From 4486cbff6855402579eff5ccbada47f15a5e8653 Mon Sep 17 00:00:00 2001 From: jprocter Date: Thu, 24 May 2007 15:16:11 +0000 Subject: [PATCH] jalview 2.0 XML schema versions for backwards compatibility in future castor upgrades --- build.xml | 32 + schemas/jalview.nodesc.properties | 13 + schemas/jalviewJvV1.xsd | 145 ++ schemas/vamsasJvV1.xsd | 74 + src/jalview/binding/Alignment.java | 342 ++- src/jalview/binding/Annotation.java | 864 ++++---- src/jalview/binding/AnnotationElement.java | 597 +++--- src/jalview/binding/Colour.java | 342 ++- src/jalview/binding/Feature.java | 621 +++--- src/jalview/binding/FeatureSettings.java | 549 ++--- src/jalview/binding/Features.java | 234 +- src/jalview/binding/JGroup.java | 1489 +++++++------ src/jalview/binding/JSeq.java | 1260 ++++++----- src/jalview/binding/JalviewModel.java | 447 ++-- src/jalview/binding/JalviewModelSequence.java | 1826 ++++++++-------- src/jalview/binding/JalviewUserColours.java | 598 +++--- src/jalview/binding/Pdbentry.java | 652 +++--- src/jalview/binding/PdbentryItem.java | 389 ++-- src/jalview/binding/Pdbids.java | 234 +- src/jalview/binding/Property.java | 342 ++- src/jalview/binding/Sequence.java | 234 +- src/jalview/binding/SequenceSet.java | 1018 ++++----- src/jalview/binding/SequenceType.java | 419 ++-- src/jalview/binding/Setting.java | 503 +++-- src/jalview/binding/Tree.java | 1655 +++++++------- src/jalview/binding/UserColourScheme.java | 234 +- src/jalview/binding/UserColours.java | 342 ++- src/jalview/binding/VAMSAS.java | 1157 +++++----- src/jalview/binding/VamsasModel.java | 234 +- src/jalview/binding/Viewport.java | 2852 +++++++++++++------------ 30 files changed, 9919 insertions(+), 9779 deletions(-) create mode 100644 schemas/jalview.nodesc.properties create mode 100644 schemas/jalviewJvV1.xsd create mode 100644 schemas/vamsasJvV1.xsd diff --git a/build.xml b/build.xml index 89bd1ca..aa0ca67 100755 --- a/build.xml +++ b/build.xml @@ -416,6 +416,38 @@ verbose="true" properties="${schemaDir}/jalview.properties" + /> + + + + + + + + + diff --git a/schemas/jalview.nodesc.properties b/schemas/jalview.nodesc.properties new file mode 100644 index 0000000..2b221fd --- /dev/null +++ b/schemas/jalview.nodesc.properties @@ -0,0 +1,13 @@ +# +# Property file for SourceCodeGenerator for jalview project XML for parsing without descriptors +# + +#org.exolab.castor.builder.superclass=com.xyz.BaseObject + +# XML namespace mapping to Java packages +# +org.exolab.castor.builder.nspackages=\ + www.vamsas.ac.uk/jalview/version2=jalview.binding,\ + www.jalview.org/colours=jalview.binding,\ + www.jalview.org=jalview.binding + diff --git a/schemas/jalviewJvV1.xsd b/schemas/jalviewJvV1.xsd new file mode 100644 index 0000000..2022ce2 --- /dev/null +++ b/schemas/jalviewJvV1.xsd @@ -0,0 +1,145 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/schemas/vamsasJvV1.xsd b/schemas/vamsasJvV1.xsd new file mode 100644 index 0000000..b830c94 --- /dev/null +++ b/schemas/vamsasJvV1.xsd @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java index 9a38f10..5b107b5 100755 --- a/src/jalview/binding/Alignment.java +++ b/src/jalview/binding/Alignment.java @@ -1,173 +1,169 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Alignment. - * - * @version $Revision$ $Date$ - */ -public class Alignment implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _annotation - */ - private jalview.binding.Annotation _annotation; - - /** - * Field _sequenceSet - */ - private jalview.binding.SequenceSet _sequenceSet; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Alignment() { - super(); - } //-- jalview.binding.Alignment() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'annotation'. - * - * @return Annotation - * @return the value of field 'annotation'. - */ - public jalview.binding.Annotation getAnnotation() - { - return this._annotation; - } //-- jalview.binding.Annotation getAnnotation() - - /** - * Returns the value of field 'sequenceSet'. - * - * @return SequenceSet - * @return the value of field 'sequenceSet'. - */ - public jalview.binding.SequenceSet getSequenceSet() - { - return this._sequenceSet; - } //-- jalview.binding.SequenceSet getSequenceSet() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'annotation'. - * - * @param annotation the value of field 'annotation'. - */ - public void setAnnotation(jalview.binding.Annotation annotation) - { - this._annotation = annotation; - } //-- void setAnnotation(jalview.binding.Annotation) - - /** - * Sets the value of field 'sequenceSet'. - * - * @param sequenceSet the value of field 'sequenceSet'. - */ - public void setSequenceSet(jalview.binding.SequenceSet sequenceSet) - { - this._sequenceSet = sequenceSet; - } //-- void setSequenceSet(jalview.binding.SequenceSet) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class Alignment. + * + * @version $Revision$ $Date$ + */ +public class Alignment implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _annotation. + */ + private jalview.binding.Annotation _annotation; + + /** + * Field _sequenceSet. + */ + private jalview.binding.SequenceSet _sequenceSet; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Alignment() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'annotation'. + * + * @return the value of field 'Annotation'. + */ + public jalview.binding.Annotation getAnnotation( + ) { + return this._annotation; + } + + /** + * Returns the value of field 'sequenceSet'. + * + * @return the value of field 'SequenceSet'. + */ + public jalview.binding.SequenceSet getSequenceSet( + ) { + return this._sequenceSet; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'annotation'. + * + * @param annotation the value of field 'annotation'. + */ + public void setAnnotation( + final jalview.binding.Annotation annotation) { + this._annotation = annotation; + } + + /** + * Sets the value of field 'sequenceSet'. + * + * @param sequenceSet the value of field 'sequenceSet'. + */ + public void setSequenceSet( + final jalview.binding.SequenceSet sequenceSet) { + this._sequenceSet = sequenceSet; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.Alignment + */ + public static jalview.binding.Alignment unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java index 66f183d..108d3ad 100755 --- a/src/jalview/binding/Annotation.java +++ b/src/jalview/binding/Annotation.java @@ -1,432 +1,432 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Annotation. - * - * @version $Revision$ $Date$ - */ -public class Annotation implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _graph - */ - private boolean _graph; - - /** - * keeps track of state for field: _graph - */ - private boolean _has_graph; - - /** - * Field _graphType - */ - private int _graphType; - - /** - * keeps track of state for field: _graphType - */ - private boolean _has_graphType; - - /** - * Field _annotationElementList - */ - private java.util.Vector _annotationElementList; - - /** - * Field _label - */ - private java.lang.String _label; - - /** - * Field _description - */ - private java.lang.String _description; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Annotation() { - super(); - _annotationElementList = new Vector(); - } //-- jalview.binding.Annotation() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAnnotationElement - * - * - * - * @param vAnnotationElement - */ - public void addAnnotationElement(jalview.binding.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - _annotationElementList.addElement(vAnnotationElement); - } //-- void addAnnotationElement(jalview.binding.AnnotationElement) - - /** - * Method addAnnotationElement - * - * - * - * @param index - * @param vAnnotationElement - */ - public void addAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - _annotationElementList.insertElementAt(vAnnotationElement, index); - } //-- void addAnnotationElement(int, jalview.binding.AnnotationElement) - - /** - * Method deleteGraph - * - */ - public void deleteGraph() - { - this._has_graph= false; - } //-- void deleteGraph() - - /** - * Method deleteGraphType - * - */ - public void deleteGraphType() - { - this._has_graphType= false; - } //-- void deleteGraphType() - - /** - * Method enumerateAnnotationElement - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAnnotationElement() - { - return _annotationElementList.elements(); - } //-- java.util.Enumeration enumerateAnnotationElement() - - /** - * Method getAnnotationElement - * - * - * - * @param index - * @return AnnotationElement - */ - public jalview.binding.AnnotationElement getAnnotationElement(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _annotationElementList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index); - } //-- jalview.binding.AnnotationElement getAnnotationElement(int) - - /** - * Method getAnnotationElement - * - * - * - * @return AnnotationElement - */ - public jalview.binding.AnnotationElement[] getAnnotationElement() - { - int size = _annotationElementList.size(); - jalview.binding.AnnotationElement[] mArray = new jalview.binding.AnnotationElement[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index); - } - return mArray; - } //-- jalview.binding.AnnotationElement[] getAnnotationElement() - - /** - * Method getAnnotationElementCount - * - * - * - * @return int - */ - public int getAnnotationElementCount() - { - return _annotationElementList.size(); - } //-- int getAnnotationElementCount() - - /** - * Returns the value of field 'description'. - * - * @return String - * @return the value of field 'description'. - */ - public java.lang.String getDescription() - { - return this._description; - } //-- java.lang.String getDescription() - - /** - * Returns the value of field 'graph'. - * - * @return boolean - * @return the value of field 'graph'. - */ - public boolean getGraph() - { - return this._graph; - } //-- boolean getGraph() - - /** - * Returns the value of field 'graphType'. - * - * @return int - * @return the value of field 'graphType'. - */ - public int getGraphType() - { - return this._graphType; - } //-- int getGraphType() - - /** - * Returns the value of field 'label'. - * - * @return String - * @return the value of field 'label'. - */ - public java.lang.String getLabel() - { - return this._label; - } //-- java.lang.String getLabel() - - /** - * Method hasGraph - * - * - * - * @return boolean - */ - public boolean hasGraph() - { - return this._has_graph; - } //-- boolean hasGraph() - - /** - * Method hasGraphType - * - * - * - * @return boolean - */ - public boolean hasGraphType() - { - return this._has_graphType; - } //-- boolean hasGraphType() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllAnnotationElement - * - */ - public void removeAllAnnotationElement() - { - _annotationElementList.removeAllElements(); - } //-- void removeAllAnnotationElement() - - /** - * Method removeAnnotationElement - * - * - * - * @param index - * @return AnnotationElement - */ - public jalview.binding.AnnotationElement removeAnnotationElement(int index) - { - java.lang.Object obj = _annotationElementList.elementAt(index); - _annotationElementList.removeElementAt(index); - return (jalview.binding.AnnotationElement) obj; - } //-- jalview.binding.AnnotationElement removeAnnotationElement(int) - - /** - * Method setAnnotationElement - * - * - * - * @param index - * @param vAnnotationElement - */ - public void setAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _annotationElementList.size())) { - throw new IndexOutOfBoundsException(); - } - _annotationElementList.setElementAt(vAnnotationElement, index); - } //-- void setAnnotationElement(int, jalview.binding.AnnotationElement) - - /** - * Method setAnnotationElement - * - * - * - * @param annotationElementArray - */ - public void setAnnotationElement(jalview.binding.AnnotationElement[] annotationElementArray) - { - //-- copy array - _annotationElementList.removeAllElements(); - for (int i = 0; i < annotationElementArray.length; i++) { - _annotationElementList.addElement(annotationElementArray[i]); - } - } //-- void setAnnotationElement(jalview.binding.AnnotationElement) - - /** - * Sets the value of field 'description'. - * - * @param description the value of field 'description'. - */ - public void setDescription(java.lang.String description) - { - this._description = description; - } //-- void setDescription(java.lang.String) - - /** - * Sets the value of field 'graph'. - * - * @param graph the value of field 'graph'. - */ - public void setGraph(boolean graph) - { - this._graph = graph; - this._has_graph = true; - } //-- void setGraph(boolean) - - /** - * Sets the value of field 'graphType'. - * - * @param graphType the value of field 'graphType'. - */ - public void setGraphType(int graphType) - { - this._graphType = graphType; - this._has_graphType = true; - } //-- void setGraphType(int) - - /** - * Sets the value of field 'label'. - * - * @param label the value of field 'label'. - */ - public void setLabel(java.lang.String label) - { - this._label = label; - } //-- void setLabel(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class Annotation. + * + * @version $Revision$ $Date$ + */ +public class Annotation implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _graph. + */ + private boolean _graph; + + /** + * keeps track of state for field: _graph + */ + private boolean _has_graph; + + /** + * Field _graphType. + */ + private int _graphType; + + /** + * keeps track of state for field: _graphType + */ + private boolean _has_graphType; + + /** + * Field _annotationElementList. + */ + private java.util.Vector _annotationElementList; + + /** + * Field _label. + */ + private java.lang.String _label; + + /** + * Field _description. + */ + private java.lang.String _description; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Annotation() { + super(); + this._annotationElementList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vAnnotationElement + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAnnotationElement( + final jalview.binding.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException { + this._annotationElementList.addElement(vAnnotationElement); + } + + /** + * + * + * @param index + * @param vAnnotationElement + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAnnotationElement( + final int index, + final jalview.binding.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException { + this._annotationElementList.add(index, vAnnotationElement); + } + + /** + */ + public void deleteGraph( + ) { + this._has_graph= false; + } + + /** + */ + public void deleteGraphType( + ) { + this._has_graphType= false; + } + + /** + * Method enumerateAnnotationElement. + * + * @return an Enumeration over all + * jalview.binding.AnnotationElement elements + */ + public java.util.Enumeration enumerateAnnotationElement( + ) { + return this._annotationElementList.elements(); + } + + /** + * Method getAnnotationElement. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the jalview.binding.AnnotationElement + * at the given index + */ + public jalview.binding.AnnotationElement getAnnotationElement( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._annotationElementList.size()) { + throw new IndexOutOfBoundsException("getAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]"); + } + + return (jalview.binding.AnnotationElement) _annotationElementList.get(index); + } + + /** + * Method getAnnotationElement.Returns the contents of the + * collection in an Array.

Note: Just in case the + * collection contents are changing in another thread, we pass + * a 0-length Array of the correct type into the API call. + * This way we know that the Array returned is of + * exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.binding.AnnotationElement[] getAnnotationElement( + ) { + jalview.binding.AnnotationElement[] array = new jalview.binding.AnnotationElement[0]; + return (jalview.binding.AnnotationElement[]) this._annotationElementList.toArray(array); + } + + /** + * Method getAnnotationElementCount. + * + * @return the size of this collection + */ + public int getAnnotationElementCount( + ) { + return this._annotationElementList.size(); + } + + /** + * Returns the value of field 'description'. + * + * @return the value of field 'Description'. + */ + public java.lang.String getDescription( + ) { + return this._description; + } + + /** + * Returns the value of field 'graph'. + * + * @return the value of field 'Graph'. + */ + public boolean getGraph( + ) { + return this._graph; + } + + /** + * Returns the value of field 'graphType'. + * + * @return the value of field 'GraphType'. + */ + public int getGraphType( + ) { + return this._graphType; + } + + /** + * Returns the value of field 'label'. + * + * @return the value of field 'Label'. + */ + public java.lang.String getLabel( + ) { + return this._label; + } + + /** + * Method hasGraph. + * + * @return true if at least one Graph has been added + */ + public boolean hasGraph( + ) { + return this._has_graph; + } + + /** + * Method hasGraphType. + * + * @return true if at least one GraphType has been added + */ + public boolean hasGraphType( + ) { + return this._has_graphType; + } + + /** + * Returns the value of field 'graph'. + * + * @return the value of field 'Graph'. + */ + public boolean isGraph( + ) { + return this._graph; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllAnnotationElement( + ) { + this._annotationElementList.clear(); + } + + /** + * Method removeAnnotationElement. + * + * @param vAnnotationElement + * @return true if the object was removed from the collection. + */ + public boolean removeAnnotationElement( + final jalview.binding.AnnotationElement vAnnotationElement) { + boolean removed = _annotationElementList.remove(vAnnotationElement); + return removed; + } + + /** + * Method removeAnnotationElementAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.AnnotationElement removeAnnotationElementAt( + final int index) { + java.lang.Object obj = this._annotationElementList.remove(index); + return (jalview.binding.AnnotationElement) obj; + } + + /** + * + * + * @param index + * @param vAnnotationElement + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setAnnotationElement( + final int index, + final jalview.binding.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._annotationElementList.size()) { + throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]"); + } + + this._annotationElementList.set(index, vAnnotationElement); + } + + /** + * + * + * @param vAnnotationElementArray + */ + public void setAnnotationElement( + final jalview.binding.AnnotationElement[] vAnnotationElementArray) { + //-- copy array + _annotationElementList.clear(); + + for (int i = 0; i < vAnnotationElementArray.length; i++) { + this._annotationElementList.add(vAnnotationElementArray[i]); + } + } + + /** + * Sets the value of field 'description'. + * + * @param description the value of field 'description'. + */ + public void setDescription( + final java.lang.String description) { + this._description = description; + } + + /** + * Sets the value of field 'graph'. + * + * @param graph the value of field 'graph'. + */ + public void setGraph( + final boolean graph) { + this._graph = graph; + this._has_graph = true; + } + + /** + * Sets the value of field 'graphType'. + * + * @param graphType the value of field 'graphType'. + */ + public void setGraphType( + final int graphType) { + this._graphType = graphType; + this._has_graphType = true; + } + + /** + * Sets the value of field 'label'. + * + * @param label the value of field 'label'. + */ + public void setLabel( + final java.lang.String label) { + this._label = label; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.Annotation + */ + public static jalview.binding.Annotation unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/AnnotationElement.java b/src/jalview/binding/AnnotationElement.java index e4aec31..d133fe0 100755 --- a/src/jalview/binding/AnnotationElement.java +++ b/src/jalview/binding/AnnotationElement.java @@ -1,306 +1,291 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class AnnotationElement. - * - * @version $Revision$ $Date$ - */ -public class AnnotationElement implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _position - */ - private int _position; - - /** - * keeps track of state for field: _position - */ - private boolean _has_position; - - /** - * Field _displayCharacter - */ - private java.lang.String _displayCharacter; - - /** - * Field _description - */ - private java.lang.String _description; - - /** - * Field _secondaryStructure - */ - private java.lang.String _secondaryStructure; - - /** - * Field _value - */ - private float _value; - - /** - * keeps track of state for field: _value - */ - private boolean _has_value; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AnnotationElement() { - super(); - } //-- jalview.binding.AnnotationElement() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deletePosition - * - */ - public void deletePosition() - { - this._has_position= false; - } //-- void deletePosition() - - /** - * Method deleteValue - * - */ - public void deleteValue() - { - this._has_value= false; - } //-- void deleteValue() - - /** - * Returns the value of field 'description'. - * - * @return String - * @return the value of field 'description'. - */ - public java.lang.String getDescription() - { - return this._description; - } //-- java.lang.String getDescription() - - /** - * Returns the value of field 'displayCharacter'. - * - * @return String - * @return the value of field 'displayCharacter'. - */ - public java.lang.String getDisplayCharacter() - { - return this._displayCharacter; - } //-- java.lang.String getDisplayCharacter() - - /** - * Returns the value of field 'position'. - * - * @return int - * @return the value of field 'position'. - */ - public int getPosition() - { - return this._position; - } //-- int getPosition() - - /** - * Returns the value of field 'secondaryStructure'. - * - * @return String - * @return the value of field 'secondaryStructure'. - */ - public java.lang.String getSecondaryStructure() - { - return this._secondaryStructure; - } //-- java.lang.String getSecondaryStructure() - - /** - * Returns the value of field 'value'. - * - * @return float - * @return the value of field 'value'. - */ - public float getValue() - { - return this._value; - } //-- float getValue() - - /** - * Method hasPosition - * - * - * - * @return boolean - */ - public boolean hasPosition() - { - return this._has_position; - } //-- boolean hasPosition() - - /** - * Method hasValue - * - * - * - * @return boolean - */ - public boolean hasValue() - { - return this._has_value; - } //-- boolean hasValue() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'description'. - * - * @param description the value of field 'description'. - */ - public void setDescription(java.lang.String description) - { - this._description = description; - } //-- void setDescription(java.lang.String) - - /** - * Sets the value of field 'displayCharacter'. - * - * @param displayCharacter the value of field 'displayCharacter' - */ - public void setDisplayCharacter(java.lang.String displayCharacter) - { - this._displayCharacter = displayCharacter; - } //-- void setDisplayCharacter(java.lang.String) - - /** - * Sets the value of field 'position'. - * - * @param position the value of field 'position'. - */ - public void setPosition(int position) - { - this._position = position; - this._has_position = true; - } //-- void setPosition(int) - - /** - * Sets the value of field 'secondaryStructure'. - * - * @param secondaryStructure the value of field - * 'secondaryStructure'. - */ - public void setSecondaryStructure(java.lang.String secondaryStructure) - { - this._secondaryStructure = secondaryStructure; - } //-- void setSecondaryStructure(java.lang.String) - - /** - * Sets the value of field 'value'. - * - * @param value the value of field 'value'. - */ - public void setValue(float value) - { - this._value = value; - this._has_value = true; - } //-- void setValue(float) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class AnnotationElement. + * + * @version $Revision$ $Date$ + */ +public class AnnotationElement implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _position. + */ + private int _position; + + /** + * keeps track of state for field: _position + */ + private boolean _has_position; + + /** + * Field _displayCharacter. + */ + private java.lang.String _displayCharacter; + + /** + * Field _description. + */ + private java.lang.String _description; + + /** + * Field _secondaryStructure. + */ + private java.lang.String _secondaryStructure; + + /** + * Field _value. + */ + private float _value; + + /** + * keeps track of state for field: _value + */ + private boolean _has_value; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AnnotationElement() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deletePosition( + ) { + this._has_position= false; + } + + /** + */ + public void deleteValue( + ) { + this._has_value= false; + } + + /** + * Returns the value of field 'description'. + * + * @return the value of field 'Description'. + */ + public java.lang.String getDescription( + ) { + return this._description; + } + + /** + * Returns the value of field 'displayCharacter'. + * + * @return the value of field 'DisplayCharacter'. + */ + public java.lang.String getDisplayCharacter( + ) { + return this._displayCharacter; + } + + /** + * Returns the value of field 'position'. + * + * @return the value of field 'Position'. + */ + public int getPosition( + ) { + return this._position; + } + + /** + * Returns the value of field 'secondaryStructure'. + * + * @return the value of field 'SecondaryStructure'. + */ + public java.lang.String getSecondaryStructure( + ) { + return this._secondaryStructure; + } + + /** + * Returns the value of field 'value'. + * + * @return the value of field 'Value'. + */ + public float getValue( + ) { + return this._value; + } + + /** + * Method hasPosition. + * + * @return true if at least one Position has been added + */ + public boolean hasPosition( + ) { + return this._has_position; + } + + /** + * Method hasValue. + * + * @return true if at least one Value has been added + */ + public boolean hasValue( + ) { + return this._has_value; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'description'. + * + * @param description the value of field 'description'. + */ + public void setDescription( + final java.lang.String description) { + this._description = description; + } + + /** + * Sets the value of field 'displayCharacter'. + * + * @param displayCharacter the value of field 'displayCharacter' + */ + public void setDisplayCharacter( + final java.lang.String displayCharacter) { + this._displayCharacter = displayCharacter; + } + + /** + * Sets the value of field 'position'. + * + * @param position the value of field 'position'. + */ + public void setPosition( + final int position) { + this._position = position; + this._has_position = true; + } + + /** + * Sets the value of field 'secondaryStructure'. + * + * @param secondaryStructure the value of field + * 'secondaryStructure'. + */ + public void setSecondaryStructure( + final java.lang.String secondaryStructure) { + this._secondaryStructure = secondaryStructure; + } + + /** + * Sets the value of field 'value'. + * + * @param value the value of field 'value'. + */ + public void setValue( + final float value) { + this._value = value; + this._has_value = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.AnnotationElement + */ + public static jalview.binding.AnnotationElement unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/Colour.java b/src/jalview/binding/Colour.java index a51102b..488ff98 100755 --- a/src/jalview/binding/Colour.java +++ b/src/jalview/binding/Colour.java @@ -1,173 +1,169 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Colour. - * - * @version $Revision$ $Date$ - */ -public class Colour implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _name - */ - private java.lang.String _name; - - /** - * Field _RGB - */ - private java.lang.String _RGB; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Colour() { - super(); - } //-- jalview.binding.Colour() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'name'. - * - * @return String - * @return the value of field 'name'. - */ - public java.lang.String getName() - { - return this._name; - } //-- java.lang.String getName() - - /** - * Returns the value of field 'RGB'. - * - * @return String - * @return the value of field 'RGB'. - */ - public java.lang.String getRGB() - { - return this._RGB; - } //-- java.lang.String getRGB() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'name'. - * - * @param name the value of field 'name'. - */ - public void setName(java.lang.String name) - { - this._name = name; - } //-- void setName(java.lang.String) - - /** - * Sets the value of field 'RGB'. - * - * @param RGB the value of field 'RGB'. - */ - public void setRGB(java.lang.String RGB) - { - this._RGB = RGB; - } //-- void setRGB(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class Colour. + * + * @version $Revision$ $Date$ + */ +public class Colour implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _name. + */ + private java.lang.String _name; + + /** + * Field _RGB. + */ + private java.lang.String _RGB; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Colour() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'name'. + * + * @return the value of field 'Name'. + */ + public java.lang.String getName( + ) { + return this._name; + } + + /** + * Returns the value of field 'RGB'. + * + * @return the value of field 'RGB'. + */ + public java.lang.String getRGB( + ) { + return this._RGB; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'name'. + * + * @param name the value of field 'name'. + */ + public void setName( + final java.lang.String name) { + this._name = name; + } + + /** + * Sets the value of field 'RGB'. + * + * @param RGB the value of field 'RGB'. + */ + public void setRGB( + final java.lang.String RGB) { + this._RGB = RGB; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.Colour + */ + public static jalview.binding.Colour unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/Feature.java b/src/jalview/binding/Feature.java index 5d0f79a..d429df3 100755 --- a/src/jalview/binding/Feature.java +++ b/src/jalview/binding/Feature.java @@ -1,331 +1,290 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Feature. - * - * @version $Revision$ $Date$ - */ -public class Feature implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _begin - */ - private int _begin; - - /** - * keeps track of state for field: _begin - */ - private boolean _has_begin; - - /** - * Field _end - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - /** - * Field _type - */ - private java.lang.String _type; - - /** - * Field _description - */ - private java.lang.String _description; - - /** - * Field _status - */ - private java.lang.String _status; - - /** - * Field _featureGroup - */ - private java.lang.String _featureGroup; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Feature() { - super(); - } //-- jalview.binding.Feature() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteBegin - * - */ - public void deleteBegin() - { - this._has_begin= false; - } //-- void deleteBegin() - - /** - * Method deleteEnd - * - */ - public void deleteEnd() - { - this._has_end= false; - } //-- void deleteEnd() - - /** - * Returns the value of field 'begin'. - * - * @return int - * @return the value of field 'begin'. - */ - public int getBegin() - { - return this._begin; - } //-- int getBegin() - - /** - * Returns the value of field 'description'. - * - * @return String - * @return the value of field 'description'. - */ - public java.lang.String getDescription() - { - return this._description; - } //-- java.lang.String getDescription() - - /** - * Returns the value of field 'end'. - * - * @return int - * @return the value of field 'end'. - */ - public int getEnd() - { - return this._end; - } //-- int getEnd() - - /** - * Returns the value of field 'featureGroup'. - * - * @return String - * @return the value of field 'featureGroup'. - */ - public java.lang.String getFeatureGroup() - { - return this._featureGroup; - } //-- java.lang.String getFeatureGroup() - - /** - * Returns the value of field 'status'. - * - * @return String - * @return the value of field 'status'. - */ - public java.lang.String getStatus() - { - return this._status; - } //-- java.lang.String getStatus() - - /** - * Returns the value of field 'type'. - * - * @return String - * @return the value of field 'type'. - */ - public java.lang.String getType() - { - return this._type; - } //-- java.lang.String getType() - - /** - * Method hasBegin - * - * - * - * @return boolean - */ - public boolean hasBegin() - { - return this._has_begin; - } //-- boolean hasBegin() - - /** - * Method hasEnd - * - * - * - * @return boolean - */ - public boolean hasEnd() - { - return this._has_end; - } //-- boolean hasEnd() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'begin'. - * - * @param begin the value of field 'begin'. - */ - public void setBegin(int begin) - { - this._begin = begin; - this._has_begin = true; - } //-- void setBegin(int) - - /** - * Sets the value of field 'description'. - * - * @param description the value of field 'description'. - */ - public void setDescription(java.lang.String description) - { - this._description = description; - } //-- void setDescription(java.lang.String) - - /** - * Sets the value of field 'end'. - * - * @param end the value of field 'end'. - */ - public void setEnd(int end) - { - this._end = end; - this._has_end = true; - } //-- void setEnd(int) - - /** - * Sets the value of field 'featureGroup'. - * - * @param featureGroup the value of field 'featureGroup'. - */ - public void setFeatureGroup(java.lang.String featureGroup) - { - this._featureGroup = featureGroup; - } //-- void setFeatureGroup(java.lang.String) - - /** - * Sets the value of field 'status'. - * - * @param status the value of field 'status'. - */ - public void setStatus(java.lang.String status) - { - this._status = status; - } //-- void setStatus(java.lang.String) - - /** - * Sets the value of field 'type'. - * - * @param type the value of field 'type'. - */ - public void setType(java.lang.String type) - { - this._type = type; - } //-- void setType(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Feature) Unmarshaller.unmarshal(jalview.binding.Feature.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class Feature. + * + * @version $Revision$ $Date$ + */ +public class Feature implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _begin. + */ + private int _begin; + + /** + * keeps track of state for field: _begin + */ + private boolean _has_begin; + + /** + * Field _end. + */ + private int _end; + + /** + * keeps track of state for field: _end + */ + private boolean _has_end; + + /** + * Field _type. + */ + private java.lang.String _type; + + /** + * Field _description. + */ + private java.lang.String _description; + + /** + * Field _status. + */ + private java.lang.String _status; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Feature() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteBegin( + ) { + this._has_begin= false; + } + + /** + */ + public void deleteEnd( + ) { + this._has_end= false; + } + + /** + * Returns the value of field 'begin'. + * + * @return the value of field 'Begin'. + */ + public int getBegin( + ) { + return this._begin; + } + + /** + * Returns the value of field 'description'. + * + * @return the value of field 'Description'. + */ + public java.lang.String getDescription( + ) { + return this._description; + } + + /** + * Returns the value of field 'end'. + * + * @return the value of field 'End'. + */ + public int getEnd( + ) { + return this._end; + } + + /** + * Returns the value of field 'status'. + * + * @return the value of field 'Status'. + */ + public java.lang.String getStatus( + ) { + return this._status; + } + + /** + * Returns the value of field 'type'. + * + * @return the value of field 'Type'. + */ + public java.lang.String getType( + ) { + return this._type; + } + + /** + * Method hasBegin. + * + * @return true if at least one Begin has been added + */ + public boolean hasBegin( + ) { + return this._has_begin; + } + + /** + * Method hasEnd. + * + * @return true if at least one End has been added + */ + public boolean hasEnd( + ) { + return this._has_end; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'begin'. + * + * @param begin the value of field 'begin'. + */ + public void setBegin( + final int begin) { + this._begin = begin; + this._has_begin = true; + } + + /** + * Sets the value of field 'description'. + * + * @param description the value of field 'description'. + */ + public void setDescription( + final java.lang.String description) { + this._description = description; + } + + /** + * Sets the value of field 'end'. + * + * @param end the value of field 'end'. + */ + public void setEnd( + final int end) { + this._end = end; + this._has_end = true; + } + + /** + * Sets the value of field 'status'. + * + * @param status the value of field 'status'. + */ + public void setStatus( + final java.lang.String status) { + this._status = status; + } + + /** + * Sets the value of field 'type'. + * + * @param type the value of field 'type'. + */ + public void setType( + final java.lang.String type) { + this._type = type; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.Feature + */ + public static jalview.binding.Feature unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.Feature) Unmarshaller.unmarshal(jalview.binding.Feature.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/FeatureSettings.java b/src/jalview/binding/FeatureSettings.java index 2ef3731..f3d06be 100755 --- a/src/jalview/binding/FeatureSettings.java +++ b/src/jalview/binding/FeatureSettings.java @@ -1,274 +1,275 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class FeatureSettings. - * - * @version $Revision$ $Date$ - */ -public class FeatureSettings implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _settingList - */ - private java.util.Vector _settingList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public FeatureSettings() { - super(); - _settingList = new Vector(); - } //-- jalview.binding.FeatureSettings() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addSetting - * - * - * - * @param vSetting - */ - public void addSetting(jalview.binding.Setting vSetting) - throws java.lang.IndexOutOfBoundsException - { - _settingList.addElement(vSetting); - } //-- void addSetting(jalview.binding.Setting) - - /** - * Method addSetting - * - * - * - * @param index - * @param vSetting - */ - public void addSetting(int index, jalview.binding.Setting vSetting) - throws java.lang.IndexOutOfBoundsException - { - _settingList.insertElementAt(vSetting, index); - } //-- void addSetting(int, jalview.binding.Setting) - - /** - * Method enumerateSetting - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateSetting() - { - return _settingList.elements(); - } //-- java.util.Enumeration enumerateSetting() - - /** - * Method getSetting - * - * - * - * @param index - * @return Setting - */ - public jalview.binding.Setting getSetting(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _settingList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.Setting) _settingList.elementAt(index); - } //-- jalview.binding.Setting getSetting(int) - - /** - * Method getSetting - * - * - * - * @return Setting - */ - public jalview.binding.Setting[] getSetting() - { - int size = _settingList.size(); - jalview.binding.Setting[] mArray = new jalview.binding.Setting[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.Setting) _settingList.elementAt(index); - } - return mArray; - } //-- jalview.binding.Setting[] getSetting() - - /** - * Method getSettingCount - * - * - * - * @return int - */ - public int getSettingCount() - { - return _settingList.size(); - } //-- int getSettingCount() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllSetting - * - */ - public void removeAllSetting() - { - _settingList.removeAllElements(); - } //-- void removeAllSetting() - - /** - * Method removeSetting - * - * - * - * @param index - * @return Setting - */ - public jalview.binding.Setting removeSetting(int index) - { - java.lang.Object obj = _settingList.elementAt(index); - _settingList.removeElementAt(index); - return (jalview.binding.Setting) obj; - } //-- jalview.binding.Setting removeSetting(int) - - /** - * Method setSetting - * - * - * - * @param index - * @param vSetting - */ - public void setSetting(int index, jalview.binding.Setting vSetting) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _settingList.size())) { - throw new IndexOutOfBoundsException(); - } - _settingList.setElementAt(vSetting, index); - } //-- void setSetting(int, jalview.binding.Setting) - - /** - * Method setSetting - * - * - * - * @param settingArray - */ - public void setSetting(jalview.binding.Setting[] settingArray) - { - //-- copy array - _settingList.removeAllElements(); - for (int i = 0; i < settingArray.length; i++) { - _settingList.addElement(settingArray[i]); - } - } //-- void setSetting(jalview.binding.Setting) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(jalview.binding.FeatureSettings.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class FeatureSettings. + * + * @version $Revision$ $Date$ + */ +public class FeatureSettings implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _settingList. + */ + private java.util.Vector _settingList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public FeatureSettings() { + super(); + this._settingList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vSetting + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSetting( + final jalview.binding.Setting vSetting) + throws java.lang.IndexOutOfBoundsException { + this._settingList.addElement(vSetting); + } + + /** + * + * + * @param index + * @param vSetting + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSetting( + final int index, + final jalview.binding.Setting vSetting) + throws java.lang.IndexOutOfBoundsException { + this._settingList.add(index, vSetting); + } + + /** + * Method enumerateSetting. + * + * @return an Enumeration over all jalview.binding.Setting + * elements + */ + public java.util.Enumeration enumerateSetting( + ) { + return this._settingList.elements(); + } + + /** + * Method getSetting. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the jalview.binding.Setting at the + * given index + */ + public jalview.binding.Setting getSetting( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._settingList.size()) { + throw new IndexOutOfBoundsException("getSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]"); + } + + return (jalview.binding.Setting) _settingList.get(index); + } + + /** + * Method getSetting.Returns the contents of the collection in + * an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.binding.Setting[] getSetting( + ) { + jalview.binding.Setting[] array = new jalview.binding.Setting[0]; + return (jalview.binding.Setting[]) this._settingList.toArray(array); + } + + /** + * Method getSettingCount. + * + * @return the size of this collection + */ + public int getSettingCount( + ) { + return this._settingList.size(); + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllSetting( + ) { + this._settingList.clear(); + } + + /** + * Method removeSetting. + * + * @param vSetting + * @return true if the object was removed from the collection. + */ + public boolean removeSetting( + final jalview.binding.Setting vSetting) { + boolean removed = _settingList.remove(vSetting); + return removed; + } + + /** + * Method removeSettingAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.Setting removeSettingAt( + final int index) { + java.lang.Object obj = this._settingList.remove(index); + return (jalview.binding.Setting) obj; + } + + /** + * + * + * @param index + * @param vSetting + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setSetting( + final int index, + final jalview.binding.Setting vSetting) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._settingList.size()) { + throw new IndexOutOfBoundsException("setSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]"); + } + + this._settingList.set(index, vSetting); + } + + /** + * + * + * @param vSettingArray + */ + public void setSetting( + final jalview.binding.Setting[] vSettingArray) { + //-- copy array + _settingList.clear(); + + for (int i = 0; i < vSettingArray.length; i++) { + this._settingList.add(vSettingArray[i]); + } + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.FeatureSettings + */ + public static jalview.binding.FeatureSettings unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(jalview.binding.FeatureSettings.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/Features.java b/src/jalview/binding/Features.java index 4706beb..e50ae7c 100755 --- a/src/jalview/binding/Features.java +++ b/src/jalview/binding/Features.java @@ -1,118 +1,116 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Features. - * - * @version $Revision$ $Date$ - */ -public class Features extends Feature -implements java.io.Serializable -{ - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Features() { - super(); - } //-- jalview.binding.Features() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Features) Unmarshaller.unmarshal(jalview.binding.Features.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class Features. + * + * @version $Revision$ $Date$ + */ +public class Features extends Feature +implements java.io.Serializable +{ + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Features() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.Feature + */ + public static jalview.binding.Feature unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.Feature) Unmarshaller.unmarshal(jalview.binding.Features.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/JGroup.java b/src/jalview/binding/JGroup.java index 6473149..862eebd 100755 --- a/src/jalview/binding/JGroup.java +++ b/src/jalview/binding/JGroup.java @@ -1,750 +1,739 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class JGroup. - * - * @version $Revision$ $Date$ - */ -public class JGroup implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _start - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Field _end - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - /** - * Field _name - */ - private java.lang.String _name; - - /** - * Field _colour - */ - private java.lang.String _colour; - - /** - * Field _consThreshold - */ - private int _consThreshold; - - /** - * keeps track of state for field: _consThreshold - */ - private boolean _has_consThreshold; - - /** - * Field _pidThreshold - */ - private int _pidThreshold; - - /** - * keeps track of state for field: _pidThreshold - */ - private boolean _has_pidThreshold; - - /** - * Field _outlineColour - */ - private int _outlineColour; - - /** - * keeps track of state for field: _outlineColour - */ - private boolean _has_outlineColour; - - /** - * Field _displayBoxes - */ - private boolean _displayBoxes; - - /** - * keeps track of state for field: _displayBoxes - */ - private boolean _has_displayBoxes; - - /** - * Field _displayText - */ - private boolean _displayText; - - /** - * keeps track of state for field: _displayText - */ - private boolean _has_displayText; - - /** - * Field _colourText - */ - private boolean _colourText; - - /** - * keeps track of state for field: _colourText - */ - private boolean _has_colourText; - - /** - * Field _seqList - */ - private java.util.Vector _seqList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public JGroup() { - super(); - _seqList = new Vector(); - } //-- jalview.binding.JGroup() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addSeq - * - * - * - * @param vSeq - */ - public void addSeq(int vSeq) - throws java.lang.IndexOutOfBoundsException - { - _seqList.addElement(new java.lang.Integer(vSeq)); - } //-- void addSeq(int) - - /** - * Method addSeq - * - * - * - * @param index - * @param vSeq - */ - public void addSeq(int index, int vSeq) - throws java.lang.IndexOutOfBoundsException - { - _seqList.insertElementAt(new java.lang.Integer(vSeq), index); - } //-- void addSeq(int, int) - - /** - * Method deleteColourText - * - */ - public void deleteColourText() - { - this._has_colourText= false; - } //-- void deleteColourText() - - /** - * Method deleteConsThreshold - * - */ - public void deleteConsThreshold() - { - this._has_consThreshold= false; - } //-- void deleteConsThreshold() - - /** - * Method deleteDisplayBoxes - * - */ - public void deleteDisplayBoxes() - { - this._has_displayBoxes= false; - } //-- void deleteDisplayBoxes() - - /** - * Method deleteDisplayText - * - */ - public void deleteDisplayText() - { - this._has_displayText= false; - } //-- void deleteDisplayText() - - /** - * Method deleteEnd - * - */ - public void deleteEnd() - { - this._has_end= false; - } //-- void deleteEnd() - - /** - * Method deleteOutlineColour - * - */ - public void deleteOutlineColour() - { - this._has_outlineColour= false; - } //-- void deleteOutlineColour() - - /** - * Method deletePidThreshold - * - */ - public void deletePidThreshold() - { - this._has_pidThreshold= false; - } //-- void deletePidThreshold() - - /** - * Method deleteStart - * - */ - public void deleteStart() - { - this._has_start= false; - } //-- void deleteStart() - - /** - * Method enumerateSeq - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateSeq() - { - return _seqList.elements(); - } //-- java.util.Enumeration enumerateSeq() - - /** - * Returns the value of field 'colour'. - * - * @return String - * @return the value of field 'colour'. - */ - public java.lang.String getColour() - { - return this._colour; - } //-- java.lang.String getColour() - - /** - * Returns the value of field 'colourText'. - * - * @return boolean - * @return the value of field 'colourText'. - */ - public boolean getColourText() - { - return this._colourText; - } //-- boolean getColourText() - - /** - * Returns the value of field 'consThreshold'. - * - * @return int - * @return the value of field 'consThreshold'. - */ - public int getConsThreshold() - { - return this._consThreshold; - } //-- int getConsThreshold() - - /** - * Returns the value of field 'displayBoxes'. - * - * @return boolean - * @return the value of field 'displayBoxes'. - */ - public boolean getDisplayBoxes() - { - return this._displayBoxes; - } //-- boolean getDisplayBoxes() - - /** - * Returns the value of field 'displayText'. - * - * @return boolean - * @return the value of field 'displayText'. - */ - public boolean getDisplayText() - { - return this._displayText; - } //-- boolean getDisplayText() - - /** - * Returns the value of field 'end'. - * - * @return int - * @return the value of field 'end'. - */ - public int getEnd() - { - return this._end; - } //-- int getEnd() - - /** - * Returns the value of field 'name'. - * - * @return String - * @return the value of field 'name'. - */ - public java.lang.String getName() - { - return this._name; - } //-- java.lang.String getName() - - /** - * Returns the value of field 'outlineColour'. - * - * @return int - * @return the value of field 'outlineColour'. - */ - public int getOutlineColour() - { - return this._outlineColour; - } //-- int getOutlineColour() - - /** - * Returns the value of field 'pidThreshold'. - * - * @return int - * @return the value of field 'pidThreshold'. - */ - public int getPidThreshold() - { - return this._pidThreshold; - } //-- int getPidThreshold() - - /** - * Method getSeq - * - * - * - * @param index - * @return int - */ - public int getSeq(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _seqList.size())) { - throw new IndexOutOfBoundsException(); - } - - return ((java.lang.Integer)_seqList.elementAt(index)).intValue(); - } //-- int getSeq(int) - - /** - * Method getSeq - * - * - * - * @return int - */ - public int[] getSeq() - { - int size = _seqList.size(); - int[] mArray = new int[size]; - for (int index = 0; index < size; index++) { - mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue(); - } - return mArray; - } //-- int[] getSeq() - - /** - * Method getSeqCount - * - * - * - * @return int - */ - public int getSeqCount() - { - return _seqList.size(); - } //-- int getSeqCount() - - /** - * Returns the value of field 'start'. - * - * @return int - * @return the value of field 'start'. - */ - public int getStart() - { - return this._start; - } //-- int getStart() - - /** - * Method hasColourText - * - * - * - * @return boolean - */ - public boolean hasColourText() - { - return this._has_colourText; - } //-- boolean hasColourText() - - /** - * Method hasConsThreshold - * - * - * - * @return boolean - */ - public boolean hasConsThreshold() - { - return this._has_consThreshold; - } //-- boolean hasConsThreshold() - - /** - * Method hasDisplayBoxes - * - * - * - * @return boolean - */ - public boolean hasDisplayBoxes() - { - return this._has_displayBoxes; - } //-- boolean hasDisplayBoxes() - - /** - * Method hasDisplayText - * - * - * - * @return boolean - */ - public boolean hasDisplayText() - { - return this._has_displayText; - } //-- boolean hasDisplayText() - - /** - * Method hasEnd - * - * - * - * @return boolean - */ - public boolean hasEnd() - { - return this._has_end; - } //-- boolean hasEnd() - - /** - * Method hasOutlineColour - * - * - * - * @return boolean - */ - public boolean hasOutlineColour() - { - return this._has_outlineColour; - } //-- boolean hasOutlineColour() - - /** - * Method hasPidThreshold - * - * - * - * @return boolean - */ - public boolean hasPidThreshold() - { - return this._has_pidThreshold; - } //-- boolean hasPidThreshold() - - /** - * Method hasStart - * - * - * - * @return boolean - */ - public boolean hasStart() - { - return this._has_start; - } //-- boolean hasStart() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllSeq - * - */ - public void removeAllSeq() - { - _seqList.removeAllElements(); - } //-- void removeAllSeq() - - /** - * Method removeSeq - * - * - * - * @param index - * @return int - */ - public int removeSeq(int index) - { - java.lang.Object obj = _seqList.elementAt(index); - _seqList.removeElementAt(index); - return ((java.lang.Integer)obj).intValue(); - } //-- int removeSeq(int) - - /** - * Sets the value of field 'colour'. - * - * @param colour the value of field 'colour'. - */ - public void setColour(java.lang.String colour) - { - this._colour = colour; - } //-- void setColour(java.lang.String) - - /** - * Sets the value of field 'colourText'. - * - * @param colourText the value of field 'colourText'. - */ - public void setColourText(boolean colourText) - { - this._colourText = colourText; - this._has_colourText = true; - } //-- void setColourText(boolean) - - /** - * Sets the value of field 'consThreshold'. - * - * @param consThreshold the value of field 'consThreshold'. - */ - public void setConsThreshold(int consThreshold) - { - this._consThreshold = consThreshold; - this._has_consThreshold = true; - } //-- void setConsThreshold(int) - - /** - * Sets the value of field 'displayBoxes'. - * - * @param displayBoxes the value of field 'displayBoxes'. - */ - public void setDisplayBoxes(boolean displayBoxes) - { - this._displayBoxes = displayBoxes; - this._has_displayBoxes = true; - } //-- void setDisplayBoxes(boolean) - - /** - * Sets the value of field 'displayText'. - * - * @param displayText the value of field 'displayText'. - */ - public void setDisplayText(boolean displayText) - { - this._displayText = displayText; - this._has_displayText = true; - } //-- void setDisplayText(boolean) - - /** - * Sets the value of field 'end'. - * - * @param end the value of field 'end'. - */ - public void setEnd(int end) - { - this._end = end; - this._has_end = true; - } //-- void setEnd(int) - - /** - * Sets the value of field 'name'. - * - * @param name the value of field 'name'. - */ - public void setName(java.lang.String name) - { - this._name = name; - } //-- void setName(java.lang.String) - - /** - * Sets the value of field 'outlineColour'. - * - * @param outlineColour the value of field 'outlineColour'. - */ - public void setOutlineColour(int outlineColour) - { - this._outlineColour = outlineColour; - this._has_outlineColour = true; - } //-- void setOutlineColour(int) - - /** - * Sets the value of field 'pidThreshold'. - * - * @param pidThreshold the value of field 'pidThreshold'. - */ - public void setPidThreshold(int pidThreshold) - { - this._pidThreshold = pidThreshold; - this._has_pidThreshold = true; - } //-- void setPidThreshold(int) - - /** - * Method setSeq - * - * - * - * @param index - * @param vSeq - */ - public void setSeq(int index, int vSeq) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _seqList.size())) { - throw new IndexOutOfBoundsException(); - } - _seqList.setElementAt(new java.lang.Integer(vSeq), index); - } //-- void setSeq(int, int) - - /** - * Method setSeq - * - * - * - * @param seqArray - */ - public void setSeq(int[] seqArray) - { - //-- copy array - _seqList.removeAllElements(); - for (int i = 0; i < seqArray.length; i++) { - _seqList.addElement(new java.lang.Integer(seqArray[i])); - } - } //-- void setSeq(int) - - /** - * Sets the value of field 'start'. - * - * @param start the value of field 'start'. - */ - public void setStart(int start) - { - this._start = start; - this._has_start = true; - } //-- void setStart(int) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class JGroup. + * + * @version $Revision$ $Date$ + */ +public class JGroup implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _start. + */ + private int _start; + + /** + * keeps track of state for field: _start + */ + private boolean _has_start; + + /** + * Field _end. + */ + private int _end; + + /** + * keeps track of state for field: _end + */ + private boolean _has_end; + + /** + * Field _name. + */ + private java.lang.String _name; + + /** + * Field _colour. + */ + private java.lang.String _colour; + + /** + * Field _consThreshold. + */ + private int _consThreshold; + + /** + * keeps track of state for field: _consThreshold + */ + private boolean _has_consThreshold; + + /** + * Field _pidThreshold. + */ + private int _pidThreshold; + + /** + * keeps track of state for field: _pidThreshold + */ + private boolean _has_pidThreshold; + + /** + * Field _outlineColour. + */ + private int _outlineColour; + + /** + * keeps track of state for field: _outlineColour + */ + private boolean _has_outlineColour; + + /** + * Field _displayBoxes. + */ + private boolean _displayBoxes; + + /** + * keeps track of state for field: _displayBoxes + */ + private boolean _has_displayBoxes; + + /** + * Field _displayText. + */ + private boolean _displayText; + + /** + * keeps track of state for field: _displayText + */ + private boolean _has_displayText; + + /** + * Field _colourText. + */ + private boolean _colourText; + + /** + * keeps track of state for field: _colourText + */ + private boolean _has_colourText; + + /** + * Field _seqList. + */ + private java.util.Vector _seqList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JGroup() { + super(); + this._seqList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vSeq + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSeq( + final int vSeq) + throws java.lang.IndexOutOfBoundsException { + this._seqList.addElement(new java.lang.Integer(vSeq)); + } + + /** + * + * + * @param index + * @param vSeq + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSeq( + final int index, + final int vSeq) + throws java.lang.IndexOutOfBoundsException { + this._seqList.add(index, new java.lang.Integer(vSeq)); + } + + /** + */ + public void deleteColourText( + ) { + this._has_colourText= false; + } + + /** + */ + public void deleteConsThreshold( + ) { + this._has_consThreshold= false; + } + + /** + */ + public void deleteDisplayBoxes( + ) { + this._has_displayBoxes= false; + } + + /** + */ + public void deleteDisplayText( + ) { + this._has_displayText= false; + } + + /** + */ + public void deleteEnd( + ) { + this._has_end= false; + } + + /** + */ + public void deleteOutlineColour( + ) { + this._has_outlineColour= false; + } + + /** + */ + public void deletePidThreshold( + ) { + this._has_pidThreshold= false; + } + + /** + */ + public void deleteStart( + ) { + this._has_start= false; + } + + /** + * Method enumerateSeq. + * + * @return an Enumeration over all int elements + */ + public java.util.Enumeration enumerateSeq( + ) { + return this._seqList.elements(); + } + + /** + * Returns the value of field 'colour'. + * + * @return the value of field 'Colour'. + */ + public java.lang.String getColour( + ) { + return this._colour; + } + + /** + * Returns the value of field 'colourText'. + * + * @return the value of field 'ColourText'. + */ + public boolean getColourText( + ) { + return this._colourText; + } + + /** + * Returns the value of field 'consThreshold'. + * + * @return the value of field 'ConsThreshold'. + */ + public int getConsThreshold( + ) { + return this._consThreshold; + } + + /** + * Returns the value of field 'displayBoxes'. + * + * @return the value of field 'DisplayBoxes'. + */ + public boolean getDisplayBoxes( + ) { + return this._displayBoxes; + } + + /** + * Returns the value of field 'displayText'. + * + * @return the value of field 'DisplayText'. + */ + public boolean getDisplayText( + ) { + return this._displayText; + } + + /** + * Returns the value of field 'end'. + * + * @return the value of field 'End'. + */ + public int getEnd( + ) { + return this._end; + } + + /** + * Returns the value of field 'name'. + * + * @return the value of field 'Name'. + */ + public java.lang.String getName( + ) { + return this._name; + } + + /** + * Returns the value of field 'outlineColour'. + * + * @return the value of field 'OutlineColour'. + */ + public int getOutlineColour( + ) { + return this._outlineColour; + } + + /** + * Returns the value of field 'pidThreshold'. + * + * @return the value of field 'PidThreshold'. + */ + public int getPidThreshold( + ) { + return this._pidThreshold; + } + + /** + * Method getSeq. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the int at the given index + */ + public int getSeq( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._seqList.size()) { + throw new IndexOutOfBoundsException("getSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]"); + } + + return ((java.lang.Integer) _seqList.get(index)).intValue(); + } + + /** + * Method getSeq.Returns the contents of the collection in an + * Array. + * + * @return this collection as an Array + */ + public int[] getSeq( + ) { + int size = this._seqList.size(); + int[] array = new int[size]; + java.util.Iterator iter = _seqList.iterator(); + for (int index = 0; index < size; index++) { + array[index] = ((java.lang.Integer) iter.next()).intValue(); + } + return array; + } + + /** + * Method getSeqCount. + * + * @return the size of this collection + */ + public int getSeqCount( + ) { + return this._seqList.size(); + } + + /** + * Returns the value of field 'start'. + * + * @return the value of field 'Start'. + */ + public int getStart( + ) { + return this._start; + } + + /** + * Method hasColourText. + * + * @return true if at least one ColourText has been added + */ + public boolean hasColourText( + ) { + return this._has_colourText; + } + + /** + * Method hasConsThreshold. + * + * @return true if at least one ConsThreshold has been added + */ + public boolean hasConsThreshold( + ) { + return this._has_consThreshold; + } + + /** + * Method hasDisplayBoxes. + * + * @return true if at least one DisplayBoxes has been added + */ + public boolean hasDisplayBoxes( + ) { + return this._has_displayBoxes; + } + + /** + * Method hasDisplayText. + * + * @return true if at least one DisplayText has been added + */ + public boolean hasDisplayText( + ) { + return this._has_displayText; + } + + /** + * Method hasEnd. + * + * @return true if at least one End has been added + */ + public boolean hasEnd( + ) { + return this._has_end; + } + + /** + * Method hasOutlineColour. + * + * @return true if at least one OutlineColour has been added + */ + public boolean hasOutlineColour( + ) { + return this._has_outlineColour; + } + + /** + * Method hasPidThreshold. + * + * @return true if at least one PidThreshold has been added + */ + public boolean hasPidThreshold( + ) { + return this._has_pidThreshold; + } + + /** + * Method hasStart. + * + * @return true if at least one Start has been added + */ + public boolean hasStart( + ) { + return this._has_start; + } + + /** + * Returns the value of field 'colourText'. + * + * @return the value of field 'ColourText'. + */ + public boolean isColourText( + ) { + return this._colourText; + } + + /** + * Returns the value of field 'displayBoxes'. + * + * @return the value of field 'DisplayBoxes'. + */ + public boolean isDisplayBoxes( + ) { + return this._displayBoxes; + } + + /** + * Returns the value of field 'displayText'. + * + * @return the value of field 'DisplayText'. + */ + public boolean isDisplayText( + ) { + return this._displayText; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllSeq( + ) { + this._seqList.clear(); + } + + /** + * Method removeSeq. + * + * @param vSeq + * @return true if the object was removed from the collection. + */ + public boolean removeSeq( + final int vSeq) { + boolean removed = _seqList.remove(new java.lang.Integer(vSeq)); + return removed; + } + + /** + * Method removeSeqAt. + * + * @param index + * @return the element removed from the collection + */ + public int removeSeqAt( + final int index) { + java.lang.Object obj = this._seqList.remove(index); + return ((java.lang.Integer) obj).intValue(); + } + + /** + * Sets the value of field 'colour'. + * + * @param colour the value of field 'colour'. + */ + public void setColour( + final java.lang.String colour) { + this._colour = colour; + } + + /** + * Sets the value of field 'colourText'. + * + * @param colourText the value of field 'colourText'. + */ + public void setColourText( + final boolean colourText) { + this._colourText = colourText; + this._has_colourText = true; + } + + /** + * Sets the value of field 'consThreshold'. + * + * @param consThreshold the value of field 'consThreshold'. + */ + public void setConsThreshold( + final int consThreshold) { + this._consThreshold = consThreshold; + this._has_consThreshold = true; + } + + /** + * Sets the value of field 'displayBoxes'. + * + * @param displayBoxes the value of field 'displayBoxes'. + */ + public void setDisplayBoxes( + final boolean displayBoxes) { + this._displayBoxes = displayBoxes; + this._has_displayBoxes = true; + } + + /** + * Sets the value of field 'displayText'. + * + * @param displayText the value of field 'displayText'. + */ + public void setDisplayText( + final boolean displayText) { + this._displayText = displayText; + this._has_displayText = true; + } + + /** + * Sets the value of field 'end'. + * + * @param end the value of field 'end'. + */ + public void setEnd( + final int end) { + this._end = end; + this._has_end = true; + } + + /** + * Sets the value of field 'name'. + * + * @param name the value of field 'name'. + */ + public void setName( + final java.lang.String name) { + this._name = name; + } + + /** + * Sets the value of field 'outlineColour'. + * + * @param outlineColour the value of field 'outlineColour'. + */ + public void setOutlineColour( + final int outlineColour) { + this._outlineColour = outlineColour; + this._has_outlineColour = true; + } + + /** + * Sets the value of field 'pidThreshold'. + * + * @param pidThreshold the value of field 'pidThreshold'. + */ + public void setPidThreshold( + final int pidThreshold) { + this._pidThreshold = pidThreshold; + this._has_pidThreshold = true; + } + + /** + * + * + * @param index + * @param vSeq + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setSeq( + final int index, + final int vSeq) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._seqList.size()) { + throw new IndexOutOfBoundsException("setSeq: Index value '" + index + "' not in range [0.." + (this._seqList.size() - 1) + "]"); + } + + this._seqList.set(index, new java.lang.Integer(vSeq)); + } + + /** + * + * + * @param vSeqArray + */ + public void setSeq( + final int[] vSeqArray) { + //-- copy array + _seqList.clear(); + + for (int i = 0; i < vSeqArray.length; i++) { + this._seqList.add(new java.lang.Integer(vSeqArray[i])); + } + } + + /** + * Sets the value of field 'start'. + * + * @param start the value of field 'start'. + */ + public void setStart( + final int start) { + this._start = start; + this._has_start = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.JGroup + */ + public static jalview.binding.JGroup unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java index ee55945..14b1f2f 100755 --- a/src/jalview/binding/JSeq.java +++ b/src/jalview/binding/JSeq.java @@ -1,637 +1,623 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class JSeq. - * - * @version $Revision$ $Date$ - */ -public class JSeq implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _colour - */ - private int _colour; - - /** - * keeps track of state for field: _colour - */ - private boolean _has_colour; - - /** - * Field _start - */ - private int _start; - - /** - * keeps track of state for field: _start - */ - private boolean _has_start; - - /** - * Field _end - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - /** - * Field _id - */ - private int _id; - - /** - * keeps track of state for field: _id - */ - private boolean _has_id; - - /** - * Field _featuresList - */ - private java.util.Vector _featuresList; - - /** - * Field _pdbidsList - */ - private java.util.Vector _pdbidsList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public JSeq() { - super(); - _featuresList = new Vector(); - _pdbidsList = new Vector(); - } //-- jalview.binding.JSeq() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addFeatures - * - * - * - * @param vFeatures - */ - public void addFeatures(jalview.binding.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - _featuresList.addElement(vFeatures); - } //-- void addFeatures(jalview.binding.Features) - - /** - * Method addFeatures - * - * - * - * @param index - * @param vFeatures - */ - public void addFeatures(int index, jalview.binding.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - _featuresList.insertElementAt(vFeatures, index); - } //-- void addFeatures(int, jalview.binding.Features) - - /** - * Method addPdbids - * - * - * - * @param vPdbids - */ - public void addPdbids(jalview.binding.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException - { - _pdbidsList.addElement(vPdbids); - } //-- void addPdbids(jalview.binding.Pdbids) - - /** - * Method addPdbids - * - * - * - * @param index - * @param vPdbids - */ - public void addPdbids(int index, jalview.binding.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException - { - _pdbidsList.insertElementAt(vPdbids, index); - } //-- void addPdbids(int, jalview.binding.Pdbids) - - /** - * Method deleteColour - * - */ - public void deleteColour() - { - this._has_colour= false; - } //-- void deleteColour() - - /** - * Method deleteEnd - * - */ - public void deleteEnd() - { - this._has_end= false; - } //-- void deleteEnd() - - /** - * Method deleteId - * - */ - public void deleteId() - { - this._has_id= false; - } //-- void deleteId() - - /** - * Method deleteStart - * - */ - public void deleteStart() - { - this._has_start= false; - } //-- void deleteStart() - - /** - * Method enumerateFeatures - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateFeatures() - { - return _featuresList.elements(); - } //-- java.util.Enumeration enumerateFeatures() - - /** - * Method enumeratePdbids - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumeratePdbids() - { - return _pdbidsList.elements(); - } //-- java.util.Enumeration enumeratePdbids() - - /** - * Returns the value of field 'colour'. - * - * @return int - * @return the value of field 'colour'. - */ - public int getColour() - { - return this._colour; - } //-- int getColour() - - /** - * Returns the value of field 'end'. - * - * @return int - * @return the value of field 'end'. - */ - public int getEnd() - { - return this._end; - } //-- int getEnd() - - /** - * Method getFeatures - * - * - * - * @param index - * @return Features - */ - public jalview.binding.Features getFeatures(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _featuresList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.Features) _featuresList.elementAt(index); - } //-- jalview.binding.Features getFeatures(int) - - /** - * Method getFeatures - * - * - * - * @return Features - */ - public jalview.binding.Features[] getFeatures() - { - int size = _featuresList.size(); - jalview.binding.Features[] mArray = new jalview.binding.Features[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.Features) _featuresList.elementAt(index); - } - return mArray; - } //-- jalview.binding.Features[] getFeatures() - - /** - * Method getFeaturesCount - * - * - * - * @return int - */ - public int getFeaturesCount() - { - return _featuresList.size(); - } //-- int getFeaturesCount() - - /** - * Returns the value of field 'id'. - * - * @return int - * @return the value of field 'id'. - */ - public int getId() - { - return this._id; - } //-- int getId() - - /** - * Method getPdbids - * - * - * - * @param index - * @return Pdbids - */ - public jalview.binding.Pdbids getPdbids(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _pdbidsList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.Pdbids) _pdbidsList.elementAt(index); - } //-- jalview.binding.Pdbids getPdbids(int) - - /** - * Method getPdbids - * - * - * - * @return Pdbids - */ - public jalview.binding.Pdbids[] getPdbids() - { - int size = _pdbidsList.size(); - jalview.binding.Pdbids[] mArray = new jalview.binding.Pdbids[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.Pdbids) _pdbidsList.elementAt(index); - } - return mArray; - } //-- jalview.binding.Pdbids[] getPdbids() - - /** - * Method getPdbidsCount - * - * - * - * @return int - */ - public int getPdbidsCount() - { - return _pdbidsList.size(); - } //-- int getPdbidsCount() - - /** - * Returns the value of field 'start'. - * - * @return int - * @return the value of field 'start'. - */ - public int getStart() - { - return this._start; - } //-- int getStart() - - /** - * Method hasColour - * - * - * - * @return boolean - */ - public boolean hasColour() - { - return this._has_colour; - } //-- boolean hasColour() - - /** - * Method hasEnd - * - * - * - * @return boolean - */ - public boolean hasEnd() - { - return this._has_end; - } //-- boolean hasEnd() - - /** - * Method hasId - * - * - * - * @return boolean - */ - public boolean hasId() - { - return this._has_id; - } //-- boolean hasId() - - /** - * Method hasStart - * - * - * - * @return boolean - */ - public boolean hasStart() - { - return this._has_start; - } //-- boolean hasStart() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllFeatures - * - */ - public void removeAllFeatures() - { - _featuresList.removeAllElements(); - } //-- void removeAllFeatures() - - /** - * Method removeAllPdbids - * - */ - public void removeAllPdbids() - { - _pdbidsList.removeAllElements(); - } //-- void removeAllPdbids() - - /** - * Method removeFeatures - * - * - * - * @param index - * @return Features - */ - public jalview.binding.Features removeFeatures(int index) - { - java.lang.Object obj = _featuresList.elementAt(index); - _featuresList.removeElementAt(index); - return (jalview.binding.Features) obj; - } //-- jalview.binding.Features removeFeatures(int) - - /** - * Method removePdbids - * - * - * - * @param index - * @return Pdbids - */ - public jalview.binding.Pdbids removePdbids(int index) - { - java.lang.Object obj = _pdbidsList.elementAt(index); - _pdbidsList.removeElementAt(index); - return (jalview.binding.Pdbids) obj; - } //-- jalview.binding.Pdbids removePdbids(int) - - /** - * Sets the value of field 'colour'. - * - * @param colour the value of field 'colour'. - */ - public void setColour(int colour) - { - this._colour = colour; - this._has_colour = true; - } //-- void setColour(int) - - /** - * Sets the value of field 'end'. - * - * @param end the value of field 'end'. - */ - public void setEnd(int end) - { - this._end = end; - this._has_end = true; - } //-- void setEnd(int) - - /** - * Method setFeatures - * - * - * - * @param index - * @param vFeatures - */ - public void setFeatures(int index, jalview.binding.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _featuresList.size())) { - throw new IndexOutOfBoundsException(); - } - _featuresList.setElementAt(vFeatures, index); - } //-- void setFeatures(int, jalview.binding.Features) - - /** - * Method setFeatures - * - * - * - * @param featuresArray - */ - public void setFeatures(jalview.binding.Features[] featuresArray) - { - //-- copy array - _featuresList.removeAllElements(); - for (int i = 0; i < featuresArray.length; i++) { - _featuresList.addElement(featuresArray[i]); - } - } //-- void setFeatures(jalview.binding.Features) - - /** - * Sets the value of field 'id'. - * - * @param id the value of field 'id'. - */ - public void setId(int id) - { - this._id = id; - this._has_id = true; - } //-- void setId(int) - - /** - * Method setPdbids - * - * - * - * @param index - * @param vPdbids - */ - public void setPdbids(int index, jalview.binding.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _pdbidsList.size())) { - throw new IndexOutOfBoundsException(); - } - _pdbidsList.setElementAt(vPdbids, index); - } //-- void setPdbids(int, jalview.binding.Pdbids) - - /** - * Method setPdbids - * - * - * - * @param pdbidsArray - */ - public void setPdbids(jalview.binding.Pdbids[] pdbidsArray) - { - //-- copy array - _pdbidsList.removeAllElements(); - for (int i = 0; i < pdbidsArray.length; i++) { - _pdbidsList.addElement(pdbidsArray[i]); - } - } //-- void setPdbids(jalview.binding.Pdbids) - - /** - * Sets the value of field 'start'. - * - * @param start the value of field 'start'. - */ - public void setStart(int start) - { - this._start = start; - this._has_start = true; - } //-- void setStart(int) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class JSeq. + * + * @version $Revision$ $Date$ + */ +public class JSeq implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _colour. + */ + private int _colour; + + /** + * keeps track of state for field: _colour + */ + private boolean _has_colour; + + /** + * Field _start. + */ + private int _start; + + /** + * keeps track of state for field: _start + */ + private boolean _has_start; + + /** + * Field _end. + */ + private int _end; + + /** + * keeps track of state for field: _end + */ + private boolean _has_end; + + /** + * Field _id. + */ + private int _id; + + /** + * keeps track of state for field: _id + */ + private boolean _has_id; + + /** + * Field _featuresList. + */ + private java.util.Vector _featuresList; + + /** + * Field _pdbidsList. + */ + private java.util.Vector _pdbidsList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JSeq() { + super(); + this._featuresList = new java.util.Vector(); + this._pdbidsList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vFeatures + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addFeatures( + final jalview.binding.Features vFeatures) + throws java.lang.IndexOutOfBoundsException { + this._featuresList.addElement(vFeatures); + } + + /** + * + * + * @param index + * @param vFeatures + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addFeatures( + final int index, + final jalview.binding.Features vFeatures) + throws java.lang.IndexOutOfBoundsException { + this._featuresList.add(index, vFeatures); + } + + /** + * + * + * @param vPdbids + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addPdbids( + final jalview.binding.Pdbids vPdbids) + throws java.lang.IndexOutOfBoundsException { + this._pdbidsList.addElement(vPdbids); + } + + /** + * + * + * @param index + * @param vPdbids + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addPdbids( + final int index, + final jalview.binding.Pdbids vPdbids) + throws java.lang.IndexOutOfBoundsException { + this._pdbidsList.add(index, vPdbids); + } + + /** + */ + public void deleteColour( + ) { + this._has_colour= false; + } + + /** + */ + public void deleteEnd( + ) { + this._has_end= false; + } + + /** + */ + public void deleteId( + ) { + this._has_id= false; + } + + /** + */ + public void deleteStart( + ) { + this._has_start= false; + } + + /** + * Method enumerateFeatures. + * + * @return an Enumeration over all jalview.binding.Features + * elements + */ + public java.util.Enumeration enumerateFeatures( + ) { + return this._featuresList.elements(); + } + + /** + * Method enumeratePdbids. + * + * @return an Enumeration over all jalview.binding.Pdbids + * elements + */ + public java.util.Enumeration enumeratePdbids( + ) { + return this._pdbidsList.elements(); + } + + /** + * Returns the value of field 'colour'. + * + * @return the value of field 'Colour'. + */ + public int getColour( + ) { + return this._colour; + } + + /** + * Returns the value of field 'end'. + * + * @return the value of field 'End'. + */ + public int getEnd( + ) { + return this._end; + } + + /** + * Method getFeatures. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the jalview.binding.Features at the + * given index + */ + public jalview.binding.Features getFeatures( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._featuresList.size()) { + throw new IndexOutOfBoundsException("getFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]"); + } + + return (jalview.binding.Features) _featuresList.get(index); + } + + /** + * Method getFeatures.Returns the contents of the collection in + * an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.binding.Features[] getFeatures( + ) { + jalview.binding.Features[] array = new jalview.binding.Features[0]; + return (jalview.binding.Features[]) this._featuresList.toArray(array); + } + + /** + * Method getFeaturesCount. + * + * @return the size of this collection + */ + public int getFeaturesCount( + ) { + return this._featuresList.size(); + } + + /** + * Returns the value of field 'id'. + * + * @return the value of field 'Id'. + */ + public int getId( + ) { + return this._id; + } + + /** + * Method getPdbids. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the jalview.binding.Pdbids at the given + * index + */ + public jalview.binding.Pdbids getPdbids( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._pdbidsList.size()) { + throw new IndexOutOfBoundsException("getPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]"); + } + + return (jalview.binding.Pdbids) _pdbidsList.get(index); + } + + /** + * Method getPdbids.Returns the contents of the collection in + * an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.binding.Pdbids[] getPdbids( + ) { + jalview.binding.Pdbids[] array = new jalview.binding.Pdbids[0]; + return (jalview.binding.Pdbids[]) this._pdbidsList.toArray(array); + } + + /** + * Method getPdbidsCount. + * + * @return the size of this collection + */ + public int getPdbidsCount( + ) { + return this._pdbidsList.size(); + } + + /** + * Returns the value of field 'start'. + * + * @return the value of field 'Start'. + */ + public int getStart( + ) { + return this._start; + } + + /** + * Method hasColour. + * + * @return true if at least one Colour has been added + */ + public boolean hasColour( + ) { + return this._has_colour; + } + + /** + * Method hasEnd. + * + * @return true if at least one End has been added + */ + public boolean hasEnd( + ) { + return this._has_end; + } + + /** + * Method hasId. + * + * @return true if at least one Id has been added + */ + public boolean hasId( + ) { + return this._has_id; + } + + /** + * Method hasStart. + * + * @return true if at least one Start has been added + */ + public boolean hasStart( + ) { + return this._has_start; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllFeatures( + ) { + this._featuresList.clear(); + } + + /** + */ + public void removeAllPdbids( + ) { + this._pdbidsList.clear(); + } + + /** + * Method removeFeatures. + * + * @param vFeatures + * @return true if the object was removed from the collection. + */ + public boolean removeFeatures( + final jalview.binding.Features vFeatures) { + boolean removed = _featuresList.remove(vFeatures); + return removed; + } + + /** + * Method removeFeaturesAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.Features removeFeaturesAt( + final int index) { + java.lang.Object obj = this._featuresList.remove(index); + return (jalview.binding.Features) obj; + } + + /** + * Method removePdbids. + * + * @param vPdbids + * @return true if the object was removed from the collection. + */ + public boolean removePdbids( + final jalview.binding.Pdbids vPdbids) { + boolean removed = _pdbidsList.remove(vPdbids); + return removed; + } + + /** + * Method removePdbidsAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.Pdbids removePdbidsAt( + final int index) { + java.lang.Object obj = this._pdbidsList.remove(index); + return (jalview.binding.Pdbids) obj; + } + + /** + * Sets the value of field 'colour'. + * + * @param colour the value of field 'colour'. + */ + public void setColour( + final int colour) { + this._colour = colour; + this._has_colour = true; + } + + /** + * Sets the value of field 'end'. + * + * @param end the value of field 'end'. + */ + public void setEnd( + final int end) { + this._end = end; + this._has_end = true; + } + + /** + * + * + * @param index + * @param vFeatures + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setFeatures( + final int index, + final jalview.binding.Features vFeatures) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._featuresList.size()) { + throw new IndexOutOfBoundsException("setFeatures: Index value '" + index + "' not in range [0.." + (this._featuresList.size() - 1) + "]"); + } + + this._featuresList.set(index, vFeatures); + } + + /** + * + * + * @param vFeaturesArray + */ + public void setFeatures( + final jalview.binding.Features[] vFeaturesArray) { + //-- copy array + _featuresList.clear(); + + for (int i = 0; i < vFeaturesArray.length; i++) { + this._featuresList.add(vFeaturesArray[i]); + } + } + + /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId( + final int id) { + this._id = id; + this._has_id = true; + } + + /** + * + * + * @param index + * @param vPdbids + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setPdbids( + final int index, + final jalview.binding.Pdbids vPdbids) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._pdbidsList.size()) { + throw new IndexOutOfBoundsException("setPdbids: Index value '" + index + "' not in range [0.." + (this._pdbidsList.size() - 1) + "]"); + } + + this._pdbidsList.set(index, vPdbids); + } + + /** + * + * + * @param vPdbidsArray + */ + public void setPdbids( + final jalview.binding.Pdbids[] vPdbidsArray) { + //-- copy array + _pdbidsList.clear(); + + for (int i = 0; i < vPdbidsArray.length; i++) { + this._pdbidsList.add(vPdbidsArray[i]); + } + } + + /** + * Sets the value of field 'start'. + * + * @param start the value of field 'start'. + */ + public void setStart( + final int start) { + this._start = start; + this._has_start = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.JSeq + */ + public static jalview.binding.JSeq unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/JalviewModel.java b/src/jalview/binding/JalviewModel.java index 8edd012..21f8be9 100755 --- a/src/jalview/binding/JalviewModel.java +++ b/src/jalview/binding/JalviewModel.java @@ -1,227 +1,220 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Date; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class JalviewModel. - * - * @version $Revision$ $Date$ - */ -public class JalviewModel implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _creationDate - */ - private java.util.Date _creationDate; - - /** - * Field _version - */ - private java.lang.String _version; - - /** - * Field _vamsasModel - */ - private jalview.binding.VamsasModel _vamsasModel; - - /** - * Field _jalviewModelSequence - */ - private jalview.binding.JalviewModelSequence _jalviewModelSequence; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public JalviewModel() { - super(); - } //-- jalview.binding.JalviewModel() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'creationDate'. - * - * @return Date - * @return the value of field 'creationDate'. - */ - public java.util.Date getCreationDate() - { - return this._creationDate; - } //-- java.util.Date getCreationDate() - - /** - * Returns the value of field 'jalviewModelSequence'. - * - * @return JalviewModelSequence - * @return the value of field 'jalviewModelSequence'. - */ - public jalview.binding.JalviewModelSequence getJalviewModelSequence() - { - return this._jalviewModelSequence; - } //-- jalview.binding.JalviewModelSequence getJalviewModelSequence() - - /** - * Returns the value of field 'vamsasModel'. - * - * @return VamsasModel - * @return the value of field 'vamsasModel'. - */ - public jalview.binding.VamsasModel getVamsasModel() - { - return this._vamsasModel; - } //-- jalview.binding.VamsasModel getVamsasModel() - - /** - * Returns the value of field 'version'. - * - * @return String - * @return the value of field 'version'. - */ - public java.lang.String getVersion() - { - return this._version; - } //-- java.lang.String getVersion() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'creationDate'. - * - * @param creationDate the value of field 'creationDate'. - */ - public void setCreationDate(java.util.Date creationDate) - { - this._creationDate = creationDate; - } //-- void setCreationDate(java.util.Date) - - /** - * Sets the value of field 'jalviewModelSequence'. - * - * @param jalviewModelSequence the value of field - * 'jalviewModelSequence'. - */ - public void setJalviewModelSequence(jalview.binding.JalviewModelSequence jalviewModelSequence) - { - this._jalviewModelSequence = jalviewModelSequence; - } //-- void setJalviewModelSequence(jalview.binding.JalviewModelSequence) - - /** - * Sets the value of field 'vamsasModel'. - * - * @param vamsasModel the value of field 'vamsasModel'. - */ - public void setVamsasModel(jalview.binding.VamsasModel vamsasModel) - { - this._vamsasModel = vamsasModel; - } //-- void setVamsasModel(jalview.binding.VamsasModel) - - /** - * Sets the value of field 'version'. - * - * @param version the value of field 'version'. - */ - public void setVersion(java.lang.String version) - { - this._version = version; - } //-- void setVersion(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class JalviewModel. + * + * @version $Revision$ $Date$ + */ +public class JalviewModel implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _creationDate. + */ + private java.util.Date _creationDate; + + /** + * Field _version. + */ + private java.lang.String _version; + + /** + * Field _vamsasModel. + */ + private jalview.binding.VamsasModel _vamsasModel; + + /** + * Field _jalviewModelSequence. + */ + private jalview.binding.JalviewModelSequence _jalviewModelSequence; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JalviewModel() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'creationDate'. + * + * @return the value of field 'CreationDate'. + */ + public java.util.Date getCreationDate( + ) { + return this._creationDate; + } + + /** + * Returns the value of field 'jalviewModelSequence'. + * + * @return the value of field 'JalviewModelSequence'. + */ + public jalview.binding.JalviewModelSequence getJalviewModelSequence( + ) { + return this._jalviewModelSequence; + } + + /** + * Returns the value of field 'vamsasModel'. + * + * @return the value of field 'VamsasModel'. + */ + public jalview.binding.VamsasModel getVamsasModel( + ) { + return this._vamsasModel; + } + + /** + * Returns the value of field 'version'. + * + * @return the value of field 'Version'. + */ + public java.lang.String getVersion( + ) { + return this._version; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'creationDate'. + * + * @param creationDate the value of field 'creationDate'. + */ + public void setCreationDate( + final java.util.Date creationDate) { + this._creationDate = creationDate; + } + + /** + * Sets the value of field 'jalviewModelSequence'. + * + * @param jalviewModelSequence the value of field + * 'jalviewModelSequence'. + */ + public void setJalviewModelSequence( + final jalview.binding.JalviewModelSequence jalviewModelSequence) { + this._jalviewModelSequence = jalviewModelSequence; + } + + /** + * Sets the value of field 'vamsasModel'. + * + * @param vamsasModel the value of field 'vamsasModel'. + */ + public void setVamsasModel( + final jalview.binding.VamsasModel vamsasModel) { + this._vamsasModel = vamsasModel; + } + + /** + * Sets the value of field 'version'. + * + * @param version the value of field 'version'. + */ + public void setVersion( + final java.lang.String version) { + this._version = version; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.JalviewModel + */ + public static jalview.binding.JalviewModel unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java index cbb50d5..5ebcee6 100755 --- a/src/jalview/binding/JalviewModelSequence.java +++ b/src/jalview/binding/JalviewModelSequence.java @@ -1,904 +1,922 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class JalviewModelSequence. - * - * @version $Revision$ $Date$ - */ -public class JalviewModelSequence implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _JSeqList - */ - private java.util.Vector _JSeqList; - - /** - * Field _JGroupList - */ - private java.util.Vector _JGroupList; - - /** - * Field _viewportList - */ - private java.util.Vector _viewportList; - - /** - * Field _userColoursList - */ - private java.util.Vector _userColoursList; - - /** - * Field _treeList - */ - private java.util.Vector _treeList; - - /** - * Field _featureSettings - */ - private jalview.binding.FeatureSettings _featureSettings; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public JalviewModelSequence() { - super(); - _JSeqList = new Vector(); - _JGroupList = new Vector(); - _viewportList = new Vector(); - _userColoursList = new Vector(); - _treeList = new Vector(); - } //-- jalview.binding.JalviewModelSequence() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addJGroup - * - * - * - * @param vJGroup - */ - public void addJGroup(jalview.binding.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException - { - _JGroupList.addElement(vJGroup); - } //-- void addJGroup(jalview.binding.JGroup) - - /** - * Method addJGroup - * - * - * - * @param index - * @param vJGroup - */ - public void addJGroup(int index, jalview.binding.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException - { - _JGroupList.insertElementAt(vJGroup, index); - } //-- void addJGroup(int, jalview.binding.JGroup) - - /** - * Method addJSeq - * - * - * - * @param vJSeq - */ - public void addJSeq(jalview.binding.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException - { - _JSeqList.addElement(vJSeq); - } //-- void addJSeq(jalview.binding.JSeq) - - /** - * Method addJSeq - * - * - * - * @param index - * @param vJSeq - */ - public void addJSeq(int index, jalview.binding.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException - { - _JSeqList.insertElementAt(vJSeq, index); - } //-- void addJSeq(int, jalview.binding.JSeq) - - /** - * Method addTree - * - * - * - * @param vTree - */ - public void addTree(jalview.binding.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.addElement(vTree); - } //-- void addTree(jalview.binding.Tree) - - /** - * Method addTree - * - * - * - * @param index - * @param vTree - */ - public void addTree(int index, jalview.binding.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.insertElementAt(vTree, index); - } //-- void addTree(int, jalview.binding.Tree) - - /** - * Method addUserColours - * - * - * - * @param vUserColours - */ - public void addUserColours(jalview.binding.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException - { - _userColoursList.addElement(vUserColours); - } //-- void addUserColours(jalview.binding.UserColours) - - /** - * Method addUserColours - * - * - * - * @param index - * @param vUserColours - */ - public void addUserColours(int index, jalview.binding.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException - { - _userColoursList.insertElementAt(vUserColours, index); - } //-- void addUserColours(int, jalview.binding.UserColours) - - /** - * Method addViewport - * - * - * - * @param vViewport - */ - public void addViewport(jalview.binding.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - _viewportList.addElement(vViewport); - } //-- void addViewport(jalview.binding.Viewport) - - /** - * Method addViewport - * - * - * - * @param index - * @param vViewport - */ - public void addViewport(int index, jalview.binding.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - _viewportList.insertElementAt(vViewport, index); - } //-- void addViewport(int, jalview.binding.Viewport) - - /** - * Method enumerateJGroup - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateJGroup() - { - return _JGroupList.elements(); - } //-- java.util.Enumeration enumerateJGroup() - - /** - * Method enumerateJSeq - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateJSeq() - { - return _JSeqList.elements(); - } //-- java.util.Enumeration enumerateJSeq() - - /** - * Method enumerateTree - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateTree() - { - return _treeList.elements(); - } //-- java.util.Enumeration enumerateTree() - - /** - * Method enumerateUserColours - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateUserColours() - { - return _userColoursList.elements(); - } //-- java.util.Enumeration enumerateUserColours() - - /** - * Method enumerateViewport - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateViewport() - { - return _viewportList.elements(); - } //-- java.util.Enumeration enumerateViewport() - - /** - * Returns the value of field 'featureSettings'. - * - * @return FeatureSettings - * @return the value of field 'featureSettings'. - */ - public jalview.binding.FeatureSettings getFeatureSettings() - { - return this._featureSettings; - } //-- jalview.binding.FeatureSettings getFeatureSettings() - - /** - * Method getJGroup - * - * - * - * @param index - * @return JGroup - */ - public jalview.binding.JGroup getJGroup(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _JGroupList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.JGroup) _JGroupList.elementAt(index); - } //-- jalview.binding.JGroup getJGroup(int) - - /** - * Method getJGroup - * - * - * - * @return JGroup - */ - public jalview.binding.JGroup[] getJGroup() - { - int size = _JGroupList.size(); - jalview.binding.JGroup[] mArray = new jalview.binding.JGroup[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.JGroup) _JGroupList.elementAt(index); - } - return mArray; - } //-- jalview.binding.JGroup[] getJGroup() - - /** - * Method getJGroupCount - * - * - * - * @return int - */ - public int getJGroupCount() - { - return _JGroupList.size(); - } //-- int getJGroupCount() - - /** - * Method getJSeq - * - * - * - * @param index - * @return JSeq - */ - public jalview.binding.JSeq getJSeq(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _JSeqList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.JSeq) _JSeqList.elementAt(index); - } //-- jalview.binding.JSeq getJSeq(int) - - /** - * Method getJSeq - * - * - * - * @return JSeq - */ - public jalview.binding.JSeq[] getJSeq() - { - int size = _JSeqList.size(); - jalview.binding.JSeq[] mArray = new jalview.binding.JSeq[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.JSeq) _JSeqList.elementAt(index); - } - return mArray; - } //-- jalview.binding.JSeq[] getJSeq() - - /** - * Method getJSeqCount - * - * - * - * @return int - */ - public int getJSeqCount() - { - return _JSeqList.size(); - } //-- int getJSeqCount() - - /** - * Method getTree - * - * - * - * @param index - * @return Tree - */ - public jalview.binding.Tree getTree(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.Tree) _treeList.elementAt(index); - } //-- jalview.binding.Tree getTree(int) - - /** - * Method getTree - * - * - * - * @return Tree - */ - public jalview.binding.Tree[] getTree() - { - int size = _treeList.size(); - jalview.binding.Tree[] mArray = new jalview.binding.Tree[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.Tree) _treeList.elementAt(index); - } - return mArray; - } //-- jalview.binding.Tree[] getTree() - - /** - * Method getTreeCount - * - * - * - * @return int - */ - public int getTreeCount() - { - return _treeList.size(); - } //-- int getTreeCount() - - /** - * Method getUserColours - * - * - * - * @param index - * @return UserColours - */ - public jalview.binding.UserColours getUserColours(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _userColoursList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.UserColours) _userColoursList.elementAt(index); - } //-- jalview.binding.UserColours getUserColours(int) - - /** - * Method getUserColours - * - * - * - * @return UserColours - */ - public jalview.binding.UserColours[] getUserColours() - { - int size = _userColoursList.size(); - jalview.binding.UserColours[] mArray = new jalview.binding.UserColours[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(index); - } - return mArray; - } //-- jalview.binding.UserColours[] getUserColours() - - /** - * Method getUserColoursCount - * - * - * - * @return int - */ - public int getUserColoursCount() - { - return _userColoursList.size(); - } //-- int getUserColoursCount() - - /** - * Method getViewport - * - * - * - * @param index - * @return Viewport - */ - public jalview.binding.Viewport getViewport(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _viewportList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.Viewport) _viewportList.elementAt(index); - } //-- jalview.binding.Viewport getViewport(int) - - /** - * Method getViewport - * - * - * - * @return Viewport - */ - public jalview.binding.Viewport[] getViewport() - { - int size = _viewportList.size(); - jalview.binding.Viewport[] mArray = new jalview.binding.Viewport[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.Viewport) _viewportList.elementAt(index); - } - return mArray; - } //-- jalview.binding.Viewport[] getViewport() - - /** - * Method getViewportCount - * - * - * - * @return int - */ - public int getViewportCount() - { - return _viewportList.size(); - } //-- int getViewportCount() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllJGroup - * - */ - public void removeAllJGroup() - { - _JGroupList.removeAllElements(); - } //-- void removeAllJGroup() - - /** - * Method removeAllJSeq - * - */ - public void removeAllJSeq() - { - _JSeqList.removeAllElements(); - } //-- void removeAllJSeq() - - /** - * Method removeAllTree - * - */ - public void removeAllTree() - { - _treeList.removeAllElements(); - } //-- void removeAllTree() - - /** - * Method removeAllUserColours - * - */ - public void removeAllUserColours() - { - _userColoursList.removeAllElements(); - } //-- void removeAllUserColours() - - /** - * Method removeAllViewport - * - */ - public void removeAllViewport() - { - _viewportList.removeAllElements(); - } //-- void removeAllViewport() - - /** - * Method removeJGroup - * - * - * - * @param index - * @return JGroup - */ - public jalview.binding.JGroup removeJGroup(int index) - { - java.lang.Object obj = _JGroupList.elementAt(index); - _JGroupList.removeElementAt(index); - return (jalview.binding.JGroup) obj; - } //-- jalview.binding.JGroup removeJGroup(int) - - /** - * Method removeJSeq - * - * - * - * @param index - * @return JSeq - */ - public jalview.binding.JSeq removeJSeq(int index) - { - java.lang.Object obj = _JSeqList.elementAt(index); - _JSeqList.removeElementAt(index); - return (jalview.binding.JSeq) obj; - } //-- jalview.binding.JSeq removeJSeq(int) - - /** - * Method removeTree - * - * - * - * @param index - * @return Tree - */ - public jalview.binding.Tree removeTree(int index) - { - java.lang.Object obj = _treeList.elementAt(index); - _treeList.removeElementAt(index); - return (jalview.binding.Tree) obj; - } //-- jalview.binding.Tree removeTree(int) - - /** - * Method removeUserColours - * - * - * - * @param index - * @return UserColours - */ - public jalview.binding.UserColours removeUserColours(int index) - { - java.lang.Object obj = _userColoursList.elementAt(index); - _userColoursList.removeElementAt(index); - return (jalview.binding.UserColours) obj; - } //-- jalview.binding.UserColours removeUserColours(int) - - /** - * Method removeViewport - * - * - * - * @param index - * @return Viewport - */ - public jalview.binding.Viewport removeViewport(int index) - { - java.lang.Object obj = _viewportList.elementAt(index); - _viewportList.removeElementAt(index); - return (jalview.binding.Viewport) obj; - } //-- jalview.binding.Viewport removeViewport(int) - - /** - * Sets the value of field 'featureSettings'. - * - * @param featureSettings the value of field 'featureSettings'. - */ - public void setFeatureSettings(jalview.binding.FeatureSettings featureSettings) - { - this._featureSettings = featureSettings; - } //-- void setFeatureSettings(jalview.binding.FeatureSettings) - - /** - * Method setJGroup - * - * - * - * @param index - * @param vJGroup - */ - public void setJGroup(int index, jalview.binding.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _JGroupList.size())) { - throw new IndexOutOfBoundsException(); - } - _JGroupList.setElementAt(vJGroup, index); - } //-- void setJGroup(int, jalview.binding.JGroup) - - /** - * Method setJGroup - * - * - * - * @param JGroupArray - */ - public void setJGroup(jalview.binding.JGroup[] JGroupArray) - { - //-- copy array - _JGroupList.removeAllElements(); - for (int i = 0; i < JGroupArray.length; i++) { - _JGroupList.addElement(JGroupArray[i]); - } - } //-- void setJGroup(jalview.binding.JGroup) - - /** - * Method setJSeq - * - * - * - * @param index - * @param vJSeq - */ - public void setJSeq(int index, jalview.binding.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _JSeqList.size())) { - throw new IndexOutOfBoundsException(); - } - _JSeqList.setElementAt(vJSeq, index); - } //-- void setJSeq(int, jalview.binding.JSeq) - - /** - * Method setJSeq - * - * - * - * @param JSeqArray - */ - public void setJSeq(jalview.binding.JSeq[] JSeqArray) - { - //-- copy array - _JSeqList.removeAllElements(); - for (int i = 0; i < JSeqArray.length; i++) { - _JSeqList.addElement(JSeqArray[i]); - } - } //-- void setJSeq(jalview.binding.JSeq) - - /** - * Method setTree - * - * - * - * @param index - * @param vTree - */ - public void setTree(int index, jalview.binding.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException(); - } - _treeList.setElementAt(vTree, index); - } //-- void setTree(int, jalview.binding.Tree) - - /** - * Method setTree - * - * - * - * @param treeArray - */ - public void setTree(jalview.binding.Tree[] treeArray) - { - //-- copy array - _treeList.removeAllElements(); - for (int i = 0; i < treeArray.length; i++) { - _treeList.addElement(treeArray[i]); - } - } //-- void setTree(jalview.binding.Tree) - - /** - * Method setUserColours - * - * - * - * @param index - * @param vUserColours - */ - public void setUserColours(int index, jalview.binding.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _userColoursList.size())) { - throw new IndexOutOfBoundsException(); - } - _userColoursList.setElementAt(vUserColours, index); - } //-- void setUserColours(int, jalview.binding.UserColours) - - /** - * Method setUserColours - * - * - * - * @param userColoursArray - */ - public void setUserColours(jalview.binding.UserColours[] userColoursArray) - { - //-- copy array - _userColoursList.removeAllElements(); - for (int i = 0; i < userColoursArray.length; i++) { - _userColoursList.addElement(userColoursArray[i]); - } - } //-- void setUserColours(jalview.binding.UserColours) - - /** - * Method setViewport - * - * - * - * @param index - * @param vViewport - */ - public void setViewport(int index, jalview.binding.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _viewportList.size())) { - throw new IndexOutOfBoundsException(); - } - _viewportList.setElementAt(vViewport, index); - } //-- void setViewport(int, jalview.binding.Viewport) - - /** - * Method setViewport - * - * - * - * @param viewportArray - */ - public void setViewport(jalview.binding.Viewport[] viewportArray) - { - //-- copy array - _viewportList.removeAllElements(); - for (int i = 0; i < viewportArray.length; i++) { - _viewportList.addElement(viewportArray[i]); - } - } //-- void setViewport(jalview.binding.Viewport) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class JalviewModelSequence. + * + * @version $Revision$ $Date$ + */ +public class JalviewModelSequence implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _JSeqList. + */ + private java.util.Vector _JSeqList; + + /** + * Field _JGroupList. + */ + private java.util.Vector _JGroupList; + + /** + * Field _viewportList. + */ + private java.util.Vector _viewportList; + + /** + * Field _userColoursList. + */ + private java.util.Vector _userColoursList; + + /** + * Field _treeList. + */ + private java.util.Vector _treeList; + + /** + * Field _featureSettings. + */ + private jalview.binding.FeatureSettings _featureSettings; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JalviewModelSequence() { + super(); + this._JSeqList = new java.util.Vector(); + this._JGroupList = new java.util.Vector(); + this._viewportList = new java.util.Vector(); + this._userColoursList = new java.util.Vector(); + this._treeList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vJGroup + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addJGroup( + final jalview.binding.JGroup vJGroup) + throws java.lang.IndexOutOfBoundsException { + this._JGroupList.addElement(vJGroup); + } + + /** + * + * + * @param index + * @param vJGroup + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addJGroup( + final int index, + final jalview.binding.JGroup vJGroup) + throws java.lang.IndexOutOfBoundsException { + this._JGroupList.add(index, vJGroup); + } + + /** + * + * + * @param vJSeq + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addJSeq( + final jalview.binding.JSeq vJSeq) + throws java.lang.IndexOutOfBoundsException { + this._JSeqList.addElement(vJSeq); + } + + /** + * + * + * @param index + * @param vJSeq + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addJSeq( + final int index, + final jalview.binding.JSeq vJSeq) + throws java.lang.IndexOutOfBoundsException { + this._JSeqList.add(index, vJSeq); + } + + /** + * + * + * @param vTree + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addTree( + final jalview.binding.Tree vTree) + throws java.lang.IndexOutOfBoundsException { + this._treeList.addElement(vTree); + } + + /** + * + * + * @param index + * @param vTree + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addTree( + final int index, + final jalview.binding.Tree vTree) + throws java.lang.IndexOutOfBoundsException { + this._treeList.add(index, vTree); + } + + /** + * + * + * @param vUserColours + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addUserColours( + final jalview.binding.UserColours vUserColours) + throws java.lang.IndexOutOfBoundsException { + this._userColoursList.addElement(vUserColours); + } + + /** + * + * + * @param index + * @param vUserColours + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addUserColours( + final int index, + final jalview.binding.UserColours vUserColours) + throws java.lang.IndexOutOfBoundsException { + this._userColoursList.add(index, vUserColours); + } + + /** + * + * + * @param vViewport + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addViewport( + final jalview.binding.Viewport vViewport) + throws java.lang.IndexOutOfBoundsException { + this._viewportList.addElement(vViewport); + } + + /** + * + * + * @param index + * @param vViewport + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addViewport( + final int index, + final jalview.binding.Viewport vViewport) + throws java.lang.IndexOutOfBoundsException { + this._viewportList.add(index, vViewport); + } + + /** + * Method enumerateJGroup. + * + * @return an Enumeration over all jalview.binding.JGroup + * elements + */ + public java.util.Enumeration enumerateJGroup( + ) { + return this._JGroupList.elements(); + } + + /** + * Method enumerateJSeq. + * + * @return an Enumeration over all jalview.binding.JSeq elements + */ + public java.util.Enumeration enumerateJSeq( + ) { + return this._JSeqList.elements(); + } + + /** + * Method enumerateTree. + * + * @return an Enumeration over all jalview.binding.Tree elements + */ + public java.util.Enumeration enumerateTree( + ) { + return this._treeList.elements(); + } + + /** + * Method enumerateUserColours. + * + * @return an Enumeration over all jalview.binding.UserColours + * elements + */ + public java.util.Enumeration enumerateUserColours( + ) { + return this._userColoursList.elements(); + } + + /** + * Method enumerateViewport. + * + * @return an Enumeration over all jalview.binding.Viewport + * elements + */ + public java.util.Enumeration enumerateViewport( + ) { + return this._viewportList.elements(); + } + + /** + * Returns the value of field 'featureSettings'. + * + * @return the value of field 'FeatureSettings'. + */ + public jalview.binding.FeatureSettings getFeatureSettings( + ) { + return this._featureSettings; + } + + /** + * Method getJGroup. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the jalview.binding.JGroup at the given + * index + */ + public jalview.binding.JGroup getJGroup( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._JGroupList.size()) { + throw new IndexOutOfBoundsException("getJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]"); + } + + return (jalview.binding.JGroup) _JGroupList.get(index); + } + + /** + * Method getJGroup.Returns the contents of the collection in + * an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.binding.JGroup[] getJGroup( + ) { + jalview.binding.JGroup[] array = new jalview.binding.JGroup[0]; + return (jalview.binding.JGroup[]) this._JGroupList.toArray(array); + } + + /** + * Method getJGroupCount. + * + * @return the size of this collection + */ + public int getJGroupCount( + ) { + return this._JGroupList.size(); + } + + /** + * Method getJSeq. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the jalview.binding.JSeq at the given + * index + */ + public jalview.binding.JSeq getJSeq( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._JSeqList.size()) { + throw new IndexOutOfBoundsException("getJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]"); + } + + return (jalview.binding.JSeq) _JSeqList.get(index); + } + + /** + * Method getJSeq.Returns the contents of the collection in an + * Array.

Note: Just in case the collection contents are + * changing in another thread, we pass a 0-length Array of the + * correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.binding.JSeq[] getJSeq( + ) { + jalview.binding.JSeq[] array = new jalview.binding.JSeq[0]; + return (jalview.binding.JSeq[]) this._JSeqList.toArray(array); + } + + /** + * Method getJSeqCount. + * + * @return the size of this collection + */ + public int getJSeqCount( + ) { + return this._JSeqList.size(); + } + + /** + * Method getTree. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the jalview.binding.Tree at the given + * index + */ + public jalview.binding.Tree getTree( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._treeList.size()) { + throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]"); + } + + return (jalview.binding.Tree) _treeList.get(index); + } + + /** + * Method getTree.Returns the contents of the collection in an + * Array.

Note: Just in case the collection contents are + * changing in another thread, we pass a 0-length Array of the + * correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.binding.Tree[] getTree( + ) { + jalview.binding.Tree[] array = new jalview.binding.Tree[0]; + return (jalview.binding.Tree[]) this._treeList.toArray(array); + } + + /** + * Method getTreeCount. + * + * @return the size of this collection + */ + public int getTreeCount( + ) { + return this._treeList.size(); + } + + /** + * Method getUserColours. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the jalview.binding.UserColours at the + * given index + */ + public jalview.binding.UserColours getUserColours( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._userColoursList.size()) { + throw new IndexOutOfBoundsException("getUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]"); + } + + return (jalview.binding.UserColours) _userColoursList.get(index); + } + + /** + * Method getUserColours.Returns the contents of the collection + * in an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.binding.UserColours[] getUserColours( + ) { + jalview.binding.UserColours[] array = new jalview.binding.UserColours[0]; + return (jalview.binding.UserColours[]) this._userColoursList.toArray(array); + } + + /** + * Method getUserColoursCount. + * + * @return the size of this collection + */ + public int getUserColoursCount( + ) { + return this._userColoursList.size(); + } + + /** + * Method getViewport. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the jalview.binding.Viewport at the + * given index + */ + public jalview.binding.Viewport getViewport( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._viewportList.size()) { + throw new IndexOutOfBoundsException("getViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]"); + } + + return (jalview.binding.Viewport) _viewportList.get(index); + } + + /** + * Method getViewport.Returns the contents of the collection in + * an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.binding.Viewport[] getViewport( + ) { + jalview.binding.Viewport[] array = new jalview.binding.Viewport[0]; + return (jalview.binding.Viewport[]) this._viewportList.toArray(array); + } + + /** + * Method getViewportCount. + * + * @return the size of this collection + */ + public int getViewportCount( + ) { + return this._viewportList.size(); + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllJGroup( + ) { + this._JGroupList.clear(); + } + + /** + */ + public void removeAllJSeq( + ) { + this._JSeqList.clear(); + } + + /** + */ + public void removeAllTree( + ) { + this._treeList.clear(); + } + + /** + */ + public void removeAllUserColours( + ) { + this._userColoursList.clear(); + } + + /** + */ + public void removeAllViewport( + ) { + this._viewportList.clear(); + } + + /** + * Method removeJGroup. + * + * @param vJGroup + * @return true if the object was removed from the collection. + */ + public boolean removeJGroup( + final jalview.binding.JGroup vJGroup) { + boolean removed = _JGroupList.remove(vJGroup); + return removed; + } + + /** + * Method removeJGroupAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.JGroup removeJGroupAt( + final int index) { + java.lang.Object obj = this._JGroupList.remove(index); + return (jalview.binding.JGroup) obj; + } + + /** + * Method removeJSeq. + * + * @param vJSeq + * @return true if the object was removed from the collection. + */ + public boolean removeJSeq( + final jalview.binding.JSeq vJSeq) { + boolean removed = _JSeqList.remove(vJSeq); + return removed; + } + + /** + * Method removeJSeqAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.JSeq removeJSeqAt( + final int index) { + java.lang.Object obj = this._JSeqList.remove(index); + return (jalview.binding.JSeq) obj; + } + + /** + * Method removeTree. + * + * @param vTree + * @return true if the object was removed from the collection. + */ + public boolean removeTree( + final jalview.binding.Tree vTree) { + boolean removed = _treeList.remove(vTree); + return removed; + } + + /** + * Method removeTreeAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.Tree removeTreeAt( + final int index) { + java.lang.Object obj = this._treeList.remove(index); + return (jalview.binding.Tree) obj; + } + + /** + * Method removeUserColours. + * + * @param vUserColours + * @return true if the object was removed from the collection. + */ + public boolean removeUserColours( + final jalview.binding.UserColours vUserColours) { + boolean removed = _userColoursList.remove(vUserColours); + return removed; + } + + /** + * Method removeUserColoursAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.UserColours removeUserColoursAt( + final int index) { + java.lang.Object obj = this._userColoursList.remove(index); + return (jalview.binding.UserColours) obj; + } + + /** + * Method removeViewport. + * + * @param vViewport + * @return true if the object was removed from the collection. + */ + public boolean removeViewport( + final jalview.binding.Viewport vViewport) { + boolean removed = _viewportList.remove(vViewport); + return removed; + } + + /** + * Method removeViewportAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.Viewport removeViewportAt( + final int index) { + java.lang.Object obj = this._viewportList.remove(index); + return (jalview.binding.Viewport) obj; + } + + /** + * Sets the value of field 'featureSettings'. + * + * @param featureSettings the value of field 'featureSettings'. + */ + public void setFeatureSettings( + final jalview.binding.FeatureSettings featureSettings) { + this._featureSettings = featureSettings; + } + + /** + * + * + * @param index + * @param vJGroup + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setJGroup( + final int index, + final jalview.binding.JGroup vJGroup) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._JGroupList.size()) { + throw new IndexOutOfBoundsException("setJGroup: Index value '" + index + "' not in range [0.." + (this._JGroupList.size() - 1) + "]"); + } + + this._JGroupList.set(index, vJGroup); + } + + /** + * + * + * @param vJGroupArray + */ + public void setJGroup( + final jalview.binding.JGroup[] vJGroupArray) { + //-- copy array + _JGroupList.clear(); + + for (int i = 0; i < vJGroupArray.length; i++) { + this._JGroupList.add(vJGroupArray[i]); + } + } + + /** + * + * + * @param index + * @param vJSeq + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setJSeq( + final int index, + final jalview.binding.JSeq vJSeq) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._JSeqList.size()) { + throw new IndexOutOfBoundsException("setJSeq: Index value '" + index + "' not in range [0.." + (this._JSeqList.size() - 1) + "]"); + } + + this._JSeqList.set(index, vJSeq); + } + + /** + * + * + * @param vJSeqArray + */ + public void setJSeq( + final jalview.binding.JSeq[] vJSeqArray) { + //-- copy array + _JSeqList.clear(); + + for (int i = 0; i < vJSeqArray.length; i++) { + this._JSeqList.add(vJSeqArray[i]); + } + } + + /** + * + * + * @param index + * @param vTree + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setTree( + final int index, + final jalview.binding.Tree vTree) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._treeList.size()) { + throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]"); + } + + this._treeList.set(index, vTree); + } + + /** + * + * + * @param vTreeArray + */ + public void setTree( + final jalview.binding.Tree[] vTreeArray) { + //-- copy array + _treeList.clear(); + + for (int i = 0; i < vTreeArray.length; i++) { + this._treeList.add(vTreeArray[i]); + } + } + + /** + * + * + * @param index + * @param vUserColours + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setUserColours( + final int index, + final jalview.binding.UserColours vUserColours) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._userColoursList.size()) { + throw new IndexOutOfBoundsException("setUserColours: Index value '" + index + "' not in range [0.." + (this._userColoursList.size() - 1) + "]"); + } + + this._userColoursList.set(index, vUserColours); + } + + /** + * + * + * @param vUserColoursArray + */ + public void setUserColours( + final jalview.binding.UserColours[] vUserColoursArray) { + //-- copy array + _userColoursList.clear(); + + for (int i = 0; i < vUserColoursArray.length; i++) { + this._userColoursList.add(vUserColoursArray[i]); + } + } + + /** + * + * + * @param index + * @param vViewport + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setViewport( + final int index, + final jalview.binding.Viewport vViewport) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._viewportList.size()) { + throw new IndexOutOfBoundsException("setViewport: Index value '" + index + "' not in range [0.." + (this._viewportList.size() - 1) + "]"); + } + + this._viewportList.set(index, vViewport); + } + + /** + * + * + * @param vViewportArray + */ + public void setViewport( + final jalview.binding.Viewport[] vViewportArray) { + //-- copy array + _viewportList.clear(); + + for (int i = 0; i < vViewportArray.length; i++) { + this._viewportList.add(vViewportArray[i]); + } + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.JalviewModelSequence + */ + public static jalview.binding.JalviewModelSequence unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/JalviewUserColours.java b/src/jalview/binding/JalviewUserColours.java index eeb051b..b5d0335 100755 --- a/src/jalview/binding/JalviewUserColours.java +++ b/src/jalview/binding/JalviewUserColours.java @@ -1,300 +1,298 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class JalviewUserColours. - * - * @version $Revision$ $Date$ - */ -public class JalviewUserColours implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _schemeName - */ - private java.lang.String _schemeName; - - /** - * Field _colourList - */ - private java.util.Vector _colourList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public JalviewUserColours() { - super(); - _colourList = new Vector(); - } //-- jalview.binding.JalviewUserColours() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addColour - * - * - * - * @param vColour - */ - public void addColour(jalview.binding.Colour vColour) - throws java.lang.IndexOutOfBoundsException - { - _colourList.addElement(vColour); - } //-- void addColour(jalview.binding.Colour) - - /** - * Method addColour - * - * - * - * @param index - * @param vColour - */ - public void addColour(int index, jalview.binding.Colour vColour) - throws java.lang.IndexOutOfBoundsException - { - _colourList.insertElementAt(vColour, index); - } //-- void addColour(int, jalview.binding.Colour) - - /** - * Method enumerateColour - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateColour() - { - return _colourList.elements(); - } //-- java.util.Enumeration enumerateColour() - - /** - * Method getColour - * - * - * - * @param index - * @return Colour - */ - public jalview.binding.Colour getColour(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _colourList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.Colour) _colourList.elementAt(index); - } //-- jalview.binding.Colour getColour(int) - - /** - * Method getColour - * - * - * - * @return Colour - */ - public jalview.binding.Colour[] getColour() - { - int size = _colourList.size(); - jalview.binding.Colour[] mArray = new jalview.binding.Colour[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.Colour) _colourList.elementAt(index); - } - return mArray; - } //-- jalview.binding.Colour[] getColour() - - /** - * Method getColourCount - * - * - * - * @return int - */ - public int getColourCount() - { - return _colourList.size(); - } //-- int getColourCount() - - /** - * Returns the value of field 'schemeName'. - * - * @return String - * @return the value of field 'schemeName'. - */ - public java.lang.String getSchemeName() - { - return this._schemeName; - } //-- java.lang.String getSchemeName() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllColour - * - */ - public void removeAllColour() - { - _colourList.removeAllElements(); - } //-- void removeAllColour() - - /** - * Method removeColour - * - * - * - * @param index - * @return Colour - */ - public jalview.binding.Colour removeColour(int index) - { - java.lang.Object obj = _colourList.elementAt(index); - _colourList.removeElementAt(index); - return (jalview.binding.Colour) obj; - } //-- jalview.binding.Colour removeColour(int) - - /** - * Method setColour - * - * - * - * @param index - * @param vColour - */ - public void setColour(int index, jalview.binding.Colour vColour) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _colourList.size())) { - throw new IndexOutOfBoundsException(); - } - _colourList.setElementAt(vColour, index); - } //-- void setColour(int, jalview.binding.Colour) - - /** - * Method setColour - * - * - * - * @param colourArray - */ - public void setColour(jalview.binding.Colour[] colourArray) - { - //-- copy array - _colourList.removeAllElements(); - for (int i = 0; i < colourArray.length; i++) { - _colourList.addElement(colourArray[i]); - } - } //-- void setColour(jalview.binding.Colour) - - /** - * Sets the value of field 'schemeName'. - * - * @param schemeName the value of field 'schemeName'. - */ - public void setSchemeName(java.lang.String schemeName) - { - this._schemeName = schemeName; - } //-- void setSchemeName(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class JalviewUserColours. + * + * @version $Revision$ $Date$ + */ +public class JalviewUserColours implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _schemeName. + */ + private java.lang.String _schemeName; + + /** + * Field _colourList. + */ + private java.util.Vector _colourList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JalviewUserColours() { + super(); + this._colourList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vColour + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addColour( + final Colour vColour) + throws java.lang.IndexOutOfBoundsException { + this._colourList.addElement(vColour); + } + + /** + * + * + * @param index + * @param vColour + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addColour( + final int index, + final Colour vColour) + throws java.lang.IndexOutOfBoundsException { + this._colourList.add(index, vColour); + } + + /** + * Method enumerateColour. + * + * @return an Enumeration over all Colour elements + */ + public java.util.Enumeration enumerateColour( + ) { + return this._colourList.elements(); + } + + /** + * Method getColour. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the Colour at the given index + */ + public Colour getColour( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._colourList.size()) { + throw new IndexOutOfBoundsException("getColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]"); + } + + return (Colour) _colourList.get(index); + } + + /** + * Method getColour.Returns the contents of the collection in + * an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public Colour[] getColour( + ) { + Colour[] array = new Colour[0]; + return (Colour[]) this._colourList.toArray(array); + } + + /** + * Method getColourCount. + * + * @return the size of this collection + */ + public int getColourCount( + ) { + return this._colourList.size(); + } + + /** + * Returns the value of field 'schemeName'. + * + * @return the value of field 'SchemeName'. + */ + public java.lang.String getSchemeName( + ) { + return this._schemeName; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllColour( + ) { + this._colourList.clear(); + } + + /** + * Method removeColour. + * + * @param vColour + * @return true if the object was removed from the collection. + */ + public boolean removeColour( + final Colour vColour) { + boolean removed = _colourList.remove(vColour); + return removed; + } + + /** + * Method removeColourAt. + * + * @param index + * @return the element removed from the collection + */ + public Colour removeColourAt( + final int index) { + java.lang.Object obj = this._colourList.remove(index); + return (Colour) obj; + } + + /** + * + * + * @param index + * @param vColour + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setColour( + final int index, + final Colour vColour) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._colourList.size()) { + throw new IndexOutOfBoundsException("setColour: Index value '" + index + "' not in range [0.." + (this._colourList.size() - 1) + "]"); + } + + this._colourList.set(index, vColour); + } + + /** + * + * + * @param vColourArray + */ + public void setColour( + final Colour[] vColourArray) { + //-- copy array + _colourList.clear(); + + for (int i = 0; i < vColourArray.length; i++) { + this._colourList.add(vColourArray[i]); + } + } + + /** + * Sets the value of field 'schemeName'. + * + * @param schemeName the value of field 'schemeName'. + */ + public void setSchemeName( + final java.lang.String schemeName) { + this._schemeName = schemeName; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.JalviewUserColours + */ + public static jalview.binding.JalviewUserColours unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/Pdbentry.java b/src/jalview/binding/Pdbentry.java index 7e0ae30..cac4cf6 100755 --- a/src/jalview/binding/Pdbentry.java +++ b/src/jalview/binding/Pdbentry.java @@ -1,326 +1,326 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Pdbentry. - * - * @version $Revision$ $Date$ - */ -public class Pdbentry implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _id - */ - private java.lang.String _id; - - /** - * Field _type - */ - private java.lang.String _type; - - /** - * Field _items - */ - private java.util.Vector _items; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Pdbentry() { - super(); - _items = new Vector(); - } //-- jalview.binding.Pdbentry() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addPdbentryItem - * - * - * - * @param vPdbentryItem - */ - public void addPdbentryItem(jalview.binding.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - _items.addElement(vPdbentryItem); - } //-- void addPdbentryItem(jalview.binding.PdbentryItem) - - /** - * Method addPdbentryItem - * - * - * - * @param index - * @param vPdbentryItem - */ - public void addPdbentryItem(int index, jalview.binding.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - _items.insertElementAt(vPdbentryItem, index); - } //-- void addPdbentryItem(int, jalview.binding.PdbentryItem) - - /** - * Method enumeratePdbentryItem - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumeratePdbentryItem() - { - return _items.elements(); - } //-- java.util.Enumeration enumeratePdbentryItem() - - /** - * Returns the value of field 'id'. - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Method getPdbentryItem - * - * - * - * @param index - * @return PdbentryItem - */ - public jalview.binding.PdbentryItem getPdbentryItem(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _items.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.PdbentryItem) _items.elementAt(index); - } //-- jalview.binding.PdbentryItem getPdbentryItem(int) - - /** - * Method getPdbentryItem - * - * - * - * @return PdbentryItem - */ - public jalview.binding.PdbentryItem[] getPdbentryItem() - { - int size = _items.size(); - jalview.binding.PdbentryItem[] mArray = new jalview.binding.PdbentryItem[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.PdbentryItem) _items.elementAt(index); - } - return mArray; - } //-- jalview.binding.PdbentryItem[] getPdbentryItem() - - /** - * Method getPdbentryItemCount - * - * - * - * @return int - */ - public int getPdbentryItemCount() - { - return _items.size(); - } //-- int getPdbentryItemCount() - - /** - * Returns the value of field 'type'. - * - * @return String - * @return the value of field 'type'. - */ - public java.lang.String getType() - { - return this._type; - } //-- java.lang.String getType() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllPdbentryItem - * - */ - public void removeAllPdbentryItem() - { - _items.removeAllElements(); - } //-- void removeAllPdbentryItem() - - /** - * Method removePdbentryItem - * - * - * - * @param index - * @return PdbentryItem - */ - public jalview.binding.PdbentryItem removePdbentryItem(int index) - { - java.lang.Object obj = _items.elementAt(index); - _items.removeElementAt(index); - return (jalview.binding.PdbentryItem) obj; - } //-- jalview.binding.PdbentryItem removePdbentryItem(int) - - /** - * Sets the value of field 'id'. - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Method setPdbentryItem - * - * - * - * @param index - * @param vPdbentryItem - */ - public void setPdbentryItem(int index, jalview.binding.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _items.size())) { - throw new IndexOutOfBoundsException(); - } - _items.setElementAt(vPdbentryItem, index); - } //-- void setPdbentryItem(int, jalview.binding.PdbentryItem) - - /** - * Method setPdbentryItem - * - * - * - * @param pdbentryItemArray - */ - public void setPdbentryItem(jalview.binding.PdbentryItem[] pdbentryItemArray) - { - //-- copy array - _items.removeAllElements(); - for (int i = 0; i < pdbentryItemArray.length; i++) { - _items.addElement(pdbentryItemArray[i]); - } - } //-- void setPdbentryItem(jalview.binding.PdbentryItem) - - /** - * Sets the value of field 'type'. - * - * @param type the value of field 'type'. - */ - public void setType(java.lang.String type) - { - this._type = type; - } //-- void setType(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbentry.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class Pdbentry. + * + * @version $Revision$ $Date$ + */ +public class Pdbentry implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _id. + */ + private java.lang.String _id; + + /** + * Field _type. + */ + private java.lang.String _type; + + /** + * Field _items. + */ + private java.util.Vector _items; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Pdbentry() { + super(); + this._items = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vPdbentryItem + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addPdbentryItem( + final jalview.binding.PdbentryItem vPdbentryItem) + throws java.lang.IndexOutOfBoundsException { + this._items.addElement(vPdbentryItem); + } + + /** + * + * + * @param index + * @param vPdbentryItem + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addPdbentryItem( + final int index, + final jalview.binding.PdbentryItem vPdbentryItem) + throws java.lang.IndexOutOfBoundsException { + this._items.add(index, vPdbentryItem); + } + + /** + * Method enumeratePdbentryItem. + * + * @return an Enumeration over all jalview.binding.PdbentryItem + * elements + */ + public java.util.Enumeration enumeratePdbentryItem( + ) { + return this._items.elements(); + } + + /** + * Returns the value of field 'id'. + * + * @return the value of field 'Id'. + */ + public java.lang.String getId( + ) { + return this._id; + } + + /** + * Method getPdbentryItem. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the jalview.binding.PdbentryItem at the + * given index + */ + public jalview.binding.PdbentryItem getPdbentryItem( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._items.size()) { + throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]"); + } + + return (jalview.binding.PdbentryItem) _items.get(index); + } + + /** + * Method getPdbentryItem.Returns the contents of the + * collection in an Array.

Note: Just in case the + * collection contents are changing in another thread, we pass + * a 0-length Array of the correct type into the API call. + * This way we know that the Array returned is of + * exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.binding.PdbentryItem[] getPdbentryItem( + ) { + jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0]; + return (jalview.binding.PdbentryItem[]) this._items.toArray(array); + } + + /** + * Method getPdbentryItemCount. + * + * @return the size of this collection + */ + public int getPdbentryItemCount( + ) { + return this._items.size(); + } + + /** + * Returns the value of field 'type'. + * + * @return the value of field 'Type'. + */ + public java.lang.String getType( + ) { + return this._type; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllPdbentryItem( + ) { + this._items.clear(); + } + + /** + * Method removePdbentryItem. + * + * @param vPdbentryItem + * @return true if the object was removed from the collection. + */ + public boolean removePdbentryItem( + final jalview.binding.PdbentryItem vPdbentryItem) { + boolean removed = _items.remove(vPdbentryItem); + return removed; + } + + /** + * Method removePdbentryItemAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.PdbentryItem removePdbentryItemAt( + final int index) { + java.lang.Object obj = this._items.remove(index); + return (jalview.binding.PdbentryItem) obj; + } + + /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId( + final java.lang.String id) { + this._id = id; + } + + /** + * + * + * @param index + * @param vPdbentryItem + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setPdbentryItem( + final int index, + final jalview.binding.PdbentryItem vPdbentryItem) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._items.size()) { + throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]"); + } + + this._items.set(index, vPdbentryItem); + } + + /** + * + * + * @param vPdbentryItemArray + */ + public void setPdbentryItem( + final jalview.binding.PdbentryItem[] vPdbentryItemArray) { + //-- copy array + _items.clear(); + + for (int i = 0; i < vPdbentryItemArray.length; i++) { + this._items.add(vPdbentryItemArray[i]); + } + } + + /** + * Sets the value of field 'type'. + * + * @param type the value of field 'type'. + */ + public void setType( + final java.lang.String type) { + this._type = type; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.Pdbentry + */ + public static jalview.binding.Pdbentry unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbentry.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/PdbentryItem.java b/src/jalview/binding/PdbentryItem.java index d797520..83bc40a 100755 --- a/src/jalview/binding/PdbentryItem.java +++ b/src/jalview/binding/PdbentryItem.java @@ -1,197 +1,192 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.Serializable; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class PdbentryItem. - * - * @version $Revision$ $Date$ - */ -public class PdbentryItem implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _propertyList - */ - private java.util.Vector _propertyList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public PdbentryItem() { - super(); - _propertyList = new Vector(); - } //-- jalview.binding.PdbentryItem() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addProperty - * - * - * - * @param vProperty - */ - public void addProperty(jalview.binding.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.addElement(vProperty); - } //-- void addProperty(jalview.binding.Property) - - /** - * Method addProperty - * - * - * - * @param index - * @param vProperty - */ - public void addProperty(int index, jalview.binding.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - _propertyList.insertElementAt(vProperty, index); - } //-- void addProperty(int, jalview.binding.Property) - - /** - * Method enumerateProperty - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateProperty() - { - return _propertyList.elements(); - } //-- java.util.Enumeration enumerateProperty() - - /** - * Method getProperty - * - * - * - * @param index - * @return Property - */ - public jalview.binding.Property getProperty(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.Property) _propertyList.elementAt(index); - } //-- jalview.binding.Property getProperty(int) - - /** - * Method getProperty - * - * - * - * @return Property - */ - public jalview.binding.Property[] getProperty() - { - int size = _propertyList.size(); - jalview.binding.Property[] mArray = new jalview.binding.Property[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.Property) _propertyList.elementAt(index); - } - return mArray; - } //-- jalview.binding.Property[] getProperty() - - /** - * Method getPropertyCount - * - * - * - * @return int - */ - public int getPropertyCount() - { - return _propertyList.size(); - } //-- int getPropertyCount() - - /** - * Method removeAllProperty - * - */ - public void removeAllProperty() - { - _propertyList.removeAllElements(); - } //-- void removeAllProperty() - - /** - * Method removeProperty - * - * - * - * @param index - * @return Property - */ - public jalview.binding.Property removeProperty(int index) - { - java.lang.Object obj = _propertyList.elementAt(index); - _propertyList.removeElementAt(index); - return (jalview.binding.Property) obj; - } //-- jalview.binding.Property removeProperty(int) - - /** - * Method setProperty - * - * - * - * @param index - * @param vProperty - */ - public void setProperty(int index, jalview.binding.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _propertyList.size())) { - throw new IndexOutOfBoundsException(); - } - _propertyList.setElementAt(vProperty, index); - } //-- void setProperty(int, jalview.binding.Property) - - /** - * Method setProperty - * - * - * - * @param propertyArray - */ - public void setProperty(jalview.binding.Property[] propertyArray) - { - //-- copy array - _propertyList.removeAllElements(); - for (int i = 0; i < propertyArray.length; i++) { - _propertyList.addElement(propertyArray[i]); - } - } //-- void setProperty(jalview.binding.Property) - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + +/** + * Class PdbentryItem. + * + * @version $Revision$ $Date$ + */ +public class PdbentryItem implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _propertyList. + */ + private java.util.Vector _propertyList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public PdbentryItem() { + super(); + this._propertyList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vProperty + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addProperty( + final jalview.binding.Property vProperty) + throws java.lang.IndexOutOfBoundsException { + this._propertyList.addElement(vProperty); + } + + /** + * + * + * @param index + * @param vProperty + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addProperty( + final int index, + final jalview.binding.Property vProperty) + throws java.lang.IndexOutOfBoundsException { + this._propertyList.add(index, vProperty); + } + + /** + * Method enumerateProperty. + * + * @return an Enumeration over all jalview.binding.Property + * elements + */ + public java.util.Enumeration enumerateProperty( + ) { + return this._propertyList.elements(); + } + + /** + * Method getProperty. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the jalview.binding.Property at the + * given index + */ + public jalview.binding.Property getProperty( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._propertyList.size()) { + throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]"); + } + + return (jalview.binding.Property) _propertyList.get(index); + } + + /** + * Method getProperty.Returns the contents of the collection in + * an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.binding.Property[] getProperty( + ) { + jalview.binding.Property[] array = new jalview.binding.Property[0]; + return (jalview.binding.Property[]) this._propertyList.toArray(array); + } + + /** + * Method getPropertyCount. + * + * @return the size of this collection + */ + public int getPropertyCount( + ) { + return this._propertyList.size(); + } + + /** + */ + public void removeAllProperty( + ) { + this._propertyList.clear(); + } + + /** + * Method removeProperty. + * + * @param vProperty + * @return true if the object was removed from the collection. + */ + public boolean removeProperty( + final jalview.binding.Property vProperty) { + boolean removed = _propertyList.remove(vProperty); + return removed; + } + + /** + * Method removePropertyAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.Property removePropertyAt( + final int index) { + java.lang.Object obj = this._propertyList.remove(index); + return (jalview.binding.Property) obj; + } + + /** + * + * + * @param index + * @param vProperty + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setProperty( + final int index, + final jalview.binding.Property vProperty) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._propertyList.size()) { + throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]"); + } + + this._propertyList.set(index, vProperty); + } + + /** + * + * + * @param vPropertyArray + */ + public void setProperty( + final jalview.binding.Property[] vPropertyArray) { + //-- copy array + _propertyList.clear(); + + for (int i = 0; i < vPropertyArray.length; i++) { + this._propertyList.add(vPropertyArray[i]); + } + } + +} diff --git a/src/jalview/binding/Pdbids.java b/src/jalview/binding/Pdbids.java index 4875b8b..b4745a2 100755 --- a/src/jalview/binding/Pdbids.java +++ b/src/jalview/binding/Pdbids.java @@ -1,118 +1,116 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Pdbids. - * - * @version $Revision$ $Date$ - */ -public class Pdbids extends Pdbentry -implements java.io.Serializable -{ - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Pdbids() { - super(); - } //-- jalview.binding.Pdbids() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Pdbids) Unmarshaller.unmarshal(jalview.binding.Pdbids.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class Pdbids. + * + * @version $Revision$ $Date$ + */ +public class Pdbids extends Pdbentry +implements java.io.Serializable +{ + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Pdbids() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.Pdbentry + */ + public static jalview.binding.Pdbentry unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbids.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/Property.java b/src/jalview/binding/Property.java index c0a1cdd..f1114f7 100755 --- a/src/jalview/binding/Property.java +++ b/src/jalview/binding/Property.java @@ -1,173 +1,169 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Property. - * - * @version $Revision$ $Date$ - */ -public class Property implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _name - */ - private java.lang.String _name; - - /** - * Field _value - */ - private java.lang.String _value; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Property() { - super(); - } //-- jalview.binding.Property() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'name'. - * - * @return String - * @return the value of field 'name'. - */ - public java.lang.String getName() - { - return this._name; - } //-- java.lang.String getName() - - /** - * Returns the value of field 'value'. - * - * @return String - * @return the value of field 'value'. - */ - public java.lang.String getValue() - { - return this._value; - } //-- java.lang.String getValue() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'name'. - * - * @param name the value of field 'name'. - */ - public void setName(java.lang.String name) - { - this._name = name; - } //-- void setName(java.lang.String) - - /** - * Sets the value of field 'value'. - * - * @param value the value of field 'value'. - */ - public void setValue(java.lang.String value) - { - this._value = value; - } //-- void setValue(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Property) Unmarshaller.unmarshal(jalview.binding.Property.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class Property. + * + * @version $Revision$ $Date$ + */ +public class Property implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _name. + */ + private java.lang.String _name; + + /** + * Field _value. + */ + private java.lang.String _value; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Property() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'name'. + * + * @return the value of field 'Name'. + */ + public java.lang.String getName( + ) { + return this._name; + } + + /** + * Returns the value of field 'value'. + * + * @return the value of field 'Value'. + */ + public java.lang.String getValue( + ) { + return this._value; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'name'. + * + * @param name the value of field 'name'. + */ + public void setName( + final java.lang.String name) { + this._name = name; + } + + /** + * Sets the value of field 'value'. + * + * @param value the value of field 'value'. + */ + public void setValue( + final java.lang.String value) { + this._value = value; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.Property + */ + public static jalview.binding.Property unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.Property) Unmarshaller.unmarshal(jalview.binding.Property.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/Sequence.java b/src/jalview/binding/Sequence.java index f3fd4e4..9c8cbc2 100755 --- a/src/jalview/binding/Sequence.java +++ b/src/jalview/binding/Sequence.java @@ -1,118 +1,116 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Sequence. - * - * @version $Revision$ $Date$ - */ -public class Sequence extends SequenceType -implements java.io.Serializable -{ - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Sequence() { - super(); - } //-- jalview.binding.Sequence() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Sequence) Unmarshaller.unmarshal(jalview.binding.Sequence.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class Sequence. + * + * @version $Revision$ $Date$ + */ +public class Sequence extends SequenceType +implements java.io.Serializable +{ + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Sequence() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.SequenceType + */ + public static jalview.binding.SequenceType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.Sequence.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java index 7ed3b52..13a9020 100755 --- a/src/jalview/binding/SequenceSet.java +++ b/src/jalview/binding/SequenceSet.java @@ -1,504 +1,514 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class SequenceSet. - * - * @version $Revision$ $Date$ - */ -public class SequenceSet implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _gapChar - */ - private java.lang.String _gapChar; - - /** - * Field _aligned - */ - private boolean _aligned; - - /** - * keeps track of state for field: _aligned - */ - private boolean _has_aligned; - - /** - * Field _sequenceList - */ - private java.util.Vector _sequenceList; - - /** - * Field _annotationList - */ - private java.util.Vector _annotationList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceSet() { - super(); - _sequenceList = new Vector(); - _annotationList = new Vector(); - } //-- jalview.binding.SequenceSet() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAnnotation - * - * - * - * @param vAnnotation - */ - public void addAnnotation(jalview.binding.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException - { - _annotationList.addElement(vAnnotation); - } //-- void addAnnotation(jalview.binding.Annotation) - - /** - * Method addAnnotation - * - * - * - * @param index - * @param vAnnotation - */ - public void addAnnotation(int index, jalview.binding.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException - { - _annotationList.insertElementAt(vAnnotation, index); - } //-- void addAnnotation(int, jalview.binding.Annotation) - - /** - * Method addSequence - * - * - * - * @param vSequence - */ - public void addSequence(jalview.binding.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - _sequenceList.addElement(vSequence); - } //-- void addSequence(jalview.binding.Sequence) - - /** - * Method addSequence - * - * - * - * @param index - * @param vSequence - */ - public void addSequence(int index, jalview.binding.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - _sequenceList.insertElementAt(vSequence, index); - } //-- void addSequence(int, jalview.binding.Sequence) - - /** - * Method deleteAligned - * - */ - public void deleteAligned() - { - this._has_aligned= false; - } //-- void deleteAligned() - - /** - * Method enumerateAnnotation - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAnnotation() - { - return _annotationList.elements(); - } //-- java.util.Enumeration enumerateAnnotation() - - /** - * Method enumerateSequence - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateSequence() - { - return _sequenceList.elements(); - } //-- java.util.Enumeration enumerateSequence() - - /** - * Returns the value of field 'aligned'. - * - * @return boolean - * @return the value of field 'aligned'. - */ - public boolean getAligned() - { - return this._aligned; - } //-- boolean getAligned() - - /** - * Method getAnnotation - * - * - * - * @param index - * @return Annotation - */ - public jalview.binding.Annotation getAnnotation(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _annotationList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.Annotation) _annotationList.elementAt(index); - } //-- jalview.binding.Annotation getAnnotation(int) - - /** - * Method getAnnotation - * - * - * - * @return Annotation - */ - public jalview.binding.Annotation[] getAnnotation() - { - int size = _annotationList.size(); - jalview.binding.Annotation[] mArray = new jalview.binding.Annotation[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index); - } - return mArray; - } //-- jalview.binding.Annotation[] getAnnotation() - - /** - * Method getAnnotationCount - * - * - * - * @return int - */ - public int getAnnotationCount() - { - return _annotationList.size(); - } //-- int getAnnotationCount() - - /** - * Returns the value of field 'gapChar'. - * - * @return String - * @return the value of field 'gapChar'. - */ - public java.lang.String getGapChar() - { - return this._gapChar; - } //-- java.lang.String getGapChar() - - /** - * Method getSequence - * - * - * - * @param index - * @return Sequence - */ - public jalview.binding.Sequence getSequence(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _sequenceList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.Sequence) _sequenceList.elementAt(index); - } //-- jalview.binding.Sequence getSequence(int) - - /** - * Method getSequence - * - * - * - * @return Sequence - */ - public jalview.binding.Sequence[] getSequence() - { - int size = _sequenceList.size(); - jalview.binding.Sequence[] mArray = new jalview.binding.Sequence[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index); - } - return mArray; - } //-- jalview.binding.Sequence[] getSequence() - - /** - * Method getSequenceCount - * - * - * - * @return int - */ - public int getSequenceCount() - { - return _sequenceList.size(); - } //-- int getSequenceCount() - - /** - * Method hasAligned - * - * - * - * @return boolean - */ - public boolean hasAligned() - { - return this._has_aligned; - } //-- boolean hasAligned() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAllAnnotation - * - */ - public void removeAllAnnotation() - { - _annotationList.removeAllElements(); - } //-- void removeAllAnnotation() - - /** - * Method removeAllSequence - * - */ - public void removeAllSequence() - { - _sequenceList.removeAllElements(); - } //-- void removeAllSequence() - - /** - * Method removeAnnotation - * - * - * - * @param index - * @return Annotation - */ - public jalview.binding.Annotation removeAnnotation(int index) - { - java.lang.Object obj = _annotationList.elementAt(index); - _annotationList.removeElementAt(index); - return (jalview.binding.Annotation) obj; - } //-- jalview.binding.Annotation removeAnnotation(int) - - /** - * Method removeSequence - * - * - * - * @param index - * @return Sequence - */ - public jalview.binding.Sequence removeSequence(int index) - { - java.lang.Object obj = _sequenceList.elementAt(index); - _sequenceList.removeElementAt(index); - return (jalview.binding.Sequence) obj; - } //-- jalview.binding.Sequence removeSequence(int) - - /** - * Sets the value of field 'aligned'. - * - * @param aligned the value of field 'aligned'. - */ - public void setAligned(boolean aligned) - { - this._aligned = aligned; - this._has_aligned = true; - } //-- void setAligned(boolean) - - /** - * Method setAnnotation - * - * - * - * @param index - * @param vAnnotation - */ - public void setAnnotation(int index, jalview.binding.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _annotationList.size())) { - throw new IndexOutOfBoundsException(); - } - _annotationList.setElementAt(vAnnotation, index); - } //-- void setAnnotation(int, jalview.binding.Annotation) - - /** - * Method setAnnotation - * - * - * - * @param annotationArray - */ - public void setAnnotation(jalview.binding.Annotation[] annotationArray) - { - //-- copy array - _annotationList.removeAllElements(); - for (int i = 0; i < annotationArray.length; i++) { - _annotationList.addElement(annotationArray[i]); - } - } //-- void setAnnotation(jalview.binding.Annotation) - - /** - * Sets the value of field 'gapChar'. - * - * @param gapChar the value of field 'gapChar'. - */ - public void setGapChar(java.lang.String gapChar) - { - this._gapChar = gapChar; - } //-- void setGapChar(java.lang.String) - - /** - * Method setSequence - * - * - * - * @param index - * @param vSequence - */ - public void setSequence(int index, jalview.binding.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _sequenceList.size())) { - throw new IndexOutOfBoundsException(); - } - _sequenceList.setElementAt(vSequence, index); - } //-- void setSequence(int, jalview.binding.Sequence) - - /** - * Method setSequence - * - * - * - * @param sequenceArray - */ - public void setSequence(jalview.binding.Sequence[] sequenceArray) - { - //-- copy array - _sequenceList.removeAllElements(); - for (int i = 0; i < sequenceArray.length; i++) { - _sequenceList.addElement(sequenceArray[i]); - } - } //-- void setSequence(jalview.binding.Sequence) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class SequenceSet. + * + * @version $Revision$ $Date$ + */ +public class SequenceSet implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _gapChar. + */ + private java.lang.String _gapChar; + + /** + * Field _aligned. + */ + private boolean _aligned; + + /** + * keeps track of state for field: _aligned + */ + private boolean _has_aligned; + + /** + * Field _sequenceList. + */ + private java.util.Vector _sequenceList; + + /** + * Field _annotationList. + */ + private java.util.Vector _annotationList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceSet() { + super(); + this._sequenceList = new java.util.Vector(); + this._annotationList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vAnnotation + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAnnotation( + final jalview.binding.Annotation vAnnotation) + throws java.lang.IndexOutOfBoundsException { + this._annotationList.addElement(vAnnotation); + } + + /** + * + * + * @param index + * @param vAnnotation + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAnnotation( + final int index, + final jalview.binding.Annotation vAnnotation) + throws java.lang.IndexOutOfBoundsException { + this._annotationList.add(index, vAnnotation); + } + + /** + * + * + * @param vSequence + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSequence( + final jalview.binding.Sequence vSequence) + throws java.lang.IndexOutOfBoundsException { + this._sequenceList.addElement(vSequence); + } + + /** + * + * + * @param index + * @param vSequence + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSequence( + final int index, + final jalview.binding.Sequence vSequence) + throws java.lang.IndexOutOfBoundsException { + this._sequenceList.add(index, vSequence); + } + + /** + */ + public void deleteAligned( + ) { + this._has_aligned= false; + } + + /** + * Method enumerateAnnotation. + * + * @return an Enumeration over all jalview.binding.Annotation + * elements + */ + public java.util.Enumeration enumerateAnnotation( + ) { + return this._annotationList.elements(); + } + + /** + * Method enumerateSequence. + * + * @return an Enumeration over all jalview.binding.Sequence + * elements + */ + public java.util.Enumeration enumerateSequence( + ) { + return this._sequenceList.elements(); + } + + /** + * Returns the value of field 'aligned'. + * + * @return the value of field 'Aligned'. + */ + public boolean getAligned( + ) { + return this._aligned; + } + + /** + * Method getAnnotation. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the jalview.binding.Annotation at the + * given index + */ + public jalview.binding.Annotation getAnnotation( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._annotationList.size()) { + throw new IndexOutOfBoundsException("getAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]"); + } + + return (jalview.binding.Annotation) _annotationList.get(index); + } + + /** + * Method getAnnotation.Returns the contents of the collection + * in an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.binding.Annotation[] getAnnotation( + ) { + jalview.binding.Annotation[] array = new jalview.binding.Annotation[0]; + return (jalview.binding.Annotation[]) this._annotationList.toArray(array); + } + + /** + * Method getAnnotationCount. + * + * @return the size of this collection + */ + public int getAnnotationCount( + ) { + return this._annotationList.size(); + } + + /** + * Returns the value of field 'gapChar'. + * + * @return the value of field 'GapChar'. + */ + public java.lang.String getGapChar( + ) { + return this._gapChar; + } + + /** + * Method getSequence. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the jalview.binding.Sequence at the + * given index + */ + public jalview.binding.Sequence getSequence( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._sequenceList.size()) { + throw new IndexOutOfBoundsException("getSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]"); + } + + return (jalview.binding.Sequence) _sequenceList.get(index); + } + + /** + * Method getSequence.Returns the contents of the collection in + * an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public jalview.binding.Sequence[] getSequence( + ) { + jalview.binding.Sequence[] array = new jalview.binding.Sequence[0]; + return (jalview.binding.Sequence[]) this._sequenceList.toArray(array); + } + + /** + * Method getSequenceCount. + * + * @return the size of this collection + */ + public int getSequenceCount( + ) { + return this._sequenceList.size(); + } + + /** + * Method hasAligned. + * + * @return true if at least one Aligned has been added + */ + public boolean hasAligned( + ) { + return this._has_aligned; + } + + /** + * Returns the value of field 'aligned'. + * + * @return the value of field 'Aligned'. + */ + public boolean isAligned( + ) { + return this._aligned; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + */ + public void removeAllAnnotation( + ) { + this._annotationList.clear(); + } + + /** + */ + public void removeAllSequence( + ) { + this._sequenceList.clear(); + } + + /** + * Method removeAnnotation. + * + * @param vAnnotation + * @return true if the object was removed from the collection. + */ + public boolean removeAnnotation( + final jalview.binding.Annotation vAnnotation) { + boolean removed = _annotationList.remove(vAnnotation); + return removed; + } + + /** + * Method removeAnnotationAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.Annotation removeAnnotationAt( + final int index) { + java.lang.Object obj = this._annotationList.remove(index); + return (jalview.binding.Annotation) obj; + } + + /** + * Method removeSequence. + * + * @param vSequence + * @return true if the object was removed from the collection. + */ + public boolean removeSequence( + final jalview.binding.Sequence vSequence) { + boolean removed = _sequenceList.remove(vSequence); + return removed; + } + + /** + * Method removeSequenceAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.binding.Sequence removeSequenceAt( + final int index) { + java.lang.Object obj = this._sequenceList.remove(index); + return (jalview.binding.Sequence) obj; + } + + /** + * Sets the value of field 'aligned'. + * + * @param aligned the value of field 'aligned'. + */ + public void setAligned( + final boolean aligned) { + this._aligned = aligned; + this._has_aligned = true; + } + + /** + * + * + * @param index + * @param vAnnotation + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setAnnotation( + final int index, + final jalview.binding.Annotation vAnnotation) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._annotationList.size()) { + throw new IndexOutOfBoundsException("setAnnotation: Index value '" + index + "' not in range [0.." + (this._annotationList.size() - 1) + "]"); + } + + this._annotationList.set(index, vAnnotation); + } + + /** + * + * + * @param vAnnotationArray + */ + public void setAnnotation( + final jalview.binding.Annotation[] vAnnotationArray) { + //-- copy array + _annotationList.clear(); + + for (int i = 0; i < vAnnotationArray.length; i++) { + this._annotationList.add(vAnnotationArray[i]); + } + } + + /** + * Sets the value of field 'gapChar'. + * + * @param gapChar the value of field 'gapChar'. + */ + public void setGapChar( + final java.lang.String gapChar) { + this._gapChar = gapChar; + } + + /** + * + * + * @param index + * @param vSequence + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setSequence( + final int index, + final jalview.binding.Sequence vSequence) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._sequenceList.size()) { + throw new IndexOutOfBoundsException("setSequence: Index value '" + index + "' not in range [0.." + (this._sequenceList.size() - 1) + "]"); + } + + this._sequenceList.set(index, vSequence); + } + + /** + * + * + * @param vSequenceArray + */ + public void setSequence( + final jalview.binding.Sequence[] vSequenceArray) { + //-- copy array + _sequenceList.clear(); + + for (int i = 0; i < vSequenceArray.length; i++) { + this._sequenceList.add(vSequenceArray[i]); + } + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.SequenceSet + */ + public static jalview.binding.SequenceSet unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/SequenceType.java b/src/jalview/binding/SequenceType.java index 1c66a2a..1bb2a62 100755 --- a/src/jalview/binding/SequenceType.java +++ b/src/jalview/binding/SequenceType.java @@ -1,225 +1,194 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class SequenceType. - * - * @version $Revision$ $Date$ - */ -public class SequenceType implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _id - */ - private java.lang.String _id; - - /** - * Field _description - */ - private java.lang.String _description; - - /** - * Field _sequence - */ - private java.lang.String _sequence; - - /** - * Field _name - */ - private java.lang.String _name; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceType() { - super(); - } //-- jalview.binding.SequenceType() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'description'. - * - * @return String - * @return the value of field 'description'. - */ - public java.lang.String getDescription() - { - return this._description; - } //-- java.lang.String getDescription() - - /** - * Returns the value of field 'id'. - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'name'. - * - * @return String - * @return the value of field 'name'. - */ - public java.lang.String getName() - { - return this._name; - } //-- java.lang.String getName() - - /** - * Returns the value of field 'sequence'. - * - * @return String - * @return the value of field 'sequence'. - */ - public java.lang.String getSequence() - { - return this._sequence; - } //-- java.lang.String getSequence() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'description'. - * - * @param description the value of field 'description'. - */ - public void setDescription(java.lang.String description) - { - this._description = description; - } //-- void setDescription(java.lang.String) - - /** - * Sets the value of field 'id'. - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'name'. - * - * @param name the value of field 'name'. - */ - public void setName(java.lang.String name) - { - this._name = name; - } //-- void setName(java.lang.String) - - /** - * Sets the value of field 'sequence'. - * - * @param sequence the value of field 'sequence'. - */ - public void setSequence(java.lang.String sequence) - { - this._sequence = sequence; - } //-- void setSequence(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.SequenceType.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class SequenceType. + * + * @version $Revision$ $Date$ + */ +public class SequenceType implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _id. + */ + private java.lang.String _id; + + /** + * Field _sequence. + */ + private java.lang.String _sequence; + + /** + * Field _name. + */ + private java.lang.String _name; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceType() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'id'. + * + * @return the value of field 'Id'. + */ + public java.lang.String getId( + ) { + return this._id; + } + + /** + * Returns the value of field 'name'. + * + * @return the value of field 'Name'. + */ + public java.lang.String getName( + ) { + return this._name; + } + + /** + * Returns the value of field 'sequence'. + * + * @return the value of field 'Sequence'. + */ + public java.lang.String getSequence( + ) { + return this._sequence; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId( + final java.lang.String id) { + this._id = id; + } + + /** + * Sets the value of field 'name'. + * + * @param name the value of field 'name'. + */ + public void setName( + final java.lang.String name) { + this._name = name; + } + + /** + * Sets the value of field 'sequence'. + * + * @param sequence the value of field 'sequence'. + */ + public void setSequence( + final java.lang.String sequence) { + this._sequence = sequence; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.SequenceType + */ + public static jalview.binding.SequenceType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.SequenceType.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/Setting.java b/src/jalview/binding/Setting.java index 7b56676..9cd84b4 100755 --- a/src/jalview/binding/Setting.java +++ b/src/jalview/binding/Setting.java @@ -1,253 +1,250 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Setting. - * - * @version $Revision$ $Date$ - */ -public class Setting implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _type - */ - private java.lang.String _type; - - /** - * Field _colour - */ - private int _colour; - - /** - * keeps track of state for field: _colour - */ - private boolean _has_colour; - - /** - * Field _display - */ - private boolean _display; - - /** - * keeps track of state for field: _display - */ - private boolean _has_display; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Setting() { - super(); - } //-- jalview.binding.Setting() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteColour - * - */ - public void deleteColour() - { - this._has_colour= false; - } //-- void deleteColour() - - /** - * Method deleteDisplay - * - */ - public void deleteDisplay() - { - this._has_display= false; - } //-- void deleteDisplay() - - /** - * Returns the value of field 'colour'. - * - * @return int - * @return the value of field 'colour'. - */ - public int getColour() - { - return this._colour; - } //-- int getColour() - - /** - * Returns the value of field 'display'. - * - * @return boolean - * @return the value of field 'display'. - */ - public boolean getDisplay() - { - return this._display; - } //-- boolean getDisplay() - - /** - * Returns the value of field 'type'. - * - * @return String - * @return the value of field 'type'. - */ - public java.lang.String getType() - { - return this._type; - } //-- java.lang.String getType() - - /** - * Method hasColour - * - * - * - * @return boolean - */ - public boolean hasColour() - { - return this._has_colour; - } //-- boolean hasColour() - - /** - * Method hasDisplay - * - * - * - * @return boolean - */ - public boolean hasDisplay() - { - return this._has_display; - } //-- boolean hasDisplay() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'colour'. - * - * @param colour the value of field 'colour'. - */ - public void setColour(int colour) - { - this._colour = colour; - this._has_colour = true; - } //-- void setColour(int) - - /** - * Sets the value of field 'display'. - * - * @param display the value of field 'display'. - */ - public void setDisplay(boolean display) - { - this._display = display; - this._has_display = true; - } //-- void setDisplay(boolean) - - /** - * Sets the value of field 'type'. - * - * @param type the value of field 'type'. - */ - public void setType(java.lang.String type) - { - this._type = type; - } //-- void setType(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Setting) Unmarshaller.unmarshal(jalview.binding.Setting.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class Setting. + * + * @version $Revision$ $Date$ + */ +public class Setting implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _type. + */ + private java.lang.String _type; + + /** + * Field _colour. + */ + private int _colour; + + /** + * keeps track of state for field: _colour + */ + private boolean _has_colour; + + /** + * Field _display. + */ + private boolean _display; + + /** + * keeps track of state for field: _display + */ + private boolean _has_display; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Setting() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteColour( + ) { + this._has_colour= false; + } + + /** + */ + public void deleteDisplay( + ) { + this._has_display= false; + } + + /** + * Returns the value of field 'colour'. + * + * @return the value of field 'Colour'. + */ + public int getColour( + ) { + return this._colour; + } + + /** + * Returns the value of field 'display'. + * + * @return the value of field 'Display'. + */ + public boolean getDisplay( + ) { + return this._display; + } + + /** + * Returns the value of field 'type'. + * + * @return the value of field 'Type'. + */ + public java.lang.String getType( + ) { + return this._type; + } + + /** + * Method hasColour. + * + * @return true if at least one Colour has been added + */ + public boolean hasColour( + ) { + return this._has_colour; + } + + /** + * Method hasDisplay. + * + * @return true if at least one Display has been added + */ + public boolean hasDisplay( + ) { + return this._has_display; + } + + /** + * Returns the value of field 'display'. + * + * @return the value of field 'Display'. + */ + public boolean isDisplay( + ) { + return this._display; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'colour'. + * + * @param colour the value of field 'colour'. + */ + public void setColour( + final int colour) { + this._colour = colour; + this._has_colour = true; + } + + /** + * Sets the value of field 'display'. + * + * @param display the value of field 'display'. + */ + public void setDisplay( + final boolean display) { + this._display = display; + this._has_display = true; + } + + /** + * Sets the value of field 'type'. + * + * @param type the value of field 'type'. + */ + public void setType( + final java.lang.String type) { + this._type = type; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.Setting + */ + public static jalview.binding.Setting unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.Setting) Unmarshaller.unmarshal(jalview.binding.Setting.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/Tree.java b/src/jalview/binding/Tree.java index 94922ac..5f138d0 100755 --- a/src/jalview/binding/Tree.java +++ b/src/jalview/binding/Tree.java @@ -1,835 +1,820 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Tree. - * - * @version $Revision$ $Date$ - */ -public class Tree implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _width - */ - private int _width; - - /** - * keeps track of state for field: _width - */ - private boolean _has_width; - - /** - * Field _height - */ - private int _height; - - /** - * keeps track of state for field: _height - */ - private boolean _has_height; - - /** - * Field _xpos - */ - private int _xpos; - - /** - * keeps track of state for field: _xpos - */ - private boolean _has_xpos; - - /** - * Field _ypos - */ - private int _ypos; - - /** - * keeps track of state for field: _ypos - */ - private boolean _has_ypos; - - /** - * Field _fontName - */ - private java.lang.String _fontName; - - /** - * Field _fontSize - */ - private int _fontSize; - - /** - * keeps track of state for field: _fontSize - */ - private boolean _has_fontSize; - - /** - * Field _fontStyle - */ - private int _fontStyle; - - /** - * keeps track of state for field: _fontStyle - */ - private boolean _has_fontStyle; - - /** - * Field _threshold - */ - private float _threshold; - - /** - * keeps track of state for field: _threshold - */ - private boolean _has_threshold; - - /** - * Field _showBootstrap - */ - private boolean _showBootstrap; - - /** - * keeps track of state for field: _showBootstrap - */ - private boolean _has_showBootstrap; - - /** - * Field _showDistances - */ - private boolean _showDistances; - - /** - * keeps track of state for field: _showDistances - */ - private boolean _has_showDistances; - - /** - * Field _markUnlinked - */ - private boolean _markUnlinked; - - /** - * keeps track of state for field: _markUnlinked - */ - private boolean _has_markUnlinked; - - /** - * Field _fitToWindow - */ - private boolean _fitToWindow; - - /** - * keeps track of state for field: _fitToWindow - */ - private boolean _has_fitToWindow; - - /** - * Field _currentTree - */ - private boolean _currentTree; - - /** - * keeps track of state for field: _currentTree - */ - private boolean _has_currentTree; - - /** - * Field _title - */ - private java.lang.String _title; - - /** - * Field _newick - */ - private java.lang.String _newick; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Tree() { - super(); - } //-- jalview.binding.Tree() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteCurrentTree - * - */ - public void deleteCurrentTree() - { - this._has_currentTree= false; - } //-- void deleteCurrentTree() - - /** - * Method deleteFitToWindow - * - */ - public void deleteFitToWindow() - { - this._has_fitToWindow= false; - } //-- void deleteFitToWindow() - - /** - * Method deleteFontSize - * - */ - public void deleteFontSize() - { - this._has_fontSize= false; - } //-- void deleteFontSize() - - /** - * Method deleteFontStyle - * - */ - public void deleteFontStyle() - { - this._has_fontStyle= false; - } //-- void deleteFontStyle() - - /** - * Method deleteHeight - * - */ - public void deleteHeight() - { - this._has_height= false; - } //-- void deleteHeight() - - /** - * Method deleteMarkUnlinked - * - */ - public void deleteMarkUnlinked() - { - this._has_markUnlinked= false; - } //-- void deleteMarkUnlinked() - - /** - * Method deleteShowBootstrap - * - */ - public void deleteShowBootstrap() - { - this._has_showBootstrap= false; - } //-- void deleteShowBootstrap() - - /** - * Method deleteShowDistances - * - */ - public void deleteShowDistances() - { - this._has_showDistances= false; - } //-- void deleteShowDistances() - - /** - * Method deleteThreshold - * - */ - public void deleteThreshold() - { - this._has_threshold= false; - } //-- void deleteThreshold() - - /** - * Method deleteWidth - * - */ - public void deleteWidth() - { - this._has_width= false; - } //-- void deleteWidth() - - /** - * Method deleteXpos - * - */ - public void deleteXpos() - { - this._has_xpos= false; - } //-- void deleteXpos() - - /** - * Method deleteYpos - * - */ - public void deleteYpos() - { - this._has_ypos= false; - } //-- void deleteYpos() - - /** - * Returns the value of field 'currentTree'. - * - * @return boolean - * @return the value of field 'currentTree'. - */ - public boolean getCurrentTree() - { - return this._currentTree; - } //-- boolean getCurrentTree() - - /** - * Returns the value of field 'fitToWindow'. - * - * @return boolean - * @return the value of field 'fitToWindow'. - */ - public boolean getFitToWindow() - { - return this._fitToWindow; - } //-- boolean getFitToWindow() - - /** - * Returns the value of field 'fontName'. - * - * @return String - * @return the value of field 'fontName'. - */ - public java.lang.String getFontName() - { - return this._fontName; - } //-- java.lang.String getFontName() - - /** - * Returns the value of field 'fontSize'. - * - * @return int - * @return the value of field 'fontSize'. - */ - public int getFontSize() - { - return this._fontSize; - } //-- int getFontSize() - - /** - * Returns the value of field 'fontStyle'. - * - * @return int - * @return the value of field 'fontStyle'. - */ - public int getFontStyle() - { - return this._fontStyle; - } //-- int getFontStyle() - - /** - * Returns the value of field 'height'. - * - * @return int - * @return the value of field 'height'. - */ - public int getHeight() - { - return this._height; - } //-- int getHeight() - - /** - * Returns the value of field 'markUnlinked'. - * - * @return boolean - * @return the value of field 'markUnlinked'. - */ - public boolean getMarkUnlinked() - { - return this._markUnlinked; - } //-- boolean getMarkUnlinked() - - /** - * Returns the value of field 'newick'. - * - * @return String - * @return the value of field 'newick'. - */ - public java.lang.String getNewick() - { - return this._newick; - } //-- java.lang.String getNewick() - - /** - * Returns the value of field 'showBootstrap'. - * - * @return boolean - * @return the value of field 'showBootstrap'. - */ - public boolean getShowBootstrap() - { - return this._showBootstrap; - } //-- boolean getShowBootstrap() - - /** - * Returns the value of field 'showDistances'. - * - * @return boolean - * @return the value of field 'showDistances'. - */ - public boolean getShowDistances() - { - return this._showDistances; - } //-- boolean getShowDistances() - - /** - * Returns the value of field 'threshold'. - * - * @return float - * @return the value of field 'threshold'. - */ - public float getThreshold() - { - return this._threshold; - } //-- float getThreshold() - - /** - * Returns the value of field 'title'. - * - * @return String - * @return the value of field 'title'. - */ - public java.lang.String getTitle() - { - return this._title; - } //-- java.lang.String getTitle() - - /** - * Returns the value of field 'width'. - * - * @return int - * @return the value of field 'width'. - */ - public int getWidth() - { - return this._width; - } //-- int getWidth() - - /** - * Returns the value of field 'xpos'. - * - * @return int - * @return the value of field 'xpos'. - */ - public int getXpos() - { - return this._xpos; - } //-- int getXpos() - - /** - * Returns the value of field 'ypos'. - * - * @return int - * @return the value of field 'ypos'. - */ - public int getYpos() - { - return this._ypos; - } //-- int getYpos() - - /** - * Method hasCurrentTree - * - * - * - * @return boolean - */ - public boolean hasCurrentTree() - { - return this._has_currentTree; - } //-- boolean hasCurrentTree() - - /** - * Method hasFitToWindow - * - * - * - * @return boolean - */ - public boolean hasFitToWindow() - { - return this._has_fitToWindow; - } //-- boolean hasFitToWindow() - - /** - * Method hasFontSize - * - * - * - * @return boolean - */ - public boolean hasFontSize() - { - return this._has_fontSize; - } //-- boolean hasFontSize() - - /** - * Method hasFontStyle - * - * - * - * @return boolean - */ - public boolean hasFontStyle() - { - return this._has_fontStyle; - } //-- boolean hasFontStyle() - - /** - * Method hasHeight - * - * - * - * @return boolean - */ - public boolean hasHeight() - { - return this._has_height; - } //-- boolean hasHeight() - - /** - * Method hasMarkUnlinked - * - * - * - * @return boolean - */ - public boolean hasMarkUnlinked() - { - return this._has_markUnlinked; - } //-- boolean hasMarkUnlinked() - - /** - * Method hasShowBootstrap - * - * - * - * @return boolean - */ - public boolean hasShowBootstrap() - { - return this._has_showBootstrap; - } //-- boolean hasShowBootstrap() - - /** - * Method hasShowDistances - * - * - * - * @return boolean - */ - public boolean hasShowDistances() - { - return this._has_showDistances; - } //-- boolean hasShowDistances() - - /** - * Method hasThreshold - * - * - * - * @return boolean - */ - public boolean hasThreshold() - { - return this._has_threshold; - } //-- boolean hasThreshold() - - /** - * Method hasWidth - * - * - * - * @return boolean - */ - public boolean hasWidth() - { - return this._has_width; - } //-- boolean hasWidth() - - /** - * Method hasXpos - * - * - * - * @return boolean - */ - public boolean hasXpos() - { - return this._has_xpos; - } //-- boolean hasXpos() - - /** - * Method hasYpos - * - * - * - * @return boolean - */ - public boolean hasYpos() - { - return this._has_ypos; - } //-- boolean hasYpos() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'currentTree'. - * - * @param currentTree the value of field 'currentTree'. - */ - public void setCurrentTree(boolean currentTree) - { - this._currentTree = currentTree; - this._has_currentTree = true; - } //-- void setCurrentTree(boolean) - - /** - * Sets the value of field 'fitToWindow'. - * - * @param fitToWindow the value of field 'fitToWindow'. - */ - public void setFitToWindow(boolean fitToWindow) - { - this._fitToWindow = fitToWindow; - this._has_fitToWindow = true; - } //-- void setFitToWindow(boolean) - - /** - * Sets the value of field 'fontName'. - * - * @param fontName the value of field 'fontName'. - */ - public void setFontName(java.lang.String fontName) - { - this._fontName = fontName; - } //-- void setFontName(java.lang.String) - - /** - * Sets the value of field 'fontSize'. - * - * @param fontSize the value of field 'fontSize'. - */ - public void setFontSize(int fontSize) - { - this._fontSize = fontSize; - this._has_fontSize = true; - } //-- void setFontSize(int) - - /** - * Sets the value of field 'fontStyle'. - * - * @param fontStyle the value of field 'fontStyle'. - */ - public void setFontStyle(int fontStyle) - { - this._fontStyle = fontStyle; - this._has_fontStyle = true; - } //-- void setFontStyle(int) - - /** - * Sets the value of field 'height'. - * - * @param height the value of field 'height'. - */ - public void setHeight(int height) - { - this._height = height; - this._has_height = true; - } //-- void setHeight(int) - - /** - * Sets the value of field 'markUnlinked'. - * - * @param markUnlinked the value of field 'markUnlinked'. - */ - public void setMarkUnlinked(boolean markUnlinked) - { - this._markUnlinked = markUnlinked; - this._has_markUnlinked = true; - } //-- void setMarkUnlinked(boolean) - - /** - * Sets the value of field 'newick'. - * - * @param newick the value of field 'newick'. - */ - public void setNewick(java.lang.String newick) - { - this._newick = newick; - } //-- void setNewick(java.lang.String) - - /** - * Sets the value of field 'showBootstrap'. - * - * @param showBootstrap the value of field 'showBootstrap'. - */ - public void setShowBootstrap(boolean showBootstrap) - { - this._showBootstrap = showBootstrap; - this._has_showBootstrap = true; - } //-- void setShowBootstrap(boolean) - - /** - * Sets the value of field 'showDistances'. - * - * @param showDistances the value of field 'showDistances'. - */ - public void setShowDistances(boolean showDistances) - { - this._showDistances = showDistances; - this._has_showDistances = true; - } //-- void setShowDistances(boolean) - - /** - * Sets the value of field 'threshold'. - * - * @param threshold the value of field 'threshold'. - */ - public void setThreshold(float threshold) - { - this._threshold = threshold; - this._has_threshold = true; - } //-- void setThreshold(float) - - /** - * Sets the value of field 'title'. - * - * @param title the value of field 'title'. - */ - public void setTitle(java.lang.String title) - { - this._title = title; - } //-- void setTitle(java.lang.String) - - /** - * Sets the value of field 'width'. - * - * @param width the value of field 'width'. - */ - public void setWidth(int width) - { - this._width = width; - this._has_width = true; - } //-- void setWidth(int) - - /** - * Sets the value of field 'xpos'. - * - * @param xpos the value of field 'xpos'. - */ - public void setXpos(int xpos) - { - this._xpos = xpos; - this._has_xpos = true; - } //-- void setXpos(int) - - /** - * Sets the value of field 'ypos'. - * - * @param ypos the value of field 'ypos'. - */ - public void setYpos(int ypos) - { - this._ypos = ypos; - this._has_ypos = true; - } //-- void setYpos(int) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class Tree. + * + * @version $Revision$ $Date$ + */ +public class Tree implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _width. + */ + private int _width; + + /** + * keeps track of state for field: _width + */ + private boolean _has_width; + + /** + * Field _height. + */ + private int _height; + + /** + * keeps track of state for field: _height + */ + private boolean _has_height; + + /** + * Field _xpos. + */ + private int _xpos; + + /** + * keeps track of state for field: _xpos + */ + private boolean _has_xpos; + + /** + * Field _ypos. + */ + private int _ypos; + + /** + * keeps track of state for field: _ypos + */ + private boolean _has_ypos; + + /** + * Field _fontName. + */ + private java.lang.String _fontName; + + /** + * Field _fontSize. + */ + private int _fontSize; + + /** + * keeps track of state for field: _fontSize + */ + private boolean _has_fontSize; + + /** + * Field _fontStyle. + */ + private int _fontStyle; + + /** + * keeps track of state for field: _fontStyle + */ + private boolean _has_fontStyle; + + /** + * Field _threshold. + */ + private float _threshold; + + /** + * keeps track of state for field: _threshold + */ + private boolean _has_threshold; + + /** + * Field _showBootstrap. + */ + private boolean _showBootstrap; + + /** + * keeps track of state for field: _showBootstrap + */ + private boolean _has_showBootstrap; + + /** + * Field _showDistances. + */ + private boolean _showDistances; + + /** + * keeps track of state for field: _showDistances + */ + private boolean _has_showDistances; + + /** + * Field _markUnlinked. + */ + private boolean _markUnlinked; + + /** + * keeps track of state for field: _markUnlinked + */ + private boolean _has_markUnlinked; + + /** + * Field _fitToWindow. + */ + private boolean _fitToWindow; + + /** + * keeps track of state for field: _fitToWindow + */ + private boolean _has_fitToWindow; + + /** + * Field _currentTree. + */ + private boolean _currentTree; + + /** + * keeps track of state for field: _currentTree + */ + private boolean _has_currentTree; + + /** + * Field _title. + */ + private java.lang.String _title; + + /** + * Field _newick. + */ + private java.lang.String _newick; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Tree() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteCurrentTree( + ) { + this._has_currentTree= false; + } + + /** + */ + public void deleteFitToWindow( + ) { + this._has_fitToWindow= false; + } + + /** + */ + public void deleteFontSize( + ) { + this._has_fontSize= false; + } + + /** + */ + public void deleteFontStyle( + ) { + this._has_fontStyle= false; + } + + /** + */ + public void deleteHeight( + ) { + this._has_height= false; + } + + /** + */ + public void deleteMarkUnlinked( + ) { + this._has_markUnlinked= false; + } + + /** + */ + public void deleteShowBootstrap( + ) { + this._has_showBootstrap= false; + } + + /** + */ + public void deleteShowDistances( + ) { + this._has_showDistances= false; + } + + /** + */ + public void deleteThreshold( + ) { + this._has_threshold= false; + } + + /** + */ + public void deleteWidth( + ) { + this._has_width= false; + } + + /** + */ + public void deleteXpos( + ) { + this._has_xpos= false; + } + + /** + */ + public void deleteYpos( + ) { + this._has_ypos= false; + } + + /** + * Returns the value of field 'currentTree'. + * + * @return the value of field 'CurrentTree'. + */ + public boolean getCurrentTree( + ) { + return this._currentTree; + } + + /** + * Returns the value of field 'fitToWindow'. + * + * @return the value of field 'FitToWindow'. + */ + public boolean getFitToWindow( + ) { + return this._fitToWindow; + } + + /** + * Returns the value of field 'fontName'. + * + * @return the value of field 'FontName'. + */ + public java.lang.String getFontName( + ) { + return this._fontName; + } + + /** + * Returns the value of field 'fontSize'. + * + * @return the value of field 'FontSize'. + */ + public int getFontSize( + ) { + return this._fontSize; + } + + /** + * Returns the value of field 'fontStyle'. + * + * @return the value of field 'FontStyle'. + */ + public int getFontStyle( + ) { + return this._fontStyle; + } + + /** + * Returns the value of field 'height'. + * + * @return the value of field 'Height'. + */ + public int getHeight( + ) { + return this._height; + } + + /** + * Returns the value of field 'markUnlinked'. + * + * @return the value of field 'MarkUnlinked'. + */ + public boolean getMarkUnlinked( + ) { + return this._markUnlinked; + } + + /** + * Returns the value of field 'newick'. + * + * @return the value of field 'Newick'. + */ + public java.lang.String getNewick( + ) { + return this._newick; + } + + /** + * Returns the value of field 'showBootstrap'. + * + * @return the value of field 'ShowBootstrap'. + */ + public boolean getShowBootstrap( + ) { + return this._showBootstrap; + } + + /** + * Returns the value of field 'showDistances'. + * + * @return the value of field 'ShowDistances'. + */ + public boolean getShowDistances( + ) { + return this._showDistances; + } + + /** + * Returns the value of field 'threshold'. + * + * @return the value of field 'Threshold'. + */ + public float getThreshold( + ) { + return this._threshold; + } + + /** + * Returns the value of field 'title'. + * + * @return the value of field 'Title'. + */ + public java.lang.String getTitle( + ) { + return this._title; + } + + /** + * Returns the value of field 'width'. + * + * @return the value of field 'Width'. + */ + public int getWidth( + ) { + return this._width; + } + + /** + * Returns the value of field 'xpos'. + * + * @return the value of field 'Xpos'. + */ + public int getXpos( + ) { + return this._xpos; + } + + /** + * Returns the value of field 'ypos'. + * + * @return the value of field 'Ypos'. + */ + public int getYpos( + ) { + return this._ypos; + } + + /** + * Method hasCurrentTree. + * + * @return true if at least one CurrentTree has been added + */ + public boolean hasCurrentTree( + ) { + return this._has_currentTree; + } + + /** + * Method hasFitToWindow. + * + * @return true if at least one FitToWindow has been added + */ + public boolean hasFitToWindow( + ) { + return this._has_fitToWindow; + } + + /** + * Method hasFontSize. + * + * @return true if at least one FontSize has been added + */ + public boolean hasFontSize( + ) { + return this._has_fontSize; + } + + /** + * Method hasFontStyle. + * + * @return true if at least one FontStyle has been added + */ + public boolean hasFontStyle( + ) { + return this._has_fontStyle; + } + + /** + * Method hasHeight. + * + * @return true if at least one Height has been added + */ + public boolean hasHeight( + ) { + return this._has_height; + } + + /** + * Method hasMarkUnlinked. + * + * @return true if at least one MarkUnlinked has been added + */ + public boolean hasMarkUnlinked( + ) { + return this._has_markUnlinked; + } + + /** + * Method hasShowBootstrap. + * + * @return true if at least one ShowBootstrap has been added + */ + public boolean hasShowBootstrap( + ) { + return this._has_showBootstrap; + } + + /** + * Method hasShowDistances. + * + * @return true if at least one ShowDistances has been added + */ + public boolean hasShowDistances( + ) { + return this._has_showDistances; + } + + /** + * Method hasThreshold. + * + * @return true if at least one Threshold has been added + */ + public boolean hasThreshold( + ) { + return this._has_threshold; + } + + /** + * Method hasWidth. + * + * @return true if at least one Width has been added + */ + public boolean hasWidth( + ) { + return this._has_width; + } + + /** + * Method hasXpos. + * + * @return true if at least one Xpos has been added + */ + public boolean hasXpos( + ) { + return this._has_xpos; + } + + /** + * Method hasYpos. + * + * @return true if at least one Ypos has been added + */ + public boolean hasYpos( + ) { + return this._has_ypos; + } + + /** + * Returns the value of field 'currentTree'. + * + * @return the value of field 'CurrentTree'. + */ + public boolean isCurrentTree( + ) { + return this._currentTree; + } + + /** + * Returns the value of field 'fitToWindow'. + * + * @return the value of field 'FitToWindow'. + */ + public boolean isFitToWindow( + ) { + return this._fitToWindow; + } + + /** + * Returns the value of field 'markUnlinked'. + * + * @return the value of field 'MarkUnlinked'. + */ + public boolean isMarkUnlinked( + ) { + return this._markUnlinked; + } + + /** + * Returns the value of field 'showBootstrap'. + * + * @return the value of field 'ShowBootstrap'. + */ + public boolean isShowBootstrap( + ) { + return this._showBootstrap; + } + + /** + * Returns the value of field 'showDistances'. + * + * @return the value of field 'ShowDistances'. + */ + public boolean isShowDistances( + ) { + return this._showDistances; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'currentTree'. + * + * @param currentTree the value of field 'currentTree'. + */ + public void setCurrentTree( + final boolean currentTree) { + this._currentTree = currentTree; + this._has_currentTree = true; + } + + /** + * Sets the value of field 'fitToWindow'. + * + * @param fitToWindow the value of field 'fitToWindow'. + */ + public void setFitToWindow( + final boolean fitToWindow) { + this._fitToWindow = fitToWindow; + this._has_fitToWindow = true; + } + + /** + * Sets the value of field 'fontName'. + * + * @param fontName the value of field 'fontName'. + */ + public void setFontName( + final java.lang.String fontName) { + this._fontName = fontName; + } + + /** + * Sets the value of field 'fontSize'. + * + * @param fontSize the value of field 'fontSize'. + */ + public void setFontSize( + final int fontSize) { + this._fontSize = fontSize; + this._has_fontSize = true; + } + + /** + * Sets the value of field 'fontStyle'. + * + * @param fontStyle the value of field 'fontStyle'. + */ + public void setFontStyle( + final int fontStyle) { + this._fontStyle = fontStyle; + this._has_fontStyle = true; + } + + /** + * Sets the value of field 'height'. + * + * @param height the value of field 'height'. + */ + public void setHeight( + final int height) { + this._height = height; + this._has_height = true; + } + + /** + * Sets the value of field 'markUnlinked'. + * + * @param markUnlinked the value of field 'markUnlinked'. + */ + public void setMarkUnlinked( + final boolean markUnlinked) { + this._markUnlinked = markUnlinked; + this._has_markUnlinked = true; + } + + /** + * Sets the value of field 'newick'. + * + * @param newick the value of field 'newick'. + */ + public void setNewick( + final java.lang.String newick) { + this._newick = newick; + } + + /** + * Sets the value of field 'showBootstrap'. + * + * @param showBootstrap the value of field 'showBootstrap'. + */ + public void setShowBootstrap( + final boolean showBootstrap) { + this._showBootstrap = showBootstrap; + this._has_showBootstrap = true; + } + + /** + * Sets the value of field 'showDistances'. + * + * @param showDistances the value of field 'showDistances'. + */ + public void setShowDistances( + final boolean showDistances) { + this._showDistances = showDistances; + this._has_showDistances = true; + } + + /** + * Sets the value of field 'threshold'. + * + * @param threshold the value of field 'threshold'. + */ + public void setThreshold( + final float threshold) { + this._threshold = threshold; + this._has_threshold = true; + } + + /** + * Sets the value of field 'title'. + * + * @param title the value of field 'title'. + */ + public void setTitle( + final java.lang.String title) { + this._title = title; + } + + /** + * Sets the value of field 'width'. + * + * @param width the value of field 'width'. + */ + public void setWidth( + final int width) { + this._width = width; + this._has_width = true; + } + + /** + * Sets the value of field 'xpos'. + * + * @param xpos the value of field 'xpos'. + */ + public void setXpos( + final int xpos) { + this._xpos = xpos; + this._has_xpos = true; + } + + /** + * Sets the value of field 'ypos'. + * + * @param ypos the value of field 'ypos'. + */ + public void setYpos( + final int ypos) { + this._ypos = ypos; + this._has_ypos = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.Tree + */ + public static jalview.binding.Tree unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/UserColourScheme.java b/src/jalview/binding/UserColourScheme.java index 79ea637..24c97ff 100755 --- a/src/jalview/binding/UserColourScheme.java +++ b/src/jalview/binding/UserColourScheme.java @@ -1,118 +1,116 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class UserColourScheme. - * - * @version $Revision$ $Date$ - */ -public class UserColourScheme extends JalviewUserColours -implements java.io.Serializable -{ - - - //----------------/ - //- Constructors -/ - //----------------/ - - public UserColourScheme() { - super(); - } //-- jalview.binding.UserColourScheme() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.UserColourScheme) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class UserColourScheme. + * + * @version $Revision$ $Date$ + */ +public class UserColourScheme extends JalviewUserColours +implements java.io.Serializable +{ + + + //----------------/ + //- Constructors -/ + //----------------/ + + public UserColourScheme() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.JalviewUserColours + */ + public static jalview.binding.JalviewUserColours unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/UserColours.java b/src/jalview/binding/UserColours.java index 241aaab..bdefe05 100755 --- a/src/jalview/binding/UserColours.java +++ b/src/jalview/binding/UserColours.java @@ -1,173 +1,169 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class UserColours. - * - * @version $Revision$ $Date$ - */ -public class UserColours implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _id - */ - private java.lang.String _id; - - /** - * Field _userColourScheme - */ - private jalview.binding.UserColourScheme _userColourScheme; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public UserColours() { - super(); - } //-- jalview.binding.UserColours() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'id'. - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'userColourScheme'. - * - * @return UserColourScheme - * @return the value of field 'userColourScheme'. - */ - public jalview.binding.UserColourScheme getUserColourScheme() - { - return this._userColourScheme; - } //-- jalview.binding.UserColourScheme getUserColourScheme() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'id'. - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'userColourScheme'. - * - * @param userColourScheme the value of field 'userColourScheme' - */ - public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme) - { - this._userColourScheme = userColourScheme; - } //-- void setUserColourScheme(jalview.binding.UserColourScheme) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class UserColours. + * + * @version $Revision$ $Date$ + */ +public class UserColours implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _id. + */ + private java.lang.String _id; + + /** + * Field _userColourScheme. + */ + private jalview.binding.UserColourScheme _userColourScheme; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public UserColours() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'id'. + * + * @return the value of field 'Id'. + */ + public java.lang.String getId( + ) { + return this._id; + } + + /** + * Returns the value of field 'userColourScheme'. + * + * @return the value of field 'UserColourScheme'. + */ + public jalview.binding.UserColourScheme getUserColourScheme( + ) { + return this._userColourScheme; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId( + final java.lang.String id) { + this._id = id; + } + + /** + * Sets the value of field 'userColourScheme'. + * + * @param userColourScheme the value of field 'userColourScheme' + */ + public void setUserColourScheme( + final jalview.binding.UserColourScheme userColourScheme) { + this._userColourScheme = userColourScheme; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.UserColours + */ + public static jalview.binding.UserColours unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java index b4237b8..1c92bd3 100755 --- a/src/jalview/binding/VAMSAS.java +++ b/src/jalview/binding/VAMSAS.java @@ -1,576 +1,581 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import java.util.Enumeration; -import java.util.Vector; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class VAMSAS. - * - * @version $Revision$ $Date$ - */ -public class VAMSAS implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _alignmentList - */ - private java.util.Vector _alignmentList; - - /** - * Field _treeList - */ - private java.util.Vector _treeList; - - /** - * Field _sequenceSetList - */ - private java.util.Vector _sequenceSetList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public VAMSAS() { - super(); - _alignmentList = new Vector(); - _treeList = new Vector(); - _sequenceSetList = new Vector(); - } //-- jalview.binding.VAMSAS() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAlignment - * - * - * - * @param vAlignment - */ - public void addAlignment(jalview.binding.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - _alignmentList.addElement(vAlignment); - } //-- void addAlignment(jalview.binding.Alignment) - - /** - * Method addAlignment - * - * - * - * @param index - * @param vAlignment - */ - public void addAlignment(int index, jalview.binding.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - _alignmentList.insertElementAt(vAlignment, index); - } //-- void addAlignment(int, jalview.binding.Alignment) - - /** - * Method addSequenceSet - * - * - * - * @param vSequenceSet - */ - public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - _sequenceSetList.addElement(vSequenceSet); - } //-- void addSequenceSet(jalview.binding.SequenceSet) - - /** - * Method addSequenceSet - * - * - * - * @param index - * @param vSequenceSet - */ - public void addSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - _sequenceSetList.insertElementAt(vSequenceSet, index); - } //-- void addSequenceSet(int, jalview.binding.SequenceSet) - - /** - * Method addTree - * - * - * - * @param vTree - */ - public void addTree(java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.addElement(vTree); - } //-- void addTree(java.lang.String) - - /** - * Method addTree - * - * - * - * @param index - * @param vTree - */ - public void addTree(int index, java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.insertElementAt(vTree, index); - } //-- void addTree(int, java.lang.String) - - /** - * Method enumerateAlignment - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAlignment() - { - return _alignmentList.elements(); - } //-- java.util.Enumeration enumerateAlignment() - - /** - * Method enumerateSequenceSet - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateSequenceSet() - { - return _sequenceSetList.elements(); - } //-- java.util.Enumeration enumerateSequenceSet() - - /** - * Method enumerateTree - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateTree() - { - return _treeList.elements(); - } //-- java.util.Enumeration enumerateTree() - - /** - * Method getAlignment - * - * - * - * @param index - * @return Alignment - */ - public jalview.binding.Alignment getAlignment(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.Alignment) _alignmentList.elementAt(index); - } //-- jalview.binding.Alignment getAlignment(int) - - /** - * Method getAlignment - * - * - * - * @return Alignment - */ - public jalview.binding.Alignment[] getAlignment() - { - int size = _alignmentList.size(); - jalview.binding.Alignment[] mArray = new jalview.binding.Alignment[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(index); - } - return mArray; - } //-- jalview.binding.Alignment[] getAlignment() - - /** - * Method getAlignmentCount - * - * - * - * @return int - */ - public int getAlignmentCount() - { - return _alignmentList.size(); - } //-- int getAlignmentCount() - - /** - * Method getSequenceSet - * - * - * - * @param index - * @return SequenceSet - */ - public jalview.binding.SequenceSet getSequenceSet(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _sequenceSetList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index); - } //-- jalview.binding.SequenceSet getSequenceSet(int) - - /** - * Method getSequenceSet - * - * - * - * @return SequenceSet - */ - public jalview.binding.SequenceSet[] getSequenceSet() - { - int size = _sequenceSetList.size(); - jalview.binding.SequenceSet[] mArray = new jalview.binding.SequenceSet[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index); - } - return mArray; - } //-- jalview.binding.SequenceSet[] getSequenceSet() - - /** - * Method getSequenceSetCount - * - * - * - * @return int - */ - public int getSequenceSetCount() - { - return _sequenceSetList.size(); - } //-- int getSequenceSetCount() - - /** - * Method getTree - * - * - * - * @param index - * @return String - */ - public java.lang.String getTree(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException(); - } - - return (String)_treeList.elementAt(index); - } //-- java.lang.String getTree(int) - - /** - * Method getTree - * - * - * - * @return String - */ - public java.lang.String[] getTree() - { - int size = _treeList.size(); - java.lang.String[] mArray = new java.lang.String[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (String)_treeList.elementAt(index); - } - return mArray; - } //-- java.lang.String[] getTree() - - /** - * Method getTreeCount - * - * - * - * @return int - */ - public int getTreeCount() - { - return _treeList.size(); - } //-- int getTreeCount() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method removeAlignment - * - * - * - * @param index - * @return Alignment - */ - public jalview.binding.Alignment removeAlignment(int index) - { - java.lang.Object obj = _alignmentList.elementAt(index); - _alignmentList.removeElementAt(index); - return (jalview.binding.Alignment) obj; - } //-- jalview.binding.Alignment removeAlignment(int) - - /** - * Method removeAllAlignment - * - */ - public void removeAllAlignment() - { - _alignmentList.removeAllElements(); - } //-- void removeAllAlignment() - - /** - * Method removeAllSequenceSet - * - */ - public void removeAllSequenceSet() - { - _sequenceSetList.removeAllElements(); - } //-- void removeAllSequenceSet() - - /** - * Method removeAllTree - * - */ - public void removeAllTree() - { - _treeList.removeAllElements(); - } //-- void removeAllTree() - - /** - * Method removeSequenceSet - * - * - * - * @param index - * @return SequenceSet - */ - public jalview.binding.SequenceSet removeSequenceSet(int index) - { - java.lang.Object obj = _sequenceSetList.elementAt(index); - _sequenceSetList.removeElementAt(index); - return (jalview.binding.SequenceSet) obj; - } //-- jalview.binding.SequenceSet removeSequenceSet(int) - - /** - * Method removeTree - * - * - * - * @param index - * @return String - */ - public java.lang.String removeTree(int index) - { - java.lang.Object obj = _treeList.elementAt(index); - _treeList.removeElementAt(index); - return (String)obj; - } //-- java.lang.String removeTree(int) - - /** - * Method setAlignment - * - * - * - * @param index - * @param vAlignment - */ - public void setAlignment(int index, jalview.binding.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _alignmentList.size())) { - throw new IndexOutOfBoundsException(); - } - _alignmentList.setElementAt(vAlignment, index); - } //-- void setAlignment(int, jalview.binding.Alignment) - - /** - * Method setAlignment - * - * - * - * @param alignmentArray - */ - public void setAlignment(jalview.binding.Alignment[] alignmentArray) - { - //-- copy array - _alignmentList.removeAllElements(); - for (int i = 0; i < alignmentArray.length; i++) { - _alignmentList.addElement(alignmentArray[i]); - } - } //-- void setAlignment(jalview.binding.Alignment) - - /** - * Method setSequenceSet - * - * - * - * @param index - * @param vSequenceSet - */ - public void setSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _sequenceSetList.size())) { - throw new IndexOutOfBoundsException(); - } - _sequenceSetList.setElementAt(vSequenceSet, index); - } //-- void setSequenceSet(int, jalview.binding.SequenceSet) - - /** - * Method setSequenceSet - * - * - * - * @param sequenceSetArray - */ - public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray) - { - //-- copy array - _sequenceSetList.removeAllElements(); - for (int i = 0; i < sequenceSetArray.length; i++) { - _sequenceSetList.addElement(sequenceSetArray[i]); - } - } //-- void setSequenceSet(jalview.binding.SequenceSet) - - /** - * Method setTree - * - * - * - * @param index - * @param vTree - */ - public void setTree(int index, java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _treeList.size())) { - throw new IndexOutOfBoundsException(); - } - _treeList.setElementAt(vTree, index); - } //-- void setTree(int, java.lang.String) - - /** - * Method setTree - * - * - * - * @param treeArray - */ - public void setTree(java.lang.String[] treeArray) - { - //-- copy array - _treeList.removeAllElements(); - for (int i = 0; i < treeArray.length; i++) { - _treeList.addElement(treeArray[i]); - } - } //-- void setTree(java.lang.String) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class VAMSAS. + * + * @version $Revision$ $Date$ + */ +public class VAMSAS implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _alignmentList. + */ + private java.util.Vector _alignmentList; + + /** + * Field _treeList. + */ + private java.util.Vector _treeList; + + /** + * Field _sequenceSetList. + */ + private java.util.Vector _sequenceSetList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public VAMSAS() { + super(); + this._alignmentList = new java.util.Vector(); + this._treeList = new java.util.Vector(); + this._sequenceSetList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vAlignment + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAlignment( + final Alignment vAlignment) + throws java.lang.IndexOutOfBoundsException { + this._alignmentList.addElement(vAlignment); + } + + /** + * + * + * @param index + * @param vAlignment + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAlignment( + final int index, + final Alignment vAlignment) + throws java.lang.IndexOutOfBoundsException { + this._alignmentList.add(index, vAlignment); + } + + /** + * + * + * @param vSequenceSet + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSequenceSet( + final SequenceSet vSequenceSet) + throws java.lang.IndexOutOfBoundsException { + this._sequenceSetList.addElement(vSequenceSet); + } + + /** + * + * + * @param index + * @param vSequenceSet + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSequenceSet( + final int index, + final SequenceSet vSequenceSet) + throws java.lang.IndexOutOfBoundsException { + this._sequenceSetList.add(index, vSequenceSet); + } + + /** + * + * + * @param vTree + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addTree( + final java.lang.String vTree) + throws java.lang.IndexOutOfBoundsException { + this._treeList.addElement(vTree); + } + + /** + * + * + * @param index + * @param vTree + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addTree( + final int index, + final java.lang.String vTree) + throws java.lang.IndexOutOfBoundsException { + this._treeList.add(index, vTree); + } + + /** + * Method enumerateAlignment. + * + * @return an Enumeration over all Alignment elements + */ + public java.util.Enumeration enumerateAlignment( + ) { + return this._alignmentList.elements(); + } + + /** + * Method enumerateSequenceSet. + * + * @return an Enumeration over all SequenceSet elements + */ + public java.util.Enumeration enumerateSequenceSet( + ) { + return this._sequenceSetList.elements(); + } + + /** + * Method enumerateTree. + * + * @return an Enumeration over all java.lang.String elements + */ + public java.util.Enumeration enumerateTree( + ) { + return this._treeList.elements(); + } + + /** + * Method getAlignment. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the Alignment at the given index + */ + public Alignment getAlignment( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alignmentList.size()) { + throw new IndexOutOfBoundsException("getAlignment: Index value '" + index + "' not in range [0.." + (this._alignmentList.size() - 1) + "]"); + } + + return (Alignment) _alignmentList.get(index); + } + + /** + * Method getAlignment.Returns the contents of the collection + * in an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public Alignment[] getAlignment( + ) { + Alignment[] array = new Alignment[0]; + return (Alignment[]) this._alignmentList.toArray(array); + } + + /** + * Method getAlignmentCount. + * + * @return the size of this collection + */ + public int getAlignmentCount( + ) { + return this._alignmentList.size(); + } + + /** + * Method getSequenceSet. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the SequenceSet at the given index + */ + public SequenceSet getSequenceSet( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._sequenceSetList.size()) { + throw new IndexOutOfBoundsException("getSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]"); + } + + return (SequenceSet) _sequenceSetList.get(index); + } + + /** + * Method getSequenceSet.Returns the contents of the collection + * in an Array.

Note: Just in case the collection contents + * are changing in another thread, we pass a 0-length Array of + * the correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public SequenceSet[] getSequenceSet( + ) { + SequenceSet[] array = new SequenceSet[0]; + return (SequenceSet[]) this._sequenceSetList.toArray(array); + } + + /** + * Method getSequenceSetCount. + * + * @return the size of this collection + */ + public int getSequenceSetCount( + ) { + return this._sequenceSetList.size(); + } + + /** + * Method getTree. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the java.lang.String at the given index + */ + public java.lang.String getTree( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._treeList.size()) { + throw new IndexOutOfBoundsException("getTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]"); + } + + return (java.lang.String) _treeList.get(index); + } + + /** + * Method getTree.Returns the contents of the collection in an + * Array.

Note: Just in case the collection contents are + * changing in another thread, we pass a 0-length Array of the + * correct type into the API call. This way we know + * that the Array returned is of exactly the correct length. + * + * @return this collection as an Array + */ + public java.lang.String[] getTree( + ) { + java.lang.String[] array = new java.lang.String[0]; + return (java.lang.String[]) this._treeList.toArray(array); + } + + /** + * Method getTreeCount. + * + * @return the size of this collection + */ + public int getTreeCount( + ) { + return this._treeList.size(); + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Method removeAlignment. + * + * @param vAlignment + * @return true if the object was removed from the collection. + */ + public boolean removeAlignment( + final Alignment vAlignment) { + boolean removed = _alignmentList.remove(vAlignment); + return removed; + } + + /** + * Method removeAlignmentAt. + * + * @param index + * @return the element removed from the collection + */ + public Alignment removeAlignmentAt( + final int index) { + java.lang.Object obj = this._alignmentList.remove(index); + return (Alignment) obj; + } + + /** + */ + public void removeAllAlignment( + ) { + this._alignmentList.clear(); + } + + /** + */ + public void removeAllSequenceSet( + ) { + this._sequenceSetList.clear(); + } + + /** + */ + public void removeAllTree( + ) { + this._treeList.clear(); + } + + /** + * Method removeSequenceSet. + * + * @param vSequenceSet + * @return true if the object was removed from the collection. + */ + public boolean removeSequenceSet( + final SequenceSet vSequenceSet) { + boolean removed = _sequenceSetList.remove(vSequenceSet); + return removed; + } + + /** + * Method removeSequenceSetAt. + * + * @param index + * @return the element removed from the collection + */ + public SequenceSet removeSequenceSetAt( + final int index) { + java.lang.Object obj = this._sequenceSetList.remove(index); + return (SequenceSet) obj; + } + + /** + * Method removeTree. + * + * @param vTree + * @return true if the object was removed from the collection. + */ + public boolean removeTree( + final java.lang.String vTree) { + boolean removed = _treeList.remove(vTree); + return removed; + } + + /** + * Method removeTreeAt. + * + * @param index + * @return the element removed from the collection + */ + public java.lang.String removeTreeAt( + final int index) { + java.lang.Object obj = this._treeList.remove(index); + return (java.lang.String) obj; + } + + /** + * + * + * @param index + * @param vAlignment + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setAlignment( + final int index, + final Alignment vAlignment) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alignmentList.size()) { + throw new IndexOutOfBoundsException("setAlignment: Index value '" + index + "' not in range [0.." + (this._alignmentList.size() - 1) + "]"); + } + + this._alignmentList.set(index, vAlignment); + } + + /** + * + * + * @param vAlignmentArray + */ + public void setAlignment( + final Alignment[] vAlignmentArray) { + //-- copy array + _alignmentList.clear(); + + for (int i = 0; i < vAlignmentArray.length; i++) { + this._alignmentList.add(vAlignmentArray[i]); + } + } + + /** + * + * + * @param index + * @param vSequenceSet + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setSequenceSet( + final int index, + final SequenceSet vSequenceSet) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._sequenceSetList.size()) { + throw new IndexOutOfBoundsException("setSequenceSet: Index value '" + index + "' not in range [0.." + (this._sequenceSetList.size() - 1) + "]"); + } + + this._sequenceSetList.set(index, vSequenceSet); + } + + /** + * + * + * @param vSequenceSetArray + */ + public void setSequenceSet( + final SequenceSet[] vSequenceSetArray) { + //-- copy array + _sequenceSetList.clear(); + + for (int i = 0; i < vSequenceSetArray.length; i++) { + this._sequenceSetList.add(vSequenceSetArray[i]); + } + } + + /** + * + * + * @param index + * @param vTree + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setTree( + final int index, + final java.lang.String vTree) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._treeList.size()) { + throw new IndexOutOfBoundsException("setTree: Index value '" + index + "' not in range [0.." + (this._treeList.size() - 1) + "]"); + } + + this._treeList.set(index, vTree); + } + + /** + * + * + * @param vTreeArray + */ + public void setTree( + final java.lang.String[] vTreeArray) { + //-- copy array + _treeList.clear(); + + for (int i = 0; i < vTreeArray.length; i++) { + this._treeList.add(vTreeArray[i]); + } + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.VAMSAS + */ + public static jalview.binding.VAMSAS unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/VamsasModel.java b/src/jalview/binding/VamsasModel.java index a4d4362..5fda35e 100755 --- a/src/jalview/binding/VamsasModel.java +++ b/src/jalview/binding/VamsasModel.java @@ -1,118 +1,116 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class VamsasModel. - * - * @version $Revision$ $Date$ - */ -public class VamsasModel extends VAMSAS -implements java.io.Serializable -{ - - - //----------------/ - //- Constructors -/ - //----------------/ - - public VamsasModel() { - super(); - } //-- jalview.binding.VamsasModel() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.VamsasModel) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class VamsasModel. + * + * @version $Revision$ $Date$ + */ +public class VamsasModel extends VAMSAS +implements java.io.Serializable +{ + + + //----------------/ + //- Constructors -/ + //----------------/ + + public VamsasModel() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.VAMSAS + */ + public static jalview.binding.VAMSAS unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} diff --git a/src/jalview/binding/Viewport.java b/src/jalview/binding/Viewport.java index 911061b..643c323 100755 --- a/src/jalview/binding/Viewport.java +++ b/src/jalview/binding/Viewport.java @@ -1,1420 +1,1432 @@ -/* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - - //---------------------------------/ - //- Imported classes and packages -/ -//---------------------------------/ - -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -import org.exolab.castor.xml.MarshalException; -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; -import org.exolab.castor.xml.ValidationException; -import org.xml.sax.ContentHandler; - -/** - * Class Viewport. - * - * @version $Revision$ $Date$ - */ -public class Viewport implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _conservationSelected - */ - private boolean _conservationSelected; - - /** - * keeps track of state for field: _conservationSelected - */ - private boolean _has_conservationSelected; - - /** - * Field _pidSelected - */ - private boolean _pidSelected; - - /** - * keeps track of state for field: _pidSelected - */ - private boolean _has_pidSelected; - - /** - * Field _bgColour - */ - private java.lang.String _bgColour; - - /** - * Field _consThreshold - */ - private int _consThreshold; - - /** - * keeps track of state for field: _consThreshold - */ - private boolean _has_consThreshold; - - /** - * Field _pidThreshold - */ - private int _pidThreshold; - - /** - * keeps track of state for field: _pidThreshold - */ - private boolean _has_pidThreshold; - - /** - * Field _title - */ - private java.lang.String _title; - - /** - * Field _showFullId - */ - private boolean _showFullId; - - /** - * keeps track of state for field: _showFullId - */ - private boolean _has_showFullId; - - /** - * Field _showText - */ - private boolean _showText; - - /** - * keeps track of state for field: _showText - */ - private boolean _has_showText; - - /** - * Field _showColourText - */ - private boolean _showColourText; - - /** - * keeps track of state for field: _showColourText - */ - private boolean _has_showColourText; - - /** - * Field _showBoxes - */ - private boolean _showBoxes; - - /** - * keeps track of state for field: _showBoxes - */ - private boolean _has_showBoxes; - - /** - * Field _wrapAlignment - */ - private boolean _wrapAlignment; - - /** - * keeps track of state for field: _wrapAlignment - */ - private boolean _has_wrapAlignment; - - /** - * Field _renderGaps - */ - private boolean _renderGaps; - - /** - * keeps track of state for field: _renderGaps - */ - private boolean _has_renderGaps; - - /** - * Field _showSequenceFeatures - */ - private boolean _showSequenceFeatures; - - /** - * keeps track of state for field: _showSequenceFeatures - */ - private boolean _has_showSequenceFeatures; - - /** - * Field _showAnnotation - */ - private boolean _showAnnotation; - - /** - * keeps track of state for field: _showAnnotation - */ - private boolean _has_showAnnotation; - - /** - * Field _showConservation - */ - private boolean _showConservation; - - /** - * keeps track of state for field: _showConservation - */ - private boolean _has_showConservation; - - /** - * Field _showQuality - */ - private boolean _showQuality; - - /** - * keeps track of state for field: _showQuality - */ - private boolean _has_showQuality; - - /** - * Field _showIdentity - */ - private boolean _showIdentity; - - /** - * keeps track of state for field: _showIdentity - */ - private boolean _has_showIdentity; - - /** - * Field _xpos - */ - private int _xpos; - - /** - * keeps track of state for field: _xpos - */ - private boolean _has_xpos; - - /** - * Field _ypos - */ - private int _ypos; - - /** - * keeps track of state for field: _ypos - */ - private boolean _has_ypos; - - /** - * Field _width - */ - private int _width; - - /** - * keeps track of state for field: _width - */ - private boolean _has_width; - - /** - * Field _height - */ - private int _height; - - /** - * keeps track of state for field: _height - */ - private boolean _has_height; - - /** - * Field _startRes - */ - private int _startRes; - - /** - * keeps track of state for field: _startRes - */ - private boolean _has_startRes; - - /** - * Field _startSeq - */ - private int _startSeq; - - /** - * keeps track of state for field: _startSeq - */ - private boolean _has_startSeq; - - /** - * Field _fontName - */ - private java.lang.String _fontName; - - /** - * Field _fontSize - */ - private int _fontSize; - - /** - * keeps track of state for field: _fontSize - */ - private boolean _has_fontSize; - - /** - * Field _fontStyle - */ - private int _fontStyle; - - /** - * keeps track of state for field: _fontStyle - */ - private boolean _has_fontStyle; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Viewport() { - super(); - } //-- jalview.binding.Viewport() - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteConsThreshold - * - */ - public void deleteConsThreshold() - { - this._has_consThreshold= false; - } //-- void deleteConsThreshold() - - /** - * Method deleteConservationSelected - * - */ - public void deleteConservationSelected() - { - this._has_conservationSelected= false; - } //-- void deleteConservationSelected() - - /** - * Method deleteFontSize - * - */ - public void deleteFontSize() - { - this._has_fontSize= false; - } //-- void deleteFontSize() - - /** - * Method deleteFontStyle - * - */ - public void deleteFontStyle() - { - this._has_fontStyle= false; - } //-- void deleteFontStyle() - - /** - * Method deleteHeight - * - */ - public void deleteHeight() - { - this._has_height= false; - } //-- void deleteHeight() - - /** - * Method deletePidSelected - * - */ - public void deletePidSelected() - { - this._has_pidSelected= false; - } //-- void deletePidSelected() - - /** - * Method deletePidThreshold - * - */ - public void deletePidThreshold() - { - this._has_pidThreshold= false; - } //-- void deletePidThreshold() - - /** - * Method deleteRenderGaps - * - */ - public void deleteRenderGaps() - { - this._has_renderGaps= false; - } //-- void deleteRenderGaps() - - /** - * Method deleteShowAnnotation - * - */ - public void deleteShowAnnotation() - { - this._has_showAnnotation= false; - } //-- void deleteShowAnnotation() - - /** - * Method deleteShowBoxes - * - */ - public void deleteShowBoxes() - { - this._has_showBoxes= false; - } //-- void deleteShowBoxes() - - /** - * Method deleteShowColourText - * - */ - public void deleteShowColourText() - { - this._has_showColourText= false; - } //-- void deleteShowColourText() - - /** - * Method deleteShowConservation - * - */ - public void deleteShowConservation() - { - this._has_showConservation= false; - } //-- void deleteShowConservation() - - /** - * Method deleteShowFullId - * - */ - public void deleteShowFullId() - { - this._has_showFullId= false; - } //-- void deleteShowFullId() - - /** - * Method deleteShowIdentity - * - */ - public void deleteShowIdentity() - { - this._has_showIdentity= false; - } //-- void deleteShowIdentity() - - /** - * Method deleteShowQuality - * - */ - public void deleteShowQuality() - { - this._has_showQuality= false; - } //-- void deleteShowQuality() - - /** - * Method deleteShowSequenceFeatures - * - */ - public void deleteShowSequenceFeatures() - { - this._has_showSequenceFeatures= false; - } //-- void deleteShowSequenceFeatures() - - /** - * Method deleteShowText - * - */ - public void deleteShowText() - { - this._has_showText= false; - } //-- void deleteShowText() - - /** - * Method deleteStartRes - * - */ - public void deleteStartRes() - { - this._has_startRes= false; - } //-- void deleteStartRes() - - /** - * Method deleteStartSeq - * - */ - public void deleteStartSeq() - { - this._has_startSeq= false; - } //-- void deleteStartSeq() - - /** - * Method deleteWidth - * - */ - public void deleteWidth() - { - this._has_width= false; - } //-- void deleteWidth() - - /** - * Method deleteWrapAlignment - * - */ - public void deleteWrapAlignment() - { - this._has_wrapAlignment= false; - } //-- void deleteWrapAlignment() - - /** - * Method deleteXpos - * - */ - public void deleteXpos() - { - this._has_xpos= false; - } //-- void deleteXpos() - - /** - * Method deleteYpos - * - */ - public void deleteYpos() - { - this._has_ypos= false; - } //-- void deleteYpos() - - /** - * Returns the value of field 'bgColour'. - * - * @return String - * @return the value of field 'bgColour'. - */ - public java.lang.String getBgColour() - { - return this._bgColour; - } //-- java.lang.String getBgColour() - - /** - * Returns the value of field 'consThreshold'. - * - * @return int - * @return the value of field 'consThreshold'. - */ - public int getConsThreshold() - { - return this._consThreshold; - } //-- int getConsThreshold() - - /** - * Returns the value of field 'conservationSelected'. - * - * @return boolean - * @return the value of field 'conservationSelected'. - */ - public boolean getConservationSelected() - { - return this._conservationSelected; - } //-- boolean getConservationSelected() - - /** - * Returns the value of field 'fontName'. - * - * @return String - * @return the value of field 'fontName'. - */ - public java.lang.String getFontName() - { - return this._fontName; - } //-- java.lang.String getFontName() - - /** - * Returns the value of field 'fontSize'. - * - * @return int - * @return the value of field 'fontSize'. - */ - public int getFontSize() - { - return this._fontSize; - } //-- int getFontSize() - - /** - * Returns the value of field 'fontStyle'. - * - * @return int - * @return the value of field 'fontStyle'. - */ - public int getFontStyle() - { - return this._fontStyle; - } //-- int getFontStyle() - - /** - * Returns the value of field 'height'. - * - * @return int - * @return the value of field 'height'. - */ - public int getHeight() - { - return this._height; - } //-- int getHeight() - - /** - * Returns the value of field 'pidSelected'. - * - * @return boolean - * @return the value of field 'pidSelected'. - */ - public boolean getPidSelected() - { - return this._pidSelected; - } //-- boolean getPidSelected() - - /** - * Returns the value of field 'pidThreshold'. - * - * @return int - * @return the value of field 'pidThreshold'. - */ - public int getPidThreshold() - { - return this._pidThreshold; - } //-- int getPidThreshold() - - /** - * Returns the value of field 'renderGaps'. - * - * @return boolean - * @return the value of field 'renderGaps'. - */ - public boolean getRenderGaps() - { - return this._renderGaps; - } //-- boolean getRenderGaps() - - /** - * Returns the value of field 'showAnnotation'. - * - * @return boolean - * @return the value of field 'showAnnotation'. - */ - public boolean getShowAnnotation() - { - return this._showAnnotation; - } //-- boolean getShowAnnotation() - - /** - * Returns the value of field 'showBoxes'. - * - * @return boolean - * @return the value of field 'showBoxes'. - */ - public boolean getShowBoxes() - { - return this._showBoxes; - } //-- boolean getShowBoxes() - - /** - * Returns the value of field 'showColourText'. - * - * @return boolean - * @return the value of field 'showColourText'. - */ - public boolean getShowColourText() - { - return this._showColourText; - } //-- boolean getShowColourText() - - /** - * Returns the value of field 'showConservation'. - * - * @return boolean - * @return the value of field 'showConservation'. - */ - public boolean getShowConservation() - { - return this._showConservation; - } //-- boolean getShowConservation() - - /** - * Returns the value of field 'showFullId'. - * - * @return boolean - * @return the value of field 'showFullId'. - */ - public boolean getShowFullId() - { - return this._showFullId; - } //-- boolean getShowFullId() - - /** - * Returns the value of field 'showIdentity'. - * - * @return boolean - * @return the value of field 'showIdentity'. - */ - public boolean getShowIdentity() - { - return this._showIdentity; - } //-- boolean getShowIdentity() - - /** - * Returns the value of field 'showQuality'. - * - * @return boolean - * @return the value of field 'showQuality'. - */ - public boolean getShowQuality() - { - return this._showQuality; - } //-- boolean getShowQuality() - - /** - * Returns the value of field 'showSequenceFeatures'. - * - * @return boolean - * @return the value of field 'showSequenceFeatures'. - */ - public boolean getShowSequenceFeatures() - { - return this._showSequenceFeatures; - } //-- boolean getShowSequenceFeatures() - - /** - * Returns the value of field 'showText'. - * - * @return boolean - * @return the value of field 'showText'. - */ - public boolean getShowText() - { - return this._showText; - } //-- boolean getShowText() - - /** - * Returns the value of field 'startRes'. - * - * @return int - * @return the value of field 'startRes'. - */ - public int getStartRes() - { - return this._startRes; - } //-- int getStartRes() - - /** - * Returns the value of field 'startSeq'. - * - * @return int - * @return the value of field 'startSeq'. - */ - public int getStartSeq() - { - return this._startSeq; - } //-- int getStartSeq() - - /** - * Returns the value of field 'title'. - * - * @return String - * @return the value of field 'title'. - */ - public java.lang.String getTitle() - { - return this._title; - } //-- java.lang.String getTitle() - - /** - * Returns the value of field 'width'. - * - * @return int - * @return the value of field 'width'. - */ - public int getWidth() - { - return this._width; - } //-- int getWidth() - - /** - * Returns the value of field 'wrapAlignment'. - * - * @return boolean - * @return the value of field 'wrapAlignment'. - */ - public boolean getWrapAlignment() - { - return this._wrapAlignment; - } //-- boolean getWrapAlignment() - - /** - * Returns the value of field 'xpos'. - * - * @return int - * @return the value of field 'xpos'. - */ - public int getXpos() - { - return this._xpos; - } //-- int getXpos() - - /** - * Returns the value of field 'ypos'. - * - * @return int - * @return the value of field 'ypos'. - */ - public int getYpos() - { - return this._ypos; - } //-- int getYpos() - - /** - * Method hasConsThreshold - * - * - * - * @return boolean - */ - public boolean hasConsThreshold() - { - return this._has_consThreshold; - } //-- boolean hasConsThreshold() - - /** - * Method hasConservationSelected - * - * - * - * @return boolean - */ - public boolean hasConservationSelected() - { - return this._has_conservationSelected; - } //-- boolean hasConservationSelected() - - /** - * Method hasFontSize - * - * - * - * @return boolean - */ - public boolean hasFontSize() - { - return this._has_fontSize; - } //-- boolean hasFontSize() - - /** - * Method hasFontStyle - * - * - * - * @return boolean - */ - public boolean hasFontStyle() - { - return this._has_fontStyle; - } //-- boolean hasFontStyle() - - /** - * Method hasHeight - * - * - * - * @return boolean - */ - public boolean hasHeight() - { - return this._has_height; - } //-- boolean hasHeight() - - /** - * Method hasPidSelected - * - * - * - * @return boolean - */ - public boolean hasPidSelected() - { - return this._has_pidSelected; - } //-- boolean hasPidSelected() - - /** - * Method hasPidThreshold - * - * - * - * @return boolean - */ - public boolean hasPidThreshold() - { - return this._has_pidThreshold; - } //-- boolean hasPidThreshold() - - /** - * Method hasRenderGaps - * - * - * - * @return boolean - */ - public boolean hasRenderGaps() - { - return this._has_renderGaps; - } //-- boolean hasRenderGaps() - - /** - * Method hasShowAnnotation - * - * - * - * @return boolean - */ - public boolean hasShowAnnotation() - { - return this._has_showAnnotation; - } //-- boolean hasShowAnnotation() - - /** - * Method hasShowBoxes - * - * - * - * @return boolean - */ - public boolean hasShowBoxes() - { - return this._has_showBoxes; - } //-- boolean hasShowBoxes() - - /** - * Method hasShowColourText - * - * - * - * @return boolean - */ - public boolean hasShowColourText() - { - return this._has_showColourText; - } //-- boolean hasShowColourText() - - /** - * Method hasShowConservation - * - * - * - * @return boolean - */ - public boolean hasShowConservation() - { - return this._has_showConservation; - } //-- boolean hasShowConservation() - - /** - * Method hasShowFullId - * - * - * - * @return boolean - */ - public boolean hasShowFullId() - { - return this._has_showFullId; - } //-- boolean hasShowFullId() - - /** - * Method hasShowIdentity - * - * - * - * @return boolean - */ - public boolean hasShowIdentity() - { - return this._has_showIdentity; - } //-- boolean hasShowIdentity() - - /** - * Method hasShowQuality - * - * - * - * @return boolean - */ - public boolean hasShowQuality() - { - return this._has_showQuality; - } //-- boolean hasShowQuality() - - /** - * Method hasShowSequenceFeatures - * - * - * - * @return boolean - */ - public boolean hasShowSequenceFeatures() - { - return this._has_showSequenceFeatures; - } //-- boolean hasShowSequenceFeatures() - - /** - * Method hasShowText - * - * - * - * @return boolean - */ - public boolean hasShowText() - { - return this._has_showText; - } //-- boolean hasShowText() - - /** - * Method hasStartRes - * - * - * - * @return boolean - */ - public boolean hasStartRes() - { - return this._has_startRes; - } //-- boolean hasStartRes() - - /** - * Method hasStartSeq - * - * - * - * @return boolean - */ - public boolean hasStartSeq() - { - return this._has_startSeq; - } //-- boolean hasStartSeq() - - /** - * Method hasWidth - * - * - * - * @return boolean - */ - public boolean hasWidth() - { - return this._has_width; - } //-- boolean hasWidth() - - /** - * Method hasWrapAlignment - * - * - * - * @return boolean - */ - public boolean hasWrapAlignment() - { - return this._has_wrapAlignment; - } //-- boolean hasWrapAlignment() - - /** - * Method hasXpos - * - * - * - * @return boolean - */ - public boolean hasXpos() - { - return this._has_xpos; - } //-- boolean hasXpos() - - /** - * Method hasYpos - * - * - * - * @return boolean - */ - public boolean hasYpos() - { - return this._has_ypos; - } //-- boolean hasYpos() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) { - return false; - } - return true; - } //-- boolean isValid() - - /** - * Method marshal - * - * - * - * @param out - */ - public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) - - /** - * Method marshal - * - * - * - * @param handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Sets the value of field 'bgColour'. - * - * @param bgColour the value of field 'bgColour'. - */ - public void setBgColour(java.lang.String bgColour) - { - this._bgColour = bgColour; - } //-- void setBgColour(java.lang.String) - - /** - * Sets the value of field 'consThreshold'. - * - * @param consThreshold the value of field 'consThreshold'. - */ - public void setConsThreshold(int consThreshold) - { - this._consThreshold = consThreshold; - this._has_consThreshold = true; - } //-- void setConsThreshold(int) - - /** - * Sets the value of field 'conservationSelected'. - * - * @param conservationSelected the value of field - * 'conservationSelected'. - */ - public void setConservationSelected(boolean conservationSelected) - { - this._conservationSelected = conservationSelected; - this._has_conservationSelected = true; - } //-- void setConservationSelected(boolean) - - /** - * Sets the value of field 'fontName'. - * - * @param fontName the value of field 'fontName'. - */ - public void setFontName(java.lang.String fontName) - { - this._fontName = fontName; - } //-- void setFontName(java.lang.String) - - /** - * Sets the value of field 'fontSize'. - * - * @param fontSize the value of field 'fontSize'. - */ - public void setFontSize(int fontSize) - { - this._fontSize = fontSize; - this._has_fontSize = true; - } //-- void setFontSize(int) - - /** - * Sets the value of field 'fontStyle'. - * - * @param fontStyle the value of field 'fontStyle'. - */ - public void setFontStyle(int fontStyle) - { - this._fontStyle = fontStyle; - this._has_fontStyle = true; - } //-- void setFontStyle(int) - - /** - * Sets the value of field 'height'. - * - * @param height the value of field 'height'. - */ - public void setHeight(int height) - { - this._height = height; - this._has_height = true; - } //-- void setHeight(int) - - /** - * Sets the value of field 'pidSelected'. - * - * @param pidSelected the value of field 'pidSelected'. - */ - public void setPidSelected(boolean pidSelected) - { - this._pidSelected = pidSelected; - this._has_pidSelected = true; - } //-- void setPidSelected(boolean) - - /** - * Sets the value of field 'pidThreshold'. - * - * @param pidThreshold the value of field 'pidThreshold'. - */ - public void setPidThreshold(int pidThreshold) - { - this._pidThreshold = pidThreshold; - this._has_pidThreshold = true; - } //-- void setPidThreshold(int) - - /** - * Sets the value of field 'renderGaps'. - * - * @param renderGaps the value of field 'renderGaps'. - */ - public void setRenderGaps(boolean renderGaps) - { - this._renderGaps = renderGaps; - this._has_renderGaps = true; - } //-- void setRenderGaps(boolean) - - /** - * Sets the value of field 'showAnnotation'. - * - * @param showAnnotation the value of field 'showAnnotation'. - */ - public void setShowAnnotation(boolean showAnnotation) - { - this._showAnnotation = showAnnotation; - this._has_showAnnotation = true; - } //-- void setShowAnnotation(boolean) - - /** - * Sets the value of field 'showBoxes'. - * - * @param showBoxes the value of field 'showBoxes'. - */ - public void setShowBoxes(boolean showBoxes) - { - this._showBoxes = showBoxes; - this._has_showBoxes = true; - } //-- void setShowBoxes(boolean) - - /** - * Sets the value of field 'showColourText'. - * - * @param showColourText the value of field 'showColourText'. - */ - public void setShowColourText(boolean showColourText) - { - this._showColourText = showColourText; - this._has_showColourText = true; - } //-- void setShowColourText(boolean) - - /** - * Sets the value of field 'showConservation'. - * - * @param showConservation the value of field 'showConservation' - */ - public void setShowConservation(boolean showConservation) - { - this._showConservation = showConservation; - this._has_showConservation = true; - } //-- void setShowConservation(boolean) - - /** - * Sets the value of field 'showFullId'. - * - * @param showFullId the value of field 'showFullId'. - */ - public void setShowFullId(boolean showFullId) - { - this._showFullId = showFullId; - this._has_showFullId = true; - } //-- void setShowFullId(boolean) - - /** - * Sets the value of field 'showIdentity'. - * - * @param showIdentity the value of field 'showIdentity'. - */ - public void setShowIdentity(boolean showIdentity) - { - this._showIdentity = showIdentity; - this._has_showIdentity = true; - } //-- void setShowIdentity(boolean) - - /** - * Sets the value of field 'showQuality'. - * - * @param showQuality the value of field 'showQuality'. - */ - public void setShowQuality(boolean showQuality) - { - this._showQuality = showQuality; - this._has_showQuality = true; - } //-- void setShowQuality(boolean) - - /** - * Sets the value of field 'showSequenceFeatures'. - * - * @param showSequenceFeatures the value of field - * 'showSequenceFeatures'. - */ - public void setShowSequenceFeatures(boolean showSequenceFeatures) - { - this._showSequenceFeatures = showSequenceFeatures; - this._has_showSequenceFeatures = true; - } //-- void setShowSequenceFeatures(boolean) - - /** - * Sets the value of field 'showText'. - * - * @param showText the value of field 'showText'. - */ - public void setShowText(boolean showText) - { - this._showText = showText; - this._has_showText = true; - } //-- void setShowText(boolean) - - /** - * Sets the value of field 'startRes'. - * - * @param startRes the value of field 'startRes'. - */ - public void setStartRes(int startRes) - { - this._startRes = startRes; - this._has_startRes = true; - } //-- void setStartRes(int) - - /** - * Sets the value of field 'startSeq'. - * - * @param startSeq the value of field 'startSeq'. - */ - public void setStartSeq(int startSeq) - { - this._startSeq = startSeq; - this._has_startSeq = true; - } //-- void setStartSeq(int) - - /** - * Sets the value of field 'title'. - * - * @param title the value of field 'title'. - */ - public void setTitle(java.lang.String title) - { - this._title = title; - } //-- void setTitle(java.lang.String) - - /** - * Sets the value of field 'width'. - * - * @param width the value of field 'width'. - */ - public void setWidth(int width) - { - this._width = width; - this._has_width = true; - } //-- void setWidth(int) - - /** - * Sets the value of field 'wrapAlignment'. - * - * @param wrapAlignment the value of field 'wrapAlignment'. - */ - public void setWrapAlignment(boolean wrapAlignment) - { - this._wrapAlignment = wrapAlignment; - this._has_wrapAlignment = true; - } //-- void setWrapAlignment(boolean) - - /** - * Sets the value of field 'xpos'. - * - * @param xpos the value of field 'xpos'. - */ - public void setXpos(int xpos) - { - this._xpos = xpos; - this._has_xpos = true; - } //-- void setXpos(int) - - /** - * Sets the value of field 'ypos'. - * - * @param ypos the value of field 'ypos'. - */ - public void setYpos(int ypos) - { - this._ypos = ypos; - this._has_ypos = true; - } //-- void setYpos(int) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object - */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.Viewport.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) - - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class Viewport. + * + * @version $Revision$ $Date$ + */ +public class Viewport implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _conservationSelected. + */ + private boolean _conservationSelected; + + /** + * keeps track of state for field: _conservationSelected + */ + private boolean _has_conservationSelected; + + /** + * Field _pidSelected. + */ + private boolean _pidSelected; + + /** + * keeps track of state for field: _pidSelected + */ + private boolean _has_pidSelected; + + /** + * Field _bgColour. + */ + private java.lang.String _bgColour; + + /** + * Field _consThreshold. + */ + private int _consThreshold; + + /** + * keeps track of state for field: _consThreshold + */ + private boolean _has_consThreshold; + + /** + * Field _pidThreshold. + */ + private int _pidThreshold; + + /** + * keeps track of state for field: _pidThreshold + */ + private boolean _has_pidThreshold; + + /** + * Field _title. + */ + private java.lang.String _title; + + /** + * Field _showFullId. + */ + private boolean _showFullId; + + /** + * keeps track of state for field: _showFullId + */ + private boolean _has_showFullId; + + /** + * Field _showText. + */ + private boolean _showText; + + /** + * keeps track of state for field: _showText + */ + private boolean _has_showText; + + /** + * Field _showColourText. + */ + private boolean _showColourText; + + /** + * keeps track of state for field: _showColourText + */ + private boolean _has_showColourText; + + /** + * Field _showBoxes. + */ + private boolean _showBoxes; + + /** + * keeps track of state for field: _showBoxes + */ + private boolean _has_showBoxes; + + /** + * Field _wrapAlignment. + */ + private boolean _wrapAlignment; + + /** + * keeps track of state for field: _wrapAlignment + */ + private boolean _has_wrapAlignment; + + /** + * Field _renderGaps. + */ + private boolean _renderGaps; + + /** + * keeps track of state for field: _renderGaps + */ + private boolean _has_renderGaps; + + /** + * Field _showSequenceFeatures. + */ + private boolean _showSequenceFeatures; + + /** + * keeps track of state for field: _showSequenceFeatures + */ + private boolean _has_showSequenceFeatures; + + /** + * Field _showAnnotation. + */ + private boolean _showAnnotation; + + /** + * keeps track of state for field: _showAnnotation + */ + private boolean _has_showAnnotation; + + /** + * Field _showConservation. + */ + private boolean _showConservation; + + /** + * keeps track of state for field: _showConservation + */ + private boolean _has_showConservation; + + /** + * Field _showQuality. + */ + private boolean _showQuality; + + /** + * keeps track of state for field: _showQuality + */ + private boolean _has_showQuality; + + /** + * Field _showIdentity. + */ + private boolean _showIdentity; + + /** + * keeps track of state for field: _showIdentity + */ + private boolean _has_showIdentity; + + /** + * Field _xpos. + */ + private int _xpos; + + /** + * keeps track of state for field: _xpos + */ + private boolean _has_xpos; + + /** + * Field _ypos. + */ + private int _ypos; + + /** + * keeps track of state for field: _ypos + */ + private boolean _has_ypos; + + /** + * Field _width. + */ + private int _width; + + /** + * keeps track of state for field: _width + */ + private boolean _has_width; + + /** + * Field _height. + */ + private int _height; + + /** + * keeps track of state for field: _height + */ + private boolean _has_height; + + /** + * Field _startRes. + */ + private int _startRes; + + /** + * keeps track of state for field: _startRes + */ + private boolean _has_startRes; + + /** + * Field _startSeq. + */ + private int _startSeq; + + /** + * keeps track of state for field: _startSeq + */ + private boolean _has_startSeq; + + /** + * Field _fontName. + */ + private java.lang.String _fontName; + + /** + * Field _fontSize. + */ + private int _fontSize; + + /** + * keeps track of state for field: _fontSize + */ + private boolean _has_fontSize; + + /** + * Field _fontStyle. + */ + private int _fontStyle; + + /** + * keeps track of state for field: _fontStyle + */ + private boolean _has_fontStyle; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Viewport() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteConsThreshold( + ) { + this._has_consThreshold= false; + } + + /** + */ + public void deleteConservationSelected( + ) { + this._has_conservationSelected= false; + } + + /** + */ + public void deleteFontSize( + ) { + this._has_fontSize= false; + } + + /** + */ + public void deleteFontStyle( + ) { + this._has_fontStyle= false; + } + + /** + */ + public void deleteHeight( + ) { + this._has_height= false; + } + + /** + */ + public void deletePidSelected( + ) { + this._has_pidSelected= false; + } + + /** + */ + public void deletePidThreshold( + ) { + this._has_pidThreshold= false; + } + + /** + */ + public void deleteRenderGaps( + ) { + this._has_renderGaps= false; + } + + /** + */ + public void deleteShowAnnotation( + ) { + this._has_showAnnotation= false; + } + + /** + */ + public void deleteShowBoxes( + ) { + this._has_showBoxes= false; + } + + /** + */ + public void deleteShowColourText( + ) { + this._has_showColourText= false; + } + + /** + */ + public void deleteShowConservation( + ) { + this._has_showConservation= false; + } + + /** + */ + public void deleteShowFullId( + ) { + this._has_showFullId= false; + } + + /** + */ + public void deleteShowIdentity( + ) { + this._has_showIdentity= false; + } + + /** + */ + public void deleteShowQuality( + ) { + this._has_showQuality= false; + } + + /** + */ + public void deleteShowSequenceFeatures( + ) { + this._has_showSequenceFeatures= false; + } + + /** + */ + public void deleteShowText( + ) { + this._has_showText= false; + } + + /** + */ + public void deleteStartRes( + ) { + this._has_startRes= false; + } + + /** + */ + public void deleteStartSeq( + ) { + this._has_startSeq= false; + } + + /** + */ + public void deleteWidth( + ) { + this._has_width= false; + } + + /** + */ + public void deleteWrapAlignment( + ) { + this._has_wrapAlignment= false; + } + + /** + */ + public void deleteXpos( + ) { + this._has_xpos= false; + } + + /** + */ + public void deleteYpos( + ) { + this._has_ypos= false; + } + + /** + * Returns the value of field 'bgColour'. + * + * @return the value of field 'BgColour'. + */ + public java.lang.String getBgColour( + ) { + return this._bgColour; + } + + /** + * Returns the value of field 'consThreshold'. + * + * @return the value of field 'ConsThreshold'. + */ + public int getConsThreshold( + ) { + return this._consThreshold; + } + + /** + * Returns the value of field 'conservationSelected'. + * + * @return the value of field 'ConservationSelected'. + */ + public boolean getConservationSelected( + ) { + return this._conservationSelected; + } + + /** + * Returns the value of field 'fontName'. + * + * @return the value of field 'FontName'. + */ + public java.lang.String getFontName( + ) { + return this._fontName; + } + + /** + * Returns the value of field 'fontSize'. + * + * @return the value of field 'FontSize'. + */ + public int getFontSize( + ) { + return this._fontSize; + } + + /** + * Returns the value of field 'fontStyle'. + * + * @return the value of field 'FontStyle'. + */ + public int getFontStyle( + ) { + return this._fontStyle; + } + + /** + * Returns the value of field 'height'. + * + * @return the value of field 'Height'. + */ + public int getHeight( + ) { + return this._height; + } + + /** + * Returns the value of field 'pidSelected'. + * + * @return the value of field 'PidSelected'. + */ + public boolean getPidSelected( + ) { + return this._pidSelected; + } + + /** + * Returns the value of field 'pidThreshold'. + * + * @return the value of field 'PidThreshold'. + */ + public int getPidThreshold( + ) { + return this._pidThreshold; + } + + /** + * Returns the value of field 'renderGaps'. + * + * @return the value of field 'RenderGaps'. + */ + public boolean getRenderGaps( + ) { + return this._renderGaps; + } + + /** + * Returns the value of field 'showAnnotation'. + * + * @return the value of field 'ShowAnnotation'. + */ + public boolean getShowAnnotation( + ) { + return this._showAnnotation; + } + + /** + * Returns the value of field 'showBoxes'. + * + * @return the value of field 'ShowBoxes'. + */ + public boolean getShowBoxes( + ) { + return this._showBoxes; + } + + /** + * Returns the value of field 'showColourText'. + * + * @return the value of field 'ShowColourText'. + */ + public boolean getShowColourText( + ) { + return this._showColourText; + } + + /** + * Returns the value of field 'showConservation'. + * + * @return the value of field 'ShowConservation'. + */ + public boolean getShowConservation( + ) { + return this._showConservation; + } + + /** + * Returns the value of field 'showFullId'. + * + * @return the value of field 'ShowFullId'. + */ + public boolean getShowFullId( + ) { + return this._showFullId; + } + + /** + * Returns the value of field 'showIdentity'. + * + * @return the value of field 'ShowIdentity'. + */ + public boolean getShowIdentity( + ) { + return this._showIdentity; + } + + /** + * Returns the value of field 'showQuality'. + * + * @return the value of field 'ShowQuality'. + */ + public boolean getShowQuality( + ) { + return this._showQuality; + } + + /** + * Returns the value of field 'showSequenceFeatures'. + * + * @return the value of field 'ShowSequenceFeatures'. + */ + public boolean getShowSequenceFeatures( + ) { + return this._showSequenceFeatures; + } + + /** + * Returns the value of field 'showText'. + * + * @return the value of field 'ShowText'. + */ + public boolean getShowText( + ) { + return this._showText; + } + + /** + * Returns the value of field 'startRes'. + * + * @return the value of field 'StartRes'. + */ + public int getStartRes( + ) { + return this._startRes; + } + + /** + * Returns the value of field 'startSeq'. + * + * @return the value of field 'StartSeq'. + */ + public int getStartSeq( + ) { + return this._startSeq; + } + + /** + * Returns the value of field 'title'. + * + * @return the value of field 'Title'. + */ + public java.lang.String getTitle( + ) { + return this._title; + } + + /** + * Returns the value of field 'width'. + * + * @return the value of field 'Width'. + */ + public int getWidth( + ) { + return this._width; + } + + /** + * Returns the value of field 'wrapAlignment'. + * + * @return the value of field 'WrapAlignment'. + */ + public boolean getWrapAlignment( + ) { + return this._wrapAlignment; + } + + /** + * Returns the value of field 'xpos'. + * + * @return the value of field 'Xpos'. + */ + public int getXpos( + ) { + return this._xpos; + } + + /** + * Returns the value of field 'ypos'. + * + * @return the value of field 'Ypos'. + */ + public int getYpos( + ) { + return this._ypos; + } + + /** + * Method hasConsThreshold. + * + * @return true if at least one ConsThreshold has been added + */ + public boolean hasConsThreshold( + ) { + return this._has_consThreshold; + } + + /** + * Method hasConservationSelected. + * + * @return true if at least one ConservationSelected has been + * added + */ + public boolean hasConservationSelected( + ) { + return this._has_conservationSelected; + } + + /** + * Method hasFontSize. + * + * @return true if at least one FontSize has been added + */ + public boolean hasFontSize( + ) { + return this._has_fontSize; + } + + /** + * Method hasFontStyle. + * + * @return true if at least one FontStyle has been added + */ + public boolean hasFontStyle( + ) { + return this._has_fontStyle; + } + + /** + * Method hasHeight. + * + * @return true if at least one Height has been added + */ + public boolean hasHeight( + ) { + return this._has_height; + } + + /** + * Method hasPidSelected. + * + * @return true if at least one PidSelected has been added + */ + public boolean hasPidSelected( + ) { + return this._has_pidSelected; + } + + /** + * Method hasPidThreshold. + * + * @return true if at least one PidThreshold has been added + */ + public boolean hasPidThreshold( + ) { + return this._has_pidThreshold; + } + + /** + * Method hasRenderGaps. + * + * @return true if at least one RenderGaps has been added + */ + public boolean hasRenderGaps( + ) { + return this._has_renderGaps; + } + + /** + * Method hasShowAnnotation. + * + * @return true if at least one ShowAnnotation has been added + */ + public boolean hasShowAnnotation( + ) { + return this._has_showAnnotation; + } + + /** + * Method hasShowBoxes. + * + * @return true if at least one ShowBoxes has been added + */ + public boolean hasShowBoxes( + ) { + return this._has_showBoxes; + } + + /** + * Method hasShowColourText. + * + * @return true if at least one ShowColourText has been added + */ + public boolean hasShowColourText( + ) { + return this._has_showColourText; + } + + /** + * Method hasShowConservation. + * + * @return true if at least one ShowConservation has been added + */ + public boolean hasShowConservation( + ) { + return this._has_showConservation; + } + + /** + * Method hasShowFullId. + * + * @return true if at least one ShowFullId has been added + */ + public boolean hasShowFullId( + ) { + return this._has_showFullId; + } + + /** + * Method hasShowIdentity. + * + * @return true if at least one ShowIdentity has been added + */ + public boolean hasShowIdentity( + ) { + return this._has_showIdentity; + } + + /** + * Method hasShowQuality. + * + * @return true if at least one ShowQuality has been added + */ + public boolean hasShowQuality( + ) { + return this._has_showQuality; + } + + /** + * Method hasShowSequenceFeatures. + * + * @return true if at least one ShowSequenceFeatures has been + * added + */ + public boolean hasShowSequenceFeatures( + ) { + return this._has_showSequenceFeatures; + } + + /** + * Method hasShowText. + * + * @return true if at least one ShowText has been added + */ + public boolean hasShowText( + ) { + return this._has_showText; + } + + /** + * Method hasStartRes. + * + * @return true if at least one StartRes has been added + */ + public boolean hasStartRes( + ) { + return this._has_startRes; + } + + /** + * Method hasStartSeq. + * + * @return true if at least one StartSeq has been added + */ + public boolean hasStartSeq( + ) { + return this._has_startSeq; + } + + /** + * Method hasWidth. + * + * @return true if at least one Width has been added + */ + public boolean hasWidth( + ) { + return this._has_width; + } + + /** + * Method hasWrapAlignment. + * + * @return true if at least one WrapAlignment has been added + */ + public boolean hasWrapAlignment( + ) { + return this._has_wrapAlignment; + } + + /** + * Method hasXpos. + * + * @return true if at least one Xpos has been added + */ + public boolean hasXpos( + ) { + return this._has_xpos; + } + + /** + * Method hasYpos. + * + * @return true if at least one Ypos has been added + */ + public boolean hasYpos( + ) { + return this._has_ypos; + } + + /** + * Returns the value of field 'conservationSelected'. + * + * @return the value of field 'ConservationSelected'. + */ + public boolean isConservationSelected( + ) { + return this._conservationSelected; + } + + /** + * Returns the value of field 'pidSelected'. + * + * @return the value of field 'PidSelected'. + */ + public boolean isPidSelected( + ) { + return this._pidSelected; + } + + /** + * Returns the value of field 'renderGaps'. + * + * @return the value of field 'RenderGaps'. + */ + public boolean isRenderGaps( + ) { + return this._renderGaps; + } + + /** + * Returns the value of field 'showAnnotation'. + * + * @return the value of field 'ShowAnnotation'. + */ + public boolean isShowAnnotation( + ) { + return this._showAnnotation; + } + + /** + * Returns the value of field 'showBoxes'. + * + * @return the value of field 'ShowBoxes'. + */ + public boolean isShowBoxes( + ) { + return this._showBoxes; + } + + /** + * Returns the value of field 'showColourText'. + * + * @return the value of field 'ShowColourText'. + */ + public boolean isShowColourText( + ) { + return this._showColourText; + } + + /** + * Returns the value of field 'showConservation'. + * + * @return the value of field 'ShowConservation'. + */ + public boolean isShowConservation( + ) { + return this._showConservation; + } + + /** + * Returns the value of field 'showFullId'. + * + * @return the value of field 'ShowFullId'. + */ + public boolean isShowFullId( + ) { + return this._showFullId; + } + + /** + * Returns the value of field 'showIdentity'. + * + * @return the value of field 'ShowIdentity'. + */ + public boolean isShowIdentity( + ) { + return this._showIdentity; + } + + /** + * Returns the value of field 'showQuality'. + * + * @return the value of field 'ShowQuality'. + */ + public boolean isShowQuality( + ) { + return this._showQuality; + } + + /** + * Returns the value of field 'showSequenceFeatures'. + * + * @return the value of field 'ShowSequenceFeatures'. + */ + public boolean isShowSequenceFeatures( + ) { + return this._showSequenceFeatures; + } + + /** + * Returns the value of field 'showText'. + * + * @return the value of field 'ShowText'. + */ + public boolean isShowText( + ) { + return this._showText; + } + + /** + * Method isValid. + * + * @return true if this object is valid according to the schema + */ + public boolean isValid( + ) { + try { + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } + + /** + * Returns the value of field 'wrapAlignment'. + * + * @return the value of field 'WrapAlignment'. + */ + public boolean isWrapAlignment( + ) { + return this._wrapAlignment; + } + + /** + * + * + * @param out + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } + + /** + * + * + * @param handler + * @throws java.io.IOException if an IOException occurs during + * marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + */ + public void marshal( + final org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, handler); + } + + /** + * Sets the value of field 'bgColour'. + * + * @param bgColour the value of field 'bgColour'. + */ + public void setBgColour( + final java.lang.String bgColour) { + this._bgColour = bgColour; + } + + /** + * Sets the value of field 'consThreshold'. + * + * @param consThreshold the value of field 'consThreshold'. + */ + public void setConsThreshold( + final int consThreshold) { + this._consThreshold = consThreshold; + this._has_consThreshold = true; + } + + /** + * Sets the value of field 'conservationSelected'. + * + * @param conservationSelected the value of field + * 'conservationSelected'. + */ + public void setConservationSelected( + final boolean conservationSelected) { + this._conservationSelected = conservationSelected; + this._has_conservationSelected = true; + } + + /** + * Sets the value of field 'fontName'. + * + * @param fontName the value of field 'fontName'. + */ + public void setFontName( + final java.lang.String fontName) { + this._fontName = fontName; + } + + /** + * Sets the value of field 'fontSize'. + * + * @param fontSize the value of field 'fontSize'. + */ + public void setFontSize( + final int fontSize) { + this._fontSize = fontSize; + this._has_fontSize = true; + } + + /** + * Sets the value of field 'fontStyle'. + * + * @param fontStyle the value of field 'fontStyle'. + */ + public void setFontStyle( + final int fontStyle) { + this._fontStyle = fontStyle; + this._has_fontStyle = true; + } + + /** + * Sets the value of field 'height'. + * + * @param height the value of field 'height'. + */ + public void setHeight( + final int height) { + this._height = height; + this._has_height = true; + } + + /** + * Sets the value of field 'pidSelected'. + * + * @param pidSelected the value of field 'pidSelected'. + */ + public void setPidSelected( + final boolean pidSelected) { + this._pidSelected = pidSelected; + this._has_pidSelected = true; + } + + /** + * Sets the value of field 'pidThreshold'. + * + * @param pidThreshold the value of field 'pidThreshold'. + */ + public void setPidThreshold( + final int pidThreshold) { + this._pidThreshold = pidThreshold; + this._has_pidThreshold = true; + } + + /** + * Sets the value of field 'renderGaps'. + * + * @param renderGaps the value of field 'renderGaps'. + */ + public void setRenderGaps( + final boolean renderGaps) { + this._renderGaps = renderGaps; + this._has_renderGaps = true; + } + + /** + * Sets the value of field 'showAnnotation'. + * + * @param showAnnotation the value of field 'showAnnotation'. + */ + public void setShowAnnotation( + final boolean showAnnotation) { + this._showAnnotation = showAnnotation; + this._has_showAnnotation = true; + } + + /** + * Sets the value of field 'showBoxes'. + * + * @param showBoxes the value of field 'showBoxes'. + */ + public void setShowBoxes( + final boolean showBoxes) { + this._showBoxes = showBoxes; + this._has_showBoxes = true; + } + + /** + * Sets the value of field 'showColourText'. + * + * @param showColourText the value of field 'showColourText'. + */ + public void setShowColourText( + final boolean showColourText) { + this._showColourText = showColourText; + this._has_showColourText = true; + } + + /** + * Sets the value of field 'showConservation'. + * + * @param showConservation the value of field 'showConservation' + */ + public void setShowConservation( + final boolean showConservation) { + this._showConservation = showConservation; + this._has_showConservation = true; + } + + /** + * Sets the value of field 'showFullId'. + * + * @param showFullId the value of field 'showFullId'. + */ + public void setShowFullId( + final boolean showFullId) { + this._showFullId = showFullId; + this._has_showFullId = true; + } + + /** + * Sets the value of field 'showIdentity'. + * + * @param showIdentity the value of field 'showIdentity'. + */ + public void setShowIdentity( + final boolean showIdentity) { + this._showIdentity = showIdentity; + this._has_showIdentity = true; + } + + /** + * Sets the value of field 'showQuality'. + * + * @param showQuality the value of field 'showQuality'. + */ + public void setShowQuality( + final boolean showQuality) { + this._showQuality = showQuality; + this._has_showQuality = true; + } + + /** + * Sets the value of field 'showSequenceFeatures'. + * + * @param showSequenceFeatures the value of field + * 'showSequenceFeatures'. + */ + public void setShowSequenceFeatures( + final boolean showSequenceFeatures) { + this._showSequenceFeatures = showSequenceFeatures; + this._has_showSequenceFeatures = true; + } + + /** + * Sets the value of field 'showText'. + * + * @param showText the value of field 'showText'. + */ + public void setShowText( + final boolean showText) { + this._showText = showText; + this._has_showText = true; + } + + /** + * Sets the value of field 'startRes'. + * + * @param startRes the value of field 'startRes'. + */ + public void setStartRes( + final int startRes) { + this._startRes = startRes; + this._has_startRes = true; + } + + /** + * Sets the value of field 'startSeq'. + * + * @param startSeq the value of field 'startSeq'. + */ + public void setStartSeq( + final int startSeq) { + this._startSeq = startSeq; + this._has_startSeq = true; + } + + /** + * Sets the value of field 'title'. + * + * @param title the value of field 'title'. + */ + public void setTitle( + final java.lang.String title) { + this._title = title; + } + + /** + * Sets the value of field 'width'. + * + * @param width the value of field 'width'. + */ + public void setWidth( + final int width) { + this._width = width; + this._has_width = true; + } + + /** + * Sets the value of field 'wrapAlignment'. + * + * @param wrapAlignment the value of field 'wrapAlignment'. + */ + public void setWrapAlignment( + final boolean wrapAlignment) { + this._wrapAlignment = wrapAlignment; + this._has_wrapAlignment = true; + } + + /** + * Sets the value of field 'xpos'. + * + * @param xpos the value of field 'xpos'. + */ + public void setXpos( + final int xpos) { + this._xpos = xpos; + this._has_xpos = true; + } + + /** + * Sets the value of field 'ypos'. + * + * @param ypos the value of field 'ypos'. + */ + public void setYpos( + final int ypos) { + this._ypos = ypos; + this._has_ypos = true; + } + + /** + * Method unmarshal. + * + * @param reader + * @throws org.exolab.castor.xml.MarshalException if object is + * null or if any SAXException is thrown during marshaling + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + * @return the unmarshaled jalview.binding.Viewport + */ + public static jalview.binding.Viewport unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.binding.Viewport) Unmarshaller.unmarshal(jalview.binding.Viewport.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema + */ + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } + +} -- 1.7.10.2