<xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
</xs:complexType>
- <xs:element name="SequenceSet">
+ <xs:complexType name="mapListType">
+ <xs:annotation>
+ <xs:documentation>
+ developed after mapRangeType from http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes
+ </xs:documentation>
+ <xs:documentation>
+ This effectively represents a java.util.MapList object
+ </xs:documentation>
+ </xs:annotation>
+ <xs:sequence>
+ <xs:element name="mapListFrom" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> a region from start to end inclusive</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:attribute name="start" type="xs:int" use="required"/>
+ <xs:attribute name="end" type="xs:int" use="required"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="mapListTo" minOccurs="0" maxOccurs="unbounded">
+ <xs:annotation>
+ <xs:documentation> a region from start to end inclusive</xs:documentation>
+ </xs:annotation>
+ <xs:complexType>
+ <xs:attribute name="start" type="xs:int" use="required"/>
+ <xs:attribute name="end" type="xs:int" use="required"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="mapFromUnit" type="xs:positiveInteger" use="required">
+ <xs:annotation>
+ <xs:documentation>number of dictionary symbol widths involved in each
+ mapped position on this sequence (for example, 3 for a dna sequence exon
+ region that is being mapped to a protein sequence). This is optional,
+ since the unit can be usually be inferred from the dictionary type of
+ each sequence involved in the mapping. </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ <xs:attribute name="mapToUnit" type="xs:positiveInteger" use="required">
+ <xs:annotation>
+ <xs:documentation>number of dictionary symbol widths involved in each
+ mapped position on this sequence (for example, 3 for a dna sequence exon
+ region that is being mapped to a protein sequence). This is optional,
+ since the unit can be usually be inferred from the dictionary type of
+ each sequence involved in the mapping. </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:complexType>
+ <xs:element name="Mapping">
+ <xs:complexType>
+ <xs:annotation>
+ <xs:documentation>
+ Represent the jalview.datamodel.Mapping object - it also provides
+ a way of storing sequences that are mapped 'to' without adding them
+ to the sequence set (which will mean they are then added to the alignment too).
+ </xs:documentation>
+ </xs:annotation>
+ <xs:complexContent>
+ <xs:extension base="vamsas:mapListType">
+ <xs:sequence>
+ <xs:choice minOccurs="0" maxOccurs="1">
+ <xs:element ref="vamsas:Sequence"/>
+ <xs:element name="dseqFor">
+ <xs:simpleType>
+ <xs:restriction base="xs:string">
+ <xs:annotation>
+ <xs:documentation>The sequence whose dataset sequence is to be referenced here</xs:documentation>
+ </xs:annotation>
+ </xs:restriction>
+ </xs:simpleType>
+ </xs:element>
+ </xs:choice>
+ </xs:sequence>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="AlcodonFrame">
<xs:complexType>
<xs:sequence>
- <xs:element name="Sequence" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="alcodon" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
- <xs:complexContent>
- <xs:extension base="vamsas:SequenceType">
- <xs:sequence>
- <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
- <xs:complexType>
- <xs:attribute name="source" type="xs:string"/>
- <xs:attribute name="version" type="xs:string"/>
- <xs:attribute name="accessionId" type="xs:string"/>
- </xs:complexType>
- </xs:element>
- </xs:sequence>
- </xs:extension>
- </xs:complexContent>
+ <xs:attribute name="pos1" type="xs:integer"/>
+ <xs:attribute name="pos2" type="xs:integer"/>
+ <xs:attribute name="pos3" type="xs:integer"/>
</xs:complexType>
</xs:element>
- <xs:element name="Annotation" minOccurs="0" maxOccurs="unbounded">
+ <xs:element name="alcodMap" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:sequence>
- <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
- <xs:element name="label" type="xs:string"/>
- <xs:element name="description" type="xs:string" minOccurs="0"/>
- <xs:element name="thresholdLine" minOccurs="0">
- <xs:complexType>
- <xs:attribute name="label" type="xs:string"/>
- <xs:attribute name="value" type="xs:float"/>
- <xs:attribute name="colour" type="xs:int"/>
- </xs:complexType>
+ <xs:element ref="vamsas:Mapping" maxOccurs="1" minOccurs="1">
+ <xs:annotation>
+ <xs:documentation>
+ a Mapping entry and an associated protein sequence
+ </xs:documentation>
+ </xs:annotation>
</xs:element>
</xs:sequence>
- <xs:attribute name="graph" type="xs:boolean" use="required"/>
- <xs:attribute name="graphType" type="xs:int" use="optional"/>
- <xs:attribute name="sequenceRef" type="xs:string" use="optional"/>
- <xs:attribute name="graphColour" type="xs:int" use="optional"/>
- <xs:attribute name="graphGroup" type="xs:int" use="optional"/>
- <xs:attribute name="id" type="xs:string" use="optional"/>
- <xs:attribute name="scoreOnly" type="xs:boolean" use="optional" default="false"/>
- <xs:attribute name="score" type="xs:double" use="optional"/>
- <xs:attribute name="visible" type="xs:boolean" use="optional"/>
+ <xs:attribute name="dnasq" type="xs:string" use="required">
+ <xs:annotation>
+ <xs:documentation>
+ internal jalview id for the dnasq for this mapping.
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:complexType>
+
</xs:element>
+
+ </xs:sequence>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="Sequence">
+ <xs:complexType>
+ <xs:complexContent>
+ <xs:extension base="vamsas:SequenceType">
+ <xs:sequence>
+ <xs:element name="DBRef" minOccurs="0" maxOccurs="unbounded">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="vamsas:Mapping" minOccurs="0" maxOccurs="1"/>
+ </xs:sequence>
+ <xs:attribute name="source" type="xs:string"/>
+ <xs:attribute name="version" type="xs:string"/>
+ <xs:attribute name="accessionId" type="xs:string"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="dsseqid" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ dataset sequence id for this sequence. Will be created as union of sequences.
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
+ </xs:extension>
+ </xs:complexContent>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="Annotation">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element name="label" type="xs:string"/>
+ <xs:element name="description" type="xs:string" minOccurs="0"/>
+ <xs:element name="thresholdLine" minOccurs="0">
+ <xs:complexType>
+ <xs:attribute name="label" type="xs:string"/>
+ <xs:attribute name="value" type="xs:float"/>
+ <xs:attribute name="colour" type="xs:int"/>
+ </xs:complexType>
+ </xs:element>
+ </xs:sequence>
+ <xs:attribute name="graph" type="xs:boolean" use="required"/>
+ <xs:attribute name="graphType" type="xs:int" use="optional"/>
+ <xs:attribute name="sequenceRef" type="xs:string" use="optional"/>
+ <xs:attribute name="graphColour" type="xs:int" use="optional"/>
+ <xs:attribute name="graphGroup" type="xs:int" use="optional"/>
+ <xs:attribute name="id" type="xs:string" use="optional"/>
+ <xs:attribute name="scoreOnly" type="xs:boolean" use="optional" default="false"/>
+ <xs:attribute name="score" type="xs:double" use="optional"/>
+ <xs:attribute name="visible" type="xs:boolean" use="optional"/>
+ </xs:complexType>
+ </xs:element>
+ <xs:element name="SequenceSet">
+ <xs:complexType>
+ <xs:sequence>
+ <xs:element ref="vamsas:Sequence" minOccurs="0" maxOccurs="unbounded"/>
+ <xs:element ref="vamsas:Annotation" minOccurs="0" maxOccurs="unbounded"/>
<xs:element name="sequenceSetProperties" minOccurs="0" maxOccurs="unbounded">
<xs:complexType>
<xs:attribute name="key" type="xs:string"/>
<xs:attribute name="value" type="xs:string"/>
</xs:complexType>
</xs:element>
+ <xs:element ref="vamsas:AlcodonFrame" minOccurs="0" maxOccurs="unbounded"/>
</xs:sequence>
<xs:attribute name="gapChar" type="xs:string" use="required"/>
+ <xs:attribute name="datasetId" type="xs:string" use="optional">
+ <xs:annotation>
+ <xs:documentation>
+ reference to set where jalview will gather the dataset sequences for all sequences in the set.
+ </xs:documentation>
+ </xs:annotation>
+ </xs:attribute>
</xs:complexType>
</xs:element>
<xs:element name="annotationElement">
-#Sun Jun 17 14:17:08 BST 2007\r
-jalview.schemabinding.version2.AnnotationColours=jalview.schemabinding.version2.descriptors.AnnotationColoursDescriptor\r
-jalview.schemabinding.version2.Sequence=jalview.schemabinding.version2.descriptors.SequenceDescriptor\r
-jalview.schemabinding.version2.SequenceType=jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor\r
-jalview.schemabinding.version2.PdbentryItem=jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor\r
-jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor\r
+#Wed Aug 29 14:54:33 BST 2007\r
jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor\r
-jalview.schemabinding.version2.Pdbentry=jalview.schemabinding.version2.descriptors.PdbentryDescriptor\r
-jalview.schemabinding.version2.AnnotationElement=jalview.schemabinding.version2.descriptors.AnnotationElementDescriptor\r
+jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor\r
+jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor\r
+jalview.schemabinding.version2.Tree=jalview.schemabinding.version2.descriptors.TreeDescriptor\r
+jalview.schemabinding.version2.JalviewModel=jalview.schemabinding.version2.descriptors.JalviewModelDescriptor\r
+jalview.schemabinding.version2.SequenceType=jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor\r
jalview.schemabinding.version2.OtherData=jalview.schemabinding.version2.descriptors.OtherDataDescriptor\r
-jalview.schemabinding.version2.VamsasModel=jalview.schemabinding.version2.descriptors.VamsasModelDescriptor\r
-jalview.schemabinding.version2.VAMSAS=jalview.schemabinding.version2.descriptors.VAMSASDescriptor\r
-jalview.schemabinding.version2.JalviewUserColours=jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor\r
-jalview.schemabinding.version2.JalviewModelSequence=jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor\r
-jalview.schemabinding.version2.Features=jalview.schemabinding.version2.descriptors.FeaturesDescriptor\r
+jalview.schemabinding.version2.Setting=jalview.schemabinding.version2.descriptors.SettingDescriptor\r
+jalview.schemabinding.version2.AlcodonFrame=jalview.schemabinding.version2.descriptors.AlcodonFrameDescriptor\r
+jalview.schemabinding.version2.AnnotationElement=jalview.schemabinding.version2.descriptors.AnnotationElementDescriptor\r
jalview.schemabinding.version2.SequenceSet=jalview.schemabinding.version2.descriptors.SequenceSetDescriptor\r
-jalview.schemabinding.version2.DBRef=jalview.schemabinding.version2.descriptors.DBRefDescriptor\r
-jalview.schemabinding.version2.Colour=jalview.schemabinding.version2.descriptors.ColourDescriptor\r
-jalview.schemabinding.version2.Feature=jalview.schemabinding.version2.descriptors.FeatureDescriptor\r
jalview.schemabinding.version2.Viewport=jalview.schemabinding.version2.descriptors.ViewportDescriptor\r
-jalview.schemabinding.version2.JalviewModel=jalview.schemabinding.version2.descriptors.JalviewModelDescriptor\r
-jalview.schemabinding.version2.JGroup=jalview.schemabinding.version2.descriptors.JGroupDescriptor\r
-jalview.schemabinding.version2.FeatureSettings=jalview.schemabinding.version2.descriptors.FeatureSettingsDescriptor\r
+jalview.schemabinding.version2.MapListType=jalview.schemabinding.version2.descriptors.MapListTypeDescriptor\r
+jalview.schemabinding.version2.Property=jalview.schemabinding.version2.descriptors.PropertyDescriptor\r
jalview.schemabinding.version2.UserColourScheme=jalview.schemabinding.version2.descriptors.UserColourSchemeDescriptor\r
+jalview.schemabinding.version2.DBRef=jalview.schemabinding.version2.descriptors.DBRefDescriptor\r
+jalview.schemabinding.version2.AlcodMap=jalview.schemabinding.version2.descriptors.AlcodMapDescriptor\r
+jalview.schemabinding.version2.Annotation=jalview.schemabinding.version2.descriptors.AnnotationDescriptor\r
+jalview.schemabinding.version2.JSeq=jalview.schemabinding.version2.descriptors.JSeqDescriptor\r
+jalview.schemabinding.version2.Sequence=jalview.schemabinding.version2.descriptors.SequenceDescriptor\r
+jalview.schemabinding.version2.Alcodon=jalview.schemabinding.version2.descriptors.AlcodonDescriptor\r
+jalview.schemabinding.version2.AnnotationColours=jalview.schemabinding.version2.descriptors.AnnotationColoursDescriptor\r
jalview.schemabinding.version2.Pdbids=jalview.schemabinding.version2.descriptors.PdbidsDescriptor\r
-jalview.schemabinding.version2.HiddenColumns=jalview.schemabinding.version2.descriptors.HiddenColumnsDescriptor\r
+jalview.schemabinding.version2.Mapping=jalview.schemabinding.version2.descriptors.MappingDescriptor\r
+jalview.schemabinding.version2.MappingChoice=jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor\r
jalview.schemabinding.version2.Group=jalview.schemabinding.version2.descriptors.GroupDescriptor\r
-jalview.schemabinding.version2.Tree=jalview.schemabinding.version2.descriptors.TreeDescriptor\r
-jalview.schemabinding.version2.Setting=jalview.schemabinding.version2.descriptors.SettingDescriptor\r
+jalview.schemabinding.version2.Feature=jalview.schemabinding.version2.descriptors.FeatureDescriptor\r
+jalview.schemabinding.version2.JalviewModelSequence=jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor\r
jalview.schemabinding.version2.UserColours=jalview.schemabinding.version2.descriptors.UserColoursDescriptor\r
-jalview.schemabinding.version2.JSeq=jalview.schemabinding.version2.descriptors.JSeqDescriptor\r
-jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor\r
-jalview.schemabinding.version2.Property=jalview.schemabinding.version2.descriptors.PropertyDescriptor\r
-jalview.schemabinding.version2.Annotation=jalview.schemabinding.version2.descriptors.AnnotationDescriptor\r
+jalview.schemabinding.version2.Colour=jalview.schemabinding.version2.descriptors.ColourDescriptor\r
+jalview.schemabinding.version2.MapListFrom=jalview.schemabinding.version2.descriptors.MapListFromDescriptor\r
+jalview.schemabinding.version2.PdbentryItem=jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor\r
+jalview.schemabinding.version2.FeatureSettings=jalview.schemabinding.version2.descriptors.FeatureSettingsDescriptor\r
+jalview.schemabinding.version2.JGroup=jalview.schemabinding.version2.descriptors.JGroupDescriptor\r
+jalview.schemabinding.version2.MapListTo=jalview.schemabinding.version2.descriptors.MapListToDescriptor\r
+jalview.schemabinding.version2.JalviewUserColours=jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor\r
+jalview.schemabinding.version2.VamsasModel=jalview.schemabinding.version2.descriptors.VamsasModelDescriptor\r
+jalview.schemabinding.version2.Pdbentry=jalview.schemabinding.version2.descriptors.PdbentryDescriptor\r
+jalview.schemabinding.version2.HiddenColumns=jalview.schemabinding.version2.descriptors.HiddenColumnsDescriptor\r
+jalview.schemabinding.version2.DseqFor=jalview.schemabinding.version2.descriptors.DseqForDescriptor\r
+jalview.schemabinding.version2.Features=jalview.schemabinding.version2.descriptors.FeaturesDescriptor\r
+jalview.schemabinding.version2.VAMSAS=jalview.schemabinding.version2.descriptors.VAMSASDescriptor\r
+jalview.schemabinding.version2.MappingChoiceItem=jalview.schemabinding.version2.descriptors.MappingChoiceItemDescriptor\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+\r
+/**\r
+ * Class AlcodMap.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class AlcodMap implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * internal jalview id for the dnasq for this mapping.\r
+ * \r
+ */\r
+ private java.lang.String _dnasq;\r
+\r
+ /**\r
+ * a Mapping entry and an associated protein sequence\r
+ * \r
+ */\r
+ private jalview.schemabinding.version2.Mapping _mapping;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AlcodMap() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Returns the value of field 'dnasq'. The field 'dnasq' has\r
+ * the following description: internal jalview id for the dnasq\r
+ * for this mapping.\r
+ * \r
+ * \r
+ * @return the value of field 'Dnasq'.\r
+ */\r
+ public java.lang.String getDnasq(\r
+ ) {\r
+ return this._dnasq;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'mapping'. The field 'mapping'\r
+ * has the following description: a Mapping entry and an\r
+ * associated protein sequence\r
+ * \r
+ * \r
+ * @return the value of field 'Mapping'.\r
+ */\r
+ public jalview.schemabinding.version2.Mapping getMapping(\r
+ ) {\r
+ return this._mapping;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
+ * \r
+ * @return true if this object is valid according to the schema\r
+ */\r
+ public boolean isValid(\r
+ ) {\r
+ try {\r
+ validate();\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, out);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, handler);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'dnasq'. The field 'dnasq' has the\r
+ * following description: internal jalview id for the dnasq for\r
+ * this mapping.\r
+ * \r
+ * \r
+ * @param dnasq the value of field 'dnasq'.\r
+ */\r
+ public void setDnasq(\r
+ final java.lang.String dnasq) {\r
+ this._dnasq = dnasq;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'mapping'. The field 'mapping' has\r
+ * the following description: a Mapping entry and an associated\r
+ * protein sequence\r
+ * \r
+ * \r
+ * @param mapping the value of field 'mapping'.\r
+ */\r
+ public void setMapping(\r
+ final jalview.schemabinding.version2.Mapping mapping) {\r
+ this._mapping = mapping;\r
+ }\r
+\r
+ /**\r
+ * Method unmarshal.\r
+ * \r
+ * @param reader\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.AlcodMap\r
+ */\r
+ public static jalview.schemabinding.version2.AlcodMap unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.AlcodMap) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodMap.class, reader);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+\r
+/**\r
+ * Class Alcodon.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class Alcodon implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _pos1.\r
+ */\r
+ private long _pos1;\r
+\r
+ /**\r
+ * keeps track of state for field: _pos1\r
+ */\r
+ private boolean _has_pos1;\r
+\r
+ /**\r
+ * Field _pos2.\r
+ */\r
+ private long _pos2;\r
+\r
+ /**\r
+ * keeps track of state for field: _pos2\r
+ */\r
+ private boolean _has_pos2;\r
+\r
+ /**\r
+ * Field _pos3.\r
+ */\r
+ private long _pos3;\r
+\r
+ /**\r
+ * keeps track of state for field: _pos3\r
+ */\r
+ private boolean _has_pos3;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Alcodon() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ */\r
+ public void deletePos1(\r
+ ) {\r
+ this._has_pos1= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deletePos2(\r
+ ) {\r
+ this._has_pos2= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deletePos3(\r
+ ) {\r
+ this._has_pos3= false;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'pos1'.\r
+ * \r
+ * @return the value of field 'Pos1'.\r
+ */\r
+ public long getPos1(\r
+ ) {\r
+ return this._pos1;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'pos2'.\r
+ * \r
+ * @return the value of field 'Pos2'.\r
+ */\r
+ public long getPos2(\r
+ ) {\r
+ return this._pos2;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'pos3'.\r
+ * \r
+ * @return the value of field 'Pos3'.\r
+ */\r
+ public long getPos3(\r
+ ) {\r
+ return this._pos3;\r
+ }\r
+\r
+ /**\r
+ * Method hasPos1.\r
+ * \r
+ * @return true if at least one Pos1 has been added\r
+ */\r
+ public boolean hasPos1(\r
+ ) {\r
+ return this._has_pos1;\r
+ }\r
+\r
+ /**\r
+ * Method hasPos2.\r
+ * \r
+ * @return true if at least one Pos2 has been added\r
+ */\r
+ public boolean hasPos2(\r
+ ) {\r
+ return this._has_pos2;\r
+ }\r
+\r
+ /**\r
+ * Method hasPos3.\r
+ * \r
+ * @return true if at least one Pos3 has been added\r
+ */\r
+ public boolean hasPos3(\r
+ ) {\r
+ return this._has_pos3;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
+ * \r
+ * @return true if this object is valid according to the schema\r
+ */\r
+ public boolean isValid(\r
+ ) {\r
+ try {\r
+ validate();\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, out);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, handler);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'pos1'.\r
+ * \r
+ * @param pos1 the value of field 'pos1'.\r
+ */\r
+ public void setPos1(\r
+ final long pos1) {\r
+ this._pos1 = pos1;\r
+ this._has_pos1 = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'pos2'.\r
+ * \r
+ * @param pos2 the value of field 'pos2'.\r
+ */\r
+ public void setPos2(\r
+ final long pos2) {\r
+ this._pos2 = pos2;\r
+ this._has_pos2 = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'pos3'.\r
+ * \r
+ * @param pos3 the value of field 'pos3'.\r
+ */\r
+ public void setPos3(\r
+ final long pos3) {\r
+ this._pos3 = pos3;\r
+ this._has_pos3 = true;\r
+ }\r
+\r
+ /**\r
+ * Method unmarshal.\r
+ * \r
+ * @param reader\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled jalview.schemabinding.version2.Alcodo\r
+ */\r
+ public static jalview.schemabinding.version2.Alcodon unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.Alcodon) Unmarshaller.unmarshal(jalview.schemabinding.version2.Alcodon.class, reader);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+\r
+/**\r
+ * Class AlcodonFrame.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class AlcodonFrame implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _alcodonList.\r
+ */\r
+ private java.util.Vector _alcodonList;\r
+\r
+ /**\r
+ * Field _alcodMapList.\r
+ */\r
+ private java.util.Vector _alcodMapList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AlcodonFrame() {\r
+ super();\r
+ this._alcodonList = new java.util.Vector();\r
+ this._alcodMapList = new java.util.Vector();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAlcodMap\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addAlcodMap(\r
+ final jalview.schemabinding.version2.AlcodMap vAlcodMap)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._alcodMapList.addElement(vAlcodMap);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAlcodMap\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addAlcodMap(\r
+ final int index,\r
+ final jalview.schemabinding.version2.AlcodMap vAlcodMap)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._alcodMapList.add(index, vAlcodMap);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAlcodon\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addAlcodon(\r
+ final jalview.schemabinding.version2.Alcodon vAlcodon)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._alcodonList.addElement(vAlcodon);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAlcodon\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addAlcodon(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Alcodon vAlcodon)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._alcodonList.add(index, vAlcodon);\r
+ }\r
+\r
+ /**\r
+ * Method enumerateAlcodMap.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.AlcodMap elements\r
+ */\r
+ public java.util.Enumeration enumerateAlcodMap(\r
+ ) {\r
+ return this._alcodMapList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateAlcodon.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.Alcodon elements\r
+ */\r
+ public java.util.Enumeration enumerateAlcodon(\r
+ ) {\r
+ return this._alcodonList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodMap.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.AlcodMap at the given index\r
+ */\r
+ public jalview.schemabinding.version2.AlcodMap getAlcodMap(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._alcodMapList.size()) {\r
+ throw new IndexOutOfBoundsException("getAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.AlcodMap) _alcodMapList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodMap.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.AlcodMap[] getAlcodMap(\r
+ ) {\r
+ jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0];\r
+ return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodMapCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getAlcodMapCount(\r
+ ) {\r
+ return this._alcodMapList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodon.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.Alcodon at the given index\r
+ */\r
+ public jalview.schemabinding.version2.Alcodon getAlcodon(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._alcodonList.size()) {\r
+ throw new IndexOutOfBoundsException("getAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodon.Returns the contents of the collection in\r
+ * an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.Alcodon[] getAlcodon(\r
+ ) {\r
+ jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0];\r
+ return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodonCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getAlcodonCount(\r
+ ) {\r
+ return this._alcodonList.size();\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
+ * \r
+ * @return true if this object is valid according to the schema\r
+ */\r
+ public boolean isValid(\r
+ ) {\r
+ try {\r
+ validate();\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, out);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, handler);\r
+ }\r
+\r
+ /**\r
+ * Method removeAlcodMap.\r
+ * \r
+ * @param vAlcodMap\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeAlcodMap(\r
+ final jalview.schemabinding.version2.AlcodMap vAlcodMap) {\r
+ boolean removed = _alcodMapList.remove(vAlcodMap);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeAlcodMapAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._alcodMapList.remove(index);\r
+ return (jalview.schemabinding.version2.AlcodMap) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeAlcodon.\r
+ * \r
+ * @param vAlcodon\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeAlcodon(\r
+ final jalview.schemabinding.version2.Alcodon vAlcodon) {\r
+ boolean removed = _alcodonList.remove(vAlcodon);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeAlcodonAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.Alcodon removeAlcodonAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._alcodonList.remove(index);\r
+ return (jalview.schemabinding.version2.Alcodon) obj;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllAlcodMap(\r
+ ) {\r
+ this._alcodMapList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllAlcodon(\r
+ ) {\r
+ this._alcodonList.clear();\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAlcodMap\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setAlcodMap(\r
+ final int index,\r
+ final jalview.schemabinding.version2.AlcodMap vAlcodMap)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._alcodMapList.size()) {\r
+ throw new IndexOutOfBoundsException("setAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._alcodMapList.set(index, vAlcodMap);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAlcodMapArray\r
+ */\r
+ public void setAlcodMap(\r
+ final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray) {\r
+ //-- copy array\r
+ _alcodMapList.clear();\r
+ \r
+ for (int i = 0; i < vAlcodMapArray.length; i++) {\r
+ this._alcodMapList.add(vAlcodMapArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAlcodon\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setAlcodon(\r
+ final int index,\r
+ final jalview.schemabinding.version2.Alcodon vAlcodon)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._alcodonList.size()) {\r
+ throw new IndexOutOfBoundsException("setAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._alcodonList.set(index, vAlcodon);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAlcodonArray\r
+ */\r
+ public void setAlcodon(\r
+ final jalview.schemabinding.version2.Alcodon[] vAlcodonArray) {\r
+ //-- copy array\r
+ _alcodonList.clear();\r
+ \r
+ for (int i = 0; i < vAlcodonArray.length; i++) {\r
+ this._alcodonList.add(vAlcodonArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Method unmarshal.\r
+ * \r
+ * @param reader\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.AlcodonFrame\r
+ */\r
+ public static jalview.schemabinding.version2.AlcodonFrame unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodonFrame.class, reader);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ }\r
+\r
+}\r
*/\r
private java.lang.String _accessionId;\r
\r
+ /**\r
+ * Field _mapping.\r
+ */\r
+ private jalview.schemabinding.version2.Mapping _mapping;\r
+\r
\r
//----------------/\r
//- Constructors -/\r
}\r
\r
/**\r
+ * Returns the value of field 'mapping'.\r
+ * \r
+ * @return the value of field 'Mapping'.\r
+ */\r
+ public jalview.schemabinding.version2.Mapping getMapping(\r
+ ) {\r
+ return this._mapping;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'source'.\r
* \r
* @return the value of field 'Source'.\r
}\r
\r
/**\r
+ * Sets the value of field 'mapping'.\r
+ * \r
+ * @param mapping the value of field 'mapping'.\r
+ */\r
+ public void setMapping(\r
+ final jalview.schemabinding.version2.Mapping mapping) {\r
+ this._mapping = mapping;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'source'.\r
* \r
* @param source the value of field 'source'.\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+\r
+/**\r
+ * a region from start to end inclusive\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class MapListFrom implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _start.\r
+ */\r
+ private int _start;\r
+\r
+ /**\r
+ * keeps track of state for field: _start\r
+ */\r
+ private boolean _has_start;\r
+\r
+ /**\r
+ * Field _end.\r
+ */\r
+ private int _end;\r
+\r
+ /**\r
+ * keeps track of state for field: _end\r
+ */\r
+ private boolean _has_end;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public MapListFrom() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ */\r
+ public void deleteEnd(\r
+ ) {\r
+ this._has_end= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteStart(\r
+ ) {\r
+ this._has_start= false;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'end'.\r
+ * \r
+ * @return the value of field 'End'.\r
+ */\r
+ public int getEnd(\r
+ ) {\r
+ return this._end;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'start'.\r
+ * \r
+ * @return the value of field 'Start'.\r
+ */\r
+ public int getStart(\r
+ ) {\r
+ return this._start;\r
+ }\r
+\r
+ /**\r
+ * Method hasEnd.\r
+ * \r
+ * @return true if at least one End has been added\r
+ */\r
+ public boolean hasEnd(\r
+ ) {\r
+ return this._has_end;\r
+ }\r
+\r
+ /**\r
+ * Method hasStart.\r
+ * \r
+ * @return true if at least one Start has been added\r
+ */\r
+ public boolean hasStart(\r
+ ) {\r
+ return this._has_start;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
+ * \r
+ * @return true if this object is valid according to the schema\r
+ */\r
+ public boolean isValid(\r
+ ) {\r
+ try {\r
+ validate();\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, out);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, handler);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'end'.\r
+ * \r
+ * @param end the value of field 'end'.\r
+ */\r
+ public void setEnd(\r
+ final int end) {\r
+ this._end = end;\r
+ this._has_end = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'start'.\r
+ * \r
+ * @param start the value of field 'start'.\r
+ */\r
+ public void setStart(\r
+ final int start) {\r
+ this._start = start;\r
+ this._has_start = true;\r
+ }\r
+\r
+ /**\r
+ * Method unmarshal.\r
+ * \r
+ * @param reader\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.MapListFrom\r
+ */\r
+ public static jalview.schemabinding.version2.MapListFrom unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.MapListFrom) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListFrom.class, reader);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+\r
+/**\r
+ * a region from start to end inclusive\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class MapListTo implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _start.\r
+ */\r
+ private int _start;\r
+\r
+ /**\r
+ * keeps track of state for field: _start\r
+ */\r
+ private boolean _has_start;\r
+\r
+ /**\r
+ * Field _end.\r
+ */\r
+ private int _end;\r
+\r
+ /**\r
+ * keeps track of state for field: _end\r
+ */\r
+ private boolean _has_end;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public MapListTo() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ */\r
+ public void deleteEnd(\r
+ ) {\r
+ this._has_end= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteStart(\r
+ ) {\r
+ this._has_start= false;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'end'.\r
+ * \r
+ * @return the value of field 'End'.\r
+ */\r
+ public int getEnd(\r
+ ) {\r
+ return this._end;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'start'.\r
+ * \r
+ * @return the value of field 'Start'.\r
+ */\r
+ public int getStart(\r
+ ) {\r
+ return this._start;\r
+ }\r
+\r
+ /**\r
+ * Method hasEnd.\r
+ * \r
+ * @return true if at least one End has been added\r
+ */\r
+ public boolean hasEnd(\r
+ ) {\r
+ return this._has_end;\r
+ }\r
+\r
+ /**\r
+ * Method hasStart.\r
+ * \r
+ * @return true if at least one Start has been added\r
+ */\r
+ public boolean hasStart(\r
+ ) {\r
+ return this._has_start;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
+ * \r
+ * @return true if this object is valid according to the schema\r
+ */\r
+ public boolean isValid(\r
+ ) {\r
+ try {\r
+ validate();\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, out);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, handler);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'end'.\r
+ * \r
+ * @param end the value of field 'end'.\r
+ */\r
+ public void setEnd(\r
+ final int end) {\r
+ this._end = end;\r
+ this._has_end = true;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'start'.\r
+ * \r
+ * @param start the value of field 'start'.\r
+ */\r
+ public void setStart(\r
+ final int start) {\r
+ this._start = start;\r
+ this._has_start = true;\r
+ }\r
+\r
+ /**\r
+ * Method unmarshal.\r
+ * \r
+ * @param reader\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.MapListTo\r
+ */\r
+ public static jalview.schemabinding.version2.MapListTo unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.MapListTo) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListTo.class, reader);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+\r
+/**\r
+ * developed after mapRangeType from\r
+ * http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes\r
+ * \r
+ * This effectively represents a java.util.MapList object\r
+ * \r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class MapListType implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * number of dictionary symbol widths involved in each\r
+ * mapped position on this sequence (for example, 3 for a dna\r
+ * sequence exon\r
+ * region that is being mapped to a protein sequence). This is\r
+ * optional,\r
+ * since the unit can be usually be inferred from the\r
+ * dictionary type of\r
+ * each sequence involved in the mapping. \r
+ */\r
+ private long _mapFromUnit;\r
+\r
+ /**\r
+ * keeps track of state for field: _mapFromUnit\r
+ */\r
+ private boolean _has_mapFromUnit;\r
+\r
+ /**\r
+ * number of dictionary symbol widths involved in each\r
+ * mapped position on this sequence (for example, 3 for a dna\r
+ * sequence exon\r
+ * region that is being mapped to a protein sequence). This is\r
+ * optional,\r
+ * since the unit can be usually be inferred from the\r
+ * dictionary type of\r
+ * each sequence involved in the mapping. \r
+ */\r
+ private long _mapToUnit;\r
+\r
+ /**\r
+ * keeps track of state for field: _mapToUnit\r
+ */\r
+ private boolean _has_mapToUnit;\r
+\r
+ /**\r
+ * a region from start to end inclusive\r
+ */\r
+ private java.util.Vector _mapListFromList;\r
+\r
+ /**\r
+ * a region from start to end inclusive\r
+ */\r
+ private java.util.Vector _mapListToList;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public MapListType() {\r
+ super();\r
+ this._mapListFromList = new java.util.Vector();\r
+ this._mapListToList = new java.util.Vector();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vMapListFrom\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addMapListFrom(\r
+ final jalview.schemabinding.version2.MapListFrom vMapListFrom)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._mapListFromList.addElement(vMapListFrom);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vMapListFrom\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addMapListFrom(\r
+ final int index,\r
+ final jalview.schemabinding.version2.MapListFrom vMapListFrom)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._mapListFromList.add(index, vMapListFrom);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vMapListTo\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addMapListTo(\r
+ final jalview.schemabinding.version2.MapListTo vMapListTo)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._mapListToList.addElement(vMapListTo);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vMapListTo\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addMapListTo(\r
+ final int index,\r
+ final jalview.schemabinding.version2.MapListTo vMapListTo)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._mapListToList.add(index, vMapListTo);\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteMapFromUnit(\r
+ ) {\r
+ this._has_mapFromUnit= false;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void deleteMapToUnit(\r
+ ) {\r
+ this._has_mapToUnit= false;\r
+ }\r
+\r
+ /**\r
+ * Method enumerateMapListFrom.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.MapListFrom elements\r
+ */\r
+ public java.util.Enumeration enumerateMapListFrom(\r
+ ) {\r
+ return this._mapListFromList.elements();\r
+ }\r
+\r
+ /**\r
+ * Method enumerateMapListTo.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.MapListTo elements\r
+ */\r
+ public java.util.Enumeration enumerateMapListTo(\r
+ ) {\r
+ return this._mapListToList.elements();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'mapFromUnit'. The field\r
+ * 'mapFromUnit' has the following description: number of\r
+ * dictionary symbol widths involved in each\r
+ * mapped position on this sequence (for example, 3 for a dna\r
+ * sequence exon\r
+ * region that is being mapped to a protein sequence). This is\r
+ * optional,\r
+ * since the unit can be usually be inferred from the\r
+ * dictionary type of\r
+ * each sequence involved in the mapping. \r
+ * \r
+ * @return the value of field 'MapFromUnit'.\r
+ */\r
+ public long getMapFromUnit(\r
+ ) {\r
+ return this._mapFromUnit;\r
+ }\r
+\r
+ /**\r
+ * Method getMapListFrom.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.MapListFrom at the given index\r
+ */\r
+ public jalview.schemabinding.version2.MapListFrom getMapListFrom(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._mapListFromList.size()) {\r
+ throw new IndexOutOfBoundsException("getMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.MapListFrom) _mapListFromList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getMapListFrom.Returns the contents of the collection\r
+ * in an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.MapListFrom[] getMapListFrom(\r
+ ) {\r
+ jalview.schemabinding.version2.MapListFrom[] array = new jalview.schemabinding.version2.MapListFrom[0];\r
+ return (jalview.schemabinding.version2.MapListFrom[]) this._mapListFromList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getMapListFromCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getMapListFromCount(\r
+ ) {\r
+ return this._mapListFromList.size();\r
+ }\r
+\r
+ /**\r
+ * Method getMapListTo.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.MapListTo at the given index\r
+ */\r
+ public jalview.schemabinding.version2.MapListTo getMapListTo(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._mapListToList.size()) {\r
+ throw new IndexOutOfBoundsException("getMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.MapListTo) _mapListToList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getMapListTo.Returns the contents of the collection\r
+ * in an Array. <p>Note: Just in case the collection contents\r
+ * are changing in another thread, we pass a 0-length Array of\r
+ * the correct type into the API call. This way we <i>know</i>\r
+ * that the Array returned is of exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.MapListTo[] getMapListTo(\r
+ ) {\r
+ jalview.schemabinding.version2.MapListTo[] array = new jalview.schemabinding.version2.MapListTo[0];\r
+ return (jalview.schemabinding.version2.MapListTo[]) this._mapListToList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getMapListToCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getMapListToCount(\r
+ ) {\r
+ return this._mapListToList.size();\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'mapToUnit'. The field\r
+ * 'mapToUnit' has the following description: number of\r
+ * dictionary symbol widths involved in each\r
+ * mapped position on this sequence (for example, 3 for a dna\r
+ * sequence exon\r
+ * region that is being mapped to a protein sequence). This is\r
+ * optional,\r
+ * since the unit can be usually be inferred from the\r
+ * dictionary type of\r
+ * each sequence involved in the mapping. \r
+ * \r
+ * @return the value of field 'MapToUnit'.\r
+ */\r
+ public long getMapToUnit(\r
+ ) {\r
+ return this._mapToUnit;\r
+ }\r
+\r
+ /**\r
+ * Method hasMapFromUnit.\r
+ * \r
+ * @return true if at least one MapFromUnit has been added\r
+ */\r
+ public boolean hasMapFromUnit(\r
+ ) {\r
+ return this._has_mapFromUnit;\r
+ }\r
+\r
+ /**\r
+ * Method hasMapToUnit.\r
+ * \r
+ * @return true if at least one MapToUnit has been added\r
+ */\r
+ public boolean hasMapToUnit(\r
+ ) {\r
+ return this._has_mapToUnit;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
+ * \r
+ * @return true if this object is valid according to the schema\r
+ */\r
+ public boolean isValid(\r
+ ) {\r
+ try {\r
+ validate();\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, out);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, handler);\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllMapListFrom(\r
+ ) {\r
+ this._mapListFromList.clear();\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllMapListTo(\r
+ ) {\r
+ this._mapListToList.clear();\r
+ }\r
+\r
+ /**\r
+ * Method removeMapListFrom.\r
+ * \r
+ * @param vMapListFrom\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeMapListFrom(\r
+ final jalview.schemabinding.version2.MapListFrom vMapListFrom) {\r
+ boolean removed = _mapListFromList.remove(vMapListFrom);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeMapListFromAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.MapListFrom removeMapListFromAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._mapListFromList.remove(index);\r
+ return (jalview.schemabinding.version2.MapListFrom) obj;\r
+ }\r
+\r
+ /**\r
+ * Method removeMapListTo.\r
+ * \r
+ * @param vMapListTo\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeMapListTo(\r
+ final jalview.schemabinding.version2.MapListTo vMapListTo) {\r
+ boolean removed = _mapListToList.remove(vMapListTo);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeMapListToAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.MapListTo removeMapListToAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._mapListToList.remove(index);\r
+ return (jalview.schemabinding.version2.MapListTo) obj;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'mapFromUnit'. The field\r
+ * 'mapFromUnit' has the following description: number of\r
+ * dictionary symbol widths involved in each\r
+ * mapped position on this sequence (for example, 3 for a dna\r
+ * sequence exon\r
+ * region that is being mapped to a protein sequence). This is\r
+ * optional,\r
+ * since the unit can be usually be inferred from the\r
+ * dictionary type of\r
+ * each sequence involved in the mapping. \r
+ * \r
+ * @param mapFromUnit the value of field 'mapFromUnit'.\r
+ */\r
+ public void setMapFromUnit(\r
+ final long mapFromUnit) {\r
+ this._mapFromUnit = mapFromUnit;\r
+ this._has_mapFromUnit = true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vMapListFrom\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setMapListFrom(\r
+ final int index,\r
+ final jalview.schemabinding.version2.MapListFrom vMapListFrom)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._mapListFromList.size()) {\r
+ throw new IndexOutOfBoundsException("setMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._mapListFromList.set(index, vMapListFrom);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vMapListFromArray\r
+ */\r
+ public void setMapListFrom(\r
+ final jalview.schemabinding.version2.MapListFrom[] vMapListFromArray) {\r
+ //-- copy array\r
+ _mapListFromList.clear();\r
+ \r
+ for (int i = 0; i < vMapListFromArray.length; i++) {\r
+ this._mapListFromList.add(vMapListFromArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vMapListTo\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setMapListTo(\r
+ final int index,\r
+ final jalview.schemabinding.version2.MapListTo vMapListTo)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._mapListToList.size()) {\r
+ throw new IndexOutOfBoundsException("setMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._mapListToList.set(index, vMapListTo);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vMapListToArray\r
+ */\r
+ public void setMapListTo(\r
+ final jalview.schemabinding.version2.MapListTo[] vMapListToArray) {\r
+ //-- copy array\r
+ _mapListToList.clear();\r
+ \r
+ for (int i = 0; i < vMapListToArray.length; i++) {\r
+ this._mapListToList.add(vMapListToArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'mapToUnit'. The field 'mapToUnit'\r
+ * has the following description: number of dictionary symbol\r
+ * widths involved in each\r
+ * mapped position on this sequence (for example, 3 for a dna\r
+ * sequence exon\r
+ * region that is being mapped to a protein sequence). This is\r
+ * optional,\r
+ * since the unit can be usually be inferred from the\r
+ * dictionary type of\r
+ * each sequence involved in the mapping. \r
+ * \r
+ * @param mapToUnit the value of field 'mapToUnit'.\r
+ */\r
+ public void setMapToUnit(\r
+ final long mapToUnit) {\r
+ this._mapToUnit = mapToUnit;\r
+ this._has_mapToUnit = true;\r
+ }\r
+\r
+ /**\r
+ * Method unmarshal.\r
+ * \r
+ * @param reader\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.MapListType\r
+ */\r
+ public static jalview.schemabinding.version2.MapListType unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.MapListType) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListType.class, reader);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+\r
+/**\r
+ * Class Mapping.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class Mapping extends jalview.schemabinding.version2.MapListType \r
+implements java.io.Serializable\r
+{\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Internal choice value storage\r
+ */\r
+ private java.lang.Object _choiceValue;\r
+\r
+ /**\r
+ * Field _mappingChoice.\r
+ */\r
+ private jalview.schemabinding.version2.MappingChoice _mappingChoice;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public Mapping() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Returns the value of field 'choiceValue'. The field\r
+ * 'choiceValue' has the following description: Internal choice\r
+ * value storage\r
+ * \r
+ * @return the value of field 'ChoiceValue'.\r
+ */\r
+ public java.lang.Object getChoiceValue(\r
+ ) {\r
+ return this._choiceValue;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'mappingChoice'.\r
+ * \r
+ * @return the value of field 'MappingChoice'.\r
+ */\r
+ public jalview.schemabinding.version2.MappingChoice getMappingChoice(\r
+ ) {\r
+ return this._mappingChoice;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
+ * \r
+ * @return true if this object is valid according to the schema\r
+ */\r
+ public boolean isValid(\r
+ ) {\r
+ try {\r
+ validate();\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, out);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, handler);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'mappingChoice'.\r
+ * \r
+ * @param mappingChoice the value of field 'mappingChoice'.\r
+ */\r
+ public void setMappingChoice(\r
+ final jalview.schemabinding.version2.MappingChoice mappingChoice) {\r
+ this._mappingChoice = mappingChoice;\r
+ this._choiceValue = mappingChoice;\r
+ }\r
+\r
+ /**\r
+ * Method unmarshal.\r
+ * \r
+ * @param reader\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.MapListType\r
+ */\r
+ public static jalview.schemabinding.version2.MapListType unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.MapListType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Mapping.class, reader);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+\r
+/**\r
+ * Class MappingChoice.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class MappingChoice implements java.io.Serializable {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _sequence.\r
+ */\r
+ private jalview.schemabinding.version2.Sequence _sequence;\r
+\r
+ /**\r
+ * Field _dseqFor.\r
+ */\r
+ private java.lang.String _dseqFor;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public MappingChoice() {\r
+ super();\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Returns the value of field 'dseqFor'.\r
+ * \r
+ * @return the value of field 'DseqFor'.\r
+ */\r
+ public java.lang.String getDseqFor(\r
+ ) {\r
+ return this._dseqFor;\r
+ }\r
+\r
+ /**\r
+ * Returns the value of field 'sequence'.\r
+ * \r
+ * @return the value of field 'Sequence'.\r
+ */\r
+ public jalview.schemabinding.version2.Sequence getSequence(\r
+ ) {\r
+ return this._sequence;\r
+ }\r
+\r
+ /**\r
+ * Method isValid.\r
+ * \r
+ * @return true if this object is valid according to the schema\r
+ */\r
+ public boolean isValid(\r
+ ) {\r
+ try {\r
+ validate();\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, out);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, handler);\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'dseqFor'.\r
+ * \r
+ * @param dseqFor the value of field 'dseqFor'.\r
+ */\r
+ public void setDseqFor(\r
+ final java.lang.String dseqFor) {\r
+ this._dseqFor = dseqFor;\r
+ }\r
+\r
+ /**\r
+ * Sets the value of field 'sequence'.\r
+ * \r
+ * @param sequence the value of field 'sequence'.\r
+ */\r
+ public void setSequence(\r
+ final jalview.schemabinding.version2.Sequence sequence) {\r
+ this._sequence = sequence;\r
+ }\r
+\r
+ /**\r
+ * Method unmarshal.\r
+ * \r
+ * @param reader\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * jalview.schemabinding.version2.MappingChoice\r
+ */\r
+ public static jalview.schemabinding.version2.MappingChoice unmarshal(\r
+ final java.io.Reader reader)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.MappingChoice) Unmarshaller.unmarshal(jalview.schemabinding.version2.MappingChoice.class, reader);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ }\r
+\r
+}\r
//--------------------------/\r
\r
/**\r
+ * dataset sequence id for this sequence. Will be created as\r
+ * union of sequences.\r
+ * \r
+ */\r
+ private java.lang.String _dsseqid;\r
+\r
+ /**\r
* Field _DBRefList.\r
*/\r
private java.util.Vector _DBRefList;\r
}\r
\r
/**\r
+ * Returns the value of field 'dsseqid'. The field 'dsseqid'\r
+ * has the following description: dataset sequence id for this\r
+ * sequence. Will be created as union of sequences.\r
+ * \r
+ * \r
+ * @return the value of field 'Dsseqid'.\r
+ */\r
+ public java.lang.String getDsseqid(\r
+ ) {\r
+ return this._dsseqid;\r
+ }\r
+\r
+ /**\r
* Method isValid.\r
* \r
* @return true if this object is valid according to the schema\r
}\r
\r
/**\r
+ * Sets the value of field 'dsseqid'. The field 'dsseqid' has\r
+ * the following description: dataset sequence id for this\r
+ * sequence. Will be created as union of sequences.\r
+ * \r
+ * \r
+ * @param dsseqid the value of field 'dsseqid'.\r
+ */\r
+ public void setDsseqid(\r
+ final java.lang.String dsseqid) {\r
+ this._dsseqid = dsseqid;\r
+ }\r
+\r
+ /**\r
* Method unmarshal.\r
* \r
* @param reader\r
private java.lang.String _gapChar;\r
\r
/**\r
+ * reference to set where jalview will gather the dataset\r
+ * sequences for all sequences in the set. \r
+ * \r
+ */\r
+ private java.lang.String _datasetId;\r
+\r
+ /**\r
* Field _sequenceList.\r
*/\r
private java.util.Vector _sequenceList;\r
*/\r
private java.util.Vector _sequenceSetPropertiesList;\r
\r
+ /**\r
+ * Field _alcodonFrameList.\r
+ */\r
+ private java.util.Vector _alcodonFrameList;\r
+\r
\r
//----------------/\r
//- Constructors -/\r
this._sequenceList = new java.util.Vector();\r
this._annotationList = new java.util.Vector();\r
this._sequenceSetPropertiesList = new java.util.Vector();\r
+ this._alcodonFrameList = new java.util.Vector();\r
}\r
\r
\r
/**\r
* \r
* \r
+ * @param vAlcodonFrame\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addAlcodonFrame(\r
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._alcodonFrameList.addElement(vAlcodonFrame);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vAlcodonFrame\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void addAlcodonFrame(\r
+ final int index,\r
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ this._alcodonFrameList.add(index, vAlcodonFrame);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
* @param vAnnotation\r
* @throws java.lang.IndexOutOfBoundsException if the index\r
* given is outside the bounds of the collection\r
}\r
\r
/**\r
+ * Method enumerateAlcodonFrame.\r
+ * \r
+ * @return an Enumeration over all\r
+ * jalview.schemabinding.version2.AlcodonFrame elements\r
+ */\r
+ public java.util.Enumeration enumerateAlcodonFrame(\r
+ ) {\r
+ return this._alcodonFrameList.elements();\r
+ }\r
+\r
+ /**\r
* Method enumerateAnnotation.\r
* \r
* @return an Enumeration over all\r
}\r
\r
/**\r
+ * Method getAlcodonFrame.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.AlcodonFrame at the given inde\r
+ */\r
+ public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._alcodonFrameList.size()) {\r
+ throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList.get(index);\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodonFrame.Returns the contents of the\r
+ * collection in an Array. <p>Note: Just in case the\r
+ * collection contents are changing in another thread, we pass\r
+ * a 0-length Array of the correct type into the API call. \r
+ * This way we <i>know</i> that the Array returned is of\r
+ * exactly the correct length.\r
+ * \r
+ * @return this collection as an Array\r
+ */\r
+ public jalview.schemabinding.version2.AlcodonFrame[] getAlcodonFrame(\r
+ ) {\r
+ jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0];\r
+ return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList.toArray(array);\r
+ }\r
+\r
+ /**\r
+ * Method getAlcodonFrameCount.\r
+ * \r
+ * @return the size of this collection\r
+ */\r
+ public int getAlcodonFrameCount(\r
+ ) {\r
+ return this._alcodonFrameList.size();\r
+ }\r
+\r
+ /**\r
* Method getAnnotation.\r
* \r
* @param index\r
}\r
\r
/**\r
+ * Returns the value of field 'datasetId'. The field\r
+ * 'datasetId' has the following description: reference to set\r
+ * where jalview will gather the dataset sequences for all\r
+ * sequences in the set. \r
+ * \r
+ * \r
+ * @return the value of field 'DatasetId'.\r
+ */\r
+ public java.lang.String getDatasetId(\r
+ ) {\r
+ return this._datasetId;\r
+ }\r
+\r
+ /**\r
* Returns the value of field 'gapChar'.\r
* \r
* @return the value of field 'GapChar'.\r
}\r
\r
/**\r
+ * Method removeAlcodonFrame.\r
+ * \r
+ * @param vAlcodonFrame\r
+ * @return true if the object was removed from the collection.\r
+ */\r
+ public boolean removeAlcodonFrame(\r
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) {\r
+ boolean removed = _alcodonFrameList.remove(vAlcodonFrame);\r
+ return removed;\r
+ }\r
+\r
+ /**\r
+ * Method removeAlcodonFrameAt.\r
+ * \r
+ * @param index\r
+ * @return the element removed from the collection\r
+ */\r
+ public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt(\r
+ final int index) {\r
+ java.lang.Object obj = this._alcodonFrameList.remove(index);\r
+ return (jalview.schemabinding.version2.AlcodonFrame) obj;\r
+ }\r
+\r
+ /**\r
+ */\r
+ public void removeAllAlcodonFrame(\r
+ ) {\r
+ this._alcodonFrameList.clear();\r
+ }\r
+\r
+ /**\r
*/\r
public void removeAllAnnotation(\r
) {\r
* \r
* \r
* @param index\r
+ * @param vAlcodonFrame\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ */\r
+ public void setAlcodonFrame(\r
+ final int index,\r
+ final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._alcodonFrameList.size()) {\r
+ throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._alcodonFrameList.set(index, vAlcodonFrame);\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param vAlcodonFrameArray\r
+ */\r
+ public void setAlcodonFrame(\r
+ final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray) {\r
+ //-- copy array\r
+ _alcodonFrameList.clear();\r
+ \r
+ for (int i = 0; i < vAlcodonFrameArray.length; i++) {\r
+ this._alcodonFrameList.add(vAlcodonFrameArray[i]);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
* @param vAnnotation\r
* @throws java.lang.IndexOutOfBoundsException if the index\r
* given is outside the bounds of the collection\r
}\r
\r
/**\r
+ * Sets the value of field 'datasetId'. The field 'datasetId'\r
+ * has the following description: reference to set where\r
+ * jalview will gather the dataset sequences for all sequences\r
+ * in the set. \r
+ * \r
+ * \r
+ * @param datasetId the value of field 'datasetId'.\r
+ */\r
+ public void setDatasetId(\r
+ final java.lang.String datasetId) {\r
+ this._datasetId = datasetId;\r
+ }\r
+\r
+ /**\r
* Sets the value of field 'gapChar'.\r
* \r
* @param gapChar the value of field 'gapChar'.\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.AlcodMap;\r
+\r
+/**\r
+ * Class AlcodMapDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class AlcodMapDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AlcodMapDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "alcodMap";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _dnasq\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dnasq", "dnasq", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AlcodMap target = (AlcodMap) object;\r
+ return target.getDnasq();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AlcodMap target = (AlcodMap) object;\r
+ target.setDnasq( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _dnasq\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _mapping\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Mapping.class, "_mapping", "Mapping", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AlcodMap target = (AlcodMap) object;\r
+ return target.getMapping();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AlcodMap target = (AlcodMap) object;\r
+ target.setMapping( (jalview.schemabinding.version2.Mapping) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Mapping();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _mapping\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.AlcodMap.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.Alcodon;\r
+\r
+/**\r
+ * Class AlcodonDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class AlcodonDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AlcodonDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "alcodon";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _pos1\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos1", "pos1", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Alcodon target = (Alcodon) object;\r
+ if (!target.hasPos1()) { return null; }\r
+ return new java.lang.Long(target.getPos1());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Alcodon target = (Alcodon) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deletePos1();\r
+ return;\r
+ }\r
+ target.setPos1( ((java.lang.Long) value).longValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _pos1\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.LongValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.LongValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _pos2\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos2", "pos2", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Alcodon target = (Alcodon) object;\r
+ if (!target.hasPos2()) { return null; }\r
+ return new java.lang.Long(target.getPos2());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Alcodon target = (Alcodon) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deletePos2();\r
+ return;\r
+ }\r
+ target.setPos2( ((java.lang.Long) value).longValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _pos2\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.LongValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.LongValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _pos3\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos3", "pos3", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Alcodon target = (Alcodon) object;\r
+ if (!target.hasPos3()) { return null; }\r
+ return new java.lang.Long(target.getPos3());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Alcodon target = (Alcodon) object;\r
+ // if null, use delete method for optional primitives \r
+ if (value == null) {\r
+ target.deletePos3();\r
+ return;\r
+ }\r
+ target.setPos3( ((java.lang.Long) value).longValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _pos3\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.LongValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.LongValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Alcodon.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.AlcodonFrame;\r
+\r
+/**\r
+ * Class AlcodonFrameDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class AlcodonFrameDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public AlcodonFrameDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "AlcodonFrame";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _alcodonList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Alcodon.class, "_alcodonList", "alcodon", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AlcodonFrame target = (AlcodonFrame) object;\r
+ return target.getAlcodon();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AlcodonFrame target = (AlcodonFrame) object;\r
+ target.addAlcodon( (jalview.schemabinding.version2.Alcodon) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ AlcodonFrame target = (AlcodonFrame) object;\r
+ target.removeAllAlcodon();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Alcodon();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _alcodonList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _alcodMapList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AlcodMap.class, "_alcodMapList", "alcodMap", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ AlcodonFrame target = (AlcodonFrame) object;\r
+ return target.getAlcodMap();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ AlcodonFrame target = (AlcodonFrame) object;\r
+ target.addAlcodMap( (jalview.schemabinding.version2.AlcodMap) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ AlcodonFrame target = (AlcodonFrame) object;\r
+ target.removeAllAlcodMap();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.AlcodMap();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _alcodMapList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.AlcodonFrame.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
_nsURI = "www.vamsas.ac.uk/jalview/version2";\r
_xmlName = "DBRef";\r
_elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
org.exolab.castor.mapping.FieldHandler handler = null;\r
org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
desc.setValidator(fieldValidator);\r
//-- initialize element descriptors\r
\r
+ //-- _mapping\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Mapping.class, "_mapping", "Mapping", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ DBRef target = (DBRef) object;\r
+ return target.getMapping();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ DBRef target = (DBRef) object;\r
+ target.setMapping( (jalview.schemabinding.version2.Mapping) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Mapping();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _mapping\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
}\r
\r
\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.MapListFrom;\r
+\r
+/**\r
+ * Class MapListFromDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class MapListFromDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public MapListFromDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "mapListFrom";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _start\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MapListFrom target = (MapListFrom) object;\r
+ if (!target.hasStart()) { return null; }\r
+ return new java.lang.Integer(target.getStart());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MapListFrom target = (MapListFrom) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setStart( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _start\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _end\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MapListFrom target = (MapListFrom) object;\r
+ if (!target.hasEnd()) { return null; }\r
+ return new java.lang.Integer(target.getEnd());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MapListFrom target = (MapListFrom) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setEnd( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _end\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.MapListFrom.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.MapListTo;\r
+\r
+/**\r
+ * Class MapListToDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class MapListToDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public MapListToDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "mapListTo";\r
+ _elementDefinition = true;\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _start\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MapListTo target = (MapListTo) object;\r
+ if (!target.hasStart()) { return null; }\r
+ return new java.lang.Integer(target.getStart());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MapListTo target = (MapListTo) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setStart( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _start\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _end\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MapListTo target = (MapListTo) object;\r
+ if (!target.hasEnd()) { return null; }\r
+ return new java.lang.Integer(target.getEnd());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MapListTo target = (MapListTo) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setEnd( ((java.lang.Integer) value).intValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _end\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.IntValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.IntValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(-2147483648);\r
+ typeValidator.setMaxInclusive(2147483647);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.MapListTo.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.MapListType;\r
+\r
+/**\r
+ * Class MapListTypeDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class MapListTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public MapListTypeDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "mapListType";\r
+ _elementDefinition = false;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsSequence();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- _mapFromUnit\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_mapFromUnit", "mapFromUnit", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MapListType target = (MapListType) object;\r
+ if (!target.hasMapFromUnit()) { return null; }\r
+ return new java.lang.Long(target.getMapFromUnit());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MapListType target = (MapListType) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setMapFromUnit( ((java.lang.Long) value).longValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _mapFromUnit\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.LongValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.LongValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(1L);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _mapToUnit\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_mapToUnit", "mapToUnit", org.exolab.castor.xml.NodeType.Attribute);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MapListType target = (MapListType) object;\r
+ if (!target.hasMapToUnit()) { return null; }\r
+ return new java.lang.Long(target.getMapToUnit());\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MapListType target = (MapListType) object;\r
+ // ignore null values for non optional primitives\r
+ if (value == null) { return; }\r
+ \r
+ target.setMapToUnit( ((java.lang.Long) value).longValue());\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setRequired(true);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _mapToUnit\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(1);\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.LongValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.LongValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setMinInclusive(1L);\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- initialize element descriptors\r
+ \r
+ //-- _mapListFromList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MapListFrom.class, "_mapListFromList", "mapListFrom", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MapListType target = (MapListType) object;\r
+ return target.getMapListFrom();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MapListType target = (MapListType) object;\r
+ target.addMapListFrom( (jalview.schemabinding.version2.MapListFrom) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ MapListType target = (MapListType) object;\r
+ target.removeAllMapListFrom();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.MapListFrom();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _mapListFromList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _mapListToList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MapListTo.class, "_mapListToList", "mapListTo", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MapListType target = (MapListType) object;\r
+ return target.getMapListTo();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MapListType target = (MapListType) object;\r
+ target.addMapListTo( (jalview.schemabinding.version2.MapListTo) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ MapListType target = (MapListType) object;\r
+ target.removeAllMapListTo();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.MapListTo();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _mapListToList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.MapListType.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.MappingChoice;\r
+\r
+/**\r
+ * Class MappingChoiceDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class MappingChoiceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public MappingChoiceDescriptor() {\r
+ super();\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _elementDefinition = false;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsChoice();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _sequence\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequence", "Sequence", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MappingChoice target = (MappingChoice) object;\r
+ return target.getSequence();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MappingChoice target = (MappingChoice) object;\r
+ target.setSequence( (jalview.schemabinding.version2.Sequence) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.Sequence();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _sequence\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ //-- _dseqFor\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dseqFor", "dseqFor", org.exolab.castor.xml.NodeType.Element);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ MappingChoice target = (MappingChoice) object;\r
+ return target.getDseqFor();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ MappingChoice target = (MappingChoice) object;\r
+ target.setDseqFor( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _dseqFor\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.MappingChoice.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
--- /dev/null
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2.descriptors;\r
+\r
+ //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import jalview.schemabinding.version2.Mapping;\r
+\r
+/**\r
+ * Class MappingDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class MappingDescriptor extends jalview.schemabinding.version2.descriptors.MapListTypeDescriptor {\r
+\r
+\r
+ //--------------------------/\r
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
+\r
+ /**\r
+ * Field _elementDefinition.\r
+ */\r
+ private boolean _elementDefinition;\r
+\r
+ /**\r
+ * Field _nsPrefix.\r
+ */\r
+ private java.lang.String _nsPrefix;\r
+\r
+ /**\r
+ * Field _nsURI.\r
+ */\r
+ private java.lang.String _nsURI;\r
+\r
+ /**\r
+ * Field _xmlName.\r
+ */\r
+ private java.lang.String _xmlName;\r
+\r
+\r
+ //----------------/\r
+ //- Constructors -/\r
+ //----------------/\r
+\r
+ public MappingDescriptor() {\r
+ super();\r
+ setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.MapListTypeDescriptor());\r
+ _nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+ _xmlName = "Mapping";\r
+ _elementDefinition = true;\r
+ \r
+ //-- set grouping compositor\r
+ setCompositorAsChoice();\r
+ org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null;\r
+ org.exolab.castor.mapping.FieldHandler handler = null;\r
+ org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
+ //-- initialize attribute descriptors\r
+ \r
+ //-- initialize element descriptors\r
+ \r
+ //-- _mappingChoice\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MappingChoice.class, "_mappingChoice", "-error-if-this-is-used-", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Mapping target = (Mapping) object;\r
+ return target.getMappingChoice();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Mapping target = (Mapping) object;\r
+ target.setMappingChoice( (jalview.schemabinding.version2.MappingChoice) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.MappingChoice();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setContainer(true);\r
+ desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor());\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _mappingChoice\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
+ }\r
+\r
+\r
+ //-----------/\r
+ //- Methods -/\r
+ //-----------/\r
+\r
+ /**\r
+ * Method getAccessMode.\r
+ * \r
+ * @return the access mode specified for this class.\r
+ */\r
+ public org.exolab.castor.mapping.AccessMode getAccessMode(\r
+ ) {\r
+ return null;\r
+ }\r
+\r
+ /**\r
+ * Method getIdentity.\r
+ * \r
+ * @return the identity field, null if this class has no\r
+ * identity.\r
+ */\r
+ public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
+ ) {\r
+ return super.getIdentity();\r
+ }\r
+\r
+ /**\r
+ * Method getJavaClass.\r
+ * \r
+ * @return the Java class represented by this descriptor.\r
+ */\r
+ public java.lang.Class getJavaClass(\r
+ ) {\r
+ return jalview.schemabinding.version2.Mapping.class;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpacePrefix.\r
+ * \r
+ * @return the namespace prefix to use when marshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpacePrefix(\r
+ ) {\r
+ return _nsPrefix;\r
+ }\r
+\r
+ /**\r
+ * Method getNameSpaceURI.\r
+ * \r
+ * @return the namespace URI used when marshaling and\r
+ * unmarshaling as XML.\r
+ */\r
+ public java.lang.String getNameSpaceURI(\r
+ ) {\r
+ return _nsURI;\r
+ }\r
+\r
+ /**\r
+ * Method getValidator.\r
+ * \r
+ * @return a specific validator for the class described by this\r
+ * ClassDescriptor.\r
+ */\r
+ public org.exolab.castor.xml.TypeValidator getValidator(\r
+ ) {\r
+ return this;\r
+ }\r
+\r
+ /**\r
+ * Method getXMLName.\r
+ * \r
+ * @return the XML Name for the Class being described.\r
+ */\r
+ public java.lang.String getXMLName(\r
+ ) {\r
+ return _xmlName;\r
+ }\r
+\r
+ /**\r
+ * Method isElementDefinition.\r
+ * \r
+ * @return true if XML schema definition of this Class is that\r
+ * of a global\r
+ * element or element with anonymous type definition.\r
+ */\r
+ public boolean isElementDefinition(\r
+ ) {\r
+ return _elementDefinition;\r
+ }\r
+\r
+}\r
org.exolab.castor.xml.FieldValidator fieldValidator = null;\r
//-- initialize attribute descriptors\r
\r
+ //-- _dsseqid\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dsseqid", "dsseqid", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ Sequence target = (Sequence) object;\r
+ return target.getDsseqid();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ Sequence target = (Sequence) object;\r
+ target.setDsseqid( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _dsseqid\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
//-- initialize element descriptors\r
\r
//-- _DBRefList\r
typeValidator.setWhiteSpace("preserve");\r
}\r
desc.setValidator(fieldValidator);\r
+ //-- _datasetId\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_datasetId", "datasetId", org.exolab.castor.xml.NodeType.Attribute);\r
+ desc.setImmutable(true);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceSet target = (SequenceSet) object;\r
+ return target.getDatasetId();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.setDatasetId( (java.lang.String) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return null;\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setMultivalued(false);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _datasetId\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ { //-- local scope\r
+ org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+ typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+ fieldValidator.setValidator(typeValidator);\r
+ typeValidator.setWhiteSpace("preserve");\r
+ }\r
+ desc.setValidator(fieldValidator);\r
//-- initialize element descriptors\r
\r
//-- _sequenceList\r
{ //-- local scope\r
}\r
desc.setValidator(fieldValidator);\r
+ //-- _alcodonFrameList\r
+ desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AlcodonFrame.class, "_alcodonFrameList", "AlcodonFrame", org.exolab.castor.xml.NodeType.Element);\r
+ handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+ public java.lang.Object getValue( java.lang.Object object ) \r
+ throws IllegalStateException\r
+ {\r
+ SequenceSet target = (SequenceSet) object;\r
+ return target.getAlcodonFrame();\r
+ }\r
+ public void setValue( java.lang.Object object, java.lang.Object value) \r
+ throws IllegalStateException, IllegalArgumentException\r
+ {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.addAlcodonFrame( (jalview.schemabinding.version2.AlcodonFrame) value);\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
+ try {\r
+ SequenceSet target = (SequenceSet) object;\r
+ target.removeAllAlcodonFrame();\r
+ } catch (java.lang.Exception ex) {\r
+ throw new IllegalStateException(ex.toString());\r
+ }\r
+ }\r
+ public java.lang.Object newInstance(java.lang.Object parent) {\r
+ return new jalview.schemabinding.version2.AlcodonFrame();\r
+ }\r
+ };\r
+ desc.setHandler(handler);\r
+ desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+ desc.setMultivalued(true);\r
+ addFieldDescriptor(desc);\r
+ \r
+ //-- validation code for: _alcodonFrameList\r
+ fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+ fieldValidator.setMinOccurs(0);\r
+ { //-- local scope\r
+ }\r
+ desc.setValidator(fieldValidator);\r
}\r
\r
\r
git://source.jalview.org / jalview.git / commitdiff