\r
- /**\r
- * Sets the value of field 'displayText'.\r
- * \r
- * @param displayText the value of field 'displayText'.\r
- */\r
- public void setDisplayText(boolean displayText)\r
- {\r
- this._displayText = displayText;\r
- this._has_displayText = true;\r
- } //-- void setDisplayText(boolean) \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 'name'.\r
- * \r
- * @param name the value of field 'name'.\r
- */\r
- public void setName(java.lang.String name)\r
- {\r
- this._name = name;\r
- } //-- void setName(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'outlineColour'.\r
- * \r
- * @param outlineColour the value of field 'outlineColour'.\r
- */\r
- public void setOutlineColour(int outlineColour)\r
- {\r
- this._outlineColour = outlineColour;\r
- this._has_outlineColour = true;\r
- } //-- void setOutlineColour(int) \r
-\r
- /**\r
- * Sets the value of field 'pidThreshold'.\r
- * \r
- * @param pidThreshold the value of field 'pidThreshold'.\r
- */\r
- public void setPidThreshold(int pidThreshold)\r
- {\r
- this._pidThreshold = pidThreshold;\r
- this._has_pidThreshold = true;\r
- } //-- void setPidThreshold(int) \r
-\r
- /**\r
- * Method setSeq\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vSeq\r
- */\r
- public void setSeq(int index, int vSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _seqList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _seqList.setElementAt(new java.lang.Integer(vSeq), index);\r
- } //-- void setSeq(int, int) \r
-\r
- /**\r
- * Method setSeq\r
- * \r
- * \r
- * \r
- * @param seqArray\r
- */\r
- public void setSeq(int[] seqArray)\r
- {\r
- //-- copy array\r
- _seqList.removeAllElements();\r
- for (int i = 0; i < seqArray.length; i++) {\r
- _seqList.addElement(new java.lang.Integer(seqArray[i]));\r
- }\r
- } //-- void setSeq(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.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class JGroup.
+ *
+ * @version $Revision$ $Date$
+ */
+public class JGroup implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _start.
+ */
+ private int _start;
+
+ /**
+ * keeps track of state for field: _start
+ */
+ private boolean _has_start;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _colour.
+ */
+ private java.lang.String _colour;
+
+ /**
+ * Field _consThreshold.
+ */
+ private int _consThreshold;
+
+ /**
+ * keeps track of state for field: _consThreshold
+ */
+ private boolean _has_consThreshold;
+
+ /**
+ * Field _pidThreshold.
+ */
+ private int _pidThreshold;
+
+ /**
+ * keeps track of state for field: _pidThreshold
+ */
+ private boolean _has_pidThreshold;
+
+ /**
+ * Field _outlineColour.
+ */
+ private int _outlineColour;
+
+ /**
+ * keeps track of state for field: _outlineColour
+ */
+ private boolean _has_outlineColour;
+
+ /**
+ * Field _displayBoxes.
+ */
+ private boolean _displayBoxes;
+
+ /**
+ * keeps track of state for field: _displayBoxes
+ */
+ private boolean _has_displayBoxes;
+
+ /**
+ * Field _displayText.
+ */
+ private boolean _displayText;
+
+ /**
+ * keeps track of state for field: _displayText
+ */
+ private boolean _has_displayText;
+
+ /**
+ * Field _colourText.
+ */
+ private boolean _colourText;
+
+ /**
+ * keeps track of state for field: _colourText
+ */
+ private boolean _has_colourText;
+
+ /**
+ * Field _seqList.
+ */
+ private java.util.Vector _seqList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public JGroup() {
+ super();
+ this._seqList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSeq(
+ final int vSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ this._seqList.addElement(new java.lang.Integer(vSeq));
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSeq(
+ final int index,
+ final int vSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ this._seqList.add(index, new java.lang.Integer(vSeq));
+ }
+
+ /**
+ */
+ public void deleteColourText(
+ ) {
+ this._has_colourText= false;
+ }
+
+ /**
+ */
+ public void deleteConsThreshold(
+ ) {
+ this._has_consThreshold= false;
+ }
+
+ /**
+ */
+ public void deleteDisplayBoxes(
+ ) {
+ this._has_displayBoxes= false;
+ }
+
+ /**
+ */
+ public void deleteDisplayText(
+ ) {
+ this._has_displayText= false;
+ }
+
+ /**
+ */
+ public void deleteEnd(
+ ) {
+ this._has_end= false;
+ }
+
+ /**
+ */
+ public void deleteOutlineColour(
+ ) {
+ this._has_outlineColour= false;
+ }
+
+ /**
+ */
+ public void deletePidThreshold(
+ ) {
+ this._has_pidThreshold= false;
+ }
+
+ /**
+ */
+ public void deleteStart(
+ ) {
+ this._has_start= false;
+ }
+
+ /**
+ * Method enumerateSeq.
+ *
+ * @return an Enumeration over all int elements
+ */
+ public java.util.Enumeration enumerateSeq(
+ ) {
+ return this._seqList.elements();
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public java.lang.String getColour(
+ ) {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'colourText'.
+ *
+ * @return the value of field 'ColourText'.
+ */
+ public boolean getColourText(
+ ) {
+ return this._colourText;
+ }
+
+ /**
+ * Returns the value of field 'consThreshold'.
+ *
+ * @return the value of field 'ConsThreshold'.
+ */
+ public int getConsThreshold(
+ ) {
+ return this._consThreshold;
+ }
+
+ /**
+ * Returns the value of field 'displayBoxes'.
+ *
+ * @return the value of field 'DisplayBoxes'.
+ */
+ public boolean getDisplayBoxes(
+ ) {
+ return this._displayBoxes;
+ }
+
+ /**
+ * Returns the value of field 'displayText'.
+ *
+ * @return the value of field 'DisplayText'.
+ */
+ public boolean getDisplayText(
+ ) {
+ return this._displayText;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd(
+ ) {
+ return this._end;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName(
+ ) {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'outlineColour'.
+ *
+ * @return the value of field 'OutlineColour'.
+ */
+ public int getOutlineColour(
+ ) {
+ return this._outlineColour;
+ }
+
+ /**
+ * Returns the value of field 'pidThreshold'.
+ *
+ * @return the value of field 'PidThreshold'.
+ */
+ public int getPidThreshold(
+ ) {
+ return this._pidThreshold;
+ }
+
+ /**
+ * Method getSeq.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the int at the given index
+ */
+ public int getSeq(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._seqList.size()) {
+ throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+ }
+
+ return ((java.lang.Integer) _seqList.get(index)).intValue();
+ }
+
+ /**
+ * Method getSeq.Returns the contents of the collection in an
+ * Array.
+ *
+ * @return this collection as an Array
+ */
+ public int[] getSeq(
+ ) {
+ int size = this._seqList.size();
+ int[] array = new int[size];
+ java.util.Iterator iter = _seqList.iterator();
+ for (int index = 0; index < size; index++) {
+ array[index] = ((java.lang.Integer) iter.next()).intValue();
+ }
+ return array;
+ }
+
+ /**
+ * Method getSeqCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSeqCount(
+ ) {
+ return this._seqList.size();
+ }
+
+ /**
+ * Returns the value of field 'start'.
+ *
+ * @return the value of field 'Start'.
+ */
+ public int getStart(
+ ) {
+ return this._start;
+ }
+
+ /**
+ * Method hasColourText.
+ *
+ * @return true if at least one ColourText has been added
+ */
+ public boolean hasColourText(
+ ) {
+ return this._has_colourText;
+ }
+
+ /**
+ * Method hasConsThreshold.
+ *
+ * @return true if at least one ConsThreshold has been added
+ */
+ public boolean hasConsThreshold(
+ ) {
+ return this._has_consThreshold;
+ }
+
+ /**
+ * Method hasDisplayBoxes.
+ *
+ * @return true if at least one DisplayBoxes has been added
+ */
+ public boolean hasDisplayBoxes(
+ ) {
+ return this._has_displayBoxes;
+ }
+
+ /**
+ * Method hasDisplayText.
+ *
+ * @return true if at least one DisplayText has been added
+ */
+ public boolean hasDisplayText(
+ ) {
+ return this._has_displayText;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd(
+ ) {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasOutlineColour.
+ *
+ * @return true if at least one OutlineColour has been added
+ */
+ public boolean hasOutlineColour(
+ ) {
+ return this._has_outlineColour;
+ }
+
+ /**
+ * Method hasPidThreshold.
+ *
+ * @return true if at least one PidThreshold has been added
+ */
+ public boolean hasPidThreshold(
+ ) {
+ return this._has_pidThreshold;
+ }
+
+ /**
+ * Method hasStart.
+ *
+ * @return true if at least one Start has been added
+ */
+ public boolean hasStart(
+ ) {
+ return this._has_start;
+ }
+
+ /**
+ * Returns the value of field 'colourText'.
+ *
+ * @return the value of field 'ColourText'.
+ */
+ public boolean isColourText(
+ ) {
+ return this._colourText;
+ }
+
+ /**
+ * Returns the value of field 'displayBoxes'.
+ *
+ * @return the value of field 'DisplayBoxes'.
+ */
+ public boolean isDisplayBoxes(
+ ) {
+ return this._displayBoxes;
+ }
+
+ /**
+ * Returns the value of field 'displayText'.
+ *
+ * @return the value of field 'DisplayText'.
+ */
+ public boolean isDisplayText(
+ ) {
+ return this._displayText;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllSeq(
+ ) {
+ this._seqList.clear();
+ }
+
+ /**
+ * Method removeSeq.
+ *
+ * @param vSeq
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSeq(
+ final int vSeq) {
+ boolean removed = _seqList.remove(new java.lang.Integer(vSeq));
+ return removed;
+ }
+
+ /**
+ * Method removeSeqAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public int removeSeqAt(
+ final int index) {
+ java.lang.Object obj = this._seqList.remove(index);
+ return ((java.lang.Integer) obj).intValue();
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour the value of field 'colour'.
+ */
+ public void setColour(
+ final java.lang.String colour) {
+ this._colour = colour;
+ }
+
+ /**
+ * Sets the value of field 'colourText'.
+ *
+ * @param colourText the value of field 'colourText'.
+ */
+ public void setColourText(
+ final boolean colourText) {
+ this._colourText = colourText;
+ this._has_colourText = true;
+ }
+
+ /**
+ * Sets the value of field 'consThreshold'.
+ *
+ * @param consThreshold the value of field 'consThreshold'.
+ */
+ public void setConsThreshold(
+ final int consThreshold) {
+ this._consThreshold = consThreshold;
+ this._has_consThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'displayBoxes'.
+ *
+ * @param displayBoxes the value of field 'displayBoxes'.
+ */
+ public void setDisplayBoxes(
+ final boolean displayBoxes) {
+ this._displayBoxes = displayBoxes;
+ this._has_displayBoxes = true;
+ }
+
+ /**
+ * Sets the value of field 'displayText'.
+ *
+ * @param displayText the value of field 'displayText'.
+ */
+ public void setDisplayText(
+ final boolean displayText) {
+ this._displayText = displayText;
+ this._has_displayText = true;
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end the value of field 'end'.
+ */
+ public void setEnd(
+ final int end) {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name the value of field 'name'.
+ */
+ public void setName(
+ final java.lang.String name) {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'outlineColour'.
+ *
+ * @param outlineColour the value of field 'outlineColour'.
+ */
+ public void setOutlineColour(
+ final int outlineColour) {
+ this._outlineColour = outlineColour;
+ this._has_outlineColour = true;
+ }
+
+ /**
+ * Sets the value of field 'pidThreshold'.
+ *
+ * @param pidThreshold the value of field 'pidThreshold'.
+ */
+ public void setPidThreshold(
+ final int pidThreshold) {
+ this._pidThreshold = pidThreshold;
+ this._has_pidThreshold = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setSeq(
+ final int index,
+ final int vSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._seqList.size()) {
+ throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]");
+ }
+
+ this._seqList.set(index, new java.lang.Integer(vSeq));
+ }
+
+ /**
+ *
+ *
+ * @param vSeqArray
+ */
+ public void setSeq(
+ final int[] vSeqArray) {
+ //-- copy array
+ _seqList.clear();
+
+ for (int i = 0; i < vSeqArray.length; i++) {
+ this._seqList.add(new java.lang.Integer(vSeqArray[i]));
+ }
+ }
+
+ /**
+ * Sets the value of field 'start'.
+ *
+ * @param start the value of field 'start'.
+ */
+ public void setStart(
+ final int start) {
+ this._start = start;
+ this._has_start = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JGroup
+ */
+ public static jalview.binding.JGroup unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 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
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class JSeq.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class JSeq implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _colour\r
- */\r
- private int _colour;\r
-\r
- /**\r
- * keeps track of state for field: _colour\r
- */\r
- private boolean _has_colour;\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
- * Field _id\r
- */\r
- private int _id;\r
-\r
- /**\r
- * keeps track of state for field: _id\r
- */\r
- private boolean _has_id;\r
-\r
- /**\r
- * Field _featuresList\r
- */\r
- private java.util.Vector _featuresList;\r
-\r
- /**\r
- * Field _pdbidsList\r
- */\r
- private java.util.Vector _pdbidsList;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public JSeq() {\r
- super();\r
- _featuresList = new Vector();\r
- _pdbidsList = new Vector();\r
- } //-- jalview.binding.JSeq()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addFeatures\r
- * \r
- * \r
- * \r
- * @param vFeatures\r
- */\r
- public void addFeatures(jalview.binding.Features vFeatures)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _featuresList.addElement(vFeatures);\r
- } //-- void addFeatures(jalview.binding.Features) \r
-\r
- /**\r
- * Method addFeatures\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vFeatures\r
- */\r
- public void addFeatures(int index, jalview.binding.Features vFeatures)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _featuresList.insertElementAt(vFeatures, index);\r
- } //-- void addFeatures(int, jalview.binding.Features) \r
-\r
- /**\r
- * Method addPdbids\r
- * \r
- * \r
- * \r
- * @param vPdbids\r
- */\r
- public void addPdbids(jalview.binding.Pdbids vPdbids)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _pdbidsList.addElement(vPdbids);\r
- } //-- void addPdbids(jalview.binding.Pdbids) \r
-\r
- /**\r
- * Method addPdbids\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vPdbids\r
- */\r
- public void addPdbids(int index, jalview.binding.Pdbids vPdbids)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _pdbidsList.insertElementAt(vPdbids, index);\r
- } //-- void addPdbids(int, jalview.binding.Pdbids) \r
-\r
- /**\r
- * Method deleteColour\r
- * \r
- */\r
- public void deleteColour()\r
- {\r
- this._has_colour= false;\r
- } //-- void deleteColour() \r
-\r
- /**\r
- * Method deleteEnd\r
- * \r
- */\r
- public void deleteEnd()\r
- {\r
- this._has_end= false;\r
- } //-- void deleteEnd() \r
-\r
- /**\r
- * Method deleteId\r
- * \r
- */\r
- public void deleteId()\r
- {\r
- this._has_id= false;\r
- } //-- void deleteId() \r
-\r
- /**\r
- * Method deleteStart\r
- * \r
- */\r
- public void deleteStart()\r
- {\r
- this._has_start= false;\r
- } //-- void deleteStart() \r
-\r
- /**\r
- * Method enumerateFeatures\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateFeatures()\r
- {\r
- return _featuresList.elements();\r
- } //-- java.util.Enumeration enumerateFeatures() \r
-\r
- /**\r
- * Method enumeratePdbids\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumeratePdbids()\r
- {\r
- return _pdbidsList.elements();\r
- } //-- java.util.Enumeration enumeratePdbids() \r
-\r
- /**\r
- * Returns the value of field 'colour'.\r
- * \r
- * @return int\r
- * @return the value of field 'colour'.\r
- */\r
- public int getColour()\r
- {\r
- return this._colour;\r
- } //-- int getColour() \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
- * Method getFeatures\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Features\r
- */\r
- public jalview.binding.Features getFeatures(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _featuresList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.binding.Features) _featuresList.elementAt(index);\r
- } //-- jalview.binding.Features getFeatures(int) \r
-\r
- /**\r
- * Method getFeatures\r
- * \r
- * \r
- * \r
- * @return Features\r
- */\r
- public jalview.binding.Features[] getFeatures()\r
- {\r
- int size = _featuresList.size();\r
- jalview.binding.Features[] mArray = new jalview.binding.Features[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.Features) _featuresList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.Features[] getFeatures() \r
-\r
- /**\r
- * Method getFeaturesCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getFeaturesCount()\r
- {\r
- return _featuresList.size();\r
- } //-- int getFeaturesCount() \r
-\r
- /**\r
- * Returns the value of field 'id'.\r
- * \r
- * @return int\r
- * @return the value of field 'id'.\r
- */\r
- public int getId()\r
- {\r
- return this._id;\r
- } //-- int getId() \r
-\r
- /**\r
- * Method getPdbids\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Pdbids\r
- */\r
- public jalview.binding.Pdbids getPdbids(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _pdbidsList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.binding.Pdbids) _pdbidsList.elementAt(index);\r
- } //-- jalview.binding.Pdbids getPdbids(int) \r
-\r
- /**\r
- * Method getPdbids\r
- * \r
- * \r
- * \r
- * @return Pdbids\r
- */\r
- public jalview.binding.Pdbids[] getPdbids()\r
- {\r
- int size = _pdbidsList.size();\r
- jalview.binding.Pdbids[] mArray = new jalview.binding.Pdbids[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.Pdbids) _pdbidsList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.Pdbids[] getPdbids() \r
-\r
- /**\r
- * Method getPdbidsCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getPdbidsCount()\r
- {\r
- return _pdbidsList.size();\r
- } //-- int getPdbidsCount() \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 hasColour\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasColour()\r
- {\r
- return this._has_colour;\r
- } //-- boolean hasColour() \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 hasId\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasId()\r
- {\r
- return this._has_id;\r
- } //-- boolean hasId() \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
- * Method removeAllFeatures\r
- * \r
- */\r
- public void removeAllFeatures()\r
- {\r
- _featuresList.removeAllElements();\r
- } //-- void removeAllFeatures() \r
-\r
- /**\r
- * Method removeAllPdbids\r
- * \r
- */\r
- public void removeAllPdbids()\r
- {\r
- _pdbidsList.removeAllElements();\r
- } //-- void removeAllPdbids() \r
-\r
- /**\r
- * Method removeFeatures\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Features\r
- */\r
- public jalview.binding.Features removeFeatures(int index)\r
- {\r
- java.lang.Object obj = _featuresList.elementAt(index);\r
- _featuresList.removeElementAt(index);\r
- return (jalview.binding.Features) obj;\r
- } //-- jalview.binding.Features removeFeatures(int) \r
-\r
- /**\r
- * Method removePdbids\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Pdbids\r
- */\r
- public jalview.binding.Pdbids removePdbids(int index)\r
- {\r
- java.lang.Object obj = _pdbidsList.elementAt(index);\r
- _pdbidsList.removeElementAt(index);\r
- return (jalview.binding.Pdbids) obj;\r
- } //-- jalview.binding.Pdbids removePdbids(int) \r
-\r
- /**\r
- * Sets the value of field 'colour'.\r
- * \r
- * @param colour the value of field 'colour'.\r
- */\r
- public void setColour(int colour)\r
- {\r
- this._colour = colour;\r
- this._has_colour = true;\r
- } //-- void setColour(int) \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
- * Method setFeatures\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vFeatures\r
- */\r
- public void setFeatures(int index, jalview.binding.Features vFeatures)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _featuresList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _featuresList.setElementAt(vFeatures, index);\r
- } //-- void setFeatures(int, jalview.binding.Features) \r
-\r
- /**\r
- * Method setFeatures\r
- * \r
- * \r
- * \r
- * @param featuresArray\r
- */\r
- public void setFeatures(jalview.binding.Features[] featuresArray)\r
- {\r
- //-- copy array\r
- _featuresList.removeAllElements();\r
- for (int i = 0; i < featuresArray.length; i++) {\r
- _featuresList.addElement(featuresArray[i]);\r
- }\r
- } //-- void setFeatures(jalview.binding.Features) \r
-\r
- /**\r
- * Sets the value of field 'id'.\r
- * \r
- * @param id the value of field 'id'.\r
- */\r
- public void setId(int id)\r
- {\r
- this._id = id;\r
- this._has_id = true;\r
- } //-- void setId(int) \r
-\r
- /**\r
- * Method setPdbids\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vPdbids\r
- */\r
- public void setPdbids(int index, jalview.binding.Pdbids vPdbids)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _pdbidsList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _pdbidsList.setElementAt(vPdbids, index);\r
- } //-- void setPdbids(int, jalview.binding.Pdbids) \r
-\r
- /**\r
- * Method setPdbids\r
- * \r
- * \r
- * \r
- * @param pdbidsArray\r
- */\r
- public void setPdbids(jalview.binding.Pdbids[] pdbidsArray)\r
- {\r
- //-- copy array\r
- _pdbidsList.removeAllElements();\r
- for (int i = 0; i < pdbidsArray.length; i++) {\r
- _pdbidsList.addElement(pdbidsArray[i]);\r
- }\r
- } //-- void setPdbids(jalview.binding.Pdbids) \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.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class JSeq.
+ *
+ * @version $Revision$ $Date$
+ */
+public class JSeq implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _colour.
+ */
+ private int _colour;
+
+ /**
+ * keeps track of state for field: _colour
+ */
+ private boolean _has_colour;
+
+ /**
+ * Field _start.
+ */
+ private int _start;
+
+ /**
+ * keeps track of state for field: _start
+ */
+ private boolean _has_start;
+
+ /**
+ * Field _end.
+ */
+ private int _end;
+
+ /**
+ * keeps track of state for field: _end
+ */
+ private boolean _has_end;
+
+ /**
+ * Field _id.
+ */
+ private int _id;
+
+ /**
+ * keeps track of state for field: _id
+ */
+ private boolean _has_id;
+
+ /**
+ * Field _featuresList.
+ */
+ private java.util.Vector _featuresList;
+
+ /**
+ * Field _pdbidsList.
+ */
+ private java.util.Vector _pdbidsList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public JSeq() {
+ super();
+ this._featuresList = new java.util.Vector();
+ this._pdbidsList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vFeatures
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addFeatures(
+ final jalview.binding.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException {
+ this._featuresList.addElement(vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vFeatures
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addFeatures(
+ final int index,
+ final jalview.binding.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException {
+ this._featuresList.add(index, vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param vPdbids
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addPdbids(
+ final jalview.binding.Pdbids vPdbids)
+ throws java.lang.IndexOutOfBoundsException {
+ this._pdbidsList.addElement(vPdbids);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbids
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addPdbids(
+ final int index,
+ final jalview.binding.Pdbids vPdbids)
+ throws java.lang.IndexOutOfBoundsException {
+ this._pdbidsList.add(index, vPdbids);
+ }
+
+ /**
+ */
+ public void deleteColour(
+ ) {
+ this._has_colour= false;
+ }
+
+ /**
+ */
+ public void deleteEnd(
+ ) {
+ this._has_end= false;
+ }
+
+ /**
+ */
+ public void deleteId(
+ ) {
+ this._has_id= false;
+ }
+
+ /**
+ */
+ public void deleteStart(
+ ) {
+ this._has_start= false;
+ }
+
+ /**
+ * Method enumerateFeatures.
+ *
+ * @return an Enumeration over all jalview.binding.Features
+ * elements
+ */
+ public java.util.Enumeration enumerateFeatures(
+ ) {
+ return this._featuresList.elements();
+ }
+
+ /**
+ * Method enumeratePdbids.
+ *
+ * @return an Enumeration over all jalview.binding.Pdbids
+ * elements
+ */
+ public java.util.Enumeration enumeratePdbids(
+ ) {
+ return this._pdbidsList.elements();
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public int getColour(
+ ) {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'end'.
+ *
+ * @return the value of field 'End'.
+ */
+ public int getEnd(
+ ) {
+ return this._end;
+ }
+
+ /**
+ * Method getFeatures.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Features at the
+ * given index
+ */
+ public jalview.binding.Features getFeatures(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._featuresList.size()) {
+ throw new IndexOutOfBoundsException("getFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Features) _featuresList.get(index);
+ }
+
+ /**
+ * Method getFeatures.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Features[] getFeatures(
+ ) {
+ jalview.binding.Features[] array = new jalview.binding.Features[0];
+ return (jalview.binding.Features[]) this._featuresList.toArray(array);
+ }
+
+ /**
+ * Method getFeaturesCount.
+ *
+ * @return the size of this collection
+ */
+ public int getFeaturesCount(
+ ) {
+ return this._featuresList.size();
+ }
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public int getId(
+ ) {
+ return this._id;
+ }
+
+ /**
+ * Method getPdbids.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Pdbids at the given
+ * index
+ */
+ public jalview.binding.Pdbids getPdbids(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._pdbidsList.size()) {
+ throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Pdbids) _pdbidsList.get(index);
+ }
+
+ /**
+ * Method getPdbids.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Pdbids[] getPdbids(
+ ) {
+ jalview.binding.Pdbids[] array = new jalview.binding.Pdbids[0];
+ return (jalview.binding.Pdbids[]) this._pdbidsList.toArray(array);
+ }
+
+ /**
+ * Method getPdbidsCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPdbidsCount(
+ ) {
+ return this._pdbidsList.size();
+ }
+
+ /**
+ * Returns the value of field 'start'.
+ *
+ * @return the value of field 'Start'.
+ */
+ public int getStart(
+ ) {
+ return this._start;
+ }
+
+ /**
+ * Method hasColour.
+ *
+ * @return true if at least one Colour has been added
+ */
+ public boolean hasColour(
+ ) {
+ return this._has_colour;
+ }
+
+ /**
+ * Method hasEnd.
+ *
+ * @return true if at least one End has been added
+ */
+ public boolean hasEnd(
+ ) {
+ return this._has_end;
+ }
+
+ /**
+ * Method hasId.
+ *
+ * @return true if at least one Id has been added
+ */
+ public boolean hasId(
+ ) {
+ return this._has_id;
+ }
+
+ /**
+ * Method hasStart.
+ *
+ * @return true if at least one Start has been added
+ */
+ public boolean hasStart(
+ ) {
+ return this._has_start;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllFeatures(
+ ) {
+ this._featuresList.clear();
+ }
+
+ /**
+ */
+ public void removeAllPdbids(
+ ) {
+ this._pdbidsList.clear();
+ }
+
+ /**
+ * Method removeFeatures.
+ *
+ * @param vFeatures
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeFeatures(
+ final jalview.binding.Features vFeatures) {
+ boolean removed = _featuresList.remove(vFeatures);
+ return removed;
+ }
+
+ /**
+ * Method removeFeaturesAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Features removeFeaturesAt(
+ final int index) {
+ java.lang.Object obj = this._featuresList.remove(index);
+ return (jalview.binding.Features) obj;
+ }
+
+ /**
+ * Method removePdbids.
+ *
+ * @param vPdbids
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removePdbids(
+ final jalview.binding.Pdbids vPdbids) {
+ boolean removed = _pdbidsList.remove(vPdbids);
+ return removed;
+ }
+
+ /**
+ * Method removePdbidsAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Pdbids removePdbidsAt(
+ final int index) {
+ java.lang.Object obj = this._pdbidsList.remove(index);
+ return (jalview.binding.Pdbids) obj;
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour the value of field 'colour'.
+ */
+ public void setColour(
+ final int colour) {
+ this._colour = colour;
+ this._has_colour = true;
+ }
+
+ /**
+ * Sets the value of field 'end'.
+ *
+ * @param end the value of field 'end'.
+ */
+ public void setEnd(
+ final int end) {
+ this._end = end;
+ this._has_end = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vFeatures
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setFeatures(
+ final int index,
+ final jalview.binding.Features vFeatures)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._featuresList.size()) {
+ throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]");
+ }
+
+ this._featuresList.set(index, vFeatures);
+ }
+
+ /**
+ *
+ *
+ * @param vFeaturesArray
+ */
+ public void setFeatures(
+ final jalview.binding.Features[] vFeaturesArray) {
+ //-- copy array
+ _featuresList.clear();
+
+ for (int i = 0; i < vFeaturesArray.length; i++) {
+ this._featuresList.add(vFeaturesArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(
+ final int id) {
+ this._id = id;
+ this._has_id = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbids
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setPdbids(
+ final int index,
+ final jalview.binding.Pdbids vPdbids)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._pdbidsList.size()) {
+ throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]");
+ }
+
+ this._pdbidsList.set(index, vPdbids);
+ }
+
+ /**
+ *
+ *
+ * @param vPdbidsArray
+ */
+ public void setPdbids(
+ final jalview.binding.Pdbids[] vPdbidsArray) {
+ //-- copy array
+ _pdbidsList.clear();
+
+ for (int i = 0; i < vPdbidsArray.length; i++) {
+ this._pdbidsList.add(vPdbidsArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'start'.
+ *
+ * @param start the value of field 'start'.
+ */
+ public void setStart(
+ final int start) {
+ this._start = start;
+ this._has_start = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JSeq
+ */
+ public static jalview.binding.JSeq unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 java.util.Date;\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 JalviewModel.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class JalviewModel implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _creationDate\r
- */\r
- private java.util.Date _creationDate;\r
-\r
- /**\r
- * Field _version\r
- */\r
- private java.lang.String _version;\r
-\r
- /**\r
- * Field _vamsasModel\r
- */\r
- private jalview.binding.VamsasModel _vamsasModel;\r
-\r
- /**\r
- * Field _jalviewModelSequence\r
- */\r
- private jalview.binding.JalviewModelSequence _jalviewModelSequence;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public JalviewModel() {\r
- super();\r
- } //-- jalview.binding.JalviewModel()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Returns the value of field 'creationDate'.\r
- * \r
- * @return Date\r
- * @return the value of field 'creationDate'.\r
- */\r
- public java.util.Date getCreationDate()\r
- {\r
- return this._creationDate;\r
- } //-- java.util.Date getCreationDate() \r
-\r
- /**\r
- * Returns the value of field 'jalviewModelSequence'.\r
- * \r
- * @return JalviewModelSequence\r
- * @return the value of field 'jalviewModelSequence'.\r
- */\r
- public jalview.binding.JalviewModelSequence getJalviewModelSequence()\r
- {\r
- return this._jalviewModelSequence;\r
- } //-- jalview.binding.JalviewModelSequence getJalviewModelSequence() \r
-\r
- /**\r
- * Returns the value of field 'vamsasModel'.\r
- * \r
- * @return VamsasModel\r
- * @return the value of field 'vamsasModel'.\r
- */\r
- public jalview.binding.VamsasModel getVamsasModel()\r
- {\r
- return this._vamsasModel;\r
- } //-- jalview.binding.VamsasModel getVamsasModel() \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 'creationDate'.\r
- * \r
- * @param creationDate the value of field 'creationDate'.\r
- */\r
- public void setCreationDate(java.util.Date creationDate)\r
- {\r
- this._creationDate = creationDate;\r
- } //-- void setCreationDate(java.util.Date) \r
-\r
- /**\r
- * Sets the value of field 'jalviewModelSequence'.\r
- * \r
- * @param jalviewModelSequence the value of field\r
- * 'jalviewModelSequence'.\r
- */\r
- public void setJalviewModelSequence(jalview.binding.JalviewModelSequence jalviewModelSequence)\r
- {\r
- this._jalviewModelSequence = jalviewModelSequence;\r
- } //-- void setJalviewModelSequence(jalview.binding.JalviewModelSequence) \r
-\r
- /**\r
- * Sets the value of field 'vamsasModel'.\r
- * \r
- * @param vamsasModel the value of field 'vamsasModel'.\r
- */\r
- public void setVamsasModel(jalview.binding.VamsasModel vamsasModel)\r
- {\r
- this._vamsasModel = vamsasModel;\r
- } //-- void setVamsasModel(jalview.binding.VamsasModel) \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.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class JalviewModel.
+ *
+ * @version $Revision$ $Date$
+ */
+public class JalviewModel implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _creationDate.
+ */
+ private java.util.Date _creationDate;
+
+ /**
+ * Field _version.
+ */
+ private java.lang.String _version;
+
+ /**
+ * Field _vamsasModel.
+ */
+ private jalview.binding.VamsasModel _vamsasModel;
+
+ /**
+ * Field _jalviewModelSequence.
+ */
+ private jalview.binding.JalviewModelSequence _jalviewModelSequence;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public JalviewModel() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Returns the value of field 'creationDate'.
+ *
+ * @return the value of field 'CreationDate'.
+ */
+ public java.util.Date getCreationDate(
+ ) {
+ return this._creationDate;
+ }
+
+ /**
+ * Returns the value of field 'jalviewModelSequence'.
+ *
+ * @return the value of field 'JalviewModelSequence'.
+ */
+ public jalview.binding.JalviewModelSequence getJalviewModelSequence(
+ ) {
+ return this._jalviewModelSequence;
+ }
+
+ /**
+ * Returns the value of field 'vamsasModel'.
+ *
+ * @return the value of field 'VamsasModel'.
+ */
+ public jalview.binding.VamsasModel getVamsasModel(
+ ) {
+ return this._vamsasModel;
+ }
+
+ /**
+ * Returns the value of field 'version'.
+ *
+ * @return the value of field 'Version'.
+ */
+ public java.lang.String getVersion(
+ ) {
+ return this._version;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'creationDate'.
+ *
+ * @param creationDate the value of field 'creationDate'.
+ */
+ public void setCreationDate(
+ final java.util.Date creationDate) {
+ this._creationDate = creationDate;
+ }
+
+ /**
+ * Sets the value of field 'jalviewModelSequence'.
+ *
+ * @param jalviewModelSequence the value of field
+ * 'jalviewModelSequence'.
+ */
+ public void setJalviewModelSequence(
+ final jalview.binding.JalviewModelSequence jalviewModelSequence) {
+ this._jalviewModelSequence = jalviewModelSequence;
+ }
+
+ /**
+ * Sets the value of field 'vamsasModel'.
+ *
+ * @param vamsasModel the value of field 'vamsasModel'.
+ */
+ public void setVamsasModel(
+ final jalview.binding.VamsasModel vamsasModel) {
+ this._vamsasModel = vamsasModel;
+ }
+
+ /**
+ * Sets the value of field 'version'.
+ *
+ * @param version the value of field 'version'.
+ */
+ public void setVersion(
+ final java.lang.String version) {
+ this._version = version;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JalviewModel
+ */
+ public static jalview.binding.JalviewModel unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 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
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class JalviewModelSequence.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class JalviewModelSequence implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _JSeqList\r
- */\r
- private java.util.Vector _JSeqList;\r
-\r
- /**\r
- * Field _JGroupList\r
- */\r
- private java.util.Vector _JGroupList;\r
-\r
- /**\r
- * Field _viewportList\r
- */\r
- private java.util.Vector _viewportList;\r
-\r
- /**\r
- * Field _userColoursList\r
- */\r
- private java.util.Vector _userColoursList;\r
-\r
- /**\r
- * Field _treeList\r
- */\r
- private java.util.Vector _treeList;\r
-\r
- /**\r
- * Field _featureSettings\r
- */\r
- private jalview.binding.FeatureSettings _featureSettings;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public JalviewModelSequence() {\r
- super();\r
- _JSeqList = new Vector();\r
- _JGroupList = new Vector();\r
- _viewportList = new Vector();\r
- _userColoursList = new Vector();\r
- _treeList = new Vector();\r
- } //-- jalview.binding.JalviewModelSequence()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addJGroup\r
- * \r
- * \r
- * \r
- * @param vJGroup\r
- */\r
- public void addJGroup(jalview.binding.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JGroupList.addElement(vJGroup);\r
- } //-- void addJGroup(jalview.binding.JGroup) \r
-\r
- /**\r
- * Method addJGroup\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vJGroup\r
- */\r
- public void addJGroup(int index, jalview.binding.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JGroupList.insertElementAt(vJGroup, index);\r
- } //-- void addJGroup(int, jalview.binding.JGroup) \r
-\r
- /**\r
- * Method addJSeq\r
- * \r
- * \r
- * \r
- * @param vJSeq\r
- */\r
- public void addJSeq(jalview.binding.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JSeqList.addElement(vJSeq);\r
- } //-- void addJSeq(jalview.binding.JSeq) \r
-\r
- /**\r
- * Method addJSeq\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vJSeq\r
- */\r
- public void addJSeq(int index, jalview.binding.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _JSeqList.insertElementAt(vJSeq, index);\r
- } //-- void addJSeq(int, jalview.binding.JSeq) \r
-\r
- /**\r
- * Method addTree\r
- * \r
- * \r
- * \r
- * @param vTree\r
- */\r
- public void addTree(jalview.binding.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _treeList.addElement(vTree);\r
- } //-- void addTree(jalview.binding.Tree) \r
-\r
- /**\r
- * Method addTree\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vTree\r
- */\r
- public void addTree(int index, jalview.binding.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _treeList.insertElementAt(vTree, index);\r
- } //-- void addTree(int, jalview.binding.Tree) \r
-\r
- /**\r
- * Method addUserColours\r
- * \r
- * \r
- * \r
- * @param vUserColours\r
- */\r
- public void addUserColours(jalview.binding.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _userColoursList.addElement(vUserColours);\r
- } //-- void addUserColours(jalview.binding.UserColours) \r
-\r
- /**\r
- * Method addUserColours\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vUserColours\r
- */\r
- public void addUserColours(int index, jalview.binding.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _userColoursList.insertElementAt(vUserColours, index);\r
- } //-- void addUserColours(int, jalview.binding.UserColours) \r
-\r
- /**\r
- * Method addViewport\r
- * \r
- * \r
- * \r
- * @param vViewport\r
- */\r
- public void addViewport(jalview.binding.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _viewportList.addElement(vViewport);\r
- } //-- void addViewport(jalview.binding.Viewport) \r
-\r
- /**\r
- * Method addViewport\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vViewport\r
- */\r
- public void addViewport(int index, jalview.binding.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _viewportList.insertElementAt(vViewport, index);\r
- } //-- void addViewport(int, jalview.binding.Viewport) \r
-\r
- /**\r
- * Method enumerateJGroup\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateJGroup()\r
- {\r
- return _JGroupList.elements();\r
- } //-- java.util.Enumeration enumerateJGroup() \r
-\r
- /**\r
- * Method enumerateJSeq\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateJSeq()\r
- {\r
- return _JSeqList.elements();\r
- } //-- java.util.Enumeration enumerateJSeq() \r
-\r
- /**\r
- * Method enumerateTree\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateTree()\r
- {\r
- return _treeList.elements();\r
- } //-- java.util.Enumeration enumerateTree() \r
-\r
- /**\r
- * Method enumerateUserColours\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateUserColours()\r
- {\r
- return _userColoursList.elements();\r
- } //-- java.util.Enumeration enumerateUserColours() \r
-\r
- /**\r
- * Method enumerateViewport\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateViewport()\r
- {\r
- return _viewportList.elements();\r
- } //-- java.util.Enumeration enumerateViewport() \r
-\r
- /**\r
- * Returns the value of field 'featureSettings'.\r
- * \r
- * @return FeatureSettings\r
- * @return the value of field 'featureSettings'.\r
- */\r
- public jalview.binding.FeatureSettings getFeatureSettings()\r
- {\r
- return this._featureSettings;\r
- } //-- jalview.binding.FeatureSettings getFeatureSettings() \r
-\r
- /**\r
- * Method getJGroup\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return JGroup\r
- */\r
- public jalview.binding.JGroup getJGroup(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _JGroupList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.binding.JGroup) _JGroupList.elementAt(index);\r
- } //-- jalview.binding.JGroup getJGroup(int) \r
-\r
- /**\r
- * Method getJGroup\r
- * \r
- * \r
- * \r
- * @return JGroup\r
- */\r
- public jalview.binding.JGroup[] getJGroup()\r
- {\r
- int size = _JGroupList.size();\r
- jalview.binding.JGroup[] mArray = new jalview.binding.JGroup[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.JGroup) _JGroupList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.JGroup[] getJGroup() \r
-\r
- /**\r
- * Method getJGroupCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getJGroupCount()\r
- {\r
- return _JGroupList.size();\r
- } //-- int getJGroupCount() \r
-\r
- /**\r
- * Method getJSeq\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return JSeq\r
- */\r
- public jalview.binding.JSeq getJSeq(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _JSeqList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.binding.JSeq) _JSeqList.elementAt(index);\r
- } //-- jalview.binding.JSeq getJSeq(int) \r
-\r
- /**\r
- * Method getJSeq\r
- * \r
- * \r
- * \r
- * @return JSeq\r
- */\r
- public jalview.binding.JSeq[] getJSeq()\r
- {\r
- int size = _JSeqList.size();\r
- jalview.binding.JSeq[] mArray = new jalview.binding.JSeq[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.JSeq) _JSeqList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.JSeq[] getJSeq() \r
-\r
- /**\r
- * Method getJSeqCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getJSeqCount()\r
- {\r
- return _JSeqList.size();\r
- } //-- int getJSeqCount() \r
-\r
- /**\r
- * Method getTree\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Tree\r
- */\r
- public jalview.binding.Tree getTree(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _treeList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.binding.Tree) _treeList.elementAt(index);\r
- } //-- jalview.binding.Tree getTree(int) \r
-\r
- /**\r
- * Method getTree\r
- * \r
- * \r
- * \r
- * @return Tree\r
- */\r
- public jalview.binding.Tree[] getTree()\r
- {\r
- int size = _treeList.size();\r
- jalview.binding.Tree[] mArray = new jalview.binding.Tree[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.Tree) _treeList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.Tree[] getTree() \r
-\r
- /**\r
- * Method getTreeCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getTreeCount()\r
- {\r
- return _treeList.size();\r
- } //-- int getTreeCount() \r
-\r
- /**\r
- * Method getUserColours\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return UserColours\r
- */\r
- public jalview.binding.UserColours getUserColours(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _userColoursList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
- } //-- jalview.binding.UserColours getUserColours(int) \r
-\r
- /**\r
- * Method getUserColours\r
- * \r
- * \r
- * \r
- * @return UserColours\r
- */\r
- public jalview.binding.UserColours[] getUserColours()\r
- {\r
- int size = _userColoursList.size();\r
- jalview.binding.UserColours[] mArray = new jalview.binding.UserColours[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.UserColours[] getUserColours() \r
-\r
- /**\r
- * Method getUserColoursCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getUserColoursCount()\r
- {\r
- return _userColoursList.size();\r
- } //-- int getUserColoursCount() \r
-\r
- /**\r
- * Method getViewport\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Viewport\r
- */\r
- public jalview.binding.Viewport getViewport(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _viewportList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.binding.Viewport) _viewportList.elementAt(index);\r
- } //-- jalview.binding.Viewport getViewport(int) \r
-\r
- /**\r
- * Method getViewport\r
- * \r
- * \r
- * \r
- * @return Viewport\r
- */\r
- public jalview.binding.Viewport[] getViewport()\r
- {\r
- int size = _viewportList.size();\r
- jalview.binding.Viewport[] mArray = new jalview.binding.Viewport[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.Viewport) _viewportList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.Viewport[] getViewport() \r
-\r
- /**\r
- * Method getViewportCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getViewportCount()\r
- {\r
- return _viewportList.size();\r
- } //-- int getViewportCount() \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
- * Method removeAllJGroup\r
- * \r
- */\r
- public void removeAllJGroup()\r
- {\r
- _JGroupList.removeAllElements();\r
- } //-- void removeAllJGroup() \r
-\r
- /**\r
- * Method removeAllJSeq\r
- * \r
- */\r
- public void removeAllJSeq()\r
- {\r
- _JSeqList.removeAllElements();\r
- } //-- void removeAllJSeq() \r
-\r
- /**\r
- * Method removeAllTree\r
- * \r
- */\r
- public void removeAllTree()\r
- {\r
- _treeList.removeAllElements();\r
- } //-- void removeAllTree() \r
-\r
- /**\r
- * Method removeAllUserColours\r
- * \r
- */\r
- public void removeAllUserColours()\r
- {\r
- _userColoursList.removeAllElements();\r
- } //-- void removeAllUserColours() \r
-\r
- /**\r
- * Method removeAllViewport\r
- * \r
- */\r
- public void removeAllViewport()\r
- {\r
- _viewportList.removeAllElements();\r
- } //-- void removeAllViewport() \r
-\r
- /**\r
- * Method removeJGroup\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return JGroup\r
- */\r
- public jalview.binding.JGroup removeJGroup(int index)\r
- {\r
- java.lang.Object obj = _JGroupList.elementAt(index);\r
- _JGroupList.removeElementAt(index);\r
- return (jalview.binding.JGroup) obj;\r
- } //-- jalview.binding.JGroup removeJGroup(int) \r
-\r
- /**\r
- * Method removeJSeq\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return JSeq\r
- */\r
- public jalview.binding.JSeq removeJSeq(int index)\r
- {\r
- java.lang.Object obj = _JSeqList.elementAt(index);\r
- _JSeqList.removeElementAt(index);\r
- return (jalview.binding.JSeq) obj;\r
- } //-- jalview.binding.JSeq removeJSeq(int) \r
-\r
- /**\r
- * Method removeTree\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Tree\r
- */\r
- public jalview.binding.Tree removeTree(int index)\r
- {\r
- java.lang.Object obj = _treeList.elementAt(index);\r
- _treeList.removeElementAt(index);\r
- return (jalview.binding.Tree) obj;\r
- } //-- jalview.binding.Tree removeTree(int) \r
-\r
- /**\r
- * Method removeUserColours\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return UserColours\r
- */\r
- public jalview.binding.UserColours removeUserColours(int index)\r
- {\r
- java.lang.Object obj = _userColoursList.elementAt(index);\r
- _userColoursList.removeElementAt(index);\r
- return (jalview.binding.UserColours) obj;\r
- } //-- jalview.binding.UserColours removeUserColours(int) \r
-\r
- /**\r
- * Method removeViewport\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Viewport\r
- */\r
- public jalview.binding.Viewport removeViewport(int index)\r
- {\r
- java.lang.Object obj = _viewportList.elementAt(index);\r
- _viewportList.removeElementAt(index);\r
- return (jalview.binding.Viewport) obj;\r
- } //-- jalview.binding.Viewport removeViewport(int) \r
-\r
- /**\r
- * Sets the value of field 'featureSettings'.\r
- * \r
- * @param featureSettings the value of field 'featureSettings'.\r
- */\r
- public void setFeatureSettings(jalview.binding.FeatureSettings featureSettings)\r
- {\r
- this._featureSettings = featureSettings;\r
- } //-- void setFeatureSettings(jalview.binding.FeatureSettings) \r
-\r
- /**\r
- * Method setJGroup\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vJGroup\r
- */\r
- public void setJGroup(int index, jalview.binding.JGroup vJGroup)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _JGroupList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _JGroupList.setElementAt(vJGroup, index);\r
- } //-- void setJGroup(int, jalview.binding.JGroup) \r
-\r
- /**\r
- * Method setJGroup\r
- * \r
- * \r
- * \r
- * @param JGroupArray\r
- */\r
- public void setJGroup(jalview.binding.JGroup[] JGroupArray)\r
- {\r
- //-- copy array\r
- _JGroupList.removeAllElements();\r
- for (int i = 0; i < JGroupArray.length; i++) {\r
- _JGroupList.addElement(JGroupArray[i]);\r
- }\r
- } //-- void setJGroup(jalview.binding.JGroup) \r
-\r
- /**\r
- * Method setJSeq\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vJSeq\r
- */\r
- public void setJSeq(int index, jalview.binding.JSeq vJSeq)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _JSeqList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _JSeqList.setElementAt(vJSeq, index);\r
- } //-- void setJSeq(int, jalview.binding.JSeq) \r
-\r
- /**\r
- * Method setJSeq\r
- * \r
- * \r
- * \r
- * @param JSeqArray\r
- */\r
- public void setJSeq(jalview.binding.JSeq[] JSeqArray)\r
- {\r
- //-- copy array\r
- _JSeqList.removeAllElements();\r
- for (int i = 0; i < JSeqArray.length; i++) {\r
- _JSeqList.addElement(JSeqArray[i]);\r
- }\r
- } //-- void setJSeq(jalview.binding.JSeq) \r
-\r
- /**\r
- * Method setTree\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vTree\r
- */\r
- public void setTree(int index, jalview.binding.Tree vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _treeList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _treeList.setElementAt(vTree, index);\r
- } //-- void setTree(int, jalview.binding.Tree) \r
-\r
- /**\r
- * Method setTree\r
- * \r
- * \r
- * \r
- * @param treeArray\r
- */\r
- public void setTree(jalview.binding.Tree[] treeArray)\r
- {\r
- //-- copy array\r
- _treeList.removeAllElements();\r
- for (int i = 0; i < treeArray.length; i++) {\r
- _treeList.addElement(treeArray[i]);\r
- }\r
- } //-- void setTree(jalview.binding.Tree) \r
-\r
- /**\r
- * Method setUserColours\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vUserColours\r
- */\r
- public void setUserColours(int index, jalview.binding.UserColours vUserColours)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _userColoursList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _userColoursList.setElementAt(vUserColours, index);\r
- } //-- void setUserColours(int, jalview.binding.UserColours) \r
-\r
- /**\r
- * Method setUserColours\r
- * \r
- * \r
- * \r
- * @param userColoursArray\r
- */\r
- public void setUserColours(jalview.binding.UserColours[] userColoursArray)\r
- {\r
- //-- copy array\r
- _userColoursList.removeAllElements();\r
- for (int i = 0; i < userColoursArray.length; i++) {\r
- _userColoursList.addElement(userColoursArray[i]);\r
- }\r
- } //-- void setUserColours(jalview.binding.UserColours) \r
-\r
- /**\r
- * Method setViewport\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vViewport\r
- */\r
- public void setViewport(int index, jalview.binding.Viewport vViewport)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _viewportList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _viewportList.setElementAt(vViewport, index);\r
- } //-- void setViewport(int, jalview.binding.Viewport) \r
-\r
- /**\r
- * Method setViewport\r
- * \r
- * \r
- * \r
- * @param viewportArray\r
- */\r
- public void setViewport(jalview.binding.Viewport[] viewportArray)\r
- {\r
- //-- copy array\r
- _viewportList.removeAllElements();\r
- for (int i = 0; i < viewportArray.length; i++) {\r
- _viewportList.addElement(viewportArray[i]);\r
- }\r
- } //-- void setViewport(jalview.binding.Viewport) \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.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class JalviewModelSequence.
+ *
+ * @version $Revision$ $Date$
+ */
+public class JalviewModelSequence implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _JSeqList.
+ */
+ private java.util.Vector _JSeqList;
+
+ /**
+ * Field _JGroupList.
+ */
+ private java.util.Vector _JGroupList;
+
+ /**
+ * Field _viewportList.
+ */
+ private java.util.Vector _viewportList;
+
+ /**
+ * Field _userColoursList.
+ */
+ private java.util.Vector _userColoursList;
+
+ /**
+ * Field _treeList.
+ */
+ private java.util.Vector _treeList;
+
+ /**
+ * Field _featureSettings.
+ */
+ private jalview.binding.FeatureSettings _featureSettings;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public JalviewModelSequence() {
+ super();
+ this._JSeqList = new java.util.Vector();
+ this._JGroupList = new java.util.Vector();
+ this._viewportList = new java.util.Vector();
+ this._userColoursList = new java.util.Vector();
+ this._treeList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addJGroup(
+ final jalview.binding.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException {
+ this._JGroupList.addElement(vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addJGroup(
+ final int index,
+ final jalview.binding.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException {
+ this._JGroupList.add(index, vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addJSeq(
+ final jalview.binding.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ this._JSeqList.addElement(vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addJSeq(
+ final int index,
+ final jalview.binding.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ this._JSeqList.add(index, vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addTree(
+ final jalview.binding.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treeList.addElement(vTree);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addTree(
+ final int index,
+ final jalview.binding.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treeList.add(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addUserColours(
+ final jalview.binding.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException {
+ this._userColoursList.addElement(vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addUserColours(
+ final int index,
+ final jalview.binding.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException {
+ this._userColoursList.add(index, vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addViewport(
+ final jalview.binding.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException {
+ this._viewportList.addElement(vViewport);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addViewport(
+ final int index,
+ final jalview.binding.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException {
+ this._viewportList.add(index, vViewport);
+ }
+
+ /**
+ * Method enumerateJGroup.
+ *
+ * @return an Enumeration over all jalview.binding.JGroup
+ * elements
+ */
+ public java.util.Enumeration enumerateJGroup(
+ ) {
+ return this._JGroupList.elements();
+ }
+
+ /**
+ * Method enumerateJSeq.
+ *
+ * @return an Enumeration over all jalview.binding.JSeq elements
+ */
+ public java.util.Enumeration enumerateJSeq(
+ ) {
+ return this._JSeqList.elements();
+ }
+
+ /**
+ * Method enumerateTree.
+ *
+ * @return an Enumeration over all jalview.binding.Tree elements
+ */
+ public java.util.Enumeration enumerateTree(
+ ) {
+ return this._treeList.elements();
+ }
+
+ /**
+ * Method enumerateUserColours.
+ *
+ * @return an Enumeration over all jalview.binding.UserColours
+ * elements
+ */
+ public java.util.Enumeration enumerateUserColours(
+ ) {
+ return this._userColoursList.elements();
+ }
+
+ /**
+ * Method enumerateViewport.
+ *
+ * @return an Enumeration over all jalview.binding.Viewport
+ * elements
+ */
+ public java.util.Enumeration enumerateViewport(
+ ) {
+ return this._viewportList.elements();
+ }
+
+ /**
+ * Returns the value of field 'featureSettings'.
+ *
+ * @return the value of field 'FeatureSettings'.
+ */
+ public jalview.binding.FeatureSettings getFeatureSettings(
+ ) {
+ return this._featureSettings;
+ }
+
+ /**
+ * Method getJGroup.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.JGroup at the given
+ * index
+ */
+ public jalview.binding.JGroup getJGroup(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._JGroupList.size()) {
+ throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.JGroup) _JGroupList.get(index);
+ }
+
+ /**
+ * Method getJGroup.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.JGroup[] getJGroup(
+ ) {
+ jalview.binding.JGroup[] array = new jalview.binding.JGroup[0];
+ return (jalview.binding.JGroup[]) this._JGroupList.toArray(array);
+ }
+
+ /**
+ * Method getJGroupCount.
+ *
+ * @return the size of this collection
+ */
+ public int getJGroupCount(
+ ) {
+ return this._JGroupList.size();
+ }
+
+ /**
+ * Method getJSeq.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.JSeq at the given
+ * index
+ */
+ public jalview.binding.JSeq getJSeq(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._JSeqList.size()) {
+ throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.JSeq) _JSeqList.get(index);
+ }
+
+ /**
+ * Method getJSeq.Returns the contents of the collection in an
+ * Array. <p>Note: Just in case the collection contents are
+ * changing in another thread, we pass a 0-length Array of the
+ * correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.JSeq[] getJSeq(
+ ) {
+ jalview.binding.JSeq[] array = new jalview.binding.JSeq[0];
+ return (jalview.binding.JSeq[]) this._JSeqList.toArray(array);
+ }
+
+ /**
+ * Method getJSeqCount.
+ *
+ * @return the size of this collection
+ */
+ public int getJSeqCount(
+ ) {
+ return this._JSeqList.size();
+ }
+
+ /**
+ * Method getTree.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Tree at the given
+ * index
+ */
+ public jalview.binding.Tree getTree(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Tree) _treeList.get(index);
+ }
+
+ /**
+ * Method getTree.Returns the contents of the collection in an
+ * Array. <p>Note: Just in case the collection contents are
+ * changing in another thread, we pass a 0-length Array of the
+ * correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Tree[] getTree(
+ ) {
+ jalview.binding.Tree[] array = new jalview.binding.Tree[0];
+ return (jalview.binding.Tree[]) this._treeList.toArray(array);
+ }
+
+ /**
+ * Method getTreeCount.
+ *
+ * @return the size of this collection
+ */
+ public int getTreeCount(
+ ) {
+ return this._treeList.size();
+ }
+
+ /**
+ * Method getUserColours.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.UserColours at the
+ * given index
+ */
+ public jalview.binding.UserColours getUserColours(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._userColoursList.size()) {
+ throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.UserColours) _userColoursList.get(index);
+ }
+
+ /**
+ * Method getUserColours.Returns the contents of the collection
+ * in an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.UserColours[] getUserColours(
+ ) {
+ jalview.binding.UserColours[] array = new jalview.binding.UserColours[0];
+ return (jalview.binding.UserColours[]) this._userColoursList.toArray(array);
+ }
+
+ /**
+ * Method getUserColoursCount.
+ *
+ * @return the size of this collection
+ */
+ public int getUserColoursCount(
+ ) {
+ return this._userColoursList.size();
+ }
+
+ /**
+ * Method getViewport.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Viewport at the
+ * given index
+ */
+ public jalview.binding.Viewport getViewport(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._viewportList.size()) {
+ throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Viewport) _viewportList.get(index);
+ }
+
+ /**
+ * Method getViewport.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Viewport[] getViewport(
+ ) {
+ jalview.binding.Viewport[] array = new jalview.binding.Viewport[0];
+ return (jalview.binding.Viewport[]) this._viewportList.toArray(array);
+ }
+
+ /**
+ * Method getViewportCount.
+ *
+ * @return the size of this collection
+ */
+ public int getViewportCount(
+ ) {
+ return this._viewportList.size();
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllJGroup(
+ ) {
+ this._JGroupList.clear();
+ }
+
+ /**
+ */
+ public void removeAllJSeq(
+ ) {
+ this._JSeqList.clear();
+ }
+
+ /**
+ */
+ public void removeAllTree(
+ ) {
+ this._treeList.clear();
+ }
+
+ /**
+ */
+ public void removeAllUserColours(
+ ) {
+ this._userColoursList.clear();
+ }
+
+ /**
+ */
+ public void removeAllViewport(
+ ) {
+ this._viewportList.clear();
+ }
+
+ /**
+ * Method removeJGroup.
+ *
+ * @param vJGroup
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeJGroup(
+ final jalview.binding.JGroup vJGroup) {
+ boolean removed = _JGroupList.remove(vJGroup);
+ return removed;
+ }
+
+ /**
+ * Method removeJGroupAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.JGroup removeJGroupAt(
+ final int index) {
+ java.lang.Object obj = this._JGroupList.remove(index);
+ return (jalview.binding.JGroup) obj;
+ }
+
+ /**
+ * Method removeJSeq.
+ *
+ * @param vJSeq
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeJSeq(
+ final jalview.binding.JSeq vJSeq) {
+ boolean removed = _JSeqList.remove(vJSeq);
+ return removed;
+ }
+
+ /**
+ * Method removeJSeqAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.JSeq removeJSeqAt(
+ final int index) {
+ java.lang.Object obj = this._JSeqList.remove(index);
+ return (jalview.binding.JSeq) obj;
+ }
+
+ /**
+ * Method removeTree.
+ *
+ * @param vTree
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeTree(
+ final jalview.binding.Tree vTree) {
+ boolean removed = _treeList.remove(vTree);
+ return removed;
+ }
+
+ /**
+ * Method removeTreeAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Tree removeTreeAt(
+ final int index) {
+ java.lang.Object obj = this._treeList.remove(index);
+ return (jalview.binding.Tree) obj;
+ }
+
+ /**
+ * Method removeUserColours.
+ *
+ * @param vUserColours
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeUserColours(
+ final jalview.binding.UserColours vUserColours) {
+ boolean removed = _userColoursList.remove(vUserColours);
+ return removed;
+ }
+
+ /**
+ * Method removeUserColoursAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.UserColours removeUserColoursAt(
+ final int index) {
+ java.lang.Object obj = this._userColoursList.remove(index);
+ return (jalview.binding.UserColours) obj;
+ }
+
+ /**
+ * Method removeViewport.
+ *
+ * @param vViewport
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeViewport(
+ final jalview.binding.Viewport vViewport) {
+ boolean removed = _viewportList.remove(vViewport);
+ return removed;
+ }
+
+ /**
+ * Method removeViewportAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Viewport removeViewportAt(
+ final int index) {
+ java.lang.Object obj = this._viewportList.remove(index);
+ return (jalview.binding.Viewport) obj;
+ }
+
+ /**
+ * Sets the value of field 'featureSettings'.
+ *
+ * @param featureSettings the value of field 'featureSettings'.
+ */
+ public void setFeatureSettings(
+ final jalview.binding.FeatureSettings featureSettings) {
+ this._featureSettings = featureSettings;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJGroup
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setJGroup(
+ final int index,
+ final jalview.binding.JGroup vJGroup)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._JGroupList.size()) {
+ throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]");
+ }
+
+ this._JGroupList.set(index, vJGroup);
+ }
+
+ /**
+ *
+ *
+ * @param vJGroupArray
+ */
+ public void setJGroup(
+ final jalview.binding.JGroup[] vJGroupArray) {
+ //-- copy array
+ _JGroupList.clear();
+
+ for (int i = 0; i < vJGroupArray.length; i++) {
+ this._JGroupList.add(vJGroupArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vJSeq
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setJSeq(
+ final int index,
+ final jalview.binding.JSeq vJSeq)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._JSeqList.size()) {
+ throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]");
+ }
+
+ this._JSeqList.set(index, vJSeq);
+ }
+
+ /**
+ *
+ *
+ * @param vJSeqArray
+ */
+ public void setJSeq(
+ final jalview.binding.JSeq[] vJSeqArray) {
+ //-- copy array
+ _JSeqList.clear();
+
+ for (int i = 0; i < vJSeqArray.length; i++) {
+ this._JSeqList.add(vJSeqArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setTree(
+ final int index,
+ final jalview.binding.Tree vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ this._treeList.set(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vTreeArray
+ */
+ public void setTree(
+ final jalview.binding.Tree[] vTreeArray) {
+ //-- copy array
+ _treeList.clear();
+
+ for (int i = 0; i < vTreeArray.length; i++) {
+ this._treeList.add(vTreeArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vUserColours
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setUserColours(
+ final int index,
+ final jalview.binding.UserColours vUserColours)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._userColoursList.size()) {
+ throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]");
+ }
+
+ this._userColoursList.set(index, vUserColours);
+ }
+
+ /**
+ *
+ *
+ * @param vUserColoursArray
+ */
+ public void setUserColours(
+ final jalview.binding.UserColours[] vUserColoursArray) {
+ //-- copy array
+ _userColoursList.clear();
+
+ for (int i = 0; i < vUserColoursArray.length; i++) {
+ this._userColoursList.add(vUserColoursArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vViewport
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setViewport(
+ final int index,
+ final jalview.binding.Viewport vViewport)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._viewportList.size()) {
+ throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]");
+ }
+
+ this._viewportList.set(index, vViewport);
+ }
+
+ /**
+ *
+ *
+ * @param vViewportArray
+ */
+ public void setViewport(
+ final jalview.binding.Viewport[] vViewportArray) {
+ //-- copy array
+ _viewportList.clear();
+
+ for (int i = 0; i < vViewportArray.length; i++) {
+ this._viewportList.add(vViewportArray[i]);
+ }
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JalviewModelSequence
+ */
+ public static jalview.binding.JalviewModelSequence unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 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
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class JalviewUserColours.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class JalviewUserColours implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _schemeName\r
- */\r
- private java.lang.String _schemeName;\r
-\r
- /**\r
- * Field _colourList\r
- */\r
- private java.util.Vector _colourList;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public JalviewUserColours() {\r
- super();\r
- _colourList = new Vector();\r
- } //-- jalview.binding.JalviewUserColours()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addColour\r
- * \r
- * \r
- * \r
- * @param vColour\r
- */\r
- public void addColour(jalview.binding.Colour vColour)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _colourList.addElement(vColour);\r
- } //-- void addColour(jalview.binding.Colour) \r
-\r
- /**\r
- * Method addColour\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vColour\r
- */\r
- public void addColour(int index, jalview.binding.Colour vColour)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _colourList.insertElementAt(vColour, index);\r
- } //-- void addColour(int, jalview.binding.Colour) \r
-\r
- /**\r
- * Method enumerateColour\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateColour()\r
- {\r
- return _colourList.elements();\r
- } //-- java.util.Enumeration enumerateColour() \r
-\r
- /**\r
- * Method getColour\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Colour\r
- */\r
- public jalview.binding.Colour getColour(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _colourList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.binding.Colour) _colourList.elementAt(index);\r
- } //-- jalview.binding.Colour getColour(int) \r
-\r
- /**\r
- * Method getColour\r
- * \r
- * \r
- * \r
- * @return Colour\r
- */\r
- public jalview.binding.Colour[] getColour()\r
- {\r
- int size = _colourList.size();\r
- jalview.binding.Colour[] mArray = new jalview.binding.Colour[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.Colour) _colourList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.Colour[] getColour() \r
-\r
- /**\r
- * Method getColourCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getColourCount()\r
- {\r
- return _colourList.size();\r
- } //-- int getColourCount() \r
-\r
- /**\r
- * Returns the value of field 'schemeName'.\r
- * \r
- * @return String\r
- * @return the value of field 'schemeName'.\r
- */\r
- public java.lang.String getSchemeName()\r
- {\r
- return this._schemeName;\r
- } //-- java.lang.String getSchemeName() \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
- * Method removeAllColour\r
- * \r
- */\r
- public void removeAllColour()\r
- {\r
- _colourList.removeAllElements();\r
- } //-- void removeAllColour() \r
-\r
- /**\r
- * Method removeColour\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Colour\r
- */\r
- public jalview.binding.Colour removeColour(int index)\r
- {\r
- java.lang.Object obj = _colourList.elementAt(index);\r
- _colourList.removeElementAt(index);\r
- return (jalview.binding.Colour) obj;\r
- } //-- jalview.binding.Colour removeColour(int) \r
-\r
- /**\r
- * Method setColour\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vColour\r
- */\r
- public void setColour(int index, jalview.binding.Colour vColour)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _colourList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _colourList.setElementAt(vColour, index);\r
- } //-- void setColour(int, jalview.binding.Colour) \r
-\r
- /**\r
- * Method setColour\r
- * \r
- * \r
- * \r
- * @param colourArray\r
- */\r
- public void setColour(jalview.binding.Colour[] colourArray)\r
- {\r
- //-- copy array\r
- _colourList.removeAllElements();\r
- for (int i = 0; i < colourArray.length; i++) {\r
- _colourList.addElement(colourArray[i]);\r
- }\r
- } //-- void setColour(jalview.binding.Colour) \r
-\r
- /**\r
- * Sets the value of field 'schemeName'.\r
- * \r
- * @param schemeName the value of field 'schemeName'.\r
- */\r
- public void setSchemeName(java.lang.String schemeName)\r
- {\r
- this._schemeName = schemeName;\r
- } //-- void setSchemeName(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.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class JalviewUserColours.
+ *
+ * @version $Revision$ $Date$
+ */
+public class JalviewUserColours implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _schemeName.
+ */
+ private java.lang.String _schemeName;
+
+ /**
+ * Field _colourList.
+ */
+ private java.util.Vector _colourList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public JalviewUserColours() {
+ super();
+ this._colourList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vColour
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addColour(
+ final Colour vColour)
+ throws java.lang.IndexOutOfBoundsException {
+ this._colourList.addElement(vColour);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vColour
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addColour(
+ final int index,
+ final Colour vColour)
+ throws java.lang.IndexOutOfBoundsException {
+ this._colourList.add(index, vColour);
+ }
+
+ /**
+ * Method enumerateColour.
+ *
+ * @return an Enumeration over all Colour elements
+ */
+ public java.util.Enumeration enumerateColour(
+ ) {
+ return this._colourList.elements();
+ }
+
+ /**
+ * Method getColour.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the Colour at the given index
+ */
+ public Colour getColour(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._colourList.size()) {
+ throw new IndexOutOfBoundsException("getColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
+ }
+
+ return (Colour) _colourList.get(index);
+ }
+
+ /**
+ * Method getColour.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public Colour[] getColour(
+ ) {
+ Colour[] array = new Colour[0];
+ return (Colour[]) this._colourList.toArray(array);
+ }
+
+ /**
+ * Method getColourCount.
+ *
+ * @return the size of this collection
+ */
+ public int getColourCount(
+ ) {
+ return this._colourList.size();
+ }
+
+ /**
+ * Returns the value of field 'schemeName'.
+ *
+ * @return the value of field 'SchemeName'.
+ */
+ public java.lang.String getSchemeName(
+ ) {
+ return this._schemeName;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllColour(
+ ) {
+ this._colourList.clear();
+ }
+
+ /**
+ * Method removeColour.
+ *
+ * @param vColour
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeColour(
+ final Colour vColour) {
+ boolean removed = _colourList.remove(vColour);
+ return removed;
+ }
+
+ /**
+ * Method removeColourAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public Colour removeColourAt(
+ final int index) {
+ java.lang.Object obj = this._colourList.remove(index);
+ return (Colour) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vColour
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setColour(
+ final int index,
+ final Colour vColour)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._colourList.size()) {
+ throw new IndexOutOfBoundsException("setColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]");
+ }
+
+ this._colourList.set(index, vColour);
+ }
+
+ /**
+ *
+ *
+ * @param vColourArray
+ */
+ public void setColour(
+ final Colour[] vColourArray) {
+ //-- copy array
+ _colourList.clear();
+
+ for (int i = 0; i < vColourArray.length; i++) {
+ this._colourList.add(vColourArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'schemeName'.
+ *
+ * @param schemeName the value of field 'schemeName'.
+ */
+ public void setSchemeName(
+ final java.lang.String schemeName) {
+ this._schemeName = schemeName;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JalviewUserColours
+ */
+ public static jalview.binding.JalviewUserColours unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 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
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Pdbentry.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Pdbentry implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _id\r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _type\r
- */\r
- private java.lang.String _type;\r
-\r
- /**\r
- * Field _items\r
- */\r
- private java.util.Vector _items;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Pdbentry() {\r
- super();\r
- _items = new Vector();\r
- } //-- jalview.binding.Pdbentry()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addPdbentryItem\r
- * \r
- * \r
- * \r
- * @param vPdbentryItem\r
- */\r
- public void addPdbentryItem(jalview.binding.PdbentryItem vPdbentryItem)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _items.addElement(vPdbentryItem);\r
- } //-- void addPdbentryItem(jalview.binding.PdbentryItem) \r
-\r
- /**\r
- * Method addPdbentryItem\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vPdbentryItem\r
- */\r
- public void addPdbentryItem(int index, jalview.binding.PdbentryItem vPdbentryItem)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _items.insertElementAt(vPdbentryItem, index);\r
- } //-- void addPdbentryItem(int, jalview.binding.PdbentryItem) \r
-\r
- /**\r
- * Method enumeratePdbentryItem\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumeratePdbentryItem()\r
- {\r
- return _items.elements();\r
- } //-- java.util.Enumeration enumeratePdbentryItem() \r
-\r
- /**\r
- * Returns the value of field 'id'.\r
- * \r
- * @return String\r
- * @return the value of field 'id'.\r
- */\r
- public java.lang.String getId()\r
- {\r
- return this._id;\r
- } //-- java.lang.String getId() \r
-\r
- /**\r
- * Method getPdbentryItem\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return PdbentryItem\r
- */\r
- public jalview.binding.PdbentryItem getPdbentryItem(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _items.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.binding.PdbentryItem) _items.elementAt(index);\r
- } //-- jalview.binding.PdbentryItem getPdbentryItem(int) \r
-\r
- /**\r
- * Method getPdbentryItem\r
- * \r
- * \r
- * \r
- * @return PdbentryItem\r
- */\r
- public jalview.binding.PdbentryItem[] getPdbentryItem()\r
- {\r
- int size = _items.size();\r
- jalview.binding.PdbentryItem[] mArray = new jalview.binding.PdbentryItem[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.PdbentryItem) _items.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.PdbentryItem[] getPdbentryItem() \r
-\r
- /**\r
- * Method getPdbentryItemCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getPdbentryItemCount()\r
- {\r
- return _items.size();\r
- } //-- int getPdbentryItemCount() \r
-\r
- /**\r
- * Returns the value of field 'type'.\r
- * \r
- * @return String\r
- * @return the value of field 'type'.\r
- */\r
- public java.lang.String getType()\r
- {\r
- return this._type;\r
- } //-- java.lang.String getType() \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
- * Method removeAllPdbentryItem\r
- * \r
- */\r
- public void removeAllPdbentryItem()\r
- {\r
- _items.removeAllElements();\r
- } //-- void removeAllPdbentryItem() \r
-\r
- /**\r
- * Method removePdbentryItem\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return PdbentryItem\r
- */\r
- public jalview.binding.PdbentryItem removePdbentryItem(int index)\r
- {\r
- java.lang.Object obj = _items.elementAt(index);\r
- _items.removeElementAt(index);\r
- return (jalview.binding.PdbentryItem) obj;\r
- } //-- jalview.binding.PdbentryItem removePdbentryItem(int) \r
-\r
- /**\r
- * Sets the value of field 'id'.\r
- * \r
- * @param id the value of field 'id'.\r
- */\r
- public void setId(java.lang.String id)\r
- {\r
- this._id = id;\r
- } //-- void setId(java.lang.String) \r
-\r
- /**\r
- * Method setPdbentryItem\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vPdbentryItem\r
- */\r
- public void setPdbentryItem(int index, jalview.binding.PdbentryItem vPdbentryItem)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _items.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _items.setElementAt(vPdbentryItem, index);\r
- } //-- void setPdbentryItem(int, jalview.binding.PdbentryItem) \r
-\r
- /**\r
- * Method setPdbentryItem\r
- * \r
- * \r
- * \r
- * @param pdbentryItemArray\r
- */\r
- public void setPdbentryItem(jalview.binding.PdbentryItem[] pdbentryItemArray)\r
- {\r
- //-- copy array\r
- _items.removeAllElements();\r
- for (int i = 0; i < pdbentryItemArray.length; i++) {\r
- _items.addElement(pdbentryItemArray[i]);\r
- }\r
- } //-- void setPdbentryItem(jalview.binding.PdbentryItem) \r
-\r
- /**\r
- * Sets the value of field 'type'.\r
- * \r
- * @param type the value of field 'type'.\r
- */\r
- public void setType(java.lang.String type)\r
- {\r
- this._type = type;\r
- } //-- void setType(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.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbentry.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Pdbentry.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Pdbentry implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _type.
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _items.
+ */
+ private java.util.Vector _items;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Pdbentry() {
+ super();
+ this._items = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vPdbentryItem
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addPdbentryItem(
+ final jalview.binding.PdbentryItem vPdbentryItem)
+ throws java.lang.IndexOutOfBoundsException {
+ this._items.addElement(vPdbentryItem);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbentryItem
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addPdbentryItem(
+ final int index,
+ final jalview.binding.PdbentryItem vPdbentryItem)
+ throws java.lang.IndexOutOfBoundsException {
+ this._items.add(index, vPdbentryItem);
+ }
+
+ /**
+ * Method enumeratePdbentryItem.
+ *
+ * @return an Enumeration over all jalview.binding.PdbentryItem
+ * elements
+ */
+ public java.util.Enumeration enumeratePdbentryItem(
+ ) {
+ return this._items.elements();
+ }
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId(
+ ) {
+ return this._id;
+ }
+
+ /**
+ * Method getPdbentryItem.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.PdbentryItem at the
+ * given index
+ */
+ public jalview.binding.PdbentryItem getPdbentryItem(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._items.size()) {
+ throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
+ }
+
+ return (jalview.binding.PdbentryItem) _items.get(index);
+ }
+
+ /**
+ * Method getPdbentryItem.Returns the contents of the
+ * collection in an Array. <p>Note: Just in case the
+ * collection contents are changing in another thread, we pass
+ * a 0-length Array of the correct type into the API call.
+ * This way we <i>know</i> that the Array returned is of
+ * exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.PdbentryItem[] getPdbentryItem(
+ ) {
+ jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0];
+ return (jalview.binding.PdbentryItem[]) this._items.toArray(array);
+ }
+
+ /**
+ * Method getPdbentryItemCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPdbentryItemCount(
+ ) {
+ return this._items.size();
+ }
+
+ /**
+ * Returns the value of field 'type'.
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType(
+ ) {
+ return this._type;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllPdbentryItem(
+ ) {
+ this._items.clear();
+ }
+
+ /**
+ * Method removePdbentryItem.
+ *
+ * @param vPdbentryItem
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removePdbentryItem(
+ final jalview.binding.PdbentryItem vPdbentryItem) {
+ boolean removed = _items.remove(vPdbentryItem);
+ return removed;
+ }
+
+ /**
+ * Method removePdbentryItemAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.PdbentryItem removePdbentryItemAt(
+ final int index) {
+ java.lang.Object obj = this._items.remove(index);
+ return (jalview.binding.PdbentryItem) obj;
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(
+ final java.lang.String id) {
+ this._id = id;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbentryItem
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setPdbentryItem(
+ final int index,
+ final jalview.binding.PdbentryItem vPdbentryItem)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._items.size()) {
+ throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
+ }
+
+ this._items.set(index, vPdbentryItem);
+ }
+
+ /**
+ *
+ *
+ * @param vPdbentryItemArray
+ */
+ public void setPdbentryItem(
+ final jalview.binding.PdbentryItem[] vPdbentryItemArray) {
+ //-- copy array
+ _items.clear();
+
+ for (int i = 0; i < vPdbentryItemArray.length; i++) {
+ this._items.add(vPdbentryItemArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'type'.
+ *
+ * @param type the value of field 'type'.
+ */
+ public void setType(
+ final java.lang.String type) {
+ this._type = type;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Pdbentry
+ */
+ public static jalview.binding.Pdbentry unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbentry.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.Serializable;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-\r
-/**\r
- * Class PdbentryItem.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class PdbentryItem implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _propertyList\r
- */\r
- private java.util.Vector _propertyList;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public PdbentryItem() {\r
- super();\r
- _propertyList = new Vector();\r
- } //-- jalview.binding.PdbentryItem()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addProperty\r
- * \r
- * \r
- * \r
- * @param vProperty\r
- */\r
- public void addProperty(jalview.binding.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _propertyList.addElement(vProperty);\r
- } //-- void addProperty(jalview.binding.Property) \r
-\r
- /**\r
- * Method addProperty\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vProperty\r
- */\r
- public void addProperty(int index, jalview.binding.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _propertyList.insertElementAt(vProperty, index);\r
- } //-- void addProperty(int, jalview.binding.Property) \r
-\r
- /**\r
- * Method enumerateProperty\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateProperty()\r
- {\r
- return _propertyList.elements();\r
- } //-- java.util.Enumeration enumerateProperty() \r
-\r
- /**\r
- * Method getProperty\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Property\r
- */\r
- public jalview.binding.Property getProperty(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _propertyList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.binding.Property) _propertyList.elementAt(index);\r
- } //-- jalview.binding.Property getProperty(int) \r
-\r
- /**\r
- * Method getProperty\r
- * \r
- * \r
- * \r
- * @return Property\r
- */\r
- public jalview.binding.Property[] getProperty()\r
- {\r
- int size = _propertyList.size();\r
- jalview.binding.Property[] mArray = new jalview.binding.Property[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.Property) _propertyList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.Property[] getProperty() \r
-\r
- /**\r
- * Method getPropertyCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getPropertyCount()\r
- {\r
- return _propertyList.size();\r
- } //-- int getPropertyCount() \r
-\r
- /**\r
- * Method removeAllProperty\r
- * \r
- */\r
- public void removeAllProperty()\r
- {\r
- _propertyList.removeAllElements();\r
- } //-- void removeAllProperty() \r
-\r
- /**\r
- * Method removeProperty\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Property\r
- */\r
- public jalview.binding.Property removeProperty(int index)\r
- {\r
- java.lang.Object obj = _propertyList.elementAt(index);\r
- _propertyList.removeElementAt(index);\r
- return (jalview.binding.Property) obj;\r
- } //-- jalview.binding.Property removeProperty(int) \r
-\r
- /**\r
- * Method setProperty\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vProperty\r
- */\r
- public void setProperty(int index, jalview.binding.Property vProperty)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _propertyList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _propertyList.setElementAt(vProperty, index);\r
- } //-- void setProperty(int, jalview.binding.Property) \r
-\r
- /**\r
- * Method setProperty\r
- * \r
- * \r
- * \r
- * @param propertyArray\r
- */\r
- public void setProperty(jalview.binding.Property[] propertyArray)\r
- {\r
- //-- copy array\r
- _propertyList.removeAllElements();\r
- for (int i = 0; i < propertyArray.length; i++) {\r
- _propertyList.addElement(propertyArray[i]);\r
- }\r
- } //-- void setProperty(jalview.binding.Property) \r
-\r
-}\r
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+/**
+ * Class PdbentryItem.
+ *
+ * @version $Revision$ $Date$
+ */
+public class PdbentryItem implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _propertyList.
+ */
+ private java.util.Vector _propertyList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public PdbentryItem() {
+ super();
+ this._propertyList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addProperty(
+ final jalview.binding.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ this._propertyList.addElement(vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addProperty(
+ final int index,
+ final jalview.binding.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ this._propertyList.add(index, vProperty);
+ }
+
+ /**
+ * Method enumerateProperty.
+ *
+ * @return an Enumeration over all jalview.binding.Property
+ * elements
+ */
+ public java.util.Enumeration enumerateProperty(
+ ) {
+ return this._propertyList.elements();
+ }
+
+ /**
+ * Method getProperty.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Property at the
+ * given index
+ */
+ public jalview.binding.Property getProperty(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size()) {
+ throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Property) _propertyList.get(index);
+ }
+
+ /**
+ * Method getProperty.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Property[] getProperty(
+ ) {
+ jalview.binding.Property[] array = new jalview.binding.Property[0];
+ return (jalview.binding.Property[]) this._propertyList.toArray(array);
+ }
+
+ /**
+ * Method getPropertyCount.
+ *
+ * @return the size of this collection
+ */
+ public int getPropertyCount(
+ ) {
+ return this._propertyList.size();
+ }
+
+ /**
+ */
+ public void removeAllProperty(
+ ) {
+ this._propertyList.clear();
+ }
+
+ /**
+ * Method removeProperty.
+ *
+ * @param vProperty
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeProperty(
+ final jalview.binding.Property vProperty) {
+ boolean removed = _propertyList.remove(vProperty);
+ return removed;
+ }
+
+ /**
+ * Method removePropertyAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Property removePropertyAt(
+ final int index) {
+ java.lang.Object obj = this._propertyList.remove(index);
+ return (jalview.binding.Property) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vProperty
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setProperty(
+ final int index,
+ final jalview.binding.Property vProperty)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._propertyList.size()) {
+ throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
+ }
+
+ this._propertyList.set(index, vProperty);
+ }
+
+ /**
+ *
+ *
+ * @param vPropertyArray
+ */
+ public void setProperty(
+ final jalview.binding.Property[] vPropertyArray) {
+ //-- copy array
+ _propertyList.clear();
+
+ for (int i = 0; i < vPropertyArray.length; i++) {
+ this._propertyList.add(vPropertyArray[i]);
+ }
+ }
+
+}
-/*\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.binding;\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 Pdbids.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Pdbids extends Pdbentry \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Pdbids() {\r
- super();\r
- } //-- jalview.binding.Pdbids()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\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
- * 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.binding.Pdbids) Unmarshaller.unmarshal(jalview.binding.Pdbids.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Pdbids.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Pdbids extends Pdbentry
+implements java.io.Serializable
+{
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Pdbids() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Pdbentry
+ */
+ public static jalview.binding.Pdbentry unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbids.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 Property.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Property implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _name\r
- */\r
- private java.lang.String _name;\r
-\r
- /**\r
- * Field _value\r
- */\r
- private java.lang.String _value;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Property() {\r
- super();\r
- } //-- jalview.binding.Property()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Returns the value of field 'name'.\r
- * \r
- * @return String\r
- * @return the value of field 'name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- } //-- java.lang.String getName() \r
-\r
- /**\r
- * Returns the value of field 'value'.\r
- * \r
- * @return String\r
- * @return the value of field 'value'.\r
- */\r
- public java.lang.String getValue()\r
- {\r
- return this._value;\r
- } //-- java.lang.String getValue() \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 'name'.\r
- * \r
- * @param name the value of field 'name'.\r
- */\r
- public void setName(java.lang.String name)\r
- {\r
- this._name = name;\r
- } //-- void setName(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'value'.\r
- * \r
- * @param value the value of field 'value'.\r
- */\r
- public void setValue(java.lang.String value)\r
- {\r
- this._value = value;\r
- } //-- void setValue(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.binding.Property) Unmarshaller.unmarshal(jalview.binding.Property.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Property.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Property implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _value.
+ */
+ private java.lang.String _value;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Property() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName(
+ ) {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'value'.
+ *
+ * @return the value of field 'Value'.
+ */
+ public java.lang.String getValue(
+ ) {
+ return this._value;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name the value of field 'name'.
+ */
+ public void setName(
+ final java.lang.String name) {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'value'.
+ *
+ * @param value the value of field 'value'.
+ */
+ public void setValue(
+ final java.lang.String value) {
+ this._value = value;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Property
+ */
+ public static jalview.binding.Property unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Property) Unmarshaller.unmarshal(jalview.binding.Property.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 Sequence.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Sequence extends SequenceType \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Sequence() {\r
- super();\r
- } //-- jalview.binding.Sequence()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\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
- * 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.binding.Sequence) Unmarshaller.unmarshal(jalview.binding.Sequence.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Sequence.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Sequence extends SequenceType
+implements java.io.Serializable
+{
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Sequence() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.SequenceType
+ */
+ public static jalview.binding.SequenceType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.Sequence.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 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
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class SequenceSet.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class SequenceSet implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _gapChar\r
- */\r
- private java.lang.String _gapChar;\r
-\r
- /**\r
- * Field _aligned\r
- */\r
- private boolean _aligned;\r
-\r
- /**\r
- * keeps track of state for field: _aligned\r
- */\r
- private boolean _has_aligned;\r
-\r
- /**\r
- * Field _sequenceList\r
- */\r
- private java.util.Vector _sequenceList;\r
-\r
- /**\r
- * Field _annotationList\r
- */\r
- private java.util.Vector _annotationList;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public SequenceSet() {\r
- super();\r
- _sequenceList = new Vector();\r
- _annotationList = new Vector();\r
- } //-- jalview.binding.SequenceSet()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addAnnotation\r
- * \r
- * \r
- * \r
- * @param vAnnotation\r
- */\r
- public void addAnnotation(jalview.binding.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationList.addElement(vAnnotation);\r
- } //-- void addAnnotation(jalview.binding.Annotation) \r
-\r
- /**\r
- * Method addAnnotation\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vAnnotation\r
- */\r
- public void addAnnotation(int index, jalview.binding.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _annotationList.insertElementAt(vAnnotation, index);\r
- } //-- void addAnnotation(int, jalview.binding.Annotation) \r
-\r
- /**\r
- * Method addSequence\r
- * \r
- * \r
- * \r
- * @param vSequence\r
- */\r
- public void addSequence(jalview.binding.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceList.addElement(vSequence);\r
- } //-- void addSequence(jalview.binding.Sequence) \r
-\r
- /**\r
- * Method addSequence\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vSequence\r
- */\r
- public void addSequence(int index, jalview.binding.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceList.insertElementAt(vSequence, index);\r
- } //-- void addSequence(int, jalview.binding.Sequence) \r
-\r
- /**\r
- * Method deleteAligned\r
- * \r
- */\r
- public void deleteAligned()\r
- {\r
- this._has_aligned= false;\r
- } //-- void deleteAligned() \r
-\r
- /**\r
- * Method enumerateAnnotation\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateAnnotation()\r
- {\r
- return _annotationList.elements();\r
- } //-- java.util.Enumeration enumerateAnnotation() \r
-\r
- /**\r
- * Method enumerateSequence\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateSequence()\r
- {\r
- return _sequenceList.elements();\r
- } //-- java.util.Enumeration enumerateSequence() \r
-\r
- /**\r
- * Returns the value of field 'aligned'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'aligned'.\r
- */\r
- public boolean getAligned()\r
- {\r
- return this._aligned;\r
- } //-- boolean getAligned() \r
-\r
- /**\r
- * Method getAnnotation\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Annotation\r
- */\r
- public jalview.binding.Annotation getAnnotation(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _annotationList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.binding.Annotation) _annotationList.elementAt(index);\r
- } //-- jalview.binding.Annotation getAnnotation(int) \r
-\r
- /**\r
- * Method getAnnotation\r
- * \r
- * \r
- * \r
- * @return Annotation\r
- */\r
- public jalview.binding.Annotation[] getAnnotation()\r
- {\r
- int size = _annotationList.size();\r
- jalview.binding.Annotation[] mArray = new jalview.binding.Annotation[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.Annotation[] getAnnotation() \r
-\r
- /**\r
- * Method getAnnotationCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getAnnotationCount()\r
- {\r
- return _annotationList.size();\r
- } //-- int getAnnotationCount() \r
-\r
- /**\r
- * Returns the value of field 'gapChar'.\r
- * \r
- * @return String\r
- * @return the value of field 'gapChar'.\r
- */\r
- public java.lang.String getGapChar()\r
- {\r
- return this._gapChar;\r
- } //-- java.lang.String getGapChar() \r
-\r
- /**\r
- * Method getSequence\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Sequence\r
- */\r
- public jalview.binding.Sequence getSequence(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _sequenceList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.binding.Sequence) _sequenceList.elementAt(index);\r
- } //-- jalview.binding.Sequence getSequence(int) \r
-\r
- /**\r
- * Method getSequence\r
- * \r
- * \r
- * \r
- * @return Sequence\r
- */\r
- public jalview.binding.Sequence[] getSequence()\r
- {\r
- int size = _sequenceList.size();\r
- jalview.binding.Sequence[] mArray = new jalview.binding.Sequence[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.Sequence[] getSequence() \r
-\r
- /**\r
- * Method getSequenceCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getSequenceCount()\r
- {\r
- return _sequenceList.size();\r
- } //-- int getSequenceCount() \r
-\r
- /**\r
- * Method hasAligned\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasAligned()\r
- {\r
- return this._has_aligned;\r
- } //-- boolean hasAligned() \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
- * Method removeAllAnnotation\r
- * \r
- */\r
- public void removeAllAnnotation()\r
- {\r
- _annotationList.removeAllElements();\r
- } //-- void removeAllAnnotation() \r
-\r
- /**\r
- * Method removeAllSequence\r
- * \r
- */\r
- public void removeAllSequence()\r
- {\r
- _sequenceList.removeAllElements();\r
- } //-- void removeAllSequence() \r
-\r
- /**\r
- * Method removeAnnotation\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Annotation\r
- */\r
- public jalview.binding.Annotation removeAnnotation(int index)\r
- {\r
- java.lang.Object obj = _annotationList.elementAt(index);\r
- _annotationList.removeElementAt(index);\r
- return (jalview.binding.Annotation) obj;\r
- } //-- jalview.binding.Annotation removeAnnotation(int) \r
-\r
- /**\r
- * Method removeSequence\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Sequence\r
- */\r
- public jalview.binding.Sequence removeSequence(int index)\r
- {\r
- java.lang.Object obj = _sequenceList.elementAt(index);\r
- _sequenceList.removeElementAt(index);\r
- return (jalview.binding.Sequence) obj;\r
- } //-- jalview.binding.Sequence removeSequence(int) \r
-\r
- /**\r
- * Sets the value of field 'aligned'.\r
- * \r
- * @param aligned the value of field 'aligned'.\r
- */\r
- public void setAligned(boolean aligned)\r
- {\r
- this._aligned = aligned;\r
- this._has_aligned = true;\r
- } //-- void setAligned(boolean) \r
-\r
- /**\r
- * Method setAnnotation\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vAnnotation\r
- */\r
- public void setAnnotation(int index, jalview.binding.Annotation vAnnotation)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _annotationList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _annotationList.setElementAt(vAnnotation, index);\r
- } //-- void setAnnotation(int, jalview.binding.Annotation) \r
-\r
- /**\r
- * Method setAnnotation\r
- * \r
- * \r
- * \r
- * @param annotationArray\r
- */\r
- public void setAnnotation(jalview.binding.Annotation[] annotationArray)\r
- {\r
- //-- copy array\r
- _annotationList.removeAllElements();\r
- for (int i = 0; i < annotationArray.length; i++) {\r
- _annotationList.addElement(annotationArray[i]);\r
- }\r
- } //-- void setAnnotation(jalview.binding.Annotation) \r
-\r
- /**\r
- * Sets the value of field 'gapChar'.\r
- * \r
- * @param gapChar the value of field 'gapChar'.\r
- */\r
- public void setGapChar(java.lang.String gapChar)\r
- {\r
- this._gapChar = gapChar;\r
- } //-- void setGapChar(java.lang.String) \r
-\r
- /**\r
- * Method setSequence\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vSequence\r
- */\r
- public void setSequence(int index, jalview.binding.Sequence vSequence)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _sequenceList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _sequenceList.setElementAt(vSequence, index);\r
- } //-- void setSequence(int, jalview.binding.Sequence) \r
-\r
- /**\r
- * Method setSequence\r
- * \r
- * \r
- * \r
- * @param sequenceArray\r
- */\r
- public void setSequence(jalview.binding.Sequence[] sequenceArray)\r
- {\r
- //-- copy array\r
- _sequenceList.removeAllElements();\r
- for (int i = 0; i < sequenceArray.length; i++) {\r
- _sequenceList.addElement(sequenceArray[i]);\r
- }\r
- } //-- void setSequence(jalview.binding.Sequence) \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.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class SequenceSet.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SequenceSet implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _gapChar.
+ */
+ private java.lang.String _gapChar;
+
+ /**
+ * Field _aligned.
+ */
+ private boolean _aligned;
+
+ /**
+ * keeps track of state for field: _aligned
+ */
+ private boolean _has_aligned;
+
+ /**
+ * Field _sequenceList.
+ */
+ private java.util.Vector _sequenceList;
+
+ /**
+ * Field _annotationList.
+ */
+ private java.util.Vector _annotationList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public SequenceSet() {
+ super();
+ this._sequenceList = new java.util.Vector();
+ this._annotationList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vAnnotation
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAnnotation(
+ final jalview.binding.Annotation vAnnotation)
+ throws java.lang.IndexOutOfBoundsException {
+ this._annotationList.addElement(vAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotation
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAnnotation(
+ final int index,
+ final jalview.binding.Annotation vAnnotation)
+ throws java.lang.IndexOutOfBoundsException {
+ this._annotationList.add(index, vAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param vSequence
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSequence(
+ final jalview.binding.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException {
+ this._sequenceList.addElement(vSequence);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequence
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSequence(
+ final int index,
+ final jalview.binding.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException {
+ this._sequenceList.add(index, vSequence);
+ }
+
+ /**
+ */
+ public void deleteAligned(
+ ) {
+ this._has_aligned= false;
+ }
+
+ /**
+ * Method enumerateAnnotation.
+ *
+ * @return an Enumeration over all jalview.binding.Annotation
+ * elements
+ */
+ public java.util.Enumeration enumerateAnnotation(
+ ) {
+ return this._annotationList.elements();
+ }
+
+ /**
+ * Method enumerateSequence.
+ *
+ * @return an Enumeration over all jalview.binding.Sequence
+ * elements
+ */
+ public java.util.Enumeration enumerateSequence(
+ ) {
+ return this._sequenceList.elements();
+ }
+
+ /**
+ * Returns the value of field 'aligned'.
+ *
+ * @return the value of field 'Aligned'.
+ */
+ public boolean getAligned(
+ ) {
+ return this._aligned;
+ }
+
+ /**
+ * Method getAnnotation.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Annotation at the
+ * given index
+ */
+ public jalview.binding.Annotation getAnnotation(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationList.size()) {
+ throw new IndexOutOfBoundsException("getAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Annotation) _annotationList.get(index);
+ }
+
+ /**
+ * Method getAnnotation.Returns the contents of the collection
+ * in an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Annotation[] getAnnotation(
+ ) {
+ jalview.binding.Annotation[] array = new jalview.binding.Annotation[0];
+ return (jalview.binding.Annotation[]) this._annotationList.toArray(array);
+ }
+
+ /**
+ * Method getAnnotationCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAnnotationCount(
+ ) {
+ return this._annotationList.size();
+ }
+
+ /**
+ * Returns the value of field 'gapChar'.
+ *
+ * @return the value of field 'GapChar'.
+ */
+ public java.lang.String getGapChar(
+ ) {
+ return this._gapChar;
+ }
+
+ /**
+ * Method getSequence.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.Sequence at the
+ * given index
+ */
+ public jalview.binding.Sequence getSequence(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceList.size()) {
+ throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.Sequence) _sequenceList.get(index);
+ }
+
+ /**
+ * Method getSequence.Returns the contents of the collection in
+ * an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.Sequence[] getSequence(
+ ) {
+ jalview.binding.Sequence[] array = new jalview.binding.Sequence[0];
+ return (jalview.binding.Sequence[]) this._sequenceList.toArray(array);
+ }
+
+ /**
+ * Method getSequenceCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequenceCount(
+ ) {
+ return this._sequenceList.size();
+ }
+
+ /**
+ * Method hasAligned.
+ *
+ * @return true if at least one Aligned has been added
+ */
+ public boolean hasAligned(
+ ) {
+ return this._has_aligned;
+ }
+
+ /**
+ * Returns the value of field 'aligned'.
+ *
+ * @return the value of field 'Aligned'.
+ */
+ public boolean isAligned(
+ ) {
+ return this._aligned;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ */
+ public void removeAllAnnotation(
+ ) {
+ this._annotationList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSequence(
+ ) {
+ this._sequenceList.clear();
+ }
+
+ /**
+ * Method removeAnnotation.
+ *
+ * @param vAnnotation
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAnnotation(
+ final jalview.binding.Annotation vAnnotation) {
+ boolean removed = _annotationList.remove(vAnnotation);
+ return removed;
+ }
+
+ /**
+ * Method removeAnnotationAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Annotation removeAnnotationAt(
+ final int index) {
+ java.lang.Object obj = this._annotationList.remove(index);
+ return (jalview.binding.Annotation) obj;
+ }
+
+ /**
+ * Method removeSequence.
+ *
+ * @param vSequence
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequence(
+ final jalview.binding.Sequence vSequence) {
+ boolean removed = _sequenceList.remove(vSequence);
+ return removed;
+ }
+
+ /**
+ * Method removeSequenceAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.Sequence removeSequenceAt(
+ final int index) {
+ java.lang.Object obj = this._sequenceList.remove(index);
+ return (jalview.binding.Sequence) obj;
+ }
+
+ /**
+ * Sets the value of field 'aligned'.
+ *
+ * @param aligned the value of field 'aligned'.
+ */
+ public void setAligned(
+ final boolean aligned) {
+ this._aligned = aligned;
+ this._has_aligned = true;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotation
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setAnnotation(
+ final int index,
+ final jalview.binding.Annotation vAnnotation)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationList.size()) {
+ throw new IndexOutOfBoundsException("setAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]");
+ }
+
+ this._annotationList.set(index, vAnnotation);
+ }
+
+ /**
+ *
+ *
+ * @param vAnnotationArray
+ */
+ public void setAnnotation(
+ final jalview.binding.Annotation[] vAnnotationArray) {
+ //-- copy array
+ _annotationList.clear();
+
+ for (int i = 0; i < vAnnotationArray.length; i++) {
+ this._annotationList.add(vAnnotationArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'gapChar'.
+ *
+ * @param gapChar the value of field 'gapChar'.
+ */
+ public void setGapChar(
+ final java.lang.String gapChar) {
+ this._gapChar = gapChar;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequence
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setSequence(
+ final int index,
+ final jalview.binding.Sequence vSequence)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceList.size()) {
+ throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]");
+ }
+
+ this._sequenceList.set(index, vSequence);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceArray
+ */
+ public void setSequence(
+ final jalview.binding.Sequence[] vSequenceArray) {
+ //-- copy array
+ _sequenceList.clear();
+
+ for (int i = 0; i < vSequenceArray.length; i++) {
+ this._sequenceList.add(vSequenceArray[i]);
+ }
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.SequenceSet
+ */
+ public static jalview.binding.SequenceSet unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 SequenceType.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class SequenceType implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _id\r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _description\r
- */\r
- private java.lang.String _description;\r
-\r
- /**\r
- * Field _sequence\r
- */\r
- private java.lang.String _sequence;\r
-\r
- /**\r
- * Field _name\r
- */\r
- private java.lang.String _name;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public SequenceType() {\r
- super();\r
- } //-- jalview.binding.SequenceType()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Returns the value of field 'description'.\r
- * \r
- * @return String\r
- * @return the value of field 'description'.\r
- */\r
- public java.lang.String getDescription()\r
- {\r
- return this._description;\r
- } //-- java.lang.String getDescription() \r
-\r
- /**\r
- * Returns the value of field 'id'.\r
- * \r
- * @return String\r
- * @return the value of field 'id'.\r
- */\r
- public java.lang.String getId()\r
- {\r
- return this._id;\r
- } //-- java.lang.String getId() \r
-\r
- /**\r
- * Returns the value of field 'name'.\r
- * \r
- * @return String\r
- * @return the value of field 'name'.\r
- */\r
- public java.lang.String getName()\r
- {\r
- return this._name;\r
- } //-- java.lang.String getName() \r
-\r
- /**\r
- * Returns the value of field 'sequence'.\r
- * \r
- * @return String\r
- * @return the value of field 'sequence'.\r
- */\r
- public java.lang.String getSequence()\r
- {\r
- return this._sequence;\r
- } //-- java.lang.String getSequence() \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 'description'.\r
- * \r
- * @param description the value of field 'description'.\r
- */\r
- public void setDescription(java.lang.String description)\r
- {\r
- this._description = description;\r
- } //-- void setDescription(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'id'.\r
- * \r
- * @param id the value of field 'id'.\r
- */\r
- public void setId(java.lang.String id)\r
- {\r
- this._id = id;\r
- } //-- void setId(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'name'.\r
- * \r
- * @param name the value of field 'name'.\r
- */\r
- public void setName(java.lang.String name)\r
- {\r
- this._name = name;\r
- } //-- void setName(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'sequence'.\r
- * \r
- * @param sequence the value of field 'sequence'.\r
- */\r
- public void setSequence(java.lang.String sequence)\r
- {\r
- this._sequence = sequence;\r
- } //-- void setSequence(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.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.SequenceType.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class SequenceType.
+ *
+ * @version $Revision$ $Date$
+ */
+public class SequenceType implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _sequence.
+ */
+ private java.lang.String _sequence;
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public SequenceType() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId(
+ ) {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName(
+ ) {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'sequence'.
+ *
+ * @return the value of field 'Sequence'.
+ */
+ public java.lang.String getSequence(
+ ) {
+ return this._sequence;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(
+ final java.lang.String id) {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name the value of field 'name'.
+ */
+ public void setName(
+ final java.lang.String name) {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'sequence'.
+ *
+ * @param sequence the value of field 'sequence'.
+ */
+ public void setSequence(
+ final java.lang.String sequence) {
+ this._sequence = sequence;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.SequenceType
+ */
+ public static jalview.binding.SequenceType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.SequenceType.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 Setting.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Setting implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _type\r
- */\r
- private java.lang.String _type;\r
-\r
- /**\r
- * Field _colour\r
- */\r
- private int _colour;\r
-\r
- /**\r
- * keeps track of state for field: _colour\r
- */\r
- private boolean _has_colour;\r
-\r
- /**\r
- * Field _display\r
- */\r
- private boolean _display;\r
-\r
- /**\r
- * keeps track of state for field: _display\r
- */\r
- private boolean _has_display;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Setting() {\r
- super();\r
- } //-- jalview.binding.Setting()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteColour\r
- * \r
- */\r
- public void deleteColour()\r
- {\r
- this._has_colour= false;\r
- } //-- void deleteColour() \r
-\r
- /**\r
- * Method deleteDisplay\r
- * \r
- */\r
- public void deleteDisplay()\r
- {\r
- this._has_display= false;\r
- } //-- void deleteDisplay() \r
-\r
- /**\r
- * Returns the value of field 'colour'.\r
- * \r
- * @return int\r
- * @return the value of field 'colour'.\r
- */\r
- public int getColour()\r
- {\r
- return this._colour;\r
- } //-- int getColour() \r
-\r
- /**\r
- * Returns the value of field 'display'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'display'.\r
- */\r
- public boolean getDisplay()\r
- {\r
- return this._display;\r
- } //-- boolean getDisplay() \r
-\r
- /**\r
- * Returns the value of field 'type'.\r
- * \r
- * @return String\r
- * @return the value of field 'type'.\r
- */\r
- public java.lang.String getType()\r
- {\r
- return this._type;\r
- } //-- java.lang.String getType() \r
-\r
- /**\r
- * Method hasColour\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasColour()\r
- {\r
- return this._has_colour;\r
- } //-- boolean hasColour() \r
-\r
- /**\r
- * Method hasDisplay\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasDisplay()\r
- {\r
- return this._has_display;\r
- } //-- boolean hasDisplay() \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 'colour'.\r
- * \r
- * @param colour the value of field 'colour'.\r
- */\r
- public void setColour(int colour)\r
- {\r
- this._colour = colour;\r
- this._has_colour = true;\r
- } //-- void setColour(int) \r
-\r
- /**\r
- * Sets the value of field 'display'.\r
- * \r
- * @param display the value of field 'display'.\r
- */\r
- public void setDisplay(boolean display)\r
- {\r
- this._display = display;\r
- this._has_display = true;\r
- } //-- void setDisplay(boolean) \r
-\r
- /**\r
- * Sets the value of field 'type'.\r
- * \r
- * @param type the value of field 'type'.\r
- */\r
- public void setType(java.lang.String type)\r
- {\r
- this._type = type;\r
- } //-- void setType(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.binding.Setting) Unmarshaller.unmarshal(jalview.binding.Setting.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Setting.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Setting implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _type.
+ */
+ private java.lang.String _type;
+
+ /**
+ * Field _colour.
+ */
+ private int _colour;
+
+ /**
+ * keeps track of state for field: _colour
+ */
+ private boolean _has_colour;
+
+ /**
+ * Field _display.
+ */
+ private boolean _display;
+
+ /**
+ * keeps track of state for field: _display
+ */
+ private boolean _has_display;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Setting() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteColour(
+ ) {
+ this._has_colour= false;
+ }
+
+ /**
+ */
+ public void deleteDisplay(
+ ) {
+ this._has_display= false;
+ }
+
+ /**
+ * Returns the value of field 'colour'.
+ *
+ * @return the value of field 'Colour'.
+ */
+ public int getColour(
+ ) {
+ return this._colour;
+ }
+
+ /**
+ * Returns the value of field 'display'.
+ *
+ * @return the value of field 'Display'.
+ */
+ public boolean getDisplay(
+ ) {
+ return this._display;
+ }
+
+ /**
+ * Returns the value of field 'type'.
+ *
+ * @return the value of field 'Type'.
+ */
+ public java.lang.String getType(
+ ) {
+ return this._type;
+ }
+
+ /**
+ * Method hasColour.
+ *
+ * @return true if at least one Colour has been added
+ */
+ public boolean hasColour(
+ ) {
+ return this._has_colour;
+ }
+
+ /**
+ * Method hasDisplay.
+ *
+ * @return true if at least one Display has been added
+ */
+ public boolean hasDisplay(
+ ) {
+ return this._has_display;
+ }
+
+ /**
+ * Returns the value of field 'display'.
+ *
+ * @return the value of field 'Display'.
+ */
+ public boolean isDisplay(
+ ) {
+ return this._display;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'colour'.
+ *
+ * @param colour the value of field 'colour'.
+ */
+ public void setColour(
+ final int colour) {
+ this._colour = colour;
+ this._has_colour = true;
+ }
+
+ /**
+ * Sets the value of field 'display'.
+ *
+ * @param display the value of field 'display'.
+ */
+ public void setDisplay(
+ final boolean display) {
+ this._display = display;
+ this._has_display = true;
+ }
+
+ /**
+ * Sets the value of field 'type'.
+ *
+ * @param type the value of field 'type'.
+ */
+ public void setType(
+ final java.lang.String type) {
+ this._type = type;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Setting
+ */
+ public static jalview.binding.Setting unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Setting) Unmarshaller.unmarshal(jalview.binding.Setting.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 Tree.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Tree implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _width\r
- */\r
- private int _width;\r
-\r
- /**\r
- * keeps track of state for field: _width\r
- */\r
- private boolean _has_width;\r
-\r
- /**\r
- * Field _height\r
- */\r
- private int _height;\r
-\r
- /**\r
- * keeps track of state for field: _height\r
- */\r
- private boolean _has_height;\r
-\r
- /**\r
- * Field _xpos\r
- */\r
- private int _xpos;\r
-\r
- /**\r
- * keeps track of state for field: _xpos\r
- */\r
- private boolean _has_xpos;\r
-\r
- /**\r
- * Field _ypos\r
- */\r
- private int _ypos;\r
-\r
- /**\r
- * keeps track of state for field: _ypos\r
- */\r
- private boolean _has_ypos;\r
-\r
- /**\r
- * Field _fontName\r
- */\r
- private java.lang.String _fontName;\r
-\r
- /**\r
- * Field _fontSize\r
- */\r
- private int _fontSize;\r
-\r
- /**\r
- * keeps track of state for field: _fontSize\r
- */\r
- private boolean _has_fontSize;\r
-\r
- /**\r
- * Field _fontStyle\r
- */\r
- private int _fontStyle;\r
-\r
- /**\r
- * keeps track of state for field: _fontStyle\r
- */\r
- private boolean _has_fontStyle;\r
-\r
- /**\r
- * Field _threshold\r
- */\r
- private float _threshold;\r
-\r
- /**\r
- * keeps track of state for field: _threshold\r
- */\r
- private boolean _has_threshold;\r
-\r
- /**\r
- * Field _showBootstrap\r
- */\r
- private boolean _showBootstrap;\r
-\r
- /**\r
- * keeps track of state for field: _showBootstrap\r
- */\r
- private boolean _has_showBootstrap;\r
-\r
- /**\r
- * Field _showDistances\r
- */\r
- private boolean _showDistances;\r
-\r
- /**\r
- * keeps track of state for field: _showDistances\r
- */\r
- private boolean _has_showDistances;\r
-\r
- /**\r
- * Field _markUnlinked\r
- */\r
- private boolean _markUnlinked;\r
-\r
- /**\r
- * keeps track of state for field: _markUnlinked\r
- */\r
- private boolean _has_markUnlinked;\r
-\r
- /**\r
- * Field _fitToWindow\r
- */\r
- private boolean _fitToWindow;\r
-\r
- /**\r
- * keeps track of state for field: _fitToWindow\r
- */\r
- private boolean _has_fitToWindow;\r
-\r
- /**\r
- * Field _currentTree\r
- */\r
- private boolean _currentTree;\r
-\r
- /**\r
- * keeps track of state for field: _currentTree\r
- */\r
- private boolean _has_currentTree;\r
-\r
- /**\r
- * Field _title\r
- */\r
- private java.lang.String _title;\r
-\r
- /**\r
- * Field _newick\r
- */\r
- private java.lang.String _newick;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Tree() {\r
- super();\r
- } //-- jalview.binding.Tree()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteCurrentTree\r
- * \r
- */\r
- public void deleteCurrentTree()\r
- {\r
- this._has_currentTree= false;\r
- } //-- void deleteCurrentTree() \r
-\r
- /**\r
- * Method deleteFitToWindow\r
- * \r
- */\r
- public void deleteFitToWindow()\r
- {\r
- this._has_fitToWindow= false;\r
- } //-- void deleteFitToWindow() \r
-\r
- /**\r
- * Method deleteFontSize\r
- * \r
- */\r
- public void deleteFontSize()\r
- {\r
- this._has_fontSize= false;\r
- } //-- void deleteFontSize() \r
-\r
- /**\r
- * Method deleteFontStyle\r
- * \r
- */\r
- public void deleteFontStyle()\r
- {\r
- this._has_fontStyle= false;\r
- } //-- void deleteFontStyle() \r
-\r
- /**\r
- * Method deleteHeight\r
- * \r
- */\r
- public void deleteHeight()\r
- {\r
- this._has_height= false;\r
- } //-- void deleteHeight() \r
-\r
- /**\r
- * Method deleteMarkUnlinked\r
- * \r
- */\r
- public void deleteMarkUnlinked()\r
- {\r
- this._has_markUnlinked= false;\r
- } //-- void deleteMarkUnlinked() \r
-\r
- /**\r
- * Method deleteShowBootstrap\r
- * \r
- */\r
- public void deleteShowBootstrap()\r
- {\r
- this._has_showBootstrap= false;\r
- } //-- void deleteShowBootstrap() \r
-\r
- /**\r
- * Method deleteShowDistances\r
- * \r
- */\r
- public void deleteShowDistances()\r
- {\r
- this._has_showDistances= false;\r
- } //-- void deleteShowDistances() \r
-\r
- /**\r
- * Method deleteThreshold\r
- * \r
- */\r
- public void deleteThreshold()\r
- {\r
- this._has_threshold= false;\r
- } //-- void deleteThreshold() \r
-\r
- /**\r
- * Method deleteWidth\r
- * \r
- */\r
- public void deleteWidth()\r
- {\r
- this._has_width= false;\r
- } //-- void deleteWidth() \r
-\r
- /**\r
- * Method deleteXpos\r
- * \r
- */\r
- public void deleteXpos()\r
- {\r
- this._has_xpos= false;\r
- } //-- void deleteXpos() \r
-\r
- /**\r
- * Method deleteYpos\r
- * \r
- */\r
- public void deleteYpos()\r
- {\r
- this._has_ypos= false;\r
- } //-- void deleteYpos() \r
-\r
- /**\r
- * Returns the value of field 'currentTree'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'currentTree'.\r
- */\r
- public boolean getCurrentTree()\r
- {\r
- return this._currentTree;\r
- } //-- boolean getCurrentTree() \r
-\r
- /**\r
- * Returns the value of field 'fitToWindow'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'fitToWindow'.\r
- */\r
- public boolean getFitToWindow()\r
- {\r
- return this._fitToWindow;\r
- } //-- boolean getFitToWindow() \r
-\r
- /**\r
- * Returns the value of field 'fontName'.\r
- * \r
- * @return String\r
- * @return the value of field 'fontName'.\r
- */\r
- public java.lang.String getFontName()\r
- {\r
- return this._fontName;\r
- } //-- java.lang.String getFontName() \r
-\r
- /**\r
- * Returns the value of field 'fontSize'.\r
- * \r
- * @return int\r
- * @return the value of field 'fontSize'.\r
- */\r
- public int getFontSize()\r
- {\r
- return this._fontSize;\r
- } //-- int getFontSize() \r
-\r
- /**\r
- * Returns the value of field 'fontStyle'.\r
- * \r
- * @return int\r
- * @return the value of field 'fontStyle'.\r
- */\r
- public int getFontStyle()\r
- {\r
- return this._fontStyle;\r
- } //-- int getFontStyle() \r
-\r
- /**\r
- * Returns the value of field 'height'.\r
- * \r
- * @return int\r
- * @return the value of field 'height'.\r
- */\r
- public int getHeight()\r
- {\r
- return this._height;\r
- } //-- int getHeight() \r
-\r
- /**\r
- * Returns the value of field 'markUnlinked'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'markUnlinked'.\r
- */\r
- public boolean getMarkUnlinked()\r
- {\r
- return this._markUnlinked;\r
- } //-- boolean getMarkUnlinked() \r
-\r
- /**\r
- * Returns the value of field 'newick'.\r
- * \r
- * @return String\r
- * @return the value of field 'newick'.\r
- */\r
- public java.lang.String getNewick()\r
- {\r
- return this._newick;\r
- } //-- java.lang.String getNewick() \r
-\r
- /**\r
- * Returns the value of field 'showBootstrap'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'showBootstrap'.\r
- */\r
- public boolean getShowBootstrap()\r
- {\r
- return this._showBootstrap;\r
- } //-- boolean getShowBootstrap() \r
-\r
- /**\r
- * Returns the value of field 'showDistances'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'showDistances'.\r
- */\r
- public boolean getShowDistances()\r
- {\r
- return this._showDistances;\r
- } //-- boolean getShowDistances() \r
-\r
- /**\r
- * Returns the value of field 'threshold'.\r
- * \r
- * @return float\r
- * @return the value of field 'threshold'.\r
- */\r
- public float getThreshold()\r
- {\r
- return this._threshold;\r
- } //-- float getThreshold() \r
-\r
- /**\r
- * Returns the value of field 'title'.\r
- * \r
- * @return String\r
- * @return the value of field 'title'.\r
- */\r
- public java.lang.String getTitle()\r
- {\r
- return this._title;\r
- } //-- java.lang.String getTitle() \r
-\r
- /**\r
- * Returns the value of field 'width'.\r
- * \r
- * @return int\r
- * @return the value of field 'width'.\r
- */\r
- public int getWidth()\r
- {\r
- return this._width;\r
- } //-- int getWidth() \r
-\r
- /**\r
- * Returns the value of field 'xpos'.\r
- * \r
- * @return int\r
- * @return the value of field 'xpos'.\r
- */\r
- public int getXpos()\r
- {\r
- return this._xpos;\r
- } //-- int getXpos() \r
-\r
- /**\r
- * Returns the value of field 'ypos'.\r
- * \r
- * @return int\r
- * @return the value of field 'ypos'.\r
- */\r
- public int getYpos()\r
- {\r
- return this._ypos;\r
- } //-- int getYpos() \r
-\r
- /**\r
- * Method hasCurrentTree\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasCurrentTree()\r
- {\r
- return this._has_currentTree;\r
- } //-- boolean hasCurrentTree() \r
-\r
- /**\r
- * Method hasFitToWindow\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasFitToWindow()\r
- {\r
- return this._has_fitToWindow;\r
- } //-- boolean hasFitToWindow() \r
-\r
- /**\r
- * Method hasFontSize\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasFontSize()\r
- {\r
- return this._has_fontSize;\r
- } //-- boolean hasFontSize() \r
-\r
- /**\r
- * Method hasFontStyle\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasFontStyle()\r
- {\r
- return this._has_fontStyle;\r
- } //-- boolean hasFontStyle() \r
-\r
- /**\r
- * Method hasHeight\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasHeight()\r
- {\r
- return this._has_height;\r
- } //-- boolean hasHeight() \r
-\r
- /**\r
- * Method hasMarkUnlinked\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasMarkUnlinked()\r
- {\r
- return this._has_markUnlinked;\r
- } //-- boolean hasMarkUnlinked() \r
-\r
- /**\r
- * Method hasShowBootstrap\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasShowBootstrap()\r
- {\r
- return this._has_showBootstrap;\r
- } //-- boolean hasShowBootstrap() \r
-\r
- /**\r
- * Method hasShowDistances\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasShowDistances()\r
- {\r
- return this._has_showDistances;\r
- } //-- boolean hasShowDistances() \r
-\r
- /**\r
- * Method hasThreshold\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasThreshold()\r
- {\r
- return this._has_threshold;\r
- } //-- boolean hasThreshold() \r
-\r
- /**\r
- * Method hasWidth\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasWidth()\r
- {\r
- return this._has_width;\r
- } //-- boolean hasWidth() \r
-\r
- /**\r
- * Method hasXpos\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasXpos()\r
- {\r
- return this._has_xpos;\r
- } //-- boolean hasXpos() \r
-\r
- /**\r
- * Method hasYpos\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasYpos()\r
- {\r
- return this._has_ypos;\r
- } //-- boolean hasYpos() \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 'currentTree'.\r
- * \r
- * @param currentTree the value of field 'currentTree'.\r
- */\r
- public void setCurrentTree(boolean currentTree)\r
- {\r
- this._currentTree = currentTree;\r
- this._has_currentTree = true;\r
- } //-- void setCurrentTree(boolean) \r
-\r
- /**\r
- * Sets the value of field 'fitToWindow'.\r
- * \r
- * @param fitToWindow the value of field 'fitToWindow'.\r
- */\r
- public void setFitToWindow(boolean fitToWindow)\r
- {\r
- this._fitToWindow = fitToWindow;\r
- this._has_fitToWindow = true;\r
- } //-- void setFitToWindow(boolean) \r
-\r
- /**\r
- * Sets the value of field 'fontName'.\r
- * \r
- * @param fontName the value of field 'fontName'.\r
- */\r
- public void setFontName(java.lang.String fontName)\r
- {\r
- this._fontName = fontName;\r
- } //-- void setFontName(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'fontSize'.\r
- * \r
- * @param fontSize the value of field 'fontSize'.\r
- */\r
- public void setFontSize(int fontSize)\r
- {\r
- this._fontSize = fontSize;\r
- this._has_fontSize = true;\r
- } //-- void setFontSize(int) \r
-\r
- /**\r
- * Sets the value of field 'fontStyle'.\r
- * \r
- * @param fontStyle the value of field 'fontStyle'.\r
- */\r
- public void setFontStyle(int fontStyle)\r
- {\r
- this._fontStyle = fontStyle;\r
- this._has_fontStyle = true;\r
- } //-- void setFontStyle(int) \r
-\r
- /**\r
- * Sets the value of field 'height'.\r
- * \r
- * @param height the value of field 'height'.\r
- */\r
- public void setHeight(int height)\r
- {\r
- this._height = height;\r
- this._has_height = true;\r
- } //-- void setHeight(int) \r
-\r
- /**\r
- * Sets the value of field 'markUnlinked'.\r
- * \r
- * @param markUnlinked the value of field 'markUnlinked'.\r
- */\r
- public void setMarkUnlinked(boolean markUnlinked)\r
- {\r
- this._markUnlinked = markUnlinked;\r
- this._has_markUnlinked = true;\r
- } //-- void setMarkUnlinked(boolean) \r
-\r
- /**\r
- * Sets the value of field 'newick'.\r
- * \r
- * @param newick the value of field 'newick'.\r
- */\r
- public void setNewick(java.lang.String newick)\r
- {\r
- this._newick = newick;\r
- } //-- void setNewick(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'showBootstrap'.\r
- * \r
- * @param showBootstrap the value of field 'showBootstrap'.\r
- */\r
- public void setShowBootstrap(boolean showBootstrap)\r
- {\r
- this._showBootstrap = showBootstrap;\r
- this._has_showBootstrap = true;\r
- } //-- void setShowBootstrap(boolean) \r
-\r
- /**\r
- * Sets the value of field 'showDistances'.\r
- * \r
- * @param showDistances the value of field 'showDistances'.\r
- */\r
- public void setShowDistances(boolean showDistances)\r
- {\r
- this._showDistances = showDistances;\r
- this._has_showDistances = true;\r
- } //-- void setShowDistances(boolean) \r
-\r
- /**\r
- * Sets the value of field 'threshold'.\r
- * \r
- * @param threshold the value of field 'threshold'.\r
- */\r
- public void setThreshold(float threshold)\r
- {\r
- this._threshold = threshold;\r
- this._has_threshold = true;\r
- } //-- void setThreshold(float) \r
-\r
- /**\r
- * Sets the value of field 'title'.\r
- * \r
- * @param title the value of field 'title'.\r
- */\r
- public void setTitle(java.lang.String title)\r
- {\r
- this._title = title;\r
- } //-- void setTitle(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'width'.\r
- * \r
- * @param width the value of field 'width'.\r
- */\r
- public void setWidth(int width)\r
- {\r
- this._width = width;\r
- this._has_width = true;\r
- } //-- void setWidth(int) \r
-\r
- /**\r
- * Sets the value of field 'xpos'.\r
- * \r
- * @param xpos the value of field 'xpos'.\r
- */\r
- public void setXpos(int xpos)\r
- {\r
- this._xpos = xpos;\r
- this._has_xpos = true;\r
- } //-- void setXpos(int) \r
-\r
- /**\r
- * Sets the value of field 'ypos'.\r
- * \r
- * @param ypos the value of field 'ypos'.\r
- */\r
- public void setYpos(int ypos)\r
- {\r
- this._ypos = ypos;\r
- this._has_ypos = true;\r
- } //-- void setYpos(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.binding.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Tree.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Tree implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
+ * Field _fontName.
+ */
+ private java.lang.String _fontName;
+
+ /**
+ * Field _fontSize.
+ */
+ private int _fontSize;
+
+ /**
+ * keeps track of state for field: _fontSize
+ */
+ private boolean _has_fontSize;
+
+ /**
+ * Field _fontStyle.
+ */
+ private int _fontStyle;
+
+ /**
+ * keeps track of state for field: _fontStyle
+ */
+ private boolean _has_fontStyle;
+
+ /**
+ * Field _threshold.
+ */
+ private float _threshold;
+
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
+
+ /**
+ * Field _showBootstrap.
+ */
+ private boolean _showBootstrap;
+
+ /**
+ * keeps track of state for field: _showBootstrap
+ */
+ private boolean _has_showBootstrap;
+
+ /**
+ * Field _showDistances.
+ */
+ private boolean _showDistances;
+
+ /**
+ * keeps track of state for field: _showDistances
+ */
+ private boolean _has_showDistances;
+
+ /**
+ * Field _markUnlinked.
+ */
+ private boolean _markUnlinked;
+
+ /**
+ * keeps track of state for field: _markUnlinked
+ */
+ private boolean _has_markUnlinked;
+
+ /**
+ * Field _fitToWindow.
+ */
+ private boolean _fitToWindow;
+
+ /**
+ * keeps track of state for field: _fitToWindow
+ */
+ private boolean _has_fitToWindow;
+
+ /**
+ * Field _currentTree.
+ */
+ private boolean _currentTree;
+
+ /**
+ * keeps track of state for field: _currentTree
+ */
+ private boolean _has_currentTree;
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * Field _newick.
+ */
+ private java.lang.String _newick;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Tree() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteCurrentTree(
+ ) {
+ this._has_currentTree= false;
+ }
+
+ /**
+ */
+ public void deleteFitToWindow(
+ ) {
+ this._has_fitToWindow= false;
+ }
+
+ /**
+ */
+ public void deleteFontSize(
+ ) {
+ this._has_fontSize= false;
+ }
+
+ /**
+ */
+ public void deleteFontStyle(
+ ) {
+ this._has_fontStyle= false;
+ }
+
+ /**
+ */
+ public void deleteHeight(
+ ) {
+ this._has_height= false;
+ }
+
+ /**
+ */
+ public void deleteMarkUnlinked(
+ ) {
+ this._has_markUnlinked= false;
+ }
+
+ /**
+ */
+ public void deleteShowBootstrap(
+ ) {
+ this._has_showBootstrap= false;
+ }
+
+ /**
+ */
+ public void deleteShowDistances(
+ ) {
+ this._has_showDistances= false;
+ }
+
+ /**
+ */
+ public void deleteThreshold(
+ ) {
+ this._has_threshold= false;
+ }
+
+ /**
+ */
+ public void deleteWidth(
+ ) {
+ this._has_width= false;
+ }
+
+ /**
+ */
+ public void deleteXpos(
+ ) {
+ this._has_xpos= false;
+ }
+
+ /**
+ */
+ public void deleteYpos(
+ ) {
+ this._has_ypos= false;
+ }
+
+ /**
+ * Returns the value of field 'currentTree'.
+ *
+ * @return the value of field 'CurrentTree'.
+ */
+ public boolean getCurrentTree(
+ ) {
+ return this._currentTree;
+ }
+
+ /**
+ * Returns the value of field 'fitToWindow'.
+ *
+ * @return the value of field 'FitToWindow'.
+ */
+ public boolean getFitToWindow(
+ ) {
+ return this._fitToWindow;
+ }
+
+ /**
+ * Returns the value of field 'fontName'.
+ *
+ * @return the value of field 'FontName'.
+ */
+ public java.lang.String getFontName(
+ ) {
+ return this._fontName;
+ }
+
+ /**
+ * Returns the value of field 'fontSize'.
+ *
+ * @return the value of field 'FontSize'.
+ */
+ public int getFontSize(
+ ) {
+ return this._fontSize;
+ }
+
+ /**
+ * Returns the value of field 'fontStyle'.
+ *
+ * @return the value of field 'FontStyle'.
+ */
+ public int getFontStyle(
+ ) {
+ return this._fontStyle;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight(
+ ) {
+ return this._height;
+ }
+
+ /**
+ * Returns the value of field 'markUnlinked'.
+ *
+ * @return the value of field 'MarkUnlinked'.
+ */
+ public boolean getMarkUnlinked(
+ ) {
+ return this._markUnlinked;
+ }
+
+ /**
+ * Returns the value of field 'newick'.
+ *
+ * @return the value of field 'Newick'.
+ */
+ public java.lang.String getNewick(
+ ) {
+ return this._newick;
+ }
+
+ /**
+ * Returns the value of field 'showBootstrap'.
+ *
+ * @return the value of field 'ShowBootstrap'.
+ */
+ public boolean getShowBootstrap(
+ ) {
+ return this._showBootstrap;
+ }
+
+ /**
+ * Returns the value of field 'showDistances'.
+ *
+ * @return the value of field 'ShowDistances'.
+ */
+ public boolean getShowDistances(
+ ) {
+ return this._showDistances;
+ }
+
+ /**
+ * Returns the value of field 'threshold'.
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold(
+ ) {
+ return this._threshold;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle(
+ ) {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth(
+ ) {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos(
+ ) {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos(
+ ) {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasCurrentTree.
+ *
+ * @return true if at least one CurrentTree has been added
+ */
+ public boolean hasCurrentTree(
+ ) {
+ return this._has_currentTree;
+ }
+
+ /**
+ * Method hasFitToWindow.
+ *
+ * @return true if at least one FitToWindow has been added
+ */
+ public boolean hasFitToWindow(
+ ) {
+ return this._has_fitToWindow;
+ }
+
+ /**
+ * Method hasFontSize.
+ *
+ * @return true if at least one FontSize has been added
+ */
+ public boolean hasFontSize(
+ ) {
+ return this._has_fontSize;
+ }
+
+ /**
+ * Method hasFontStyle.
+ *
+ * @return true if at least one FontStyle has been added
+ */
+ public boolean hasFontStyle(
+ ) {
+ return this._has_fontStyle;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight(
+ ) {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasMarkUnlinked.
+ *
+ * @return true if at least one MarkUnlinked has been added
+ */
+ public boolean hasMarkUnlinked(
+ ) {
+ return this._has_markUnlinked;
+ }
+
+ /**
+ * Method hasShowBootstrap.
+ *
+ * @return true if at least one ShowBootstrap has been added
+ */
+ public boolean hasShowBootstrap(
+ ) {
+ return this._has_showBootstrap;
+ }
+
+ /**
+ * Method hasShowDistances.
+ *
+ * @return true if at least one ShowDistances has been added
+ */
+ public boolean hasShowDistances(
+ ) {
+ return this._has_showDistances;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold(
+ ) {
+ return this._has_threshold;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth(
+ ) {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos(
+ ) {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos(
+ ) {
+ return this._has_ypos;
+ }
+
+ /**
+ * Returns the value of field 'currentTree'.
+ *
+ * @return the value of field 'CurrentTree'.
+ */
+ public boolean isCurrentTree(
+ ) {
+ return this._currentTree;
+ }
+
+ /**
+ * Returns the value of field 'fitToWindow'.
+ *
+ * @return the value of field 'FitToWindow'.
+ */
+ public boolean isFitToWindow(
+ ) {
+ return this._fitToWindow;
+ }
+
+ /**
+ * Returns the value of field 'markUnlinked'.
+ *
+ * @return the value of field 'MarkUnlinked'.
+ */
+ public boolean isMarkUnlinked(
+ ) {
+ return this._markUnlinked;
+ }
+
+ /**
+ * Returns the value of field 'showBootstrap'.
+ *
+ * @return the value of field 'ShowBootstrap'.
+ */
+ public boolean isShowBootstrap(
+ ) {
+ return this._showBootstrap;
+ }
+
+ /**
+ * Returns the value of field 'showDistances'.
+ *
+ * @return the value of field 'ShowDistances'.
+ */
+ public boolean isShowDistances(
+ ) {
+ return this._showDistances;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'currentTree'.
+ *
+ * @param currentTree the value of field 'currentTree'.
+ */
+ public void setCurrentTree(
+ final boolean currentTree) {
+ this._currentTree = currentTree;
+ this._has_currentTree = true;
+ }
+
+ /**
+ * Sets the value of field 'fitToWindow'.
+ *
+ * @param fitToWindow the value of field 'fitToWindow'.
+ */
+ public void setFitToWindow(
+ final boolean fitToWindow) {
+ this._fitToWindow = fitToWindow;
+ this._has_fitToWindow = true;
+ }
+
+ /**
+ * Sets the value of field 'fontName'.
+ *
+ * @param fontName the value of field 'fontName'.
+ */
+ public void setFontName(
+ final java.lang.String fontName) {
+ this._fontName = fontName;
+ }
+
+ /**
+ * Sets the value of field 'fontSize'.
+ *
+ * @param fontSize the value of field 'fontSize'.
+ */
+ public void setFontSize(
+ final int fontSize) {
+ this._fontSize = fontSize;
+ this._has_fontSize = true;
+ }
+
+ /**
+ * Sets the value of field 'fontStyle'.
+ *
+ * @param fontStyle the value of field 'fontStyle'.
+ */
+ public void setFontStyle(
+ final int fontStyle) {
+ this._fontStyle = fontStyle;
+ this._has_fontStyle = true;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height the value of field 'height'.
+ */
+ public void setHeight(
+ final int height) {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ * Sets the value of field 'markUnlinked'.
+ *
+ * @param markUnlinked the value of field 'markUnlinked'.
+ */
+ public void setMarkUnlinked(
+ final boolean markUnlinked) {
+ this._markUnlinked = markUnlinked;
+ this._has_markUnlinked = true;
+ }
+
+ /**
+ * Sets the value of field 'newick'.
+ *
+ * @param newick the value of field 'newick'.
+ */
+ public void setNewick(
+ final java.lang.String newick) {
+ this._newick = newick;
+ }
+
+ /**
+ * Sets the value of field 'showBootstrap'.
+ *
+ * @param showBootstrap the value of field 'showBootstrap'.
+ */
+ public void setShowBootstrap(
+ final boolean showBootstrap) {
+ this._showBootstrap = showBootstrap;
+ this._has_showBootstrap = true;
+ }
+
+ /**
+ * Sets the value of field 'showDistances'.
+ *
+ * @param showDistances the value of field 'showDistances'.
+ */
+ public void setShowDistances(
+ final boolean showDistances) {
+ this._showDistances = showDistances;
+ this._has_showDistances = true;
+ }
+
+ /**
+ * Sets the value of field 'threshold'.
+ *
+ * @param threshold the value of field 'threshold'.
+ */
+ public void setThreshold(
+ final float threshold) {
+ this._threshold = threshold;
+ this._has_threshold = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title the value of field 'title'.
+ */
+ public void setTitle(
+ final java.lang.String title) {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width the value of field 'width'.
+ */
+ public void setWidth(
+ final int width) {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos the value of field 'xpos'.
+ */
+ public void setXpos(
+ final int xpos) {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos the value of field 'ypos'.
+ */
+ public void setYpos(
+ final int ypos) {
+ this._ypos = ypos;
+ this._has_ypos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Tree
+ */
+ public static jalview.binding.Tree unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 UserColourScheme.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class UserColourScheme extends JalviewUserColours \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public UserColourScheme() {\r
- super();\r
- } //-- jalview.binding.UserColourScheme()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\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
- * 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.binding.UserColourScheme) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class UserColourScheme.
+ *
+ * @version $Revision$ $Date$
+ */
+public class UserColourScheme extends JalviewUserColours
+implements java.io.Serializable
+{
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public UserColourScheme() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.JalviewUserColours
+ */
+ public static jalview.binding.JalviewUserColours unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 UserColours.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class UserColours implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _id\r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _userColourScheme\r
- */\r
- private jalview.binding.UserColourScheme _userColourScheme;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public UserColours() {\r
- super();\r
- } //-- jalview.binding.UserColours()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Returns the value of field 'id'.\r
- * \r
- * @return String\r
- * @return the value of field 'id'.\r
- */\r
- public java.lang.String getId()\r
- {\r
- return this._id;\r
- } //-- java.lang.String getId() \r
-\r
- /**\r
- * Returns the value of field 'userColourScheme'.\r
- * \r
- * @return UserColourScheme\r
- * @return the value of field 'userColourScheme'.\r
- */\r
- public jalview.binding.UserColourScheme getUserColourScheme()\r
- {\r
- return this._userColourScheme;\r
- } //-- jalview.binding.UserColourScheme getUserColourScheme() \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 'id'.\r
- * \r
- * @param id the value of field 'id'.\r
- */\r
- public void setId(java.lang.String id)\r
- {\r
- this._id = id;\r
- } //-- void setId(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'userColourScheme'.\r
- * \r
- * @param userColourScheme the value of field 'userColourScheme'\r
- */\r
- public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme)\r
- {\r
- this._userColourScheme = userColourScheme;\r
- } //-- void setUserColourScheme(jalview.binding.UserColourScheme) \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.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class UserColours.
+ *
+ * @version $Revision$ $Date$
+ */
+public class UserColours implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _id.
+ */
+ private java.lang.String _id;
+
+ /**
+ * Field _userColourScheme.
+ */
+ private jalview.binding.UserColourScheme _userColourScheme;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public UserColours() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId(
+ ) {
+ return this._id;
+ }
+
+ /**
+ * Returns the value of field 'userColourScheme'.
+ *
+ * @return the value of field 'UserColourScheme'.
+ */
+ public jalview.binding.UserColourScheme getUserColourScheme(
+ ) {
+ return this._userColourScheme;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'id'.
+ *
+ * @param id the value of field 'id'.
+ */
+ public void setId(
+ final java.lang.String id) {
+ this._id = id;
+ }
+
+ /**
+ * Sets the value of field 'userColourScheme'.
+ *
+ * @param userColourScheme the value of field 'userColourScheme'
+ */
+ public void setUserColourScheme(
+ final jalview.binding.UserColourScheme userColourScheme) {
+ this._userColourScheme = userColourScheme;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.UserColours
+ */
+ public static jalview.binding.UserColours unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 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
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class VAMSAS.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class VAMSAS implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _alignmentList\r
- */\r
- private java.util.Vector _alignmentList;\r
-\r
- /**\r
- * Field _treeList\r
- */\r
- private java.util.Vector _treeList;\r
-\r
- /**\r
- * Field _sequenceSetList\r
- */\r
- private java.util.Vector _sequenceSetList;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public VAMSAS() {\r
- super();\r
- _alignmentList = new Vector();\r
- _treeList = new Vector();\r
- _sequenceSetList = new Vector();\r
- } //-- jalview.binding.VAMSAS()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addAlignment\r
- * \r
- * \r
- * \r
- * @param vAlignment\r
- */\r
- public void addAlignment(jalview.binding.Alignment vAlignment)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _alignmentList.addElement(vAlignment);\r
- } //-- void addAlignment(jalview.binding.Alignment) \r
-\r
- /**\r
- * Method addAlignment\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vAlignment\r
- */\r
- public void addAlignment(int index, jalview.binding.Alignment vAlignment)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _alignmentList.insertElementAt(vAlignment, index);\r
- } //-- void addAlignment(int, jalview.binding.Alignment) \r
-\r
- /**\r
- * Method addSequenceSet\r
- * \r
- * \r
- * \r
- * @param vSequenceSet\r
- */\r
- public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceSetList.addElement(vSequenceSet);\r
- } //-- void addSequenceSet(jalview.binding.SequenceSet) \r
-\r
- /**\r
- * Method addSequenceSet\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vSequenceSet\r
- */\r
- public void addSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _sequenceSetList.insertElementAt(vSequenceSet, index);\r
- } //-- void addSequenceSet(int, jalview.binding.SequenceSet) \r
-\r
- /**\r
- * Method addTree\r
- * \r
- * \r
- * \r
- * @param vTree\r
- */\r
- public void addTree(java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _treeList.addElement(vTree);\r
- } //-- void addTree(java.lang.String) \r
-\r
- /**\r
- * Method addTree\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vTree\r
- */\r
- public void addTree(int index, java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _treeList.insertElementAt(vTree, index);\r
- } //-- void addTree(int, java.lang.String) \r
-\r
- /**\r
- * Method enumerateAlignment\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateAlignment()\r
- {\r
- return _alignmentList.elements();\r
- } //-- java.util.Enumeration enumerateAlignment() \r
-\r
- /**\r
- * Method enumerateSequenceSet\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateSequenceSet()\r
- {\r
- return _sequenceSetList.elements();\r
- } //-- java.util.Enumeration enumerateSequenceSet() \r
-\r
- /**\r
- * Method enumerateTree\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateTree()\r
- {\r
- return _treeList.elements();\r
- } //-- java.util.Enumeration enumerateTree() \r
-\r
- /**\r
- * Method getAlignment\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Alignment\r
- */\r
- public jalview.binding.Alignment getAlignment(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _alignmentList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.binding.Alignment) _alignmentList.elementAt(index);\r
- } //-- jalview.binding.Alignment getAlignment(int) \r
-\r
- /**\r
- * Method getAlignment\r
- * \r
- * \r
- * \r
- * @return Alignment\r
- */\r
- public jalview.binding.Alignment[] getAlignment()\r
- {\r
- int size = _alignmentList.size();\r
- jalview.binding.Alignment[] mArray = new jalview.binding.Alignment[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.Alignment[] getAlignment() \r
-\r
- /**\r
- * Method getAlignmentCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getAlignmentCount()\r
- {\r
- return _alignmentList.size();\r
- } //-- int getAlignmentCount() \r
-\r
- /**\r
- * Method getSequenceSet\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return SequenceSet\r
- */\r
- public jalview.binding.SequenceSet getSequenceSet(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _sequenceSetList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);\r
- } //-- jalview.binding.SequenceSet getSequenceSet(int) \r
-\r
- /**\r
- * Method getSequenceSet\r
- * \r
- * \r
- * \r
- * @return SequenceSet\r
- */\r
- public jalview.binding.SequenceSet[] getSequenceSet()\r
- {\r
- int size = _sequenceSetList.size();\r
- jalview.binding.SequenceSet[] mArray = new jalview.binding.SequenceSet[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.binding.SequenceSet[] getSequenceSet() \r
-\r
- /**\r
- * Method getSequenceSetCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getSequenceSetCount()\r
- {\r
- return _sequenceSetList.size();\r
- } //-- int getSequenceSetCount() \r
-\r
- /**\r
- * Method getTree\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return String\r
- */\r
- public java.lang.String getTree(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _treeList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (String)_treeList.elementAt(index);\r
- } //-- java.lang.String getTree(int) \r
-\r
- /**\r
- * Method getTree\r
- * \r
- * \r
- * \r
- * @return String\r
- */\r
- public java.lang.String[] getTree()\r
- {\r
- int size = _treeList.size();\r
- java.lang.String[] mArray = new java.lang.String[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (String)_treeList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- java.lang.String[] getTree() \r
-\r
- /**\r
- * Method getTreeCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getTreeCount()\r
- {\r
- return _treeList.size();\r
- } //-- int getTreeCount() \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
- * Method removeAlignment\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return Alignment\r
- */\r
- public jalview.binding.Alignment removeAlignment(int index)\r
- {\r
- java.lang.Object obj = _alignmentList.elementAt(index);\r
- _alignmentList.removeElementAt(index);\r
- return (jalview.binding.Alignment) obj;\r
- } //-- jalview.binding.Alignment removeAlignment(int) \r
-\r
- /**\r
- * Method removeAllAlignment\r
- * \r
- */\r
- public void removeAllAlignment()\r
- {\r
- _alignmentList.removeAllElements();\r
- } //-- void removeAllAlignment() \r
-\r
- /**\r
- * Method removeAllSequenceSet\r
- * \r
- */\r
- public void removeAllSequenceSet()\r
- {\r
- _sequenceSetList.removeAllElements();\r
- } //-- void removeAllSequenceSet() \r
-\r
- /**\r
- * Method removeAllTree\r
- * \r
- */\r
- public void removeAllTree()\r
- {\r
- _treeList.removeAllElements();\r
- } //-- void removeAllTree() \r
-\r
- /**\r
- * Method removeSequenceSet\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return SequenceSet\r
- */\r
- public jalview.binding.SequenceSet removeSequenceSet(int index)\r
- {\r
- java.lang.Object obj = _sequenceSetList.elementAt(index);\r
- _sequenceSetList.removeElementAt(index);\r
- return (jalview.binding.SequenceSet) obj;\r
- } //-- jalview.binding.SequenceSet removeSequenceSet(int) \r
-\r
- /**\r
- * Method removeTree\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return String\r
- */\r
- public java.lang.String removeTree(int index)\r
- {\r
- java.lang.Object obj = _treeList.elementAt(index);\r
- _treeList.removeElementAt(index);\r
- return (String)obj;\r
- } //-- java.lang.String removeTree(int) \r
-\r
- /**\r
- * Method setAlignment\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vAlignment\r
- */\r
- public void setAlignment(int index, jalview.binding.Alignment vAlignment)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _alignmentList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _alignmentList.setElementAt(vAlignment, index);\r
- } //-- void setAlignment(int, jalview.binding.Alignment) \r
-\r
- /**\r
- * Method setAlignment\r
- * \r
- * \r
- * \r
- * @param alignmentArray\r
- */\r
- public void setAlignment(jalview.binding.Alignment[] alignmentArray)\r
- {\r
- //-- copy array\r
- _alignmentList.removeAllElements();\r
- for (int i = 0; i < alignmentArray.length; i++) {\r
- _alignmentList.addElement(alignmentArray[i]);\r
- }\r
- } //-- void setAlignment(jalview.binding.Alignment) \r
-\r
- /**\r
- * Method setSequenceSet\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vSequenceSet\r
- */\r
- public void setSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _sequenceSetList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _sequenceSetList.setElementAt(vSequenceSet, index);\r
- } //-- void setSequenceSet(int, jalview.binding.SequenceSet) \r
-\r
- /**\r
- * Method setSequenceSet\r
- * \r
- * \r
- * \r
- * @param sequenceSetArray\r
- */\r
- public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray)\r
- {\r
- //-- copy array\r
- _sequenceSetList.removeAllElements();\r
- for (int i = 0; i < sequenceSetArray.length; i++) {\r
- _sequenceSetList.addElement(sequenceSetArray[i]);\r
- }\r
- } //-- void setSequenceSet(jalview.binding.SequenceSet) \r
-\r
- /**\r
- * Method setTree\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vTree\r
- */\r
- public void setTree(int index, java.lang.String vTree)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _treeList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _treeList.setElementAt(vTree, index);\r
- } //-- void setTree(int, java.lang.String) \r
-\r
- /**\r
- * Method setTree\r
- * \r
- * \r
- * \r
- * @param treeArray\r
- */\r
- public void setTree(java.lang.String[] treeArray)\r
- {\r
- //-- copy array\r
- _treeList.removeAllElements();\r
- for (int i = 0; i < treeArray.length; i++) {\r
- _treeList.addElement(treeArray[i]);\r
- }\r
- } //-- void setTree(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.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class VAMSAS.
+ *
+ * @version $Revision$ $Date$
+ */
+public class VAMSAS implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _alignmentList.
+ */
+ private java.util.Vector _alignmentList;
+
+ /**
+ * Field _treeList.
+ */
+ private java.util.Vector _treeList;
+
+ /**
+ * Field _sequenceSetList.
+ */
+ private java.util.Vector _sequenceSetList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public VAMSAS() {
+ super();
+ this._alignmentList = new java.util.Vector();
+ this._treeList = new java.util.Vector();
+ this._sequenceSetList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vAlignment
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAlignment(
+ final Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alignmentList.addElement(vAlignment);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlignment
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAlignment(
+ final int index,
+ final Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException {
+ this._alignmentList.add(index, vAlignment);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceSet
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSequenceSet(
+ final SequenceSet vSequenceSet)
+ throws java.lang.IndexOutOfBoundsException {
+ this._sequenceSetList.addElement(vSequenceSet);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequenceSet
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSequenceSet(
+ final int index,
+ final SequenceSet vSequenceSet)
+ throws java.lang.IndexOutOfBoundsException {
+ this._sequenceSetList.add(index, vSequenceSet);
+ }
+
+ /**
+ *
+ *
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addTree(
+ final java.lang.String vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treeList.addElement(vTree);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addTree(
+ final int index,
+ final java.lang.String vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ this._treeList.add(index, vTree);
+ }
+
+ /**
+ * Method enumerateAlignment.
+ *
+ * @return an Enumeration over all Alignment elements
+ */
+ public java.util.Enumeration enumerateAlignment(
+ ) {
+ return this._alignmentList.elements();
+ }
+
+ /**
+ * Method enumerateSequenceSet.
+ *
+ * @return an Enumeration over all SequenceSet elements
+ */
+ public java.util.Enumeration enumerateSequenceSet(
+ ) {
+ return this._sequenceSetList.elements();
+ }
+
+ /**
+ * Method enumerateTree.
+ *
+ * @return an Enumeration over all java.lang.String elements
+ */
+ public java.util.Enumeration enumerateTree(
+ ) {
+ return this._treeList.elements();
+ }
+
+ /**
+ * Method getAlignment.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the Alignment at the given index
+ */
+ public Alignment getAlignment(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alignmentList.size()) {
+ throw new IndexOutOfBoundsException("getAlignment: Index value '" + index + "' not in range [0.." + (this._alignmentList.size() - 1) + "]");
+ }
+
+ return (Alignment) _alignmentList.get(index);
+ }
+
+ /**
+ * Method getAlignment.Returns the contents of the collection
+ * in an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public Alignment[] getAlignment(
+ ) {
+ Alignment[] array = new Alignment[0];
+ return (Alignment[]) this._alignmentList.toArray(array);
+ }
+
+ /**
+ * Method getAlignmentCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAlignmentCount(
+ ) {
+ return this._alignmentList.size();
+ }
+
+ /**
+ * Method getSequenceSet.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the SequenceSet at the given index
+ */
+ public SequenceSet getSequenceSet(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceSetList.size()) {
+ throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
+ }
+
+ return (SequenceSet) _sequenceSetList.get(index);
+ }
+
+ /**
+ * Method getSequenceSet.Returns the contents of the collection
+ * in an Array. <p>Note: Just in case the collection contents
+ * are changing in another thread, we pass a 0-length Array of
+ * the correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public SequenceSet[] getSequenceSet(
+ ) {
+ SequenceSet[] array = new SequenceSet[0];
+ return (SequenceSet[]) this._sequenceSetList.toArray(array);
+ }
+
+ /**
+ * Method getSequenceSetCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSequenceSetCount(
+ ) {
+ return this._sequenceSetList.size();
+ }
+
+ /**
+ * Method getTree.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the java.lang.String at the given index
+ */
+ public java.lang.String getTree(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ return (java.lang.String) _treeList.get(index);
+ }
+
+ /**
+ * Method getTree.Returns the contents of the collection in an
+ * Array. <p>Note: Just in case the collection contents are
+ * changing in another thread, we pass a 0-length Array of the
+ * correct type into the API call. This way we <i>know</i>
+ * that the Array returned is of exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public java.lang.String[] getTree(
+ ) {
+ java.lang.String[] array = new java.lang.String[0];
+ return (java.lang.String[]) this._treeList.toArray(array);
+ }
+
+ /**
+ * Method getTreeCount.
+ *
+ * @return the size of this collection
+ */
+ public int getTreeCount(
+ ) {
+ return this._treeList.size();
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method removeAlignment.
+ *
+ * @param vAlignment
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAlignment(
+ final Alignment vAlignment) {
+ boolean removed = _alignmentList.remove(vAlignment);
+ return removed;
+ }
+
+ /**
+ * Method removeAlignmentAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public Alignment removeAlignmentAt(
+ final int index) {
+ java.lang.Object obj = this._alignmentList.remove(index);
+ return (Alignment) obj;
+ }
+
+ /**
+ */
+ public void removeAllAlignment(
+ ) {
+ this._alignmentList.clear();
+ }
+
+ /**
+ */
+ public void removeAllSequenceSet(
+ ) {
+ this._sequenceSetList.clear();
+ }
+
+ /**
+ */
+ public void removeAllTree(
+ ) {
+ this._treeList.clear();
+ }
+
+ /**
+ * Method removeSequenceSet.
+ *
+ * @param vSequenceSet
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSequenceSet(
+ final SequenceSet vSequenceSet) {
+ boolean removed = _sequenceSetList.remove(vSequenceSet);
+ return removed;
+ }
+
+ /**
+ * Method removeSequenceSetAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public SequenceSet removeSequenceSetAt(
+ final int index) {
+ java.lang.Object obj = this._sequenceSetList.remove(index);
+ return (SequenceSet) obj;
+ }
+
+ /**
+ * Method removeTree.
+ *
+ * @param vTree
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeTree(
+ final java.lang.String vTree) {
+ boolean removed = _treeList.remove(vTree);
+ return removed;
+ }
+
+ /**
+ * Method removeTreeAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public java.lang.String removeTreeAt(
+ final int index) {
+ java.lang.Object obj = this._treeList.remove(index);
+ return (java.lang.String) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAlignment
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setAlignment(
+ final int index,
+ final Alignment vAlignment)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._alignmentList.size()) {
+ throw new IndexOutOfBoundsException("setAlignment: Index value '" + index + "' not in range [0.." + (this._alignmentList.size() - 1) + "]");
+ }
+
+ this._alignmentList.set(index, vAlignment);
+ }
+
+ /**
+ *
+ *
+ * @param vAlignmentArray
+ */
+ public void setAlignment(
+ final Alignment[] vAlignmentArray) {
+ //-- copy array
+ _alignmentList.clear();
+
+ for (int i = 0; i < vAlignmentArray.length; i++) {
+ this._alignmentList.add(vAlignmentArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSequenceSet
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setSequenceSet(
+ final int index,
+ final SequenceSet vSequenceSet)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._sequenceSetList.size()) {
+ throw new IndexOutOfBoundsException("setSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]");
+ }
+
+ this._sequenceSetList.set(index, vSequenceSet);
+ }
+
+ /**
+ *
+ *
+ * @param vSequenceSetArray
+ */
+ public void setSequenceSet(
+ final SequenceSet[] vSequenceSetArray) {
+ //-- copy array
+ _sequenceSetList.clear();
+
+ for (int i = 0; i < vSequenceSetArray.length; i++) {
+ this._sequenceSetList.add(vSequenceSetArray[i]);
+ }
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vTree
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setTree(
+ final int index,
+ final java.lang.String vTree)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._treeList.size()) {
+ throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+ }
+
+ this._treeList.set(index, vTree);
+ }
+
+ /**
+ *
+ *
+ * @param vTreeArray
+ */
+ public void setTree(
+ final java.lang.String[] vTreeArray) {
+ //-- copy array
+ _treeList.clear();
+
+ for (int i = 0; i < vTreeArray.length; i++) {
+ this._treeList.add(vTreeArray[i]);
+ }
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.VAMSAS
+ */
+ public static jalview.binding.VAMSAS unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 VamsasModel.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class VamsasModel extends VAMSAS \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public VamsasModel() {\r
- super();\r
- } //-- jalview.binding.VamsasModel()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\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
- * 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.binding.VamsasModel) Unmarshaller.unmarshal(jalview.binding.VamsasModel.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class VamsasModel.
+ *
+ * @version $Revision$ $Date$
+ */
+public class VamsasModel extends VAMSAS
+implements java.io.Serializable
+{
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public VamsasModel() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.VAMSAS
+ */
+ public static jalview.binding.VAMSAS unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
-/*\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.binding;\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 Viewport.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Viewport implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _conservationSelected\r
- */\r
- private boolean _conservationSelected;\r
-\r
- /**\r
- * keeps track of state for field: _conservationSelected\r
- */\r
- private boolean _has_conservationSelected;\r
-\r
- /**\r
- * Field _pidSelected\r
- */\r
- private boolean _pidSelected;\r
-\r
- /**\r
- * keeps track of state for field: _pidSelected\r
- */\r
- private boolean _has_pidSelected;\r
-\r
- /**\r
- * Field _bgColour\r
- */\r
- private java.lang.String _bgColour;\r
-\r
- /**\r
- * Field _consThreshold\r
- */\r
- private int _consThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _consThreshold\r
- */\r
- private boolean _has_consThreshold;\r
-\r
- /**\r
- * Field _pidThreshold\r
- */\r
- private int _pidThreshold;\r
-\r
- /**\r
- * keeps track of state for field: _pidThreshold\r
- */\r
- private boolean _has_pidThreshold;\r
-\r
- /**\r
- * Field _title\r
- */\r
- private java.lang.String _title;\r
-\r
- /**\r
- * Field _showFullId\r
- */\r
- private boolean _showFullId;\r
-\r
- /**\r
- * keeps track of state for field: _showFullId\r
- */\r
- private boolean _has_showFullId;\r
-\r
- /**\r
- * Field _showText\r
- */\r
- private boolean _showText;\r
-\r
- /**\r
- * keeps track of state for field: _showText\r
- */\r
- private boolean _has_showText;\r
-\r
- /**\r
- * Field _showColourText\r
- */\r
- private boolean _showColourText;\r
-\r
- /**\r
- * keeps track of state for field: _showColourText\r
- */\r
- private boolean _has_showColourText;\r
-\r
- /**\r
- * Field _showBoxes\r
- */\r
- private boolean _showBoxes;\r
-\r
- /**\r
- * keeps track of state for field: _showBoxes\r
- */\r
- private boolean _has_showBoxes;\r
-\r
- /**\r
- * Field _wrapAlignment\r
- */\r
- private boolean _wrapAlignment;\r
-\r
- /**\r
- * keeps track of state for field: _wrapAlignment\r
- */\r
- private boolean _has_wrapAlignment;\r
-\r
- /**\r
- * Field _renderGaps\r
- */\r
- private boolean _renderGaps;\r
-\r
- /**\r
- * keeps track of state for field: _renderGaps\r
- */\r
- private boolean _has_renderGaps;\r
-\r
- /**\r
- * Field _showSequenceFeatures\r
- */\r
- private boolean _showSequenceFeatures;\r
-\r
- /**\r
- * keeps track of state for field: _showSequenceFeatures\r
- */\r
- private boolean _has_showSequenceFeatures;\r
-\r
- /**\r
- * Field _showAnnotation\r
- */\r
- private boolean _showAnnotation;\r
-\r
- /**\r
- * keeps track of state for field: _showAnnotation\r
- */\r
- private boolean _has_showAnnotation;\r
-\r
- /**\r
- * Field _showConservation\r
- */\r
- private boolean _showConservation;\r
-\r
- /**\r
- * keeps track of state for field: _showConservation\r
- */\r
- private boolean _has_showConservation;\r
-\r
- /**\r
- * Field _showQuality\r
- */\r
- private boolean _showQuality;\r
-\r
- /**\r
- * keeps track of state for field: _showQuality\r
- */\r
- private boolean _has_showQuality;\r
-\r
- /**\r
- * Field _showIdentity\r
- */\r
- private boolean _showIdentity;\r
-\r
- /**\r
- * keeps track of state for field: _showIdentity\r
- */\r
- private boolean _has_showIdentity;\r
-\r
- /**\r
- * Field _xpos\r
- */\r
- private int _xpos;\r
-\r
- /**\r
- * keeps track of state for field: _xpos\r
- */\r
- private boolean _has_xpos;\r
-\r
- /**\r
- * Field _ypos\r
- */\r
- private int _ypos;\r
-\r
- /**\r
- * keeps track of state for field: _ypos\r
- */\r
- private boolean _has_ypos;\r
-\r
- /**\r
- * Field _width\r
- */\r
- private int _width;\r
-\r
- /**\r
- * keeps track of state for field: _width\r
- */\r
- private boolean _has_width;\r
-\r
- /**\r
- * Field _height\r
- */\r
- private int _height;\r
-\r
- /**\r
- * keeps track of state for field: _height\r
- */\r
- private boolean _has_height;\r
-\r
- /**\r
- * Field _startRes\r
- */\r
- private int _startRes;\r
-\r
- /**\r
- * keeps track of state for field: _startRes\r
- */\r
- private boolean _has_startRes;\r
-\r
- /**\r
- * Field _startSeq\r
- */\r
- private int _startSeq;\r
-\r
- /**\r
- * keeps track of state for field: _startSeq\r
- */\r
- private boolean _has_startSeq;\r
-\r
- /**\r
- * Field _fontName\r
- */\r
- private java.lang.String _fontName;\r
-\r
- /**\r
- * Field _fontSize\r
- */\r
- private int _fontSize;\r
-\r
- /**\r
- * keeps track of state for field: _fontSize\r
- */\r
- private boolean _has_fontSize;\r
-\r
- /**\r
- * Field _fontStyle\r
- */\r
- private int _fontStyle;\r
-\r
- /**\r
- * keeps track of state for field: _fontStyle\r
- */\r
- private boolean _has_fontStyle;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Viewport() {\r
- super();\r
- } //-- jalview.binding.Viewport()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteConsThreshold\r
- * \r
- */\r
- public void deleteConsThreshold()\r
- {\r
- this._has_consThreshold= false;\r
- } //-- void deleteConsThreshold() \r
-\r
- /**\r
- * Method deleteConservationSelected\r
- * \r
- */\r
- public void deleteConservationSelected()\r
- {\r
- this._has_conservationSelected= false;\r
- } //-- void deleteConservationSelected() \r
-\r
- /**\r
- * Method deleteFontSize\r
- * \r
- */\r
- public void deleteFontSize()\r
- {\r
- this._has_fontSize= false;\r
- } //-- void deleteFontSize() \r
-\r
- /**\r
- * Method deleteFontStyle\r
- * \r
- */\r
- public void deleteFontStyle()\r
- {\r
- this._has_fontStyle= false;\r
- } //-- void deleteFontStyle() \r
-\r
- /**\r
- * Method deleteHeight\r
- * \r
- */\r
- public void deleteHeight()\r
- {\r
- this._has_height= false;\r
- } //-- void deleteHeight() \r
-\r
- /**\r
- * Method deletePidSelected\r
- * \r
- */\r
- public void deletePidSelected()\r
- {\r
- this._has_pidSelected= false;\r
- } //-- void deletePidSelected() \r
-\r
- /**\r
- * Method deletePidThreshold\r
- * \r
- */\r
- public void deletePidThreshold()\r
- {\r
- this._has_pidThreshold= false;\r
- } //-- void deletePidThreshold() \r
-\r
- /**\r
- * Method deleteRenderGaps\r
- * \r
- */\r
- public void deleteRenderGaps()\r
- {\r
- this._has_renderGaps= false;\r
- } //-- void deleteRenderGaps() \r
-\r
- /**\r
- * Method deleteShowAnnotation\r
- * \r
- */\r
- public void deleteShowAnnotation()\r
- {\r
- this._has_showAnnotation= false;\r
- } //-- void deleteShowAnnotation() \r
-\r
- /**\r
- * Method deleteShowBoxes\r
- * \r
- */\r
- public void deleteShowBoxes()\r
- {\r
- this._has_showBoxes= false;\r
- } //-- void deleteShowBoxes() \r
-\r
- /**\r
- * Method deleteShowColourText\r
- * \r
- */\r
- public void deleteShowColourText()\r
- {\r
- this._has_showColourText= false;\r
- } //-- void deleteShowColourText() \r
-\r
- /**\r
- * Method deleteShowConservation\r
- * \r
- */\r
- public void deleteShowConservation()\r
- {\r
- this._has_showConservation= false;\r
- } //-- void deleteShowConservation() \r
-\r
- /**\r
- * Method deleteShowFullId\r
- * \r
- */\r
- public void deleteShowFullId()\r
- {\r
- this._has_showFullId= false;\r
- } //-- void deleteShowFullId() \r
-\r
- /**\r
- * Method deleteShowIdentity\r
- * \r
- */\r
- public void deleteShowIdentity()\r
- {\r
- this._has_showIdentity= false;\r
- } //-- void deleteShowIdentity() \r
-\r
- /**\r
- * Method deleteShowQuality\r
- * \r
- */\r
- public void deleteShowQuality()\r
- {\r
- this._has_showQuality= false;\r
- } //-- void deleteShowQuality() \r
-\r
- /**\r
- * Method deleteShowSequenceFeatures\r
- * \r
- */\r
- public void deleteShowSequenceFeatures()\r
- {\r
- this._has_showSequenceFeatures= false;\r
- } //-- void deleteShowSequenceFeatures() \r
-\r
- /**\r
- * Method deleteShowText\r
- * \r
- */\r
- public void deleteShowText()\r
- {\r
- this._has_showText= false;\r
- } //-- void deleteShowText() \r
-\r
- /**\r
- * Method deleteStartRes\r
- * \r
- */\r
- public void deleteStartRes()\r
- {\r
- this._has_startRes= false;\r
- } //-- void deleteStartRes() \r
-\r
- /**\r
- * Method deleteStartSeq\r
- * \r
- */\r
- public void deleteStartSeq()\r
- {\r
- this._has_startSeq= false;\r
- } //-- void deleteStartSeq() \r
-\r
- /**\r
- * Method deleteWidth\r
- * \r
- */\r
- public void deleteWidth()\r
- {\r
- this._has_width= false;\r
- } //-- void deleteWidth() \r
-\r
- /**\r
- * Method deleteWrapAlignment\r
- * \r
- */\r
- public void deleteWrapAlignment()\r
- {\r
- this._has_wrapAlignment= false;\r
- } //-- void deleteWrapAlignment() \r
-\r
- /**\r
- * Method deleteXpos\r
- * \r
- */\r
- public void deleteXpos()\r
- {\r
- this._has_xpos= false;\r
- } //-- void deleteXpos() \r
-\r
- /**\r
- * Method deleteYpos\r
- * \r
- */\r
- public void deleteYpos()\r
- {\r
- this._has_ypos= false;\r
- } //-- void deleteYpos() \r
-\r
- /**\r
- * Returns the value of field 'bgColour'.\r
- * \r
- * @return String\r
- * @return the value of field 'bgColour'.\r
- */\r
- public java.lang.String getBgColour()\r
- {\r
- return this._bgColour;\r
- } //-- java.lang.String getBgColour() \r
-\r
- /**\r
- * Returns the value of field 'consThreshold'.\r
- * \r
- * @return int\r
- * @return the value of field 'consThreshold'.\r
- */\r
- public int getConsThreshold()\r
- {\r
- return this._consThreshold;\r
- } //-- int getConsThreshold() \r
-\r
- /**\r
- * Returns the value of field 'conservationSelected'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'conservationSelected'.\r
- */\r
- public boolean getConservationSelected()\r
- {\r
- return this._conservationSelected;\r
- } //-- boolean getConservationSelected() \r
-\r
- /**\r
- * Returns the value of field 'fontName'.\r
- * \r
- * @return String\r
- * @return the value of field 'fontName'.\r
- */\r
- public java.lang.String getFontName()\r
- {\r
- return this._fontName;\r
- } //-- java.lang.String getFontName() \r
-\r
- /**\r
- * Returns the value of field 'fontSize'.\r
- * \r
- * @return int\r
- * @return the value of field 'fontSize'.\r
- */\r
- public int getFontSize()\r
- {\r
- return this._fontSize;\r
- } //-- int getFontSize() \r
-\r
- /**\r
- * Returns the value of field 'fontStyle'.\r
- * \r
- * @return int\r
- * @return the value of field 'fontStyle'.\r
- */\r
- public int getFontStyle()\r
- {\r
- return this._fontStyle;\r
- } //-- int getFontStyle() \r
-\r
- /**\r
- * Returns the value of field 'height'.\r
- * \r
- * @return int\r
- * @return the value of field 'height'.\r
- */\r
- public int getHeight()\r
- {\r
- return this._height;\r
- } //-- int getHeight() \r
-\r
- /**\r
- * Returns the value of field 'pidSelected'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'pidSelected'.\r
- */\r
- public boolean getPidSelected()\r
- {\r
- return this._pidSelected;\r
- } //-- boolean getPidSelected() \r
-\r
- /**\r
- * Returns the value of field 'pidThreshold'.\r
- * \r
- * @return int\r
- * @return the value of field 'pidThreshold'.\r
- */\r
- public int getPidThreshold()\r
- {\r
- return this._pidThreshold;\r
- } //-- int getPidThreshold() \r
-\r
- /**\r
- * Returns the value of field 'renderGaps'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'renderGaps'.\r
- */\r
- public boolean getRenderGaps()\r
- {\r
- return this._renderGaps;\r
- } //-- boolean getRenderGaps() \r
-\r
- /**\r
- * Returns the value of field 'showAnnotation'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'showAnnotation'.\r
- */\r
- public boolean getShowAnnotation()\r
- {\r
- return this._showAnnotation;\r
- } //-- boolean getShowAnnotation() \r
-\r
- /**\r
- * Returns the value of field 'showBoxes'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'showBoxes'.\r
- */\r
- public boolean getShowBoxes()\r
- {\r
- return this._showBoxes;\r
- } //-- boolean getShowBoxes() \r
-\r
- /**\r
- * Returns the value of field 'showColourText'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'showColourText'.\r
- */\r
- public boolean getShowColourText()\r
- {\r
- return this._showColourText;\r
- } //-- boolean getShowColourText() \r
-\r
- /**\r
- * Returns the value of field 'showConservation'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'showConservation'.\r
- */\r
- public boolean getShowConservation()\r
- {\r
- return this._showConservation;\r
- } //-- boolean getShowConservation() \r
-\r
- /**\r
- * Returns the value of field 'showFullId'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'showFullId'.\r
- */\r
- public boolean getShowFullId()\r
- {\r
- return this._showFullId;\r
- } //-- boolean getShowFullId() \r
-\r
- /**\r
- * Returns the value of field 'showIdentity'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'showIdentity'.\r
- */\r
- public boolean getShowIdentity()\r
- {\r
- return this._showIdentity;\r
- } //-- boolean getShowIdentity() \r
-\r
- /**\r
- * Returns the value of field 'showQuality'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'showQuality'.\r
- */\r
- public boolean getShowQuality()\r
- {\r
- return this._showQuality;\r
- } //-- boolean getShowQuality() \r
-\r
- /**\r
- * Returns the value of field 'showSequenceFeatures'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'showSequenceFeatures'.\r
- */\r
- public boolean getShowSequenceFeatures()\r
- {\r
- return this._showSequenceFeatures;\r
- } //-- boolean getShowSequenceFeatures() \r
-\r
- /**\r
- * Returns the value of field 'showText'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'showText'.\r
- */\r
- public boolean getShowText()\r
- {\r
- return this._showText;\r
- } //-- boolean getShowText() \r
-\r
- /**\r
- * Returns the value of field 'startRes'.\r
- * \r
- * @return int\r
- * @return the value of field 'startRes'.\r
- */\r
- public int getStartRes()\r
- {\r
- return this._startRes;\r
- } //-- int getStartRes() \r
-\r
- /**\r
- * Returns the value of field 'startSeq'.\r
- * \r
- * @return int\r
- * @return the value of field 'startSeq'.\r
- */\r
- public int getStartSeq()\r
- {\r
- return this._startSeq;\r
- } //-- int getStartSeq() \r
-\r
- /**\r
- * Returns the value of field 'title'.\r
- * \r
- * @return String\r
- * @return the value of field 'title'.\r
- */\r
- public java.lang.String getTitle()\r
- {\r
- return this._title;\r
- } //-- java.lang.String getTitle() \r
-\r
- /**\r
- * Returns the value of field 'width'.\r
- * \r
- * @return int\r
- * @return the value of field 'width'.\r
- */\r
- public int getWidth()\r
- {\r
- return this._width;\r
- } //-- int getWidth() \r
-\r
- /**\r
- * Returns the value of field 'wrapAlignment'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'wrapAlignment'.\r
- */\r
- public boolean getWrapAlignment()\r
- {\r
- return this._wrapAlignment;\r
- } //-- boolean getWrapAlignment() \r
-\r
- /**\r
- * Returns the value of field 'xpos'.\r
- * \r
- * @return int\r
- * @return the value of field 'xpos'.\r
- */\r
- public int getXpos()\r
- {\r
- return this._xpos;\r
- } //-- int getXpos() \r
-\r
- /**\r
- * Returns the value of field 'ypos'.\r
- * \r
- * @return int\r
- * @return the value of field 'ypos'.\r
- */\r
- public int getYpos()\r
- {\r
- return this._ypos;\r
- } //-- int getYpos() \r
-\r
- /**\r
- * Method hasConsThreshold\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasConsThreshold()\r
- {\r
- return this._has_consThreshold;\r
- } //-- boolean hasConsThreshold() \r
-\r
- /**\r
- * Method hasConservationSelected\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasConservationSelected()\r
- {\r
- return this._has_conservationSelected;\r
- } //-- boolean hasConservationSelected() \r
-\r
- /**\r
- * Method hasFontSize\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasFontSize()\r
- {\r
- return this._has_fontSize;\r
- } //-- boolean hasFontSize() \r
-\r
- /**\r
- * Method hasFontStyle\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasFontStyle()\r
- {\r
- return this._has_fontStyle;\r
- } //-- boolean hasFontStyle() \r
-\r
- /**\r
- * Method hasHeight\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasHeight()\r
- {\r
- return this._has_height;\r
- } //-- boolean hasHeight() \r
-\r
- /**\r
- * Method hasPidSelected\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasPidSelected()\r
- {\r
- return this._has_pidSelected;\r
- } //-- boolean hasPidSelected() \r
-\r
- /**\r
- * Method hasPidThreshold\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasPidThreshold()\r
- {\r
- return this._has_pidThreshold;\r
- } //-- boolean hasPidThreshold() \r
-\r
- /**\r
- * Method hasRenderGaps\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasRenderGaps()\r
- {\r
- return this._has_renderGaps;\r
- } //-- boolean hasRenderGaps() \r
-\r
- /**\r
- * Method hasShowAnnotation\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasShowAnnotation()\r
- {\r
- return this._has_showAnnotation;\r
- } //-- boolean hasShowAnnotation() \r
-\r
- /**\r
- * Method hasShowBoxes\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasShowBoxes()\r
- {\r
- return this._has_showBoxes;\r
- } //-- boolean hasShowBoxes() \r
-\r
- /**\r
- * Method hasShowColourText\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasShowColourText()\r
- {\r
- return this._has_showColourText;\r
- } //-- boolean hasShowColourText() \r
-\r
- /**\r
- * Method hasShowConservation\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasShowConservation()\r
- {\r
- return this._has_showConservation;\r
- } //-- boolean hasShowConservation() \r
-\r
- /**\r
- * Method hasShowFullId\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasShowFullId()\r
- {\r
- return this._has_showFullId;\r
- } //-- boolean hasShowFullId() \r
-\r
- /**\r
- * Method hasShowIdentity\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasShowIdentity()\r
- {\r
- return this._has_showIdentity;\r
- } //-- boolean hasShowIdentity() \r
-\r
- /**\r
- * Method hasShowQuality\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasShowQuality()\r
- {\r
- return this._has_showQuality;\r
- } //-- boolean hasShowQuality() \r
-\r
- /**\r
- * Method hasShowSequenceFeatures\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasShowSequenceFeatures()\r
- {\r
- return this._has_showSequenceFeatures;\r
- } //-- boolean hasShowSequenceFeatures() \r
-\r
- /**\r
- * Method hasShowText\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasShowText()\r
- {\r
- return this._has_showText;\r
- } //-- boolean hasShowText() \r
-\r
- /**\r
- * Method hasStartRes\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasStartRes()\r
- {\r
- return this._has_startRes;\r
- } //-- boolean hasStartRes() \r
-\r
- /**\r
- * Method hasStartSeq\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasStartSeq()\r
- {\r
- return this._has_startSeq;\r
- } //-- boolean hasStartSeq() \r
-\r
- /**\r
- * Method hasWidth\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasWidth()\r
- {\r
- return this._has_width;\r
- } //-- boolean hasWidth() \r
-\r
- /**\r
- * Method hasWrapAlignment\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasWrapAlignment()\r
- {\r
- return this._has_wrapAlignment;\r
- } //-- boolean hasWrapAlignment() \r
-\r
- /**\r
- * Method hasXpos\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasXpos()\r
- {\r
- return this._has_xpos;\r
- } //-- boolean hasXpos() \r
-\r
- /**\r
- * Method hasYpos\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasYpos()\r
- {\r
- return this._has_ypos;\r
- } //-- boolean hasYpos() \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 'bgColour'.\r
- * \r
- * @param bgColour the value of field 'bgColour'.\r
- */\r
- public void setBgColour(java.lang.String bgColour)\r
- {\r
- this._bgColour = bgColour;\r
- } //-- void setBgColour(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'consThreshold'.\r
- * \r
- * @param consThreshold the value of field 'consThreshold'.\r
- */\r
- public void setConsThreshold(int consThreshold)\r
- {\r
- this._consThreshold = consThreshold;\r
- this._has_consThreshold = true;\r
- } //-- void setConsThreshold(int) \r
-\r
- /**\r
- * Sets the value of field 'conservationSelected'.\r
- * \r
- * @param conservationSelected the value of field\r
- * 'conservationSelected'.\r
- */\r
- public void setConservationSelected(boolean conservationSelected)\r
- {\r
- this._conservationSelected = conservationSelected;\r
- this._has_conservationSelected = true;\r
- } //-- void setConservationSelected(boolean) \r
-\r
- /**\r
- * Sets the value of field 'fontName'.\r
- * \r
- * @param fontName the value of field 'fontName'.\r
- */\r
- public void setFontName(java.lang.String fontName)\r
- {\r
- this._fontName = fontName;\r
- } //-- void setFontName(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'fontSize'.\r
- * \r
- * @param fontSize the value of field 'fontSize'.\r
- */\r
- public void setFontSize(int fontSize)\r
- {\r
- this._fontSize = fontSize;\r
- this._has_fontSize = true;\r
- } //-- void setFontSize(int) \r
-\r
- /**\r
- * Sets the value of field 'fontStyle'.\r
- * \r
- * @param fontStyle the value of field 'fontStyle'.\r
- */\r
- public void setFontStyle(int fontStyle)\r
- {\r
- this._fontStyle = fontStyle;\r
- this._has_fontStyle = true;\r
- } //-- void setFontStyle(int) \r
-\r
- /**\r
- * Sets the value of field 'height'.\r
- * \r
- * @param height the value of field 'height'.\r
- */\r
- public void setHeight(int height)\r
- {\r
- this._height = height;\r
- this._has_height = true;\r
- } //-- void setHeight(int) \r
-\r
- /**\r
- * Sets the value of field 'pidSelected'.\r
- * \r
- * @param pidSelected the value of field 'pidSelected'.\r
- */\r
- public void setPidSelected(boolean pidSelected)\r
- {\r
- this._pidSelected = pidSelected;\r
- this._has_pidSelected = true;\r
- } //-- void setPidSelected(boolean) \r
-\r
- /**\r
- * Sets the value of field 'pidThreshold'.\r
- * \r
- * @param pidThreshold the value of field 'pidThreshold'.\r
- */\r
- public void setPidThreshold(int pidThreshold)\r
- {\r
- this._pidThreshold = pidThreshold;\r
- this._has_pidThreshold = true;\r
- } //-- void setPidThreshold(int) \r
-\r
- /**\r
- * Sets the value of field 'renderGaps'.\r
- * \r
- * @param renderGaps the value of field 'renderGaps'.\r
- */\r
- public void setRenderGaps(boolean renderGaps)\r
- {\r
- this._renderGaps = renderGaps;\r
- this._has_renderGaps = true;\r
- } //-- void setRenderGaps(boolean) \r
-\r
- /**\r
- * Sets the value of field 'showAnnotation'.\r
- * \r
- * @param showAnnotation the value of field 'showAnnotation'.\r
- */\r
- public void setShowAnnotation(boolean showAnnotation)\r
- {\r
- this._showAnnotation = showAnnotation;\r
- this._has_showAnnotation = true;\r
- } //-- void setShowAnnotation(boolean) \r
-\r
- /**\r
- * Sets the value of field 'showBoxes'.\r
- * \r
- * @param showBoxes the value of field 'showBoxes'.\r
- */\r
- public void setShowBoxes(boolean showBoxes)\r
- {\r
- this._showBoxes = showBoxes;\r
- this._has_showBoxes = true;\r
- } //-- void setShowBoxes(boolean) \r
-\r
- /**\r
- * Sets the value of field 'showColourText'.\r
- * \r
- * @param showColourText the value of field 'showColourText'.\r
- */\r
- public void setShowColourText(boolean showColourText)\r
- {\r
- this._showColourText = showColourText;\r
- this._has_showColourText = true;\r
- } //-- void setShowColourText(boolean) \r
-\r
- /**\r
- * Sets the value of field 'showConservation'.\r
- * \r
- * @param showConservation the value of field 'showConservation'\r
- */\r
- public void setShowConservation(boolean showConservation)\r
- {\r
- this._showConservation = showConservation;\r
- this._has_showConservation = true;\r
- } //-- void setShowConservation(boolean) \r
-\r
- /**\r
- * Sets the value of field 'showFullId'.\r
- * \r
- * @param showFullId the value of field 'showFullId'.\r
- */\r
- public void setShowFullId(boolean showFullId)\r
- {\r
- this._showFullId = showFullId;\r
- this._has_showFullId = true;\r
- } //-- void setShowFullId(boolean) \r
-\r
- /**\r
- * Sets the value of field 'showIdentity'.\r
- * \r
- * @param showIdentity the value of field 'showIdentity'.\r
- */\r
- public void setShowIdentity(boolean showIdentity)\r
- {\r
- this._showIdentity = showIdentity;\r
- this._has_showIdentity = true;\r
- } //-- void setShowIdentity(boolean) \r
-\r
- /**\r
- * Sets the value of field 'showQuality'.\r
- * \r
- * @param showQuality the value of field 'showQuality'.\r
- */\r
- public void setShowQuality(boolean showQuality)\r
- {\r
- this._showQuality = showQuality;\r
- this._has_showQuality = true;\r
- } //-- void setShowQuality(boolean) \r
-\r
- /**\r
- * Sets the value of field 'showSequenceFeatures'.\r
- * \r
- * @param showSequenceFeatures the value of field\r
- * 'showSequenceFeatures'.\r
- */\r
- public void setShowSequenceFeatures(boolean showSequenceFeatures)\r
- {\r
- this._showSequenceFeatures = showSequenceFeatures;\r
- this._has_showSequenceFeatures = true;\r
- } //-- void setShowSequenceFeatures(boolean) \r
-\r
- /**\r
- * Sets the value of field 'showText'.\r
- * \r
- * @param showText the value of field 'showText'.\r
- */\r
- public void setShowText(boolean showText)\r
- {\r
- this._showText = showText;\r
- this._has_showText = true;\r
- } //-- void setShowText(boolean) \r
-\r
- /**\r
- * Sets the value of field 'startRes'.\r
- * \r
- * @param startRes the value of field 'startRes'.\r
- */\r
- public void setStartRes(int startRes)\r
- {\r
- this._startRes = startRes;\r
- this._has_startRes = true;\r
- } //-- void setStartRes(int) \r
-\r
- /**\r
- * Sets the value of field 'startSeq'.\r
- * \r
- * @param startSeq the value of field 'startSeq'.\r
- */\r
- public void setStartSeq(int startSeq)\r
- {\r
- this._startSeq = startSeq;\r
- this._has_startSeq = true;\r
- } //-- void setStartSeq(int) \r
-\r
- /**\r
- * Sets the value of field 'title'.\r
- * \r
- * @param title the value of field 'title'.\r
- */\r
- public void setTitle(java.lang.String title)\r
- {\r
- this._title = title;\r
- } //-- void setTitle(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'width'.\r
- * \r
- * @param width the value of field 'width'.\r
- */\r
- public void setWidth(int width)\r
- {\r
- this._width = width;\r
- this._has_width = true;\r
- } //-- void setWidth(int) \r
-\r
- /**\r
- * Sets the value of field 'wrapAlignment'.\r
- * \r
- * @param wrapAlignment the value of field 'wrapAlignment'.\r
- */\r
- public void setWrapAlignment(boolean wrapAlignment)\r
- {\r
- this._wrapAlignment = wrapAlignment;\r
- this._has_wrapAlignment = true;\r
- } //-- void setWrapAlignment(boolean) \r
-\r
- /**\r
- * Sets the value of field 'xpos'.\r
- * \r
- * @param xpos the value of field 'xpos'.\r
- */\r
- public void setXpos(int xpos)\r
- {\r
- this._xpos = xpos;\r
- this._has_xpos = true;\r
- } //-- void setXpos(int) \r
-\r
- /**\r
- * Sets the value of field 'ypos'.\r
- * \r
- * @param ypos the value of field 'ypos'.\r
- */\r
- public void setYpos(int ypos)\r
- {\r
- this._ypos = ypos;\r
- this._has_ypos = true;\r
- } //-- void setYpos(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.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.Viewport.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
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Viewport.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Viewport implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _conservationSelected.
+ */
+ private boolean _conservationSelected;
+
+ /**
+ * keeps track of state for field: _conservationSelected
+ */
+ private boolean _has_conservationSelected;
+
+ /**
+ * Field _pidSelected.
+ */
+ private boolean _pidSelected;
+
+ /**
+ * keeps track of state for field: _pidSelected
+ */
+ private boolean _has_pidSelected;
+
+ /**
+ * Field _bgColour.
+ */
+ private java.lang.String _bgColour;
+
+ /**
+ * Field _consThreshold.
+ */
+ private int _consThreshold;
+
+ /**
+ * keeps track of state for field: _consThreshold
+ */
+ private boolean _has_consThreshold;
+
+ /**
+ * Field _pidThreshold.
+ */
+ private int _pidThreshold;
+
+ /**
+ * keeps track of state for field: _pidThreshold
+ */
+ private boolean _has_pidThreshold;
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * Field _showFullId.
+ */
+ private boolean _showFullId;
+
+ /**
+ * keeps track of state for field: _showFullId
+ */
+ private boolean _has_showFullId;
+
+ /**
+ * Field _showText.
+ */
+ private boolean _showText;
+
+ /**
+ * keeps track of state for field: _showText
+ */
+ private boolean _has_showText;
+
+ /**
+ * Field _showColourText.
+ */
+ private boolean _showColourText;
+
+ /**
+ * keeps track of state for field: _showColourText
+ */
+ private boolean _has_showColourText;
+
+ /**
+ * Field _showBoxes.
+ */
+ private boolean _showBoxes;
+
+ /**
+ * keeps track of state for field: _showBoxes
+ */
+ private boolean _has_showBoxes;
+
+ /**
+ * Field _wrapAlignment.
+ */
+ private boolean _wrapAlignment;
+
+ /**
+ * keeps track of state for field: _wrapAlignment
+ */
+ private boolean _has_wrapAlignment;
+
+ /**
+ * Field _renderGaps.
+ */
+ private boolean _renderGaps;
+
+ /**
+ * keeps track of state for field: _renderGaps
+ */
+ private boolean _has_renderGaps;
+
+ /**
+ * Field _showSequenceFeatures.
+ */
+ private boolean _showSequenceFeatures;
+
+ /**
+ * keeps track of state for field: _showSequenceFeatures
+ */
+ private boolean _has_showSequenceFeatures;
+
+ /**
+ * Field _showAnnotation.
+ */
+ private boolean _showAnnotation;
+
+ /**
+ * keeps track of state for field: _showAnnotation
+ */
+ private boolean _has_showAnnotation;
+
+ /**
+ * Field _showConservation.
+ */
+ private boolean _showConservation;
+
+ /**
+ * keeps track of state for field: _showConservation
+ */
+ private boolean _has_showConservation;
+
+ /**
+ * Field _showQuality.
+ */
+ private boolean _showQuality;
+
+ /**
+ * keeps track of state for field: _showQuality
+ */
+ private boolean _has_showQuality;
+
+ /**
+ * Field _showIdentity.
+ */
+ private boolean _showIdentity;
+
+ /**
+ * keeps track of state for field: _showIdentity
+ */
+ private boolean _has_showIdentity;
+
+ /**
+ * Field _xpos.
+ */
+ private int _xpos;
+
+ /**
+ * keeps track of state for field: _xpos
+ */
+ private boolean _has_xpos;
+
+ /**
+ * Field _ypos.
+ */
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _has_ypos;
+
+ /**
+ * Field _width.
+ */
+ private int _width;
+
+ /**
+ * keeps track of state for field: _width
+ */
+ private boolean _has_width;
+
+ /**
+ * Field _height.
+ */
+ private int _height;
+
+ /**
+ * keeps track of state for field: _height
+ */
+ private boolean _has_height;
+
+ /**
+ * Field _startRes.
+ */
+ private int _startRes;
+
+ /**
+ * keeps track of state for field: _startRes
+ */
+ private boolean _has_startRes;
+
+ /**
+ * Field _startSeq.
+ */
+ private int _startSeq;
+
+ /**
+ * keeps track of state for field: _startSeq
+ */
+ private boolean _has_startSeq;
+
+ /**
+ * Field _fontName.
+ */
+ private java.lang.String _fontName;
+
+ /**
+ * Field _fontSize.
+ */
+ private int _fontSize;
+
+ /**
+ * keeps track of state for field: _fontSize
+ */
+ private boolean _has_fontSize;
+
+ /**
+ * Field _fontStyle.
+ */
+ private int _fontStyle;
+
+ /**
+ * keeps track of state for field: _fontStyle
+ */
+ private boolean _has_fontStyle;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Viewport() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteConsThreshold(
+ ) {
+ this._has_consThreshold= false;
+ }
+
+ /**
+ */
+ public void deleteConservationSelected(
+ ) {
+ this._has_conservationSelected= false;
+ }
+
+ /**
+ */
+ public void deleteFontSize(
+ ) {
+ this._has_fontSize= false;
+ }
+
+ /**
+ */
+ public void deleteFontStyle(
+ ) {
+ this._has_fontStyle= false;
+ }
+
+ /**
+ */
+ public void deleteHeight(
+ ) {
+ this._has_height= false;
+ }
+
+ /**
+ */
+ public void deletePidSelected(
+ ) {
+ this._has_pidSelected= false;
+ }
+
+ /**
+ */
+ public void deletePidThreshold(
+ ) {
+ this._has_pidThreshold= false;
+ }
+
+ /**
+ */
+ public void deleteRenderGaps(
+ ) {
+ this._has_renderGaps= false;
+ }
+
+ /**
+ */
+ public void deleteShowAnnotation(
+ ) {
+ this._has_showAnnotation= false;
+ }
+
+ /**
+ */
+ public void deleteShowBoxes(
+ ) {
+ this._has_showBoxes= false;
+ }
+
+ /**
+ */
+ public void deleteShowColourText(
+ ) {
+ this._has_showColourText= false;
+ }
+
+ /**
+ */
+ public void deleteShowConservation(
+ ) {
+ this._has_showConservation= false;
+ }
+
+ /**
+ */
+ public void deleteShowFullId(
+ ) {
+ this._has_showFullId= false;
+ }
+
+ /**
+ */
+ public void deleteShowIdentity(
+ ) {
+ this._has_showIdentity= false;
+ }
+
+ /**
+ */
+ public void deleteShowQuality(
+ ) {
+ this._has_showQuality= false;
+ }
+
+ /**
+ */
+ public void deleteShowSequenceFeatures(
+ ) {
+ this._has_showSequenceFeatures= false;
+ }
+
+ /**
+ */
+ public void deleteShowText(
+ ) {
+ this._has_showText= false;
+ }
+
+ /**
+ */
+ public void deleteStartRes(
+ ) {
+ this._has_startRes= false;
+ }
+
+ /**
+ */
+ public void deleteStartSeq(
+ ) {
+ this._has_startSeq= false;
+ }
+
+ /**
+ */
+ public void deleteWidth(
+ ) {
+ this._has_width= false;
+ }
+
+ /**
+ */
+ public void deleteWrapAlignment(
+ ) {
+ this._has_wrapAlignment= false;
+ }
+
+ /**
+ */
+ public void deleteXpos(
+ ) {
+ this._has_xpos= false;
+ }
+
+ /**
+ */
+ public void deleteYpos(
+ ) {
+ this._has_ypos= false;
+ }
+
+ /**
+ * Returns the value of field 'bgColour'.
+ *
+ * @return the value of field 'BgColour'.
+ */
+ public java.lang.String getBgColour(
+ ) {
+ return this._bgColour;
+ }
+
+ /**
+ * Returns the value of field 'consThreshold'.
+ *
+ * @return the value of field 'ConsThreshold'.
+ */
+ public int getConsThreshold(
+ ) {
+ return this._consThreshold;
+ }
+
+ /**
+ * Returns the value of field 'conservationSelected'.
+ *
+ * @return the value of field 'ConservationSelected'.
+ */
+ public boolean getConservationSelected(
+ ) {
+ return this._conservationSelected;
+ }
+
+ /**
+ * Returns the value of field 'fontName'.
+ *
+ * @return the value of field 'FontName'.
+ */
+ public java.lang.String getFontName(
+ ) {
+ return this._fontName;
+ }
+
+ /**
+ * Returns the value of field 'fontSize'.
+ *
+ * @return the value of field 'FontSize'.
+ */
+ public int getFontSize(
+ ) {
+ return this._fontSize;
+ }
+
+ /**
+ * Returns the value of field 'fontStyle'.
+ *
+ * @return the value of field 'FontStyle'.
+ */
+ public int getFontStyle(
+ ) {
+ return this._fontStyle;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight(
+ ) {
+ return this._height;
+ }
+
+ /**
+ * Returns the value of field 'pidSelected'.
+ *
+ * @return the value of field 'PidSelected'.
+ */
+ public boolean getPidSelected(
+ ) {
+ return this._pidSelected;
+ }
+
+ /**
+ * Returns the value of field 'pidThreshold'.
+ *
+ * @return the value of field 'PidThreshold'.
+ */
+ public int getPidThreshold(
+ ) {
+ return this._pidThreshold;
+ }
+
+ /**
+ * Returns the value of field 'renderGaps'.
+ *
+ * @return the value of field 'RenderGaps'.
+ */
+ public boolean getRenderGaps(
+ ) {
+ return this._renderGaps;
+ }
+
+ /**
+ * Returns the value of field 'showAnnotation'.
+ *
+ * @return the value of field 'ShowAnnotation'.
+ */
+ public boolean getShowAnnotation(
+ ) {
+ return this._showAnnotation;
+ }
+
+ /**
+ * Returns the value of field 'showBoxes'.
+ *
+ * @return the value of field 'ShowBoxes'.
+ */
+ public boolean getShowBoxes(
+ ) {
+ return this._showBoxes;
+ }
+
+ /**
+ * Returns the value of field 'showColourText'.
+ *
+ * @return the value of field 'ShowColourText'.
+ */
+ public boolean getShowColourText(
+ ) {
+ return this._showColourText;
+ }
+
+ /**
+ * Returns the value of field 'showConservation'.
+ *
+ * @return the value of field 'ShowConservation'.
+ */
+ public boolean getShowConservation(
+ ) {
+ return this._showConservation;
+ }
+
+ /**
+ * Returns the value of field 'showFullId'.
+ *
+ * @return the value of field 'ShowFullId'.
+ */
+ public boolean getShowFullId(
+ ) {
+ return this._showFullId;
+ }
+
+ /**
+ * Returns the value of field 'showIdentity'.
+ *
+ * @return the value of field 'ShowIdentity'.
+ */
+ public boolean getShowIdentity(
+ ) {
+ return this._showIdentity;
+ }
+
+ /**
+ * Returns the value of field 'showQuality'.
+ *
+ * @return the value of field 'ShowQuality'.
+ */
+ public boolean getShowQuality(
+ ) {
+ return this._showQuality;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceFeatures'.
+ *
+ * @return the value of field 'ShowSequenceFeatures'.
+ */
+ public boolean getShowSequenceFeatures(
+ ) {
+ return this._showSequenceFeatures;
+ }
+
+ /**
+ * Returns the value of field 'showText'.
+ *
+ * @return the value of field 'ShowText'.
+ */
+ public boolean getShowText(
+ ) {
+ return this._showText;
+ }
+
+ /**
+ * Returns the value of field 'startRes'.
+ *
+ * @return the value of field 'StartRes'.
+ */
+ public int getStartRes(
+ ) {
+ return this._startRes;
+ }
+
+ /**
+ * Returns the value of field 'startSeq'.
+ *
+ * @return the value of field 'StartSeq'.
+ */
+ public int getStartSeq(
+ ) {
+ return this._startSeq;
+ }
+
+ /**
+ * Returns the value of field 'title'.
+ *
+ * @return the value of field 'Title'.
+ */
+ public java.lang.String getTitle(
+ ) {
+ return this._title;
+ }
+
+ /**
+ * Returns the value of field 'width'.
+ *
+ * @return the value of field 'Width'.
+ */
+ public int getWidth(
+ ) {
+ return this._width;
+ }
+
+ /**
+ * Returns the value of field 'wrapAlignment'.
+ *
+ * @return the value of field 'WrapAlignment'.
+ */
+ public boolean getWrapAlignment(
+ ) {
+ return this._wrapAlignment;
+ }
+
+ /**
+ * Returns the value of field 'xpos'.
+ *
+ * @return the value of field 'Xpos'.
+ */
+ public int getXpos(
+ ) {
+ return this._xpos;
+ }
+
+ /**
+ * Returns the value of field 'ypos'.
+ *
+ * @return the value of field 'Ypos'.
+ */
+ public int getYpos(
+ ) {
+ return this._ypos;
+ }
+
+ /**
+ * Method hasConsThreshold.
+ *
+ * @return true if at least one ConsThreshold has been added
+ */
+ public boolean hasConsThreshold(
+ ) {
+ return this._has_consThreshold;
+ }
+
+ /**
+ * Method hasConservationSelected.
+ *
+ * @return true if at least one ConservationSelected has been
+ * added
+ */
+ public boolean hasConservationSelected(
+ ) {
+ return this._has_conservationSelected;
+ }
+
+ /**
+ * Method hasFontSize.
+ *
+ * @return true if at least one FontSize has been added
+ */
+ public boolean hasFontSize(
+ ) {
+ return this._has_fontSize;
+ }
+
+ /**
+ * Method hasFontStyle.
+ *
+ * @return true if at least one FontStyle has been added
+ */
+ public boolean hasFontStyle(
+ ) {
+ return this._has_fontStyle;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight(
+ ) {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasPidSelected.
+ *
+ * @return true if at least one PidSelected has been added
+ */
+ public boolean hasPidSelected(
+ ) {
+ return this._has_pidSelected;
+ }
+
+ /**
+ * Method hasPidThreshold.
+ *
+ * @return true if at least one PidThreshold has been added
+ */
+ public boolean hasPidThreshold(
+ ) {
+ return this._has_pidThreshold;
+ }
+
+ /**
+ * Method hasRenderGaps.
+ *
+ * @return true if at least one RenderGaps has been added
+ */
+ public boolean hasRenderGaps(
+ ) {
+ return this._has_renderGaps;
+ }
+
+ /**
+ * Method hasShowAnnotation.
+ *
+ * @return true if at least one ShowAnnotation has been added
+ */
+ public boolean hasShowAnnotation(
+ ) {
+ return this._has_showAnnotation;
+ }
+
+ /**
+ * Method hasShowBoxes.
+ *
+ * @return true if at least one ShowBoxes has been added
+ */
+ public boolean hasShowBoxes(
+ ) {
+ return this._has_showBoxes;
+ }
+
+ /**
+ * Method hasShowColourText.
+ *
+ * @return true if at least one ShowColourText has been added
+ */
+ public boolean hasShowColourText(
+ ) {
+ return this._has_showColourText;
+ }
+
+ /**
+ * Method hasShowConservation.
+ *
+ * @return true if at least one ShowConservation has been added
+ */
+ public boolean hasShowConservation(
+ ) {
+ return this._has_showConservation;
+ }
+
+ /**
+ * Method hasShowFullId.
+ *
+ * @return true if at least one ShowFullId has been added
+ */
+ public boolean hasShowFullId(
+ ) {
+ return this._has_showFullId;
+ }
+
+ /**
+ * Method hasShowIdentity.
+ *
+ * @return true if at least one ShowIdentity has been added
+ */
+ public boolean hasShowIdentity(
+ ) {
+ return this._has_showIdentity;
+ }
+
+ /**
+ * Method hasShowQuality.
+ *
+ * @return true if at least one ShowQuality has been added
+ */
+ public boolean hasShowQuality(
+ ) {
+ return this._has_showQuality;
+ }
+
+ /**
+ * Method hasShowSequenceFeatures.
+ *
+ * @return true if at least one ShowSequenceFeatures has been
+ * added
+ */
+ public boolean hasShowSequenceFeatures(
+ ) {
+ return this._has_showSequenceFeatures;
+ }
+
+ /**
+ * Method hasShowText.
+ *
+ * @return true if at least one ShowText has been added
+ */
+ public boolean hasShowText(
+ ) {
+ return this._has_showText;
+ }
+
+ /**
+ * Method hasStartRes.
+ *
+ * @return true if at least one StartRes has been added
+ */
+ public boolean hasStartRes(
+ ) {
+ return this._has_startRes;
+ }
+
+ /**
+ * Method hasStartSeq.
+ *
+ * @return true if at least one StartSeq has been added
+ */
+ public boolean hasStartSeq(
+ ) {
+ return this._has_startSeq;
+ }
+
+ /**
+ * Method hasWidth.
+ *
+ * @return true if at least one Width has been added
+ */
+ public boolean hasWidth(
+ ) {
+ return this._has_width;
+ }
+
+ /**
+ * Method hasWrapAlignment.
+ *
+ * @return true if at least one WrapAlignment has been added
+ */
+ public boolean hasWrapAlignment(
+ ) {
+ return this._has_wrapAlignment;
+ }
+
+ /**
+ * Method hasXpos.
+ *
+ * @return true if at least one Xpos has been added
+ */
+ public boolean hasXpos(
+ ) {
+ return this._has_xpos;
+ }
+
+ /**
+ * Method hasYpos.
+ *
+ * @return true if at least one Ypos has been added
+ */
+ public boolean hasYpos(
+ ) {
+ return this._has_ypos;
+ }
+
+ /**
+ * Returns the value of field 'conservationSelected'.
+ *
+ * @return the value of field 'ConservationSelected'.
+ */
+ public boolean isConservationSelected(
+ ) {
+ return this._conservationSelected;
+ }
+
+ /**
+ * Returns the value of field 'pidSelected'.
+ *
+ * @return the value of field 'PidSelected'.
+ */
+ public boolean isPidSelected(
+ ) {
+ return this._pidSelected;
+ }
+
+ /**
+ * Returns the value of field 'renderGaps'.
+ *
+ * @return the value of field 'RenderGaps'.
+ */
+ public boolean isRenderGaps(
+ ) {
+ return this._renderGaps;
+ }
+
+ /**
+ * Returns the value of field 'showAnnotation'.
+ *
+ * @return the value of field 'ShowAnnotation'.
+ */
+ public boolean isShowAnnotation(
+ ) {
+ return this._showAnnotation;
+ }
+
+ /**
+ * Returns the value of field 'showBoxes'.
+ *
+ * @return the value of field 'ShowBoxes'.
+ */
+ public boolean isShowBoxes(
+ ) {
+ return this._showBoxes;
+ }
+
+ /**
+ * Returns the value of field 'showColourText'.
+ *
+ * @return the value of field 'ShowColourText'.
+ */
+ public boolean isShowColourText(
+ ) {
+ return this._showColourText;
+ }
+
+ /**
+ * Returns the value of field 'showConservation'.
+ *
+ * @return the value of field 'ShowConservation'.
+ */
+ public boolean isShowConservation(
+ ) {
+ return this._showConservation;
+ }
+
+ /**
+ * Returns the value of field 'showFullId'.
+ *
+ * @return the value of field 'ShowFullId'.
+ */
+ public boolean isShowFullId(
+ ) {
+ return this._showFullId;
+ }
+
+ /**
+ * Returns the value of field 'showIdentity'.
+ *
+ * @return the value of field 'ShowIdentity'.
+ */
+ public boolean isShowIdentity(
+ ) {
+ return this._showIdentity;
+ }
+
+ /**
+ * Returns the value of field 'showQuality'.
+ *
+ * @return the value of field 'ShowQuality'.
+ */
+ public boolean isShowQuality(
+ ) {
+ return this._showQuality;
+ }
+
+ /**
+ * Returns the value of field 'showSequenceFeatures'.
+ *
+ * @return the value of field 'ShowSequenceFeatures'.
+ */
+ public boolean isShowSequenceFeatures(
+ ) {
+ return this._showSequenceFeatures;
+ }
+
+ /**
+ * Returns the value of field 'showText'.
+ *
+ * @return the value of field 'ShowText'.
+ */
+ public boolean isShowText(
+ ) {
+ return this._showText;
+ }
+
+ /**
+ * Method isValid.
+ *
+ * @return true if this object is valid according to the schema
+ */
+ public boolean isValid(
+ ) {
+ try {
+ validate();
+ } catch (org.exolab.castor.xml.ValidationException vex) {
+ return false;
+ }
+ return true;
+ }
+
+ /**
+ * Returns the value of field 'wrapAlignment'.
+ *
+ * @return the value of field 'WrapAlignment'.
+ */
+ public boolean isWrapAlignment(
+ ) {
+ return this._wrapAlignment;
+ }
+
+ /**
+ *
+ *
+ * @param out
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void marshal(
+ final java.io.Writer out)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, out);
+ }
+
+ /**
+ *
+ *
+ * @param handler
+ * @throws java.io.IOException if an IOException occurs during
+ * marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ */
+ public void marshal(
+ final org.xml.sax.ContentHandler handler)
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ Marshaller.marshal(this, handler);
+ }
+
+ /**
+ * Sets the value of field 'bgColour'.
+ *
+ * @param bgColour the value of field 'bgColour'.
+ */
+ public void setBgColour(
+ final java.lang.String bgColour) {
+ this._bgColour = bgColour;
+ }
+
+ /**
+ * Sets the value of field 'consThreshold'.
+ *
+ * @param consThreshold the value of field 'consThreshold'.
+ */
+ public void setConsThreshold(
+ final int consThreshold) {
+ this._consThreshold = consThreshold;
+ this._has_consThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'conservationSelected'.
+ *
+ * @param conservationSelected the value of field
+ * 'conservationSelected'.
+ */
+ public void setConservationSelected(
+ final boolean conservationSelected) {
+ this._conservationSelected = conservationSelected;
+ this._has_conservationSelected = true;
+ }
+
+ /**
+ * Sets the value of field 'fontName'.
+ *
+ * @param fontName the value of field 'fontName'.
+ */
+ public void setFontName(
+ final java.lang.String fontName) {
+ this._fontName = fontName;
+ }
+
+ /**
+ * Sets the value of field 'fontSize'.
+ *
+ * @param fontSize the value of field 'fontSize'.
+ */
+ public void setFontSize(
+ final int fontSize) {
+ this._fontSize = fontSize;
+ this._has_fontSize = true;
+ }
+
+ /**
+ * Sets the value of field 'fontStyle'.
+ *
+ * @param fontStyle the value of field 'fontStyle'.
+ */
+ public void setFontStyle(
+ final int fontStyle) {
+ this._fontStyle = fontStyle;
+ this._has_fontStyle = true;
+ }
+
+ /**
+ * Sets the value of field 'height'.
+ *
+ * @param height the value of field 'height'.
+ */
+ public void setHeight(
+ final int height) {
+ this._height = height;
+ this._has_height = true;
+ }
+
+ /**
+ * Sets the value of field 'pidSelected'.
+ *
+ * @param pidSelected the value of field 'pidSelected'.
+ */
+ public void setPidSelected(
+ final boolean pidSelected) {
+ this._pidSelected = pidSelected;
+ this._has_pidSelected = true;
+ }
+
+ /**
+ * Sets the value of field 'pidThreshold'.
+ *
+ * @param pidThreshold the value of field 'pidThreshold'.
+ */
+ public void setPidThreshold(
+ final int pidThreshold) {
+ this._pidThreshold = pidThreshold;
+ this._has_pidThreshold = true;
+ }
+
+ /**
+ * Sets the value of field 'renderGaps'.
+ *
+ * @param renderGaps the value of field 'renderGaps'.
+ */
+ public void setRenderGaps(
+ final boolean renderGaps) {
+ this._renderGaps = renderGaps;
+ this._has_renderGaps = true;
+ }
+
+ /**
+ * Sets the value of field 'showAnnotation'.
+ *
+ * @param showAnnotation the value of field 'showAnnotation'.
+ */
+ public void setShowAnnotation(
+ final boolean showAnnotation) {
+ this._showAnnotation = showAnnotation;
+ this._has_showAnnotation = true;
+ }
+
+ /**
+ * Sets the value of field 'showBoxes'.
+ *
+ * @param showBoxes the value of field 'showBoxes'.
+ */
+ public void setShowBoxes(
+ final boolean showBoxes) {
+ this._showBoxes = showBoxes;
+ this._has_showBoxes = true;
+ }
+
+ /**
+ * Sets the value of field 'showColourText'.
+ *
+ * @param showColourText the value of field 'showColourText'.
+ */
+ public void setShowColourText(
+ final boolean showColourText) {
+ this._showColourText = showColourText;
+ this._has_showColourText = true;
+ }
+
+ /**
+ * Sets the value of field 'showConservation'.
+ *
+ * @param showConservation the value of field 'showConservation'
+ */
+ public void setShowConservation(
+ final boolean showConservation) {
+ this._showConservation = showConservation;
+ this._has_showConservation = true;
+ }
+
+ /**
+ * Sets the value of field 'showFullId'.
+ *
+ * @param showFullId the value of field 'showFullId'.
+ */
+ public void setShowFullId(
+ final boolean showFullId) {
+ this._showFullId = showFullId;
+ this._has_showFullId = true;
+ }
+
+ /**
+ * Sets the value of field 'showIdentity'.
+ *
+ * @param showIdentity the value of field 'showIdentity'.
+ */
+ public void setShowIdentity(
+ final boolean showIdentity) {
+ this._showIdentity = showIdentity;
+ this._has_showIdentity = true;
+ }
+
+ /**
+ * Sets the value of field 'showQuality'.
+ *
+ * @param showQuality the value of field 'showQuality'.
+ */
+ public void setShowQuality(
+ final boolean showQuality) {
+ this._showQuality = showQuality;
+ this._has_showQuality = true;
+ }
+
+ /**
+ * Sets the value of field 'showSequenceFeatures'.
+ *
+ * @param showSequenceFeatures the value of field
+ * 'showSequenceFeatures'.
+ */
+ public void setShowSequenceFeatures(
+ final boolean showSequenceFeatures) {
+ this._showSequenceFeatures = showSequenceFeatures;
+ this._has_showSequenceFeatures = true;
+ }
+
+ /**
+ * Sets the value of field 'showText'.
+ *
+ * @param showText the value of field 'showText'.
+ */
+ public void setShowText(
+ final boolean showText) {
+ this._showText = showText;
+ this._has_showText = true;
+ }
+
+ /**
+ * Sets the value of field 'startRes'.
+ *
+ * @param startRes the value of field 'startRes'.
+ */
+ public void setStartRes(
+ final int startRes) {
+ this._startRes = startRes;
+ this._has_startRes = true;
+ }
+
+ /**
+ * Sets the value of field 'startSeq'.
+ *
+ * @param startSeq the value of field 'startSeq'.
+ */
+ public void setStartSeq(
+ final int startSeq) {
+ this._startSeq = startSeq;
+ this._has_startSeq = true;
+ }
+
+ /**
+ * Sets the value of field 'title'.
+ *
+ * @param title the value of field 'title'.
+ */
+ public void setTitle(
+ final java.lang.String title) {
+ this._title = title;
+ }
+
+ /**
+ * Sets the value of field 'width'.
+ *
+ * @param width the value of field 'width'.
+ */
+ public void setWidth(
+ final int width) {
+ this._width = width;
+ this._has_width = true;
+ }
+
+ /**
+ * Sets the value of field 'wrapAlignment'.
+ *
+ * @param wrapAlignment the value of field 'wrapAlignment'.
+ */
+ public void setWrapAlignment(
+ final boolean wrapAlignment) {
+ this._wrapAlignment = wrapAlignment;
+ this._has_wrapAlignment = true;
+ }
+
+ /**
+ * Sets the value of field 'xpos'.
+ *
+ * @param xpos the value of field 'xpos'.
+ */
+ public void setXpos(
+ final int xpos) {
+ this._xpos = xpos;
+ this._has_xpos = true;
+ }
+
+ /**
+ * Sets the value of field 'ypos'.
+ *
+ * @param ypos the value of field 'ypos'.
+ */
+ public void setYpos(
+ final int ypos) {
+ this._ypos = ypos;
+ this._has_ypos = true;
+ }
+
+ /**
+ * Method unmarshal.
+ *
+ * @param reader
+ * @throws org.exolab.castor.xml.MarshalException if object is
+ * null or if any SAXException is thrown during marshaling
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ * @return the unmarshaled jalview.binding.Viewport
+ */
+ public static jalview.binding.Viewport unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.Viewport.class, reader);
+ }
+
+ /**
+ *
+ *
+ * @throws org.exolab.castor.xml.ValidationException if this
+ * object is an invalid instance according to the schema
+ */
+ public void validate(
+ )
+ throws org.exolab.castor.xml.ValidationException {
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+ validator.validate(this);
+ }
+
+}
git://source.jalview.org / jalview.git / commitdiff