From: jprocter Date: Thu, 17 Feb 2011 11:29:57 +0000 (+0000) Subject: fixes JAL-778 - flag to indicate binding between an alignment panel and Jmol view... X-Git-Tag: Release_2_7~252 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a95b88b05400d7e841f9523d4c4228c678307654;p=jalview.git fixes JAL-778 - flag to indicate binding between an alignment panel and Jmol view for colouring and optionally for superposition as well. --- diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd index c847b6d..d179ab2 100755 --- a/schemas/jalview.xsd +++ b/schemas/jalview.xsd @@ -52,6 +52,20 @@ viewId will appear for each instance. + + + + Flag set if the alignment panel containing this JSeq should be explicitly linked to the Jmol view referred to/created by this structureState (since Jalview 2.7). + + + + + + + Flag set if the alignment panel containing this JSeq should be included in those used to perform a structure superposition (since Jalview 2.7). + + + diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java index 6b1efa8..5b107b5 100755 --- a/src/jalview/binding/Alignment.java +++ b/src/jalview/binding/Alignment.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,162 +19,151 @@ import org.exolab.castor.xml.Unmarshaller; * * @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; +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); } - 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 87ca721..108d3ad 100755 --- a/src/jalview/binding/Annotation.java +++ b/src/jalview/binding/Annotation.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,441 +19,414 @@ import org.exolab.castor.xml.Unmarshaller; * * @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) + "]"); +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(); } - 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; + + //-----------/ + //- 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); } - 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) + "]"); + + /** + * + * + * @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); } - 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]); + /** + * 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); } - } - - /** - * 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 7814e34..d133fe0 100755 --- a/src/jalview/binding/AnnotationElement.java +++ b/src/jalview/binding/AnnotationElement.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,287 +19,273 @@ import org.exolab.castor.xml.Unmarshaller; * * @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 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 void deletePosition() - { - this._has_position = false; - } + 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 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; + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); } - 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 b1e7916..c041723 100755 --- a/src/jalview/binding/Colour.java +++ b/src/jalview/binding/Colour.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,480 +19,465 @@ import org.exolab.castor.xml.Unmarshaller; * * @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; - - /** - * Field _minRGB. - */ - private java.lang.String _minRGB; - - /** - * loosely specified enumeration: NONE,ABOVE, or BELOW - */ - private java.lang.String _threshType; - - /** - * Field _threshold. - */ - private float _threshold; - - /** - * keeps track of state for field: _threshold - */ - private boolean _has_threshold; - - /** - * Field _max. - */ - private float _max; - - /** - * keeps track of state for field: _max - */ - private boolean _has_max; - - /** - * Field _min. - */ - private float _min; - - /** - * keeps track of state for field: _min - */ - private boolean _has_min; - - /** - * Field _colourByLabel. - */ - private boolean _colourByLabel; - - /** - * keeps track of state for field: _colourByLabel - */ - private boolean _has_colourByLabel; - - /** - * Field _autoScale. - */ - private boolean _autoScale; - - /** - * keeps track of state for field: _autoScale - */ - private boolean _has_autoScale; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Colour() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteAutoScale() - { - this._has_autoScale = false; - } - - /** - */ - public void deleteColourByLabel() - { - this._has_colourByLabel = false; - } - - /** - */ - public void deleteMax() - { - this._has_max = false; - } - - /** - */ - public void deleteMin() - { - this._has_min = false; - } - - /** - */ - public void deleteThreshold() - { - this._has_threshold = false; - } - - /** - * Returns the value of field 'autoScale'. - * - * @return the value of field 'AutoScale'. - */ - public boolean getAutoScale() - { - return this._autoScale; - } - - /** - * Returns the value of field 'colourByLabel'. - * - * @return the value of field 'ColourByLabel'. - */ - public boolean getColourByLabel() - { - return this._colourByLabel; - } - - /** - * Returns the value of field 'max'. - * - * @return the value of field 'Max'. - */ - public float getMax() - { - return this._max; - } - - /** - * Returns the value of field 'min'. - * - * @return the value of field 'Min'. - */ - public float getMin() - { - return this._min; - } - - /** - * Returns the value of field 'minRGB'. - * - * @return the value of field 'MinRGB'. - */ - public java.lang.String getMinRGB() - { - return this._minRGB; - } - - /** - * 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; - } - - /** - * Returns the value of field 'threshType'. The field 'threshType' has the - * following description: loosely specified enumeration: NONE,ABOVE, or BELOW - * - * @return the value of field 'ThreshType'. - */ - public java.lang.String getThreshType() - { - return this._threshType; - } - - /** - * Returns the value of field 'threshold'. - * - * @return the value of field 'Threshold'. - */ - public float getThreshold() - { - return this._threshold; - } - - /** - * Method hasAutoScale. - * - * @return true if at least one AutoScale has been added - */ - public boolean hasAutoScale() - { - return this._has_autoScale; - } - - /** - * Method hasColourByLabel. - * - * @return true if at least one ColourByLabel has been added - */ - public boolean hasColourByLabel() - { - return this._has_colourByLabel; - } - - /** - * Method hasMax. - * - * @return true if at least one Max has been added - */ - public boolean hasMax() - { - return this._has_max; - } - - /** - * Method hasMin. - * - * @return true if at least one Min has been added - */ - public boolean hasMin() - { - return this._has_min; - } - - /** - * Method hasThreshold. - * - * @return true if at least one Threshold has been added - */ - public boolean hasThreshold() - { - return this._has_threshold; - } - - /** - * Returns the value of field 'autoScale'. - * - * @return the value of field 'AutoScale'. - */ - public boolean isAutoScale() - { - return this._autoScale; - } - - /** - * Returns the value of field 'colourByLabel'. - * - * @return the value of field 'ColourByLabel'. - */ - public boolean isColourByLabel() - { - return this._colourByLabel; - } - - /** - * 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 'autoScale'. - * - * @param autoScale - * the value of field 'autoScale'. - */ - public void setAutoScale(final boolean autoScale) - { - this._autoScale = autoScale; - this._has_autoScale = true; - } - - /** - * Sets the value of field 'colourByLabel'. - * - * @param colourByLabel - * the value of field 'colourByLabel'. - */ - public void setColourByLabel(final boolean colourByLabel) - { - this._colourByLabel = colourByLabel; - this._has_colourByLabel = true; - } - - /** - * Sets the value of field 'max'. - * - * @param max - * the value of field 'max'. - */ - public void setMax(final float max) - { - this._max = max; - this._has_max = true; - } - - /** - * Sets the value of field 'min'. - * - * @param min - * the value of field 'min'. - */ - public void setMin(final float min) - { - this._min = min; - this._has_min = true; - } - - /** - * Sets the value of field 'minRGB'. - * - * @param minRGB - * the value of field 'minRGB'. - */ - public void setMinRGB(final java.lang.String minRGB) - { - this._minRGB = minRGB; - } - - /** - * 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; - } - - /** - * Sets the value of field 'threshType'. The field 'threshType' has the - * following description: loosely specified enumeration: NONE,ABOVE, or BELOW - * - * @param threshType - * the value of field 'threshType'. - */ - public void setThreshType(final java.lang.String threshType) - { - this._threshType = threshType; - } - - /** - * 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; - } - - /** - * 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); - } +public class Colour implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _name. + */ + private java.lang.String _name; + + /** + * Field _RGB. + */ + private java.lang.String _RGB; + + /** + * Field _minRGB. + */ + private java.lang.String _minRGB; + + /** + * loosely specified enumeration: NONE,ABOVE, or BELOW + */ + private java.lang.String _threshType; + + /** + * Field _threshold. + */ + private float _threshold; + + /** + * keeps track of state for field: _threshold + */ + private boolean _has_threshold; + + /** + * Field _max. + */ + private float _max; + + /** + * keeps track of state for field: _max + */ + private boolean _has_max; + + /** + * Field _min. + */ + private float _min; + + /** + * keeps track of state for field: _min + */ + private boolean _has_min; + + /** + * Field _colourByLabel. + */ + private boolean _colourByLabel; + + /** + * keeps track of state for field: _colourByLabel + */ + private boolean _has_colourByLabel; + + /** + * Field _autoScale. + */ + private boolean _autoScale; + + /** + * keeps track of state for field: _autoScale + */ + private boolean _has_autoScale; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Colour() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteAutoScale( + ) { + this._has_autoScale= false; + } + + /** + */ + public void deleteColourByLabel( + ) { + this._has_colourByLabel= false; + } + + /** + */ + public void deleteMax( + ) { + this._has_max= false; + } + + /** + */ + public void deleteMin( + ) { + this._has_min= false; + } + + /** + */ + public void deleteThreshold( + ) { + this._has_threshold= false; + } + + /** + * Returns the value of field 'autoScale'. + * + * @return the value of field 'AutoScale'. + */ + public boolean getAutoScale( + ) { + return this._autoScale; + } + + /** + * Returns the value of field 'colourByLabel'. + * + * @return the value of field 'ColourByLabel'. + */ + public boolean getColourByLabel( + ) { + return this._colourByLabel; + } + + /** + * Returns the value of field 'max'. + * + * @return the value of field 'Max'. + */ + public float getMax( + ) { + return this._max; + } + + /** + * Returns the value of field 'min'. + * + * @return the value of field 'Min'. + */ + public float getMin( + ) { + return this._min; + } + + /** + * Returns the value of field 'minRGB'. + * + * @return the value of field 'MinRGB'. + */ + public java.lang.String getMinRGB( + ) { + return this._minRGB; + } + + /** + * 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; + } + + /** + * Returns the value of field 'threshType'. The field + * 'threshType' has the following description: loosely + * specified enumeration: NONE,ABOVE, or BELOW + * + * @return the value of field 'ThreshType'. + */ + public java.lang.String getThreshType( + ) { + return this._threshType; + } + + /** + * Returns the value of field 'threshold'. + * + * @return the value of field 'Threshold'. + */ + public float getThreshold( + ) { + return this._threshold; + } + + /** + * Method hasAutoScale. + * + * @return true if at least one AutoScale has been added + */ + public boolean hasAutoScale( + ) { + return this._has_autoScale; + } + + /** + * Method hasColourByLabel. + * + * @return true if at least one ColourByLabel has been added + */ + public boolean hasColourByLabel( + ) { + return this._has_colourByLabel; + } + + /** + * Method hasMax. + * + * @return true if at least one Max has been added + */ + public boolean hasMax( + ) { + return this._has_max; + } + + /** + * Method hasMin. + * + * @return true if at least one Min has been added + */ + public boolean hasMin( + ) { + return this._has_min; + } + + /** + * Method hasThreshold. + * + * @return true if at least one Threshold has been added + */ + public boolean hasThreshold( + ) { + return this._has_threshold; + } + + /** + * Returns the value of field 'autoScale'. + * + * @return the value of field 'AutoScale'. + */ + public boolean isAutoScale( + ) { + return this._autoScale; + } + + /** + * Returns the value of field 'colourByLabel'. + * + * @return the value of field 'ColourByLabel'. + */ + public boolean isColourByLabel( + ) { + return this._colourByLabel; + } + + /** + * 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 'autoScale'. + * + * @param autoScale the value of field 'autoScale'. + */ + public void setAutoScale( + final boolean autoScale) { + this._autoScale = autoScale; + this._has_autoScale = true; + } + + /** + * Sets the value of field 'colourByLabel'. + * + * @param colourByLabel the value of field 'colourByLabel'. + */ + public void setColourByLabel( + final boolean colourByLabel) { + this._colourByLabel = colourByLabel; + this._has_colourByLabel = true; + } + + /** + * Sets the value of field 'max'. + * + * @param max the value of field 'max'. + */ + public void setMax( + final float max) { + this._max = max; + this._has_max = true; + } + + /** + * Sets the value of field 'min'. + * + * @param min the value of field 'min'. + */ + public void setMin( + final float min) { + this._min = min; + this._has_min = true; + } + + /** + * Sets the value of field 'minRGB'. + * + * @param minRGB the value of field 'minRGB'. + */ + public void setMinRGB( + final java.lang.String minRGB) { + this._minRGB = minRGB; + } + + /** + * 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; + } + + /** + * Sets the value of field 'threshType'. The field 'threshType' + * has the following description: loosely specified + * enumeration: NONE,ABOVE, or BELOW + * + * @param threshType the value of field 'threshType'. + */ + public void setThreshType( + final java.lang.String threshType) { + this._threshType = threshType; + } + + /** + * 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; + } + + /** + * 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 cd0c9bd..d429df3 100755 --- a/src/jalview/binding/Feature.java +++ b/src/jalview/binding/Feature.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,286 +19,272 @@ import org.exolab.castor.xml.Unmarshaller; * * @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 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 void deleteBegin() - { - this._has_begin = false; - } + 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 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; + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); } - 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 5a768c4..f3d06be 100755 --- a/src/jalview/binding/FeatureSettings.java +++ b/src/jalview/binding/FeatureSettings.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,271 +19,257 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class FeatureSettings implements java.io.Serializable -{ +public class FeatureSettings implements java.io.Serializable { - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - /** - * Field _settingList. - */ - private java.util.Vector _settingList; + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ - // ----------------/ - // - Constructors -/ - // ----------------/ + /** + * Field _settingList. + */ + private java.util.Vector _settingList; - public FeatureSettings() - { - super(); - this._settingList = new java.util.Vector(); - } - // -----------/ - // - Methods -/ - // -----------/ + //----------------/ + //- Constructors -/ + //----------------/ - /** - * - * - * @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); - } + public FeatureSettings() { + super(); + this._settingList = new java.util.Vector(); + } - /** - * - * - * @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(); - } + //-----------/ + //- Methods -/ + //-----------/ - /** - * 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) + "]"); + /** + * + * + * @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); } - return (jalview.binding.Setting) _settingList.get(index); - } + /** + * + * + * @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 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 enumerateSetting. + * + * @return an Enumeration over all jalview.binding.Setting + * elements + */ + public java.util.Enumeration enumerateSetting( + ) { + return this._settingList.elements(); + } - /** - * Method getSettingCount. - * - * @return the size of this collection - */ - public int getSettingCount() - { - return this._settingList.size(); - } + /** + * 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 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; + /** + * 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); } - 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); - } + /** + * Method getSettingCount. + * + * @return the size of this collection + */ + public int getSettingCount( + ) { + return this._settingList.size(); + } - /** - * - * - * @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 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 removeAllSetting() - { - this._settingList.clear(); - } + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } - /** - * 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; - } + /** + * + * + * @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 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; - } + /** + */ + public void removeAllSetting( + ) { + this._settingList.clear(); + } - /** - * - * - * @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) + "]"); + /** + * 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; } - this._settingList.set(index, vSetting); - } + /** + * 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 vSettingArray - */ - public void setSetting(final jalview.binding.Setting[] vSettingArray) - { - // -- copy array - _settingList.clear(); + /** + * + * + * @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); + } - for (int i = 0; i < vSettingArray.length; i++) - { - this._settingList.add(vSettingArray[i]); + /** + * + * + * @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); - } + /** + * 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); - } + /** + * + * + * @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 0d65b0c..e50ae7c 100755 --- a/src/jalview/binding/Features.java +++ b/src/jalview/binding/Features.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,106 +19,98 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class Features extends Feature implements java.io.Serializable +public class Features extends Feature +implements java.io.Serializable { - // ----------------/ - // - Constructors -/ - // ----------------/ - public Features() - { - super(); - } + //----------------/ + //- Constructors -/ + //----------------/ - // -----------/ - // - Methods -/ - // -----------/ + public Features() { + super(); + } - /** - * 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; + + //-----------/ + //- 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; } - 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 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); - } + /** + * + * + * @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); - } + /** + * 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); - } + /** + * + * + * @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 02d92292..862eebd 100755 --- a/src/jalview/binding/JGroup.java +++ b/src/jalview/binding/JGroup.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,742 +19,721 @@ import org.exolab.castor.xml.Unmarshaller; * * @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); - } +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 cbc949a..14b1f2f 100755 --- a/src/jalview/binding/JSeq.java +++ b/src/jalview/binding/JSeq.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,627 +19,605 @@ import org.exolab.castor.xml.Unmarshaller; * * @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); - } +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 8f12c0c..21f8be9 100755 --- a/src/jalview/binding/JalviewModel.java +++ b/src/jalview/binding/JalviewModel.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,215 +19,202 @@ import org.exolab.castor.xml.Unmarshaller; * * @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; +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); } - 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 6b056d3..5ebcee6 100755 --- a/src/jalview/binding/JalviewModelSequence.java +++ b/src/jalview/binding/JalviewModelSequence.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,937 +19,904 @@ import org.exolab.castor.xml.Unmarshaller; * * @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); - } +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 cf575f5..9a6465b 100755 --- a/src/jalview/binding/JalviewUserColours.java +++ b/src/jalview/binding/JalviewUserColours.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,326 +19,312 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class JalviewUserColours implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _schemeName. - */ - private java.lang.String _schemeName; - - /** - * Jalview colour scheme document version. - * - */ - private java.lang.String _version; - - /** - * 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) + "]"); +public class JalviewUserColours implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _schemeName. + */ + private java.lang.String _schemeName; + + /** + * Jalview colour scheme document version. + * + */ + private java.lang.String _version; + + /** + * Field _colourList. + */ + private java.util.Vector _colourList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JalviewUserColours() { + super(); + this._colourList = new java.util.Vector(); } - 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; - } - - /** - * Returns the value of field 'version'. The field 'version' has the following - * description: Jalview colour scheme document 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; + + //-----------/ + //- 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); } - 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 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 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) + "]"); + public int getColourCount( + ) { + return this._colourList.size(); } - 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]); + /** + * Returns the value of field 'schemeName'. + * + * @return the value of field 'SchemeName'. + */ + public java.lang.String getSchemeName( + ) { + return this._schemeName; + } + + /** + * Returns the value of field 'version'. The field 'version' + * has the following description: Jalview colour scheme + * document 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); + } + + /** + */ + 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; + } + + /** + * Sets the value of field 'version'. The field 'version' has + * the following description: Jalview colour scheme document + * 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.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); } - } - - /** - * Sets the value of field 'schemeName'. - * - * @param schemeName - * the value of field 'schemeName'. - */ - public void setSchemeName(final java.lang.String schemeName) - { - this._schemeName = schemeName; - } - - /** - * Sets the value of field 'version'. The field 'version' has the following - * description: Jalview colour scheme document 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.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 54c678c..cac4cf6 100755 --- a/src/jalview/binding/Pdbentry.java +++ b/src/jalview/binding/Pdbentry.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,326 +19,308 @@ import org.exolab.castor.xml.Unmarshaller; * * @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) - + "]"); +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(); } - 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; + + //-----------/ + //- 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; } - 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 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 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) - + "]"); + public jalview.binding.PdbentryItem[] getPdbentryItem( + ) { + jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0]; + return (jalview.binding.PdbentryItem[]) this._items.toArray(array); } - 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]); + /** + * 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); } - } - - /** - * 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 7e40e0c..83bc40a 100755 --- a/src/jalview/binding/PdbentryItem.java +++ b/src/jalview/binding/PdbentryItem.java @@ -1,20 +1,10 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; /** @@ -22,185 +12,181 @@ package jalview.binding; * * @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) + "]"); +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(); } - 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) + "]"); + public void removeAllProperty( + ) { + this._propertyList.clear(); } - 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]); + /** + * 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 4857701..b4745a2 100755 --- a/src/jalview/binding/Pdbids.java +++ b/src/jalview/binding/Pdbids.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,106 +19,98 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class Pdbids extends Pdbentry implements java.io.Serializable +public class Pdbids extends Pdbentry +implements java.io.Serializable { - // ----------------/ - // - Constructors -/ - // ----------------/ - public Pdbids() - { - super(); - } + //----------------/ + //- Constructors -/ + //----------------/ - // -----------/ - // - Methods -/ - // -----------/ + public Pdbids() { + super(); + } - /** - * 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; + + //-----------/ + //- 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; } - 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 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); - } + /** + * + * + * @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); - } + /** + * 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); - } + /** + * + * + * @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 b051b0d..f1114f7 100755 --- a/src/jalview/binding/Property.java +++ b/src/jalview/binding/Property.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,162 +19,151 @@ import org.exolab.castor.xml.Unmarshaller; * * @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; +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); } - 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 e69fa67..9c8cbc2 100755 --- a/src/jalview/binding/Sequence.java +++ b/src/jalview/binding/Sequence.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,106 +19,98 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class Sequence extends SequenceType implements java.io.Serializable +public class Sequence extends SequenceType +implements java.io.Serializable { - // ----------------/ - // - Constructors -/ - // ----------------/ - public Sequence() - { - super(); - } + //----------------/ + //- Constructors -/ + //----------------/ - // -----------/ - // - Methods -/ - // -----------/ + public Sequence() { + super(); + } - /** - * 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; + + //-----------/ + //- 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; } - 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 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); - } + /** + * + * + * @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); - } + /** + * 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); - } + /** + * + * + * @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 fa6feda..13a9020 100755 --- a/src/jalview/binding/SequenceSet.java +++ b/src/jalview/binding/SequenceSet.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,520 +19,496 @@ import org.exolab.castor.xml.Unmarshaller; * * @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); - } +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 1b420a0..1bb2a62 100755 --- a/src/jalview/binding/SequenceType.java +++ b/src/jalview/binding/SequenceType.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,188 +19,176 @@ import org.exolab.castor.xml.Unmarshaller; * * @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; +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); } - 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 a9717e7..9cd84b4 100755 --- a/src/jalview/binding/Setting.java +++ b/src/jalview/binding/Setting.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,244 +19,232 @@ import org.exolab.castor.xml.Unmarshaller; * * @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 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 void deleteColour() - { - this._has_colour = false; - } + 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 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; + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); } - 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 2e62e4a..5f138d0 100755 --- a/src/jalview/binding/Tree.java +++ b/src/jalview/binding/Tree.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,825 +19,802 @@ import org.exolab.castor.xml.Unmarshaller; * * @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); - } +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 915881b..24c97ff 100755 --- a/src/jalview/binding/UserColourScheme.java +++ b/src/jalview/binding/UserColourScheme.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,107 +19,98 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class UserColourScheme extends JalviewUserColours implements - java.io.Serializable +public class UserColourScheme extends JalviewUserColours +implements java.io.Serializable { - // ----------------/ - // - Constructors -/ - // ----------------/ - public UserColourScheme() - { - super(); - } + //----------------/ + //- Constructors -/ + //----------------/ - // -----------/ - // - Methods -/ - // -----------/ + public UserColourScheme() { + super(); + } - /** - * 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; + + //-----------/ + //- 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; } - 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 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); - } + /** + * + * + * @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); - } + /** + * 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); - } + /** + * + * + * @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 cf195e7..bdefe05 100755 --- a/src/jalview/binding/UserColours.java +++ b/src/jalview/binding/UserColours.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,163 +19,151 @@ import org.exolab.castor.xml.Unmarshaller; * * @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; +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); } - 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 d7610d4..1c92bd3 100755 --- a/src/jalview/binding/VAMSAS.java +++ b/src/jalview/binding/VAMSAS.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,584 +19,563 @@ import org.exolab.castor.xml.Unmarshaller; * * @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); - } +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 2b1bc0e..5fda35e 100755 --- a/src/jalview/binding/VamsasModel.java +++ b/src/jalview/binding/VamsasModel.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,105 +19,98 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class VamsasModel extends VAMSAS implements java.io.Serializable +public class VamsasModel extends VAMSAS +implements java.io.Serializable { - // ----------------/ - // - Constructors -/ - // ----------------/ - public VamsasModel() - { - super(); - } + //----------------/ + //- Constructors -/ + //----------------/ - // -----------/ - // - Methods -/ - // -----------/ + public VamsasModel() { + super(); + } - /** - * 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; + + //-----------/ + //- 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; } - 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 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); - } + /** + * + * + * @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); - } + /** + * 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); - } + /** + * + * + * @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 ee663c7..643c323 100755 --- a/src/jalview/binding/Viewport.java +++ b/src/jalview/binding/Viewport.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,1445 +19,1414 @@ import org.exolab.castor.xml.Unmarshaller; * * @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 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 void deleteConsThreshold() - { - this._has_consThreshold = false; - } + public boolean hasShowIdentity( + ) { + return this._has_showIdentity; + } - /** + /** + * Method hasShowQuality. + * + * @return true if at least one ShowQuality has been added */ - public void deleteConservationSelected() - { - this._has_conservationSelected = false; - } + public boolean hasShowQuality( + ) { + return this._has_showQuality; + } - /** + /** + * Method hasShowSequenceFeatures. + * + * @return true if at least one ShowSequenceFeatures has been + * added */ - public void deleteFontSize() - { - this._has_fontSize = false; - } + public boolean hasShowSequenceFeatures( + ) { + return this._has_showSequenceFeatures; + } - /** + /** + * Method hasShowText. + * + * @return true if at least one ShowText has been added */ - public void deleteFontStyle() - { - this._has_fontStyle = false; - } + public boolean hasShowText( + ) { + return this._has_showText; + } - /** + /** + * Method hasStartRes. + * + * @return true if at least one StartRes has been added */ - public void deleteHeight() - { - this._has_height = false; - } + public boolean hasStartRes( + ) { + return this._has_startRes; + } - /** + /** + * Method hasStartSeq. + * + * @return true if at least one StartSeq has been added */ - public void deletePidSelected() - { - this._has_pidSelected = false; - } + public boolean hasStartSeq( + ) { + return this._has_startSeq; + } - /** + /** + * Method hasWidth. + * + * @return true if at least one Width has been added */ - public void deletePidThreshold() - { - this._has_pidThreshold = false; - } + public boolean hasWidth( + ) { + return this._has_width; + } - /** + /** + * Method hasWrapAlignment. + * + * @return true if at least one WrapAlignment has been added */ - public void deleteRenderGaps() - { - this._has_renderGaps = false; - } + public boolean hasWrapAlignment( + ) { + return this._has_wrapAlignment; + } - /** + /** + * Method hasXpos. + * + * @return true if at least one Xpos has been added */ - public void deleteShowAnnotation() - { - this._has_showAnnotation = false; - } + public boolean hasXpos( + ) { + return this._has_xpos; + } - /** + /** + * Method hasYpos. + * + * @return true if at least one Ypos has been added */ - public void deleteShowBoxes() - { - this._has_showBoxes = false; - } + public boolean hasYpos( + ) { + return this._has_ypos; + } - /** + /** + * Returns the value of field 'conservationSelected'. + * + * @return the value of field 'ConservationSelected'. */ - public void deleteShowColourText() - { - this._has_showColourText = false; - } + public boolean isConservationSelected( + ) { + return this._conservationSelected; + } - /** + /** + * Returns the value of field 'pidSelected'. + * + * @return the value of field 'PidSelected'. */ - public void deleteShowConservation() - { - this._has_showConservation = false; - } + public boolean isPidSelected( + ) { + return this._pidSelected; + } - /** + /** + * Returns the value of field 'renderGaps'. + * + * @return the value of field 'RenderGaps'. */ - public void deleteShowFullId() - { - this._has_showFullId = false; - } + public boolean isRenderGaps( + ) { + return this._renderGaps; + } - /** + /** + * Returns the value of field 'showAnnotation'. + * + * @return the value of field 'ShowAnnotation'. */ - public void deleteShowIdentity() - { - this._has_showIdentity = false; - } + public boolean isShowAnnotation( + ) { + return this._showAnnotation; + } - /** + /** + * Returns the value of field 'showBoxes'. + * + * @return the value of field 'ShowBoxes'. */ - 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); - } + 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); + } } diff --git a/src/jalview/schemabinding/version2/.castor.cdr b/src/jalview/schemabinding/version2/.castor.cdr index 93d2e0f..e54b627 100644 --- a/src/jalview/schemabinding/version2/.castor.cdr +++ b/src/jalview/schemabinding/version2/.castor.cdr @@ -1,4 +1,4 @@ -#Mon Sep 06 13:16:48 BST 2010 +#Tue Feb 15 17:12:42 GMT 2011 jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor diff --git a/src/jalview/schemabinding/version2/AlcodMap.java b/src/jalview/schemabinding/version2/AlcodMap.java index 3b1aa1b..f43acd6 100644 --- a/src/jalview/schemabinding/version2/AlcodMap.java +++ b/src/jalview/schemabinding/version2/AlcodMap.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,174 +19,166 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class AlcodMap implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * internal jalview id for the dnasq for this mapping. - * - */ - private java.lang.String _dnasq; - - /** - * a Mapping entry and an associated protein sequence - * - */ - private jalview.schemabinding.version2.Mapping _mapping; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AlcodMap() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'dnasq'. The field 'dnasq' has the following - * description: internal jalview id for the dnasq for this mapping. - * - * - * @return the value of field 'Dnasq'. - */ - public java.lang.String getDnasq() - { - return this._dnasq; - } - - /** - * Returns the value of field 'mapping'. The field 'mapping' has the following - * description: a Mapping entry and an associated protein sequence - * - * - * @return the value of field 'Mapping'. - */ - public jalview.schemabinding.version2.Mapping getMapping() - { - return this._mapping; - } - - /** - * 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; +public class AlcodMap implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * internal jalview id for the dnasq for this mapping. + * + */ + private java.lang.String _dnasq; + + /** + * a Mapping entry and an associated protein sequence + * + */ + private jalview.schemabinding.version2.Mapping _mapping; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AlcodMap() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'dnasq'. The field 'dnasq' has + * the following description: internal jalview id for the dnasq + * for this mapping. + * + * + * @return the value of field 'Dnasq'. + */ + public java.lang.String getDnasq( + ) { + return this._dnasq; + } + + /** + * Returns the value of field 'mapping'. The field 'mapping' + * has the following description: a Mapping entry and an + * associated protein sequence + * + * + * @return the value of field 'Mapping'. + */ + public jalview.schemabinding.version2.Mapping getMapping( + ) { + return this._mapping; + } + + /** + * 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 'dnasq'. The field 'dnasq' has the + * following description: internal jalview id for the dnasq for + * this mapping. + * + * + * @param dnasq the value of field 'dnasq'. + */ + public void setDnasq( + final java.lang.String dnasq) { + this._dnasq = dnasq; + } + + /** + * Sets the value of field 'mapping'. The field 'mapping' has + * the following description: a Mapping entry and an associated + * protein sequence + * + * + * @param mapping the value of field 'mapping'. + */ + public void setMapping( + final jalview.schemabinding.version2.Mapping mapping) { + this._mapping = mapping; + } + + /** + * 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.schemabinding.version2.AlcodMap + */ + public static jalview.schemabinding.version2.AlcodMap unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.AlcodMap) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodMap.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); } - 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 'dnasq'. The field 'dnasq' has the following - * description: internal jalview id for the dnasq for this mapping. - * - * - * @param dnasq - * the value of field 'dnasq'. - */ - public void setDnasq(final java.lang.String dnasq) - { - this._dnasq = dnasq; - } - - /** - * Sets the value of field 'mapping'. The field 'mapping' has the following - * description: a Mapping entry and an associated protein sequence - * - * - * @param mapping - * the value of field 'mapping'. - */ - public void setMapping( - final jalview.schemabinding.version2.Mapping mapping) - { - this._mapping = mapping; - } - - /** - * 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.schemabinding.version2.AlcodMap - */ - public static jalview.schemabinding.version2.AlcodMap unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.AlcodMap) Unmarshaller - .unmarshal(jalview.schemabinding.version2.AlcodMap.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/schemabinding/version2/Alcodon.java b/src/jalview/schemabinding/version2/Alcodon.java index 9bd0a7f..cffbd9a 100644 --- a/src/jalview/schemabinding/version2/Alcodon.java +++ b/src/jalview/schemabinding/version2/Alcodon.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,257 +19,245 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class Alcodon implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _pos1. - */ - private long _pos1; - - /** - * keeps track of state for field: _pos1 - */ - private boolean _has_pos1; - - /** - * Field _pos2. - */ - private long _pos2; - - /** - * keeps track of state for field: _pos2 - */ - private boolean _has_pos2; - - /** - * Field _pos3. - */ - private long _pos3; - - /** - * keeps track of state for field: _pos3 - */ - private boolean _has_pos3; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Alcodon() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** +public class Alcodon implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _pos1. + */ + private long _pos1; + + /** + * keeps track of state for field: _pos1 + */ + private boolean _has_pos1; + + /** + * Field _pos2. + */ + private long _pos2; + + /** + * keeps track of state for field: _pos2 + */ + private boolean _has_pos2; + + /** + * Field _pos3. + */ + private long _pos3; + + /** + * keeps track of state for field: _pos3 + */ + private boolean _has_pos3; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Alcodon() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** */ - public void deletePos1() - { - this._has_pos1 = false; - } + public void deletePos1( + ) { + this._has_pos1= false; + } - /** + /** */ - public void deletePos2() - { - this._has_pos2 = false; - } + public void deletePos2( + ) { + this._has_pos2= false; + } + + /** + */ + public void deletePos3( + ) { + this._has_pos3= false; + } + + /** + * Returns the value of field 'pos1'. + * + * @return the value of field 'Pos1'. + */ + public long getPos1( + ) { + return this._pos1; + } + + /** + * Returns the value of field 'pos2'. + * + * @return the value of field 'Pos2'. + */ + public long getPos2( + ) { + return this._pos2; + } + + /** + * Returns the value of field 'pos3'. + * + * @return the value of field 'Pos3'. + */ + public long getPos3( + ) { + return this._pos3; + } + + /** + * Method hasPos1. + * + * @return true if at least one Pos1 has been added + */ + public boolean hasPos1( + ) { + return this._has_pos1; + } + + /** + * Method hasPos2. + * + * @return true if at least one Pos2 has been added + */ + public boolean hasPos2( + ) { + return this._has_pos2; + } + + /** + * Method hasPos3. + * + * @return true if at least one Pos3 has been added + */ + public boolean hasPos3( + ) { + return this._has_pos3; + } + + /** + * 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 'pos1'. + * + * @param pos1 the value of field 'pos1'. + */ + public void setPos1( + final long pos1) { + this._pos1 = pos1; + this._has_pos1 = true; + } + + /** + * Sets the value of field 'pos2'. + * + * @param pos2 the value of field 'pos2'. + */ + public void setPos2( + final long pos2) { + this._pos2 = pos2; + this._has_pos2 = true; + } + + /** + * Sets the value of field 'pos3'. + * + * @param pos3 the value of field 'pos3'. + */ + public void setPos3( + final long pos3) { + this._pos3 = pos3; + this._has_pos3 = 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.schemabinding.version2.Alcodo + */ + public static jalview.schemabinding.version2.Alcodon unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Alcodon) Unmarshaller.unmarshal(jalview.schemabinding.version2.Alcodon.class, reader); + } - /** + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema */ - public void deletePos3() - { - this._has_pos3 = false; - } - - /** - * Returns the value of field 'pos1'. - * - * @return the value of field 'Pos1'. - */ - public long getPos1() - { - return this._pos1; - } - - /** - * Returns the value of field 'pos2'. - * - * @return the value of field 'Pos2'. - */ - public long getPos2() - { - return this._pos2; - } - - /** - * Returns the value of field 'pos3'. - * - * @return the value of field 'Pos3'. - */ - public long getPos3() - { - return this._pos3; - } - - /** - * Method hasPos1. - * - * @return true if at least one Pos1 has been added - */ - public boolean hasPos1() - { - return this._has_pos1; - } - - /** - * Method hasPos2. - * - * @return true if at least one Pos2 has been added - */ - public boolean hasPos2() - { - return this._has_pos2; - } - - /** - * Method hasPos3. - * - * @return true if at least one Pos3 has been added - */ - public boolean hasPos3() - { - return this._has_pos3; - } - - /** - * 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; + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); } - 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 'pos1'. - * - * @param pos1 - * the value of field 'pos1'. - */ - public void setPos1(final long pos1) - { - this._pos1 = pos1; - this._has_pos1 = true; - } - - /** - * Sets the value of field 'pos2'. - * - * @param pos2 - * the value of field 'pos2'. - */ - public void setPos2(final long pos2) - { - this._pos2 = pos2; - this._has_pos2 = true; - } - - /** - * Sets the value of field 'pos3'. - * - * @param pos3 - * the value of field 'pos3'. - */ - public void setPos3(final long pos3) - { - this._pos3 = pos3; - this._has_pos3 = 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.schemabinding.version2.Alcodo - */ - public static jalview.schemabinding.version2.Alcodon unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Alcodon) Unmarshaller.unmarshal( - jalview.schemabinding.version2.Alcodon.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/schemabinding/version2/AlcodonFrame.java b/src/jalview/schemabinding/version2/AlcodonFrame.java index 8bbe3dd..b8b2a41 100644 --- a/src/jalview/schemabinding/version2/AlcodonFrame.java +++ b/src/jalview/schemabinding/version2/AlcodonFrame.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,448 +19,414 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class AlcodonFrame implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _alcodonList. - */ - private java.util.Vector _alcodonList; - - /** - * Field _alcodMapList. - */ - private java.util.Vector _alcodMapList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AlcodonFrame() - { - super(); - this._alcodonList = new java.util.Vector(); - this._alcodMapList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vAlcodMap - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlcodMap( - final jalview.schemabinding.version2.AlcodMap vAlcodMap) - throws java.lang.IndexOutOfBoundsException - { - this._alcodMapList.addElement(vAlcodMap); - } - - /** - * - * - * @param index - * @param vAlcodMap - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlcodMap(final int index, - final jalview.schemabinding.version2.AlcodMap vAlcodMap) - throws java.lang.IndexOutOfBoundsException - { - this._alcodMapList.add(index, vAlcodMap); - } - - /** - * - * - * @param vAlcodon - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlcodon( - final jalview.schemabinding.version2.Alcodon vAlcodon) - throws java.lang.IndexOutOfBoundsException - { - this._alcodonList.addElement(vAlcodon); - } - - /** - * - * - * @param index - * @param vAlcodon - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlcodon(final int index, - final jalview.schemabinding.version2.Alcodon vAlcodon) - throws java.lang.IndexOutOfBoundsException - { - this._alcodonList.add(index, vAlcodon); - } - - /** - * Method enumerateAlcodMap. - * - * @return an Enumeration over all jalview.schemabinding.version2.AlcodMap - * elements - */ - public java.util.Enumeration enumerateAlcodMap() - { - return this._alcodMapList.elements(); - } - - /** - * Method enumerateAlcodon. - * - * @return an Enumeration over all jalview.schemabinding.version2.Alcodon - * elements - */ - public java.util.Enumeration enumerateAlcodon() - { - return this._alcodonList.elements(); - } - - /** - * Method getAlcodMap. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.AlcodMap at the - * given index - */ - public jalview.schemabinding.version2.AlcodMap getAlcodMap(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alcodMapList.size()) - { - throw new IndexOutOfBoundsException("getAlcodMap: Index value '" - + index + "' not in range [0.." - + (this._alcodMapList.size() - 1) + "]"); +public class AlcodonFrame implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _alcodonList. + */ + private java.util.Vector _alcodonList; + + /** + * Field _alcodMapList. + */ + private java.util.Vector _alcodMapList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AlcodonFrame() { + super(); + this._alcodonList = new java.util.Vector(); + this._alcodMapList = new java.util.Vector(); } - return (jalview.schemabinding.version2.AlcodMap) _alcodMapList - .get(index); - } - - /** - * Method getAlcodMap.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.schemabinding.version2.AlcodMap[] getAlcodMap() - { - jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0]; - return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList - .toArray(array); - } - - /** - * Method getAlcodMapCount. - * - * @return the size of this collection - */ - public int getAlcodMapCount() - { - return this._alcodMapList.size(); - } - - /** - * Method getAlcodon. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.Alcodon at the - * given index - */ - public jalview.schemabinding.version2.Alcodon getAlcodon(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alcodonList.size()) - { - throw new IndexOutOfBoundsException("getAlcodon: Index value '" - + index + "' not in range [0.." - + (this._alcodonList.size() - 1) + "]"); + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vAlcodMap + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAlcodMap( + final jalview.schemabinding.version2.AlcodMap vAlcodMap) + throws java.lang.IndexOutOfBoundsException { + this._alcodMapList.addElement(vAlcodMap); } - return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index); - } - - /** - * Method getAlcodon.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.schemabinding.version2.Alcodon[] getAlcodon() - { - jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0]; - return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList - .toArray(array); - } - - /** - * Method getAlcodonCount. - * - * @return the size of this collection - */ - public int getAlcodonCount() - { - return this._alcodonList.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; + /** + * + * + * @param index + * @param vAlcodMap + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAlcodMap( + final int index, + final jalview.schemabinding.version2.AlcodMap vAlcodMap) + throws java.lang.IndexOutOfBoundsException { + this._alcodMapList.add(index, vAlcodMap); } - 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 removeAlcodMap. - * - * @param vAlcodMap - * @return true if the object was removed from the collection. - */ - public boolean removeAlcodMap( - final jalview.schemabinding.version2.AlcodMap vAlcodMap) - { - boolean removed = _alcodMapList.remove(vAlcodMap); - return removed; - } - - /** - * Method removeAlcodMapAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt( - final int index) - { - java.lang.Object obj = this._alcodMapList.remove(index); - return (jalview.schemabinding.version2.AlcodMap) obj; - } - - /** - * Method removeAlcodon. - * - * @param vAlcodon - * @return true if the object was removed from the collection. - */ - public boolean removeAlcodon( - final jalview.schemabinding.version2.Alcodon vAlcodon) - { - boolean removed = _alcodonList.remove(vAlcodon); - return removed; - } - - /** - * Method removeAlcodonAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Alcodon removeAlcodonAt( - final int index) - { - java.lang.Object obj = this._alcodonList.remove(index); - return (jalview.schemabinding.version2.Alcodon) obj; - } - - /** + + /** + * + * + * @param vAlcodon + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection */ - public void removeAllAlcodMap() - { - this._alcodMapList.clear(); - } + public void addAlcodon( + final jalview.schemabinding.version2.Alcodon vAlcodon) + throws java.lang.IndexOutOfBoundsException { + this._alcodonList.addElement(vAlcodon); + } - /** + /** + * + * + * @param index + * @param vAlcodon + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection */ - public void removeAllAlcodon() - { - this._alcodonList.clear(); - } - - /** - * - * - * @param index - * @param vAlcodMap - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAlcodMap(final int index, - final jalview.schemabinding.version2.AlcodMap vAlcodMap) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alcodMapList.size()) - { - throw new IndexOutOfBoundsException("setAlcodMap: Index value '" - + index + "' not in range [0.." - + (this._alcodMapList.size() - 1) + "]"); + public void addAlcodon( + final int index, + final jalview.schemabinding.version2.Alcodon vAlcodon) + throws java.lang.IndexOutOfBoundsException { + this._alcodonList.add(index, vAlcodon); } - this._alcodMapList.set(index, vAlcodMap); - } - - /** - * - * - * @param vAlcodMapArray - */ - public void setAlcodMap( - final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray) - { - // -- copy array - _alcodMapList.clear(); - - for (int i = 0; i < vAlcodMapArray.length; i++) - { - this._alcodMapList.add(vAlcodMapArray[i]); + /** + * Method enumerateAlcodMap. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.AlcodMap elements + */ + public java.util.Enumeration enumerateAlcodMap( + ) { + return this._alcodMapList.elements(); } - } - - /** - * - * - * @param index - * @param vAlcodon - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAlcodon(final int index, - final jalview.schemabinding.version2.Alcodon vAlcodon) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alcodonList.size()) - { - throw new IndexOutOfBoundsException("setAlcodon: Index value '" - + index + "' not in range [0.." - + (this._alcodonList.size() - 1) + "]"); + + /** + * Method enumerateAlcodon. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.Alcodon elements + */ + public java.util.Enumeration enumerateAlcodon( + ) { + return this._alcodonList.elements(); + } + + /** + * Method getAlcodMap. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.AlcodMap at the given index + */ + public jalview.schemabinding.version2.AlcodMap getAlcodMap( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alcodMapList.size()) { + throw new IndexOutOfBoundsException("getAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.AlcodMap) _alcodMapList.get(index); + } + + /** + * Method getAlcodMap.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.schemabinding.version2.AlcodMap[] getAlcodMap( + ) { + jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0]; + return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList.toArray(array); + } + + /** + * Method getAlcodMapCount. + * + * @return the size of this collection + */ + public int getAlcodMapCount( + ) { + return this._alcodMapList.size(); } - this._alcodonList.set(index, vAlcodon); - } - - /** - * - * - * @param vAlcodonArray - */ - public void setAlcodon( - final jalview.schemabinding.version2.Alcodon[] vAlcodonArray) - { - // -- copy array - _alcodonList.clear(); - - for (int i = 0; i < vAlcodonArray.length; i++) - { - this._alcodonList.add(vAlcodonArray[i]); + /** + * Method getAlcodon. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.Alcodon at the given index + */ + public jalview.schemabinding.version2.Alcodon getAlcodon( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alcodonList.size()) { + throw new IndexOutOfBoundsException("getAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index); + } + + /** + * Method getAlcodon.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.schemabinding.version2.Alcodon[] getAlcodon( + ) { + jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0]; + return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList.toArray(array); + } + + /** + * Method getAlcodonCount. + * + * @return the size of this collection + */ + public int getAlcodonCount( + ) { + return this._alcodonList.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 removeAlcodMap. + * + * @param vAlcodMap + * @return true if the object was removed from the collection. + */ + public boolean removeAlcodMap( + final jalview.schemabinding.version2.AlcodMap vAlcodMap) { + boolean removed = _alcodMapList.remove(vAlcodMap); + return removed; + } + + /** + * Method removeAlcodMapAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt( + final int index) { + java.lang.Object obj = this._alcodMapList.remove(index); + return (jalview.schemabinding.version2.AlcodMap) obj; + } + + /** + * Method removeAlcodon. + * + * @param vAlcodon + * @return true if the object was removed from the collection. + */ + public boolean removeAlcodon( + final jalview.schemabinding.version2.Alcodon vAlcodon) { + boolean removed = _alcodonList.remove(vAlcodon); + return removed; + } + + /** + * Method removeAlcodonAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Alcodon removeAlcodonAt( + final int index) { + java.lang.Object obj = this._alcodonList.remove(index); + return (jalview.schemabinding.version2.Alcodon) obj; + } + + /** + */ + public void removeAllAlcodMap( + ) { + this._alcodMapList.clear(); + } + + /** + */ + public void removeAllAlcodon( + ) { + this._alcodonList.clear(); + } + + /** + * + * + * @param index + * @param vAlcodMap + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setAlcodMap( + final int index, + final jalview.schemabinding.version2.AlcodMap vAlcodMap) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alcodMapList.size()) { + throw new IndexOutOfBoundsException("setAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]"); + } + + this._alcodMapList.set(index, vAlcodMap); + } + + /** + * + * + * @param vAlcodMapArray + */ + public void setAlcodMap( + final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray) { + //-- copy array + _alcodMapList.clear(); + + for (int i = 0; i < vAlcodMapArray.length; i++) { + this._alcodMapList.add(vAlcodMapArray[i]); + } + } + + /** + * + * + * @param index + * @param vAlcodon + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setAlcodon( + final int index, + final jalview.schemabinding.version2.Alcodon vAlcodon) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alcodonList.size()) { + throw new IndexOutOfBoundsException("setAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]"); + } + + this._alcodonList.set(index, vAlcodon); + } + + /** + * + * + * @param vAlcodonArray + */ + public void setAlcodon( + final jalview.schemabinding.version2.Alcodon[] vAlcodonArray) { + //-- copy array + _alcodonList.clear(); + + for (int i = 0; i < vAlcodonArray.length; i++) { + this._alcodonList.add(vAlcodonArray[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.schemabinding.version2.AlcodonFrame + */ + public static jalview.schemabinding.version2.AlcodonFrame unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodonFrame.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); } - } - - /** - * 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.schemabinding.version2.AlcodonFrame - */ - public static jalview.schemabinding.version2.AlcodonFrame unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller - .unmarshal(jalview.schemabinding.version2.AlcodonFrame.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/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java index ddf63fb..8c5c8ff 100755 --- a/src/jalview/schemabinding/version2/Annotation.java +++ b/src/jalview/schemabinding/version2/Annotation.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,1054 +19,1014 @@ import org.exolab.castor.xml.Unmarshaller; * * @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 _sequenceRef. - */ - private java.lang.String _sequenceRef; - - /** - * Field _groupRef. - */ - private java.lang.String _groupRef; - - /** - * Field _graphColour. - */ - private int _graphColour; - - /** - * keeps track of state for field: _graphColour - */ - private boolean _has_graphColour; - - /** - * Field _graphGroup. - */ - private int _graphGroup; - - /** - * keeps track of state for field: _graphGroup - */ - private boolean _has_graphGroup; - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _scoreOnly. - */ - private boolean _scoreOnly = false; - - /** - * keeps track of state for field: _scoreOnly - */ - private boolean _has_scoreOnly; - - /** - * Field _score. - */ - private double _score; - - /** - * keeps track of state for field: _score - */ - private boolean _has_score; - - /** - * Field _visible. - */ - private boolean _visible; - - /** - * keeps track of state for field: _visible - */ - private boolean _has_visible; - - /** - * Field _centreColLabels. - */ - private boolean _centreColLabels; - - /** - * keeps track of state for field: _centreColLabels - */ - private boolean _has_centreColLabels; - - /** - * Field _scaleColLabels. - */ - private boolean _scaleColLabels; - - /** - * keeps track of state for field: _scaleColLabels - */ - private boolean _has_scaleColLabels; - - /** - * Field _showAllColLabels. - */ - private boolean _showAllColLabels; - - /** - * keeps track of state for field: _showAllColLabels - */ - private boolean _has_showAllColLabels; - - /** - * is an autocalculated annotation row - */ - private boolean _autoCalculated = false; - - /** - * keeps track of state for field: _autoCalculated - */ - private boolean _has_autoCalculated; - - /** - * Field _annotationElementList. - */ - private java.util.Vector _annotationElementList; - - /** - * Field _label. - */ - private java.lang.String _label; - - /** - * Field _description. - */ - private java.lang.String _description; - - /** - * Field _thresholdLine. - */ - private jalview.schemabinding.version2.ThresholdLine _thresholdLine; - - // ----------------/ - // - 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.schemabinding.version2.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.schemabinding.version2.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - this._annotationElementList.add(index, vAnnotationElement); - } - - /** - */ - public void deleteAutoCalculated() - { - this._has_autoCalculated = false; - } - - /** - */ - public void deleteCentreColLabels() - { - this._has_centreColLabels = false; - } - - /** - */ - public void deleteGraph() - { - this._has_graph = false; - } - - /** - */ - public void deleteGraphColour() - { - this._has_graphColour = false; - } - - /** - */ - public void deleteGraphGroup() - { - this._has_graphGroup = false; - } - - /** - */ - public void deleteGraphType() - { - this._has_graphType = false; - } - - /** - */ - public void deleteScaleColLabels() - { - this._has_scaleColLabels = false; - } - - /** - */ - public void deleteScore() - { - this._has_score = false; - } - - /** - */ - public void deleteScoreOnly() - { - this._has_scoreOnly = false; - } - - /** - */ - public void deleteShowAllColLabels() - { - this._has_showAllColLabels = false; - } - - /** - */ - public void deleteVisible() - { - this._has_visible = false; - } - - /** - * Method enumerateAnnotationElement. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.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.schemabinding.version2.AnnotationElement - * at the given index - */ - public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.AnnotationElement[] getAnnotationElement() - { - jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0]; - return (jalview.schemabinding.version2.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 'autoCalculated'. The field 'autoCalculated' has - * the following description: is an autocalculated annotation row - * - * @return the value of field 'AutoCalculated'. - */ - public boolean getAutoCalculated() - { - return this._autoCalculated; - } - - /** - * Returns the value of field 'centreColLabels'. - * - * @return the value of field 'CentreColLabels'. - */ - public boolean getCentreColLabels() - { - return this._centreColLabels; - } - - /** - * 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 'graphColour'. - * - * @return the value of field 'GraphColour'. - */ - public int getGraphColour() - { - return this._graphColour; - } - - /** - * Returns the value of field 'graphGroup'. - * - * @return the value of field 'GraphGroup'. - */ - public int getGraphGroup() - { - return this._graphGroup; - } - - /** - * Returns the value of field 'graphType'. - * - * @return the value of field 'GraphType'. - */ - public int getGraphType() - { - return this._graphType; - } - - /** - * Returns the value of field 'groupRef'. - * - * @return the value of field 'GroupRef'. - */ - public java.lang.String getGroupRef() - { - return this._groupRef; - } - - /** - * 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 'label'. - * - * @return the value of field 'Label'. - */ - public java.lang.String getLabel() - { - return this._label; - } - - /** - * Returns the value of field 'scaleColLabels'. - * - * @return the value of field 'ScaleColLabels'. - */ - public boolean getScaleColLabels() - { - return this._scaleColLabels; - } - - /** - * Returns the value of field 'score'. - * - * @return the value of field 'Score'. - */ - public double getScore() - { - return this._score; - } - - /** - * Returns the value of field 'scoreOnly'. - * - * @return the value of field 'ScoreOnly'. - */ - public boolean getScoreOnly() - { - return this._scoreOnly; - } - - /** - * Returns the value of field 'sequenceRef'. - * - * @return the value of field 'SequenceRef'. - */ - public java.lang.String getSequenceRef() - { - return this._sequenceRef; - } - - /** - * Returns the value of field 'showAllColLabels'. - * - * @return the value of field 'ShowAllColLabels'. - */ - public boolean getShowAllColLabels() - { - return this._showAllColLabels; - } - - /** - * Returns the value of field 'thresholdLine'. - * - * @return the value of field 'ThresholdLine'. - */ - public jalview.schemabinding.version2.ThresholdLine getThresholdLine() - { - return this._thresholdLine; - } - - /** - * Returns the value of field 'visible'. - * - * @return the value of field 'Visible'. - */ - public boolean getVisible() - { - return this._visible; - } - - /** - * Method hasAutoCalculated. - * - * @return true if at least one AutoCalculated has been added - */ - public boolean hasAutoCalculated() - { - return this._has_autoCalculated; - } - - /** - * Method hasCentreColLabels. - * - * @return true if at least one CentreColLabels has been added - */ - public boolean hasCentreColLabels() - { - return this._has_centreColLabels; - } - - /** - * Method hasGraph. - * - * @return true if at least one Graph has been added - */ - public boolean hasGraph() - { - return this._has_graph; - } - - /** - * Method hasGraphColour. - * - * @return true if at least one GraphColour has been added - */ - public boolean hasGraphColour() - { - return this._has_graphColour; - } - - /** - * Method hasGraphGroup. - * - * @return true if at least one GraphGroup has been added - */ - public boolean hasGraphGroup() - { - return this._has_graphGroup; - } - - /** - * Method hasGraphType. - * - * @return true if at least one GraphType has been added - */ - public boolean hasGraphType() - { - return this._has_graphType; - } - - /** - * Method hasScaleColLabels. - * - * @return true if at least one ScaleColLabels has been added - */ - public boolean hasScaleColLabels() - { - return this._has_scaleColLabels; - } - - /** - * Method hasScore. - * - * @return true if at least one Score has been added - */ - public boolean hasScore() - { - return this._has_score; - } - - /** - * Method hasScoreOnly. - * - * @return true if at least one ScoreOnly has been added - */ - public boolean hasScoreOnly() - { - return this._has_scoreOnly; - } - - /** - * Method hasShowAllColLabels. - * - * @return true if at least one ShowAllColLabels has been added - */ - public boolean hasShowAllColLabels() - { - return this._has_showAllColLabels; - } - - /** - * Method hasVisible. - * - * @return true if at least one Visible has been added - */ - public boolean hasVisible() - { - return this._has_visible; - } - - /** - * Returns the value of field 'autoCalculated'. The field 'autoCalculated' has - * the following description: is an autocalculated annotation row - * - * @return the value of field 'AutoCalculated'. - */ - public boolean isAutoCalculated() - { - return this._autoCalculated; - } - - /** - * Returns the value of field 'centreColLabels'. - * - * @return the value of field 'CentreColLabels'. - */ - public boolean isCentreColLabels() - { - return this._centreColLabels; - } - - /** - * Returns the value of field 'graph'. - * - * @return the value of field 'Graph'. - */ - public boolean isGraph() - { - return this._graph; - } - - /** - * Returns the value of field 'scaleColLabels'. - * - * @return the value of field 'ScaleColLabels'. - */ - public boolean isScaleColLabels() - { - return this._scaleColLabels; - } - - /** - * Returns the value of field 'scoreOnly'. - * - * @return the value of field 'ScoreOnly'. - */ - public boolean isScoreOnly() - { - return this._scoreOnly; - } - - /** - * Returns the value of field 'showAllColLabels'. - * - * @return the value of field 'ShowAllColLabels'. - */ - public boolean isShowAllColLabels() - { - return this._showAllColLabels; - } - - /** - * 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 'visible'. - * - * @return the value of field 'Visible'. - */ - public boolean isVisible() - { - return this._visible; - } - - /** - * - * - * @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.schemabinding.version2.AnnotationElement vAnnotationElement) - { - boolean removed = _annotationElementList.remove(vAnnotationElement); - return removed; - } - - /** - * Method removeAnnotationElementAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt( - final int index) - { - java.lang.Object obj = this._annotationElementList.remove(index); - return (jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.AnnotationElement[] vAnnotationElementArray) - { - // -- copy array - _annotationElementList.clear(); - - for (int i = 0; i < vAnnotationElementArray.length; i++) - { - this._annotationElementList.add(vAnnotationElementArray[i]); - } - } - - /** - * Sets the value of field 'autoCalculated'. The field 'autoCalculated' has - * the following description: is an autocalculated annotation row - * - * @param autoCalculated - * the value of field 'autoCalculated'. - */ - public void setAutoCalculated(final boolean autoCalculated) - { - this._autoCalculated = autoCalculated; - this._has_autoCalculated = true; - } - - /** - * Sets the value of field 'centreColLabels'. - * - * @param centreColLabels - * the value of field 'centreColLabels'. - */ - public void setCentreColLabels(final boolean centreColLabels) - { - this._centreColLabels = centreColLabels; - this._has_centreColLabels = 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 '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 'graphColour'. - * - * @param graphColour - * the value of field 'graphColour'. - */ - public void setGraphColour(final int graphColour) - { - this._graphColour = graphColour; - this._has_graphColour = true; - } - - /** - * Sets the value of field 'graphGroup'. - * - * @param graphGroup - * the value of field 'graphGroup'. - */ - public void setGraphGroup(final int graphGroup) - { - this._graphGroup = graphGroup; - this._has_graphGroup = 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 'groupRef'. - * - * @param groupRef - * the value of field 'groupRef'. - */ - public void setGroupRef(final java.lang.String groupRef) - { - this._groupRef = groupRef; - } - - /** - * 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 'label'. - * - * @param label - * the value of field 'label'. - */ - public void setLabel(final java.lang.String label) - { - this._label = label; - } - - /** - * Sets the value of field 'scaleColLabels'. - * - * @param scaleColLabels - * the value of field 'scaleColLabels'. - */ - public void setScaleColLabels(final boolean scaleColLabels) - { - this._scaleColLabels = scaleColLabels; - this._has_scaleColLabels = true; - } - - /** - * Sets the value of field 'score'. - * - * @param score - * the value of field 'score'. - */ - public void setScore(final double score) - { - this._score = score; - this._has_score = true; - } - - /** - * Sets the value of field 'scoreOnly'. - * - * @param scoreOnly - * the value of field 'scoreOnly'. - */ - public void setScoreOnly(final boolean scoreOnly) - { - this._scoreOnly = scoreOnly; - this._has_scoreOnly = true; - } - - /** - * Sets the value of field 'sequenceRef'. - * - * @param sequenceRef - * the value of field 'sequenceRef'. - */ - public void setSequenceRef(final java.lang.String sequenceRef) - { - this._sequenceRef = sequenceRef; - } - - /** - * Sets the value of field 'showAllColLabels'. - * - * @param showAllColLabels - * the value of field 'showAllColLabels' - */ - public void setShowAllColLabels(final boolean showAllColLabels) - { - this._showAllColLabels = showAllColLabels; - this._has_showAllColLabels = true; - } - - /** - * Sets the value of field 'thresholdLine'. - * - * @param thresholdLine - * the value of field 'thresholdLine'. - */ - public void setThresholdLine( - final jalview.schemabinding.version2.ThresholdLine thresholdLine) - { - this._thresholdLine = thresholdLine; - } - - /** - * Sets the value of field 'visible'. - * - * @param visible - * the value of field 'visible'. - */ - public void setVisible(final boolean visible) - { - this._visible = visible; - this._has_visible = 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.schemabinding.version2.Annotation - */ - public static jalview.schemabinding.version2.Annotation unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Annotation) Unmarshaller - .unmarshal(jalview.schemabinding.version2.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); - } +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 _sequenceRef. + */ + private java.lang.String _sequenceRef; + + /** + * Field _groupRef. + */ + private java.lang.String _groupRef; + + /** + * Field _graphColour. + */ + private int _graphColour; + + /** + * keeps track of state for field: _graphColour + */ + private boolean _has_graphColour; + + /** + * Field _graphGroup. + */ + private int _graphGroup; + + /** + * keeps track of state for field: _graphGroup + */ + private boolean _has_graphGroup; + + /** + * Field _id. + */ + private java.lang.String _id; + + /** + * Field _scoreOnly. + */ + private boolean _scoreOnly = false; + + /** + * keeps track of state for field: _scoreOnly + */ + private boolean _has_scoreOnly; + + /** + * Field _score. + */ + private double _score; + + /** + * keeps track of state for field: _score + */ + private boolean _has_score; + + /** + * Field _visible. + */ + private boolean _visible; + + /** + * keeps track of state for field: _visible + */ + private boolean _has_visible; + + /** + * Field _centreColLabels. + */ + private boolean _centreColLabels; + + /** + * keeps track of state for field: _centreColLabels + */ + private boolean _has_centreColLabels; + + /** + * Field _scaleColLabels. + */ + private boolean _scaleColLabels; + + /** + * keeps track of state for field: _scaleColLabels + */ + private boolean _has_scaleColLabels; + + /** + * Field _showAllColLabels. + */ + private boolean _showAllColLabels; + + /** + * keeps track of state for field: _showAllColLabels + */ + private boolean _has_showAllColLabels; + + /** + * is an autocalculated annotation row + */ + private boolean _autoCalculated = false; + + /** + * keeps track of state for field: _autoCalculated + */ + private boolean _has_autoCalculated; + + /** + * Field _annotationElementList. + */ + private java.util.Vector _annotationElementList; + + /** + * Field _label. + */ + private java.lang.String _label; + + /** + * Field _description. + */ + private java.lang.String _description; + + /** + * Field _thresholdLine. + */ + private jalview.schemabinding.version2.ThresholdLine _thresholdLine; + + + //----------------/ + //- 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.schemabinding.version2.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.schemabinding.version2.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException { + this._annotationElementList.add(index, vAnnotationElement); + } + + /** + */ + public void deleteAutoCalculated( + ) { + this._has_autoCalculated= false; + } + + /** + */ + public void deleteCentreColLabels( + ) { + this._has_centreColLabels= false; + } + + /** + */ + public void deleteGraph( + ) { + this._has_graph= false; + } + + /** + */ + public void deleteGraphColour( + ) { + this._has_graphColour= false; + } + + /** + */ + public void deleteGraphGroup( + ) { + this._has_graphGroup= false; + } + + /** + */ + public void deleteGraphType( + ) { + this._has_graphType= false; + } + + /** + */ + public void deleteScaleColLabels( + ) { + this._has_scaleColLabels= false; + } + + /** + */ + public void deleteScore( + ) { + this._has_score= false; + } + + /** + */ + public void deleteScoreOnly( + ) { + this._has_scoreOnly= false; + } + + /** + */ + public void deleteShowAllColLabels( + ) { + this._has_showAllColLabels= false; + } + + /** + */ + public void deleteVisible( + ) { + this._has_visible= false; + } + + /** + * Method enumerateAnnotationElement. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.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.schemabinding.version2.AnnotationElement at the + * given index + */ + public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.AnnotationElement[] getAnnotationElement( + ) { + jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0]; + return (jalview.schemabinding.version2.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 'autoCalculated'. The field + * 'autoCalculated' has the following description: is an + * autocalculated annotation row + * + * @return the value of field 'AutoCalculated'. + */ + public boolean getAutoCalculated( + ) { + return this._autoCalculated; + } + + /** + * Returns the value of field 'centreColLabels'. + * + * @return the value of field 'CentreColLabels'. + */ + public boolean getCentreColLabels( + ) { + return this._centreColLabels; + } + + /** + * 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 'graphColour'. + * + * @return the value of field 'GraphColour'. + */ + public int getGraphColour( + ) { + return this._graphColour; + } + + /** + * Returns the value of field 'graphGroup'. + * + * @return the value of field 'GraphGroup'. + */ + public int getGraphGroup( + ) { + return this._graphGroup; + } + + /** + * Returns the value of field 'graphType'. + * + * @return the value of field 'GraphType'. + */ + public int getGraphType( + ) { + return this._graphType; + } + + /** + * Returns the value of field 'groupRef'. + * + * @return the value of field 'GroupRef'. + */ + public java.lang.String getGroupRef( + ) { + return this._groupRef; + } + + /** + * 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 'label'. + * + * @return the value of field 'Label'. + */ + public java.lang.String getLabel( + ) { + return this._label; + } + + /** + * Returns the value of field 'scaleColLabels'. + * + * @return the value of field 'ScaleColLabels'. + */ + public boolean getScaleColLabels( + ) { + return this._scaleColLabels; + } + + /** + * Returns the value of field 'score'. + * + * @return the value of field 'Score'. + */ + public double getScore( + ) { + return this._score; + } + + /** + * Returns the value of field 'scoreOnly'. + * + * @return the value of field 'ScoreOnly'. + */ + public boolean getScoreOnly( + ) { + return this._scoreOnly; + } + + /** + * Returns the value of field 'sequenceRef'. + * + * @return the value of field 'SequenceRef'. + */ + public java.lang.String getSequenceRef( + ) { + return this._sequenceRef; + } + + /** + * Returns the value of field 'showAllColLabels'. + * + * @return the value of field 'ShowAllColLabels'. + */ + public boolean getShowAllColLabels( + ) { + return this._showAllColLabels; + } + + /** + * Returns the value of field 'thresholdLine'. + * + * @return the value of field 'ThresholdLine'. + */ + public jalview.schemabinding.version2.ThresholdLine getThresholdLine( + ) { + return this._thresholdLine; + } + + /** + * Returns the value of field 'visible'. + * + * @return the value of field 'Visible'. + */ + public boolean getVisible( + ) { + return this._visible; + } + + /** + * Method hasAutoCalculated. + * + * @return true if at least one AutoCalculated has been added + */ + public boolean hasAutoCalculated( + ) { + return this._has_autoCalculated; + } + + /** + * Method hasCentreColLabels. + * + * @return true if at least one CentreColLabels has been added + */ + public boolean hasCentreColLabels( + ) { + return this._has_centreColLabels; + } + + /** + * Method hasGraph. + * + * @return true if at least one Graph has been added + */ + public boolean hasGraph( + ) { + return this._has_graph; + } + + /** + * Method hasGraphColour. + * + * @return true if at least one GraphColour has been added + */ + public boolean hasGraphColour( + ) { + return this._has_graphColour; + } + + /** + * Method hasGraphGroup. + * + * @return true if at least one GraphGroup has been added + */ + public boolean hasGraphGroup( + ) { + return this._has_graphGroup; + } + + /** + * Method hasGraphType. + * + * @return true if at least one GraphType has been added + */ + public boolean hasGraphType( + ) { + return this._has_graphType; + } + + /** + * Method hasScaleColLabels. + * + * @return true if at least one ScaleColLabels has been added + */ + public boolean hasScaleColLabels( + ) { + return this._has_scaleColLabels; + } + + /** + * Method hasScore. + * + * @return true if at least one Score has been added + */ + public boolean hasScore( + ) { + return this._has_score; + } + + /** + * Method hasScoreOnly. + * + * @return true if at least one ScoreOnly has been added + */ + public boolean hasScoreOnly( + ) { + return this._has_scoreOnly; + } + + /** + * Method hasShowAllColLabels. + * + * @return true if at least one ShowAllColLabels has been added + */ + public boolean hasShowAllColLabels( + ) { + return this._has_showAllColLabels; + } + + /** + * Method hasVisible. + * + * @return true if at least one Visible has been added + */ + public boolean hasVisible( + ) { + return this._has_visible; + } + + /** + * Returns the value of field 'autoCalculated'. The field + * 'autoCalculated' has the following description: is an + * autocalculated annotation row + * + * @return the value of field 'AutoCalculated'. + */ + public boolean isAutoCalculated( + ) { + return this._autoCalculated; + } + + /** + * Returns the value of field 'centreColLabels'. + * + * @return the value of field 'CentreColLabels'. + */ + public boolean isCentreColLabels( + ) { + return this._centreColLabels; + } + + /** + * Returns the value of field 'graph'. + * + * @return the value of field 'Graph'. + */ + public boolean isGraph( + ) { + return this._graph; + } + + /** + * Returns the value of field 'scaleColLabels'. + * + * @return the value of field 'ScaleColLabels'. + */ + public boolean isScaleColLabels( + ) { + return this._scaleColLabels; + } + + /** + * Returns the value of field 'scoreOnly'. + * + * @return the value of field 'ScoreOnly'. + */ + public boolean isScoreOnly( + ) { + return this._scoreOnly; + } + + /** + * Returns the value of field 'showAllColLabels'. + * + * @return the value of field 'ShowAllColLabels'. + */ + public boolean isShowAllColLabels( + ) { + return this._showAllColLabels; + } + + /** + * 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 'visible'. + * + * @return the value of field 'Visible'. + */ + public boolean isVisible( + ) { + return this._visible; + } + + /** + * + * + * @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.schemabinding.version2.AnnotationElement vAnnotationElement) { + boolean removed = _annotationElementList.remove(vAnnotationElement); + return removed; + } + + /** + * Method removeAnnotationElementAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt( + final int index) { + java.lang.Object obj = this._annotationElementList.remove(index); + return (jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.AnnotationElement[] vAnnotationElementArray) { + //-- copy array + _annotationElementList.clear(); + + for (int i = 0; i < vAnnotationElementArray.length; i++) { + this._annotationElementList.add(vAnnotationElementArray[i]); + } + } + + /** + * Sets the value of field 'autoCalculated'. The field + * 'autoCalculated' has the following description: is an + * autocalculated annotation row + * + * @param autoCalculated the value of field 'autoCalculated'. + */ + public void setAutoCalculated( + final boolean autoCalculated) { + this._autoCalculated = autoCalculated; + this._has_autoCalculated = true; + } + + /** + * Sets the value of field 'centreColLabels'. + * + * @param centreColLabels the value of field 'centreColLabels'. + */ + public void setCentreColLabels( + final boolean centreColLabels) { + this._centreColLabels = centreColLabels; + this._has_centreColLabels = 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 '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 'graphColour'. + * + * @param graphColour the value of field 'graphColour'. + */ + public void setGraphColour( + final int graphColour) { + this._graphColour = graphColour; + this._has_graphColour = true; + } + + /** + * Sets the value of field 'graphGroup'. + * + * @param graphGroup the value of field 'graphGroup'. + */ + public void setGraphGroup( + final int graphGroup) { + this._graphGroup = graphGroup; + this._has_graphGroup = 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 'groupRef'. + * + * @param groupRef the value of field 'groupRef'. + */ + public void setGroupRef( + final java.lang.String groupRef) { + this._groupRef = groupRef; + } + + /** + * 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 'label'. + * + * @param label the value of field 'label'. + */ + public void setLabel( + final java.lang.String label) { + this._label = label; + } + + /** + * Sets the value of field 'scaleColLabels'. + * + * @param scaleColLabels the value of field 'scaleColLabels'. + */ + public void setScaleColLabels( + final boolean scaleColLabels) { + this._scaleColLabels = scaleColLabels; + this._has_scaleColLabels = true; + } + + /** + * Sets the value of field 'score'. + * + * @param score the value of field 'score'. + */ + public void setScore( + final double score) { + this._score = score; + this._has_score = true; + } + + /** + * Sets the value of field 'scoreOnly'. + * + * @param scoreOnly the value of field 'scoreOnly'. + */ + public void setScoreOnly( + final boolean scoreOnly) { + this._scoreOnly = scoreOnly; + this._has_scoreOnly = true; + } + + /** + * Sets the value of field 'sequenceRef'. + * + * @param sequenceRef the value of field 'sequenceRef'. + */ + public void setSequenceRef( + final java.lang.String sequenceRef) { + this._sequenceRef = sequenceRef; + } + + /** + * Sets the value of field 'showAllColLabels'. + * + * @param showAllColLabels the value of field 'showAllColLabels' + */ + public void setShowAllColLabels( + final boolean showAllColLabels) { + this._showAllColLabels = showAllColLabels; + this._has_showAllColLabels = true; + } + + /** + * Sets the value of field 'thresholdLine'. + * + * @param thresholdLine the value of field 'thresholdLine'. + */ + public void setThresholdLine( + final jalview.schemabinding.version2.ThresholdLine thresholdLine) { + this._thresholdLine = thresholdLine; + } + + /** + * Sets the value of field 'visible'. + * + * @param visible the value of field 'visible'. + */ + public void setVisible( + final boolean visible) { + this._visible = visible; + this._has_visible = 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.schemabinding.version2.Annotation + */ + public static jalview.schemabinding.version2.Annotation unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.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/schemabinding/version2/AnnotationColours.java b/src/jalview/schemabinding/version2/AnnotationColours.java index 19f92b8..36f9f93 100755 --- a/src/jalview/schemabinding/version2/AnnotationColours.java +++ b/src/jalview/schemabinding/version2/AnnotationColours.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,360 +19,344 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class AnnotationColours implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _aboveThreshold. - */ - private int _aboveThreshold; - - /** - * keeps track of state for field: _aboveThreshold - */ - private boolean _has_aboveThreshold; - - /** - * Field _annotation. - */ - private java.lang.String _annotation; - - /** - * Field _minColour. - */ - private int _minColour; - - /** - * keeps track of state for field: _minColour - */ - private boolean _has_minColour; - - /** - * Field _maxColour. - */ - private int _maxColour; - - /** - * keeps track of state for field: _maxColour - */ - private boolean _has_maxColour; - - /** - * Field _colourScheme. - */ - private java.lang.String _colourScheme; - - /** - * Field _threshold. - */ - private float _threshold; - - /** - * keeps track of state for field: _threshold - */ - private boolean _has_threshold; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AnnotationColours() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteAboveThreshold() - { - this._has_aboveThreshold = false; - } - - /** - */ - public void deleteMaxColour() - { - this._has_maxColour = false; - } - - /** - */ - public void deleteMinColour() - { - this._has_minColour = false; - } - - /** - */ - public void deleteThreshold() - { - this._has_threshold = false; - } - - /** - * Returns the value of field 'aboveThreshold'. - * - * @return the value of field 'AboveThreshold'. - */ - public int getAboveThreshold() - { - return this._aboveThreshold; - } - - /** - * Returns the value of field 'annotation'. - * - * @return the value of field 'Annotation'. - */ - public java.lang.String getAnnotation() - { - return this._annotation; - } - - /** - * Returns the value of field 'colourScheme'. - * - * @return the value of field 'ColourScheme'. - */ - public java.lang.String getColourScheme() - { - return this._colourScheme; - } - - /** - * Returns the value of field 'maxColour'. - * - * @return the value of field 'MaxColour'. - */ - public int getMaxColour() - { - return this._maxColour; - } - - /** - * Returns the value of field 'minColour'. - * - * @return the value of field 'MinColour'. - */ - public int getMinColour() - { - return this._minColour; - } - - /** - * Returns the value of field 'threshold'. - * - * @return the value of field 'Threshold'. - */ - public float getThreshold() - { - return this._threshold; - } - - /** - * Method hasAboveThreshold. - * - * @return true if at least one AboveThreshold has been added - */ - public boolean hasAboveThreshold() - { - return this._has_aboveThreshold; - } - - /** - * Method hasMaxColour. - * - * @return true if at least one MaxColour has been added - */ - public boolean hasMaxColour() - { - return this._has_maxColour; - } - - /** - * Method hasMinColour. - * - * @return true if at least one MinColour has been added - */ - public boolean hasMinColour() - { - return this._has_minColour; - } - - /** - * Method hasThreshold. - * - * @return true if at least one Threshold has been added - */ - public boolean hasThreshold() - { - return this._has_threshold; - } - - /** - * 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; +public class AnnotationColours implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _aboveThreshold. + */ + private int _aboveThreshold; + + /** + * keeps track of state for field: _aboveThreshold + */ + private boolean _has_aboveThreshold; + + /** + * Field _annotation. + */ + private java.lang.String _annotation; + + /** + * Field _minColour. + */ + private int _minColour; + + /** + * keeps track of state for field: _minColour + */ + private boolean _has_minColour; + + /** + * Field _maxColour. + */ + private int _maxColour; + + /** + * keeps track of state for field: _maxColour + */ + private boolean _has_maxColour; + + /** + * Field _colourScheme. + */ + private java.lang.String _colourScheme; + + /** + * Field _threshold. + */ + private float _threshold; + + /** + * keeps track of state for field: _threshold + */ + private boolean _has_threshold; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AnnotationColours() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteAboveThreshold( + ) { + this._has_aboveThreshold= false; + } + + /** + */ + public void deleteMaxColour( + ) { + this._has_maxColour= false; + } + + /** + */ + public void deleteMinColour( + ) { + this._has_minColour= false; + } + + /** + */ + public void deleteThreshold( + ) { + this._has_threshold= false; + } + + /** + * Returns the value of field 'aboveThreshold'. + * + * @return the value of field 'AboveThreshold'. + */ + public int getAboveThreshold( + ) { + return this._aboveThreshold; + } + + /** + * Returns the value of field 'annotation'. + * + * @return the value of field 'Annotation'. + */ + public java.lang.String getAnnotation( + ) { + return this._annotation; + } + + /** + * Returns the value of field 'colourScheme'. + * + * @return the value of field 'ColourScheme'. + */ + public java.lang.String getColourScheme( + ) { + return this._colourScheme; + } + + /** + * Returns the value of field 'maxColour'. + * + * @return the value of field 'MaxColour'. + */ + public int getMaxColour( + ) { + return this._maxColour; + } + + /** + * Returns the value of field 'minColour'. + * + * @return the value of field 'MinColour'. + */ + public int getMinColour( + ) { + return this._minColour; + } + + /** + * Returns the value of field 'threshold'. + * + * @return the value of field 'Threshold'. + */ + public float getThreshold( + ) { + return this._threshold; + } + + /** + * Method hasAboveThreshold. + * + * @return true if at least one AboveThreshold has been added + */ + public boolean hasAboveThreshold( + ) { + return this._has_aboveThreshold; + } + + /** + * Method hasMaxColour. + * + * @return true if at least one MaxColour has been added + */ + public boolean hasMaxColour( + ) { + return this._has_maxColour; + } + + /** + * Method hasMinColour. + * + * @return true if at least one MinColour has been added + */ + public boolean hasMinColour( + ) { + return this._has_minColour; + } + + /** + * Method hasThreshold. + * + * @return true if at least one Threshold has been added + */ + public boolean hasThreshold( + ) { + return this._has_threshold; + } + + /** + * 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 'aboveThreshold'. + * + * @param aboveThreshold the value of field 'aboveThreshold'. + */ + public void setAboveThreshold( + final int aboveThreshold) { + this._aboveThreshold = aboveThreshold; + this._has_aboveThreshold = true; + } + + /** + * Sets the value of field 'annotation'. + * + * @param annotation the value of field 'annotation'. + */ + public void setAnnotation( + final java.lang.String annotation) { + this._annotation = annotation; + } + + /** + * Sets the value of field 'colourScheme'. + * + * @param colourScheme the value of field 'colourScheme'. + */ + public void setColourScheme( + final java.lang.String colourScheme) { + this._colourScheme = colourScheme; + } + + /** + * Sets the value of field 'maxColour'. + * + * @param maxColour the value of field 'maxColour'. + */ + public void setMaxColour( + final int maxColour) { + this._maxColour = maxColour; + this._has_maxColour = true; + } + + /** + * Sets the value of field 'minColour'. + * + * @param minColour the value of field 'minColour'. + */ + public void setMinColour( + final int minColour) { + this._minColour = minColour; + this._has_minColour = 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; + } + + /** + * 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.schemabinding.version2.AnnotationColours + */ + public static jalview.schemabinding.version2.AnnotationColours unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.AnnotationColours.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); } - 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 'aboveThreshold'. - * - * @param aboveThreshold - * the value of field 'aboveThreshold'. - */ - public void setAboveThreshold(final int aboveThreshold) - { - this._aboveThreshold = aboveThreshold; - this._has_aboveThreshold = true; - } - - /** - * Sets the value of field 'annotation'. - * - * @param annotation - * the value of field 'annotation'. - */ - public void setAnnotation(final java.lang.String annotation) - { - this._annotation = annotation; - } - - /** - * Sets the value of field 'colourScheme'. - * - * @param colourScheme - * the value of field 'colourScheme'. - */ - public void setColourScheme(final java.lang.String colourScheme) - { - this._colourScheme = colourScheme; - } - - /** - * Sets the value of field 'maxColour'. - * - * @param maxColour - * the value of field 'maxColour'. - */ - public void setMaxColour(final int maxColour) - { - this._maxColour = maxColour; - this._has_maxColour = true; - } - - /** - * Sets the value of field 'minColour'. - * - * @param minColour - * the value of field 'minColour'. - */ - public void setMinColour(final int minColour) - { - this._minColour = minColour; - this._has_minColour = 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; - } - - /** - * 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.schemabinding.version2.AnnotationColours - */ - public static jalview.schemabinding.version2.AnnotationColours unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.AnnotationColours.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/schemabinding/version2/AnnotationElement.java b/src/jalview/schemabinding/version2/AnnotationElement.java index 5f2ab2c..eca3e6a 100755 --- a/src/jalview/schemabinding/version2/AnnotationElement.java +++ b/src/jalview/schemabinding/version2/AnnotationElement.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,338 +19,322 @@ import org.exolab.castor.xml.Unmarshaller; * * @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 _colour. - */ - private int _colour; - - /** - * keeps track of state for field: _colour - */ - private boolean _has_colour; - - /** - * 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 deleteColour() - { - this._has_colour = false; - } - - /** - */ - public void deletePosition() - { - this._has_position = false; - } - - /** - */ - public void deleteValue() - { - this._has_value = false; - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public int getColour() - { - return this._colour; - } - - /** - * 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 hasColour. - * - * @return true if at least one Colour has been added - */ - public boolean hasColour() - { - return this._has_colour; - } - - /** - * 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; +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 _colour. + */ + private int _colour; + + /** + * keeps track of state for field: _colour + */ + private boolean _has_colour; + + /** + * 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 deleteColour( + ) { + this._has_colour= false; + } + + /** + */ + public void deletePosition( + ) { + this._has_position= false; + } + + /** + */ + public void deleteValue( + ) { + this._has_value= false; + } + + /** + * Returns the value of field 'colour'. + * + * @return the value of field 'Colour'. + */ + public int getColour( + ) { + return this._colour; + } + + /** + * 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 hasColour. + * + * @return true if at least one Colour has been added + */ + public boolean hasColour( + ) { + return this._has_colour; + } + + /** + * 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 '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 '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.schemabinding.version2.AnnotationElement + */ + public static jalview.schemabinding.version2.AnnotationElement unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller.unmarshal(jalview.schemabinding.version2.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); } - 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 '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.schemabinding.version2.AnnotationElement - */ - public static jalview.schemabinding.version2.AnnotationElement unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.AnnotationElement) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.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/schemabinding/version2/Colour.java b/src/jalview/schemabinding/version2/Colour.java index 7f4a6b1..d7650a0 100755 --- a/src/jalview/schemabinding/version2/Colour.java +++ b/src/jalview/schemabinding/version2/Colour.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,481 +19,465 @@ import org.exolab.castor.xml.Unmarshaller; * * @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; - - /** - * Field _minRGB. - */ - private java.lang.String _minRGB; - - /** - * loosely specified enumeration: NONE,ABOVE, or BELOW - */ - private java.lang.String _threshType; - - /** - * Field _threshold. - */ - private float _threshold; - - /** - * keeps track of state for field: _threshold - */ - private boolean _has_threshold; - - /** - * Field _max. - */ - private float _max; - - /** - * keeps track of state for field: _max - */ - private boolean _has_max; - - /** - * Field _min. - */ - private float _min; - - /** - * keeps track of state for field: _min - */ - private boolean _has_min; - - /** - * Field _colourByLabel. - */ - private boolean _colourByLabel; - - /** - * keeps track of state for field: _colourByLabel - */ - private boolean _has_colourByLabel; - - /** - * Field _autoScale. - */ - private boolean _autoScale; - - /** - * keeps track of state for field: _autoScale - */ - private boolean _has_autoScale; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Colour() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteAutoScale() - { - this._has_autoScale = false; - } - - /** - */ - public void deleteColourByLabel() - { - this._has_colourByLabel = false; - } - - /** - */ - public void deleteMax() - { - this._has_max = false; - } - - /** - */ - public void deleteMin() - { - this._has_min = false; - } - - /** - */ - public void deleteThreshold() - { - this._has_threshold = false; - } - - /** - * Returns the value of field 'autoScale'. - * - * @return the value of field 'AutoScale'. - */ - public boolean getAutoScale() - { - return this._autoScale; - } - - /** - * Returns the value of field 'colourByLabel'. - * - * @return the value of field 'ColourByLabel'. - */ - public boolean getColourByLabel() - { - return this._colourByLabel; - } - - /** - * Returns the value of field 'max'. - * - * @return the value of field 'Max'. - */ - public float getMax() - { - return this._max; - } - - /** - * Returns the value of field 'min'. - * - * @return the value of field 'Min'. - */ - public float getMin() - { - return this._min; - } - - /** - * Returns the value of field 'minRGB'. - * - * @return the value of field 'MinRGB'. - */ - public java.lang.String getMinRGB() - { - return this._minRGB; - } - - /** - * 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; - } - - /** - * Returns the value of field 'threshType'. The field 'threshType' has the - * following description: loosely specified enumeration: NONE,ABOVE, or BELOW - * - * @return the value of field 'ThreshType'. - */ - public java.lang.String getThreshType() - { - return this._threshType; - } - - /** - * Returns the value of field 'threshold'. - * - * @return the value of field 'Threshold'. - */ - public float getThreshold() - { - return this._threshold; - } - - /** - * Method hasAutoScale. - * - * @return true if at least one AutoScale has been added - */ - public boolean hasAutoScale() - { - return this._has_autoScale; - } - - /** - * Method hasColourByLabel. - * - * @return true if at least one ColourByLabel has been added - */ - public boolean hasColourByLabel() - { - return this._has_colourByLabel; - } - - /** - * Method hasMax. - * - * @return true if at least one Max has been added - */ - public boolean hasMax() - { - return this._has_max; - } - - /** - * Method hasMin. - * - * @return true if at least one Min has been added - */ - public boolean hasMin() - { - return this._has_min; - } - - /** - * Method hasThreshold. - * - * @return true if at least one Threshold has been added - */ - public boolean hasThreshold() - { - return this._has_threshold; - } - - /** - * Returns the value of field 'autoScale'. - * - * @return the value of field 'AutoScale'. - */ - public boolean isAutoScale() - { - return this._autoScale; - } - - /** - * Returns the value of field 'colourByLabel'. - * - * @return the value of field 'ColourByLabel'. - */ - public boolean isColourByLabel() - { - return this._colourByLabel; - } - - /** - * 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 'autoScale'. - * - * @param autoScale - * the value of field 'autoScale'. - */ - public void setAutoScale(final boolean autoScale) - { - this._autoScale = autoScale; - this._has_autoScale = true; - } - - /** - * Sets the value of field 'colourByLabel'. - * - * @param colourByLabel - * the value of field 'colourByLabel'. - */ - public void setColourByLabel(final boolean colourByLabel) - { - this._colourByLabel = colourByLabel; - this._has_colourByLabel = true; - } - - /** - * Sets the value of field 'max'. - * - * @param max - * the value of field 'max'. - */ - public void setMax(final float max) - { - this._max = max; - this._has_max = true; - } - - /** - * Sets the value of field 'min'. - * - * @param min - * the value of field 'min'. - */ - public void setMin(final float min) - { - this._min = min; - this._has_min = true; - } - - /** - * Sets the value of field 'minRGB'. - * - * @param minRGB - * the value of field 'minRGB'. - */ - public void setMinRGB(final java.lang.String minRGB) - { - this._minRGB = minRGB; - } - - /** - * 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; - } - - /** - * Sets the value of field 'threshType'. The field 'threshType' has the - * following description: loosely specified enumeration: NONE,ABOVE, or BELOW - * - * @param threshType - * the value of field 'threshType'. - */ - public void setThreshType(final java.lang.String threshType) - { - this._threshType = threshType; - } - - /** - * 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; - } - - /** - * 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.schemabinding.version2.Colour - */ - public static jalview.schemabinding.version2.Colour unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Colour) Unmarshaller.unmarshal( - jalview.schemabinding.version2.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); - } +public class Colour implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _name. + */ + private java.lang.String _name; + + /** + * Field _RGB. + */ + private java.lang.String _RGB; + + /** + * Field _minRGB. + */ + private java.lang.String _minRGB; + + /** + * loosely specified enumeration: NONE,ABOVE, or BELOW + */ + private java.lang.String _threshType; + + /** + * Field _threshold. + */ + private float _threshold; + + /** + * keeps track of state for field: _threshold + */ + private boolean _has_threshold; + + /** + * Field _max. + */ + private float _max; + + /** + * keeps track of state for field: _max + */ + private boolean _has_max; + + /** + * Field _min. + */ + private float _min; + + /** + * keeps track of state for field: _min + */ + private boolean _has_min; + + /** + * Field _colourByLabel. + */ + private boolean _colourByLabel; + + /** + * keeps track of state for field: _colourByLabel + */ + private boolean _has_colourByLabel; + + /** + * Field _autoScale. + */ + private boolean _autoScale; + + /** + * keeps track of state for field: _autoScale + */ + private boolean _has_autoScale; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Colour() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteAutoScale( + ) { + this._has_autoScale= false; + } + + /** + */ + public void deleteColourByLabel( + ) { + this._has_colourByLabel= false; + } + + /** + */ + public void deleteMax( + ) { + this._has_max= false; + } + + /** + */ + public void deleteMin( + ) { + this._has_min= false; + } + + /** + */ + public void deleteThreshold( + ) { + this._has_threshold= false; + } + + /** + * Returns the value of field 'autoScale'. + * + * @return the value of field 'AutoScale'. + */ + public boolean getAutoScale( + ) { + return this._autoScale; + } + + /** + * Returns the value of field 'colourByLabel'. + * + * @return the value of field 'ColourByLabel'. + */ + public boolean getColourByLabel( + ) { + return this._colourByLabel; + } + + /** + * Returns the value of field 'max'. + * + * @return the value of field 'Max'. + */ + public float getMax( + ) { + return this._max; + } + + /** + * Returns the value of field 'min'. + * + * @return the value of field 'Min'. + */ + public float getMin( + ) { + return this._min; + } + + /** + * Returns the value of field 'minRGB'. + * + * @return the value of field 'MinRGB'. + */ + public java.lang.String getMinRGB( + ) { + return this._minRGB; + } + + /** + * 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; + } + + /** + * Returns the value of field 'threshType'. The field + * 'threshType' has the following description: loosely + * specified enumeration: NONE,ABOVE, or BELOW + * + * @return the value of field 'ThreshType'. + */ + public java.lang.String getThreshType( + ) { + return this._threshType; + } + + /** + * Returns the value of field 'threshold'. + * + * @return the value of field 'Threshold'. + */ + public float getThreshold( + ) { + return this._threshold; + } + + /** + * Method hasAutoScale. + * + * @return true if at least one AutoScale has been added + */ + public boolean hasAutoScale( + ) { + return this._has_autoScale; + } + + /** + * Method hasColourByLabel. + * + * @return true if at least one ColourByLabel has been added + */ + public boolean hasColourByLabel( + ) { + return this._has_colourByLabel; + } + + /** + * Method hasMax. + * + * @return true if at least one Max has been added + */ + public boolean hasMax( + ) { + return this._has_max; + } + + /** + * Method hasMin. + * + * @return true if at least one Min has been added + */ + public boolean hasMin( + ) { + return this._has_min; + } + + /** + * Method hasThreshold. + * + * @return true if at least one Threshold has been added + */ + public boolean hasThreshold( + ) { + return this._has_threshold; + } + + /** + * Returns the value of field 'autoScale'. + * + * @return the value of field 'AutoScale'. + */ + public boolean isAutoScale( + ) { + return this._autoScale; + } + + /** + * Returns the value of field 'colourByLabel'. + * + * @return the value of field 'ColourByLabel'. + */ + public boolean isColourByLabel( + ) { + return this._colourByLabel; + } + + /** + * 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 'autoScale'. + * + * @param autoScale the value of field 'autoScale'. + */ + public void setAutoScale( + final boolean autoScale) { + this._autoScale = autoScale; + this._has_autoScale = true; + } + + /** + * Sets the value of field 'colourByLabel'. + * + * @param colourByLabel the value of field 'colourByLabel'. + */ + public void setColourByLabel( + final boolean colourByLabel) { + this._colourByLabel = colourByLabel; + this._has_colourByLabel = true; + } + + /** + * Sets the value of field 'max'. + * + * @param max the value of field 'max'. + */ + public void setMax( + final float max) { + this._max = max; + this._has_max = true; + } + + /** + * Sets the value of field 'min'. + * + * @param min the value of field 'min'. + */ + public void setMin( + final float min) { + this._min = min; + this._has_min = true; + } + + /** + * Sets the value of field 'minRGB'. + * + * @param minRGB the value of field 'minRGB'. + */ + public void setMinRGB( + final java.lang.String minRGB) { + this._minRGB = minRGB; + } + + /** + * 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; + } + + /** + * Sets the value of field 'threshType'. The field 'threshType' + * has the following description: loosely specified + * enumeration: NONE,ABOVE, or BELOW + * + * @param threshType the value of field 'threshType'. + */ + public void setThreshType( + final java.lang.String threshType) { + this._threshType = threshType; + } + + /** + * 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; + } + + /** + * 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.schemabinding.version2.Colour + */ + public static jalview.schemabinding.version2.Colour unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Colour) Unmarshaller.unmarshal(jalview.schemabinding.version2.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/schemabinding/version2/DBRef.java b/src/jalview/schemabinding/version2/DBRef.java index 155d162..4d67250 100644 --- a/src/jalview/schemabinding/version2/DBRef.java +++ b/src/jalview/schemabinding/version2/DBRef.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,215 +19,201 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class DBRef implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _source. - */ - private java.lang.String _source; - - /** - * Field _version. - */ - private java.lang.String _version; - - /** - * Field _accessionId. - */ - private java.lang.String _accessionId; - - /** - * Field _mapping. - */ - private jalview.schemabinding.version2.Mapping _mapping; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public DBRef() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'accessionId'. - * - * @return the value of field 'AccessionId'. - */ - public java.lang.String getAccessionId() - { - return this._accessionId; - } - - /** - * Returns the value of field 'mapping'. - * - * @return the value of field 'Mapping'. - */ - public jalview.schemabinding.version2.Mapping getMapping() - { - return this._mapping; - } - - /** - * Returns the value of field 'source'. - * - * @return the value of field 'Source'. - */ - public java.lang.String getSource() - { - return this._source; - } - - /** - * 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; +public class DBRef implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _source. + */ + private java.lang.String _source; + + /** + * Field _version. + */ + private java.lang.String _version; + + /** + * Field _accessionId. + */ + private java.lang.String _accessionId; + + /** + * Field _mapping. + */ + private jalview.schemabinding.version2.Mapping _mapping; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public DBRef() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'accessionId'. + * + * @return the value of field 'AccessionId'. + */ + public java.lang.String getAccessionId( + ) { + return this._accessionId; + } + + /** + * Returns the value of field 'mapping'. + * + * @return the value of field 'Mapping'. + */ + public jalview.schemabinding.version2.Mapping getMapping( + ) { + return this._mapping; + } + + /** + * Returns the value of field 'source'. + * + * @return the value of field 'Source'. + */ + public java.lang.String getSource( + ) { + return this._source; + } + + /** + * 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 'accessionId'. + * + * @param accessionId the value of field 'accessionId'. + */ + public void setAccessionId( + final java.lang.String accessionId) { + this._accessionId = accessionId; + } + + /** + * Sets the value of field 'mapping'. + * + * @param mapping the value of field 'mapping'. + */ + public void setMapping( + final jalview.schemabinding.version2.Mapping mapping) { + this._mapping = mapping; + } + + /** + * Sets the value of field 'source'. + * + * @param source the value of field 'source'. + */ + public void setSource( + final java.lang.String source) { + this._source = source; + } + + /** + * 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.schemabinding.version2.DBRef + */ + public static jalview.schemabinding.version2.DBRef unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal(jalview.schemabinding.version2.DBRef.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); } - 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 'accessionId'. - * - * @param accessionId - * the value of field 'accessionId'. - */ - public void setAccessionId(final java.lang.String accessionId) - { - this._accessionId = accessionId; - } - - /** - * Sets the value of field 'mapping'. - * - * @param mapping - * the value of field 'mapping'. - */ - public void setMapping( - final jalview.schemabinding.version2.Mapping mapping) - { - this._mapping = mapping; - } - - /** - * Sets the value of field 'source'. - * - * @param source - * the value of field 'source'. - */ - public void setSource(final java.lang.String source) - { - this._source = source; - } - - /** - * 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.schemabinding.version2.DBRef - */ - public static jalview.schemabinding.version2.DBRef unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal( - jalview.schemabinding.version2.DBRef.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/schemabinding/version2/Feature.java b/src/jalview/schemabinding/version2/Feature.java index ebd7424..109ec6e 100755 --- a/src/jalview/schemabinding/version2/Feature.java +++ b/src/jalview/schemabinding/version2/Feature.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,530 +19,501 @@ import org.exolab.castor.xml.Unmarshaller; * * @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; - - /** - * Field _score. - */ - private float _score; - - /** - * keeps track of state for field: _score - */ - private boolean _has_score; - - /** - * Field _otherDataList. - */ - private java.util.Vector _otherDataList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Feature() - { - super(); - this._otherDataList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vOtherData - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addOtherData( - final jalview.schemabinding.version2.OtherData vOtherData) - throws java.lang.IndexOutOfBoundsException - { - this._otherDataList.addElement(vOtherData); - } - - /** - * - * - * @param index - * @param vOtherData - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addOtherData(final int index, - final jalview.schemabinding.version2.OtherData vOtherData) - throws java.lang.IndexOutOfBoundsException - { - this._otherDataList.add(index, vOtherData); - } - - /** - */ - public void deleteBegin() - { - this._has_begin = false; - } - - /** - */ - public void deleteEnd() - { - this._has_end = false; - } - - /** - */ - public void deleteScore() - { - this._has_score = false; - } - - /** - * Method enumerateOtherData. - * - * @return an Enumeration over all jalview.schemabinding.version2.OtherData - * elements - */ - public java.util.Enumeration enumerateOtherData() - { - return this._otherDataList.elements(); - } - - /** - * 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 'featureGroup'. - * - * @return the value of field 'FeatureGroup'. - */ - public java.lang.String getFeatureGroup() - { - return this._featureGroup; - } - - /** - * Method getOtherData. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.OtherData at the - * given index - */ - public jalview.schemabinding.version2.OtherData getOtherData( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._otherDataList.size()) - { - throw new IndexOutOfBoundsException("getOtherData: Index value '" - + index + "' not in range [0.." - + (this._otherDataList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.OtherData) _otherDataList - .get(index); - } - - /** - * Method getOtherData.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.schemabinding.version2.OtherData[] getOtherData() - { - jalview.schemabinding.version2.OtherData[] array = new jalview.schemabinding.version2.OtherData[0]; - return (jalview.schemabinding.version2.OtherData[]) this._otherDataList - .toArray(array); - } - - /** - * Method getOtherDataCount. - * - * @return the size of this collection - */ - public int getOtherDataCount() - { - return this._otherDataList.size(); - } - - /** - * Returns the value of field 'score'. - * - * @return the value of field 'Score'. - */ - public float getScore() - { - return this._score; - } - - /** - * 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 hasScore. - * - * @return true if at least one Score has been added - */ - public boolean hasScore() - { - return this._has_score; - } - - /** - * 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 removeAllOtherData() - { - this._otherDataList.clear(); - } - - /** - * Method removeOtherData. - * - * @param vOtherData - * @return true if the object was removed from the collection. - */ - public boolean removeOtherData( - final jalview.schemabinding.version2.OtherData vOtherData) - { - boolean removed = _otherDataList.remove(vOtherData); - return removed; - } - - /** - * Method removeOtherDataAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.OtherData removeOtherDataAt( - final int index) - { - java.lang.Object obj = this._otherDataList.remove(index); - return (jalview.schemabinding.version2.OtherData) obj; - } - - /** - * 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 'featureGroup'. - * - * @param featureGroup - * the value of field 'featureGroup'. - */ - public void setFeatureGroup(final java.lang.String featureGroup) - { - this._featureGroup = featureGroup; - } - - /** - * - * - * @param index - * @param vOtherData - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setOtherData(final int index, - final jalview.schemabinding.version2.OtherData vOtherData) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._otherDataList.size()) - { - throw new IndexOutOfBoundsException("setOtherData: Index value '" - + index + "' not in range [0.." - + (this._otherDataList.size() - 1) + "]"); - } - - this._otherDataList.set(index, vOtherData); - } - - /** - * - * - * @param vOtherDataArray - */ - public void setOtherData( - final jalview.schemabinding.version2.OtherData[] vOtherDataArray) - { - // -- copy array - _otherDataList.clear(); - - for (int i = 0; i < vOtherDataArray.length; i++) - { - this._otherDataList.add(vOtherDataArray[i]); - } - } - - /** - * Sets the value of field 'score'. - * - * @param score - * the value of field 'score'. - */ - public void setScore(final float score) - { - this._score = score; - this._has_score = 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.schemabinding.version2.Featur - */ - public static jalview.schemabinding.version2.Feature unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal( - jalview.schemabinding.version2.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); - } +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; + + /** + * Field _score. + */ + private float _score; + + /** + * keeps track of state for field: _score + */ + private boolean _has_score; + + /** + * Field _otherDataList. + */ + private java.util.Vector _otherDataList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Feature() { + super(); + this._otherDataList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vOtherData + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addOtherData( + final jalview.schemabinding.version2.OtherData vOtherData) + throws java.lang.IndexOutOfBoundsException { + this._otherDataList.addElement(vOtherData); + } + + /** + * + * + * @param index + * @param vOtherData + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addOtherData( + final int index, + final jalview.schemabinding.version2.OtherData vOtherData) + throws java.lang.IndexOutOfBoundsException { + this._otherDataList.add(index, vOtherData); + } + + /** + */ + public void deleteBegin( + ) { + this._has_begin= false; + } + + /** + */ + public void deleteEnd( + ) { + this._has_end= false; + } + + /** + */ + public void deleteScore( + ) { + this._has_score= false; + } + + /** + * Method enumerateOtherData. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.OtherData elements + */ + public java.util.Enumeration enumerateOtherData( + ) { + return this._otherDataList.elements(); + } + + /** + * 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 'featureGroup'. + * + * @return the value of field 'FeatureGroup'. + */ + public java.lang.String getFeatureGroup( + ) { + return this._featureGroup; + } + + /** + * Method getOtherData. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.OtherData at the given index + */ + public jalview.schemabinding.version2.OtherData getOtherData( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._otherDataList.size()) { + throw new IndexOutOfBoundsException("getOtherData: Index value '" + index + "' not in range [0.." + (this._otherDataList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.OtherData) _otherDataList.get(index); + } + + /** + * Method getOtherData.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.schemabinding.version2.OtherData[] getOtherData( + ) { + jalview.schemabinding.version2.OtherData[] array = new jalview.schemabinding.version2.OtherData[0]; + return (jalview.schemabinding.version2.OtherData[]) this._otherDataList.toArray(array); + } + + /** + * Method getOtherDataCount. + * + * @return the size of this collection + */ + public int getOtherDataCount( + ) { + return this._otherDataList.size(); + } + + /** + * Returns the value of field 'score'. + * + * @return the value of field 'Score'. + */ + public float getScore( + ) { + return this._score; + } + + /** + * 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 hasScore. + * + * @return true if at least one Score has been added + */ + public boolean hasScore( + ) { + return this._has_score; + } + + /** + * 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 removeAllOtherData( + ) { + this._otherDataList.clear(); + } + + /** + * Method removeOtherData. + * + * @param vOtherData + * @return true if the object was removed from the collection. + */ + public boolean removeOtherData( + final jalview.schemabinding.version2.OtherData vOtherData) { + boolean removed = _otherDataList.remove(vOtherData); + return removed; + } + + /** + * Method removeOtherDataAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.OtherData removeOtherDataAt( + final int index) { + java.lang.Object obj = this._otherDataList.remove(index); + return (jalview.schemabinding.version2.OtherData) obj; + } + + /** + * 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 'featureGroup'. + * + * @param featureGroup the value of field 'featureGroup'. + */ + public void setFeatureGroup( + final java.lang.String featureGroup) { + this._featureGroup = featureGroup; + } + + /** + * + * + * @param index + * @param vOtherData + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setOtherData( + final int index, + final jalview.schemabinding.version2.OtherData vOtherData) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._otherDataList.size()) { + throw new IndexOutOfBoundsException("setOtherData: Index value '" + index + "' not in range [0.." + (this._otherDataList.size() - 1) + "]"); + } + + this._otherDataList.set(index, vOtherData); + } + + /** + * + * + * @param vOtherDataArray + */ + public void setOtherData( + final jalview.schemabinding.version2.OtherData[] vOtherDataArray) { + //-- copy array + _otherDataList.clear(); + + for (int i = 0; i < vOtherDataArray.length; i++) { + this._otherDataList.add(vOtherDataArray[i]); + } + } + + /** + * Sets the value of field 'score'. + * + * @param score the value of field 'score'. + */ + public void setScore( + final float score) { + this._score = score; + this._has_score = 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.schemabinding.version2.Featur + */ + public static jalview.schemabinding.version2.Feature unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.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/schemabinding/version2/FeatureSettings.java b/src/jalview/schemabinding/version2/FeatureSettings.java index 9bacca3..5ce4054 100755 --- a/src/jalview/schemabinding/version2/FeatureSettings.java +++ b/src/jalview/schemabinding/version2/FeatureSettings.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,444 +19,414 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class FeatureSettings implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _settingList. - */ - private java.util.Vector _settingList; - - /** - * Field _groupList. - */ - private java.util.Vector _groupList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FeatureSettings() - { - super(); - this._settingList = new java.util.Vector(); - this._groupList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vGroup - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addGroup(final jalview.schemabinding.version2.Group vGroup) - throws java.lang.IndexOutOfBoundsException - { - this._groupList.addElement(vGroup); - } - - /** - * - * - * @param index - * @param vGroup - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addGroup(final int index, - final jalview.schemabinding.version2.Group vGroup) - throws java.lang.IndexOutOfBoundsException - { - this._groupList.add(index, vGroup); - } - - /** - * - * - * @param vSetting - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSetting( - final jalview.schemabinding.version2.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.schemabinding.version2.Setting vSetting) - throws java.lang.IndexOutOfBoundsException - { - this._settingList.add(index, vSetting); - } - - /** - * Method enumerateGroup. - * - * @return an Enumeration over all jalview.schemabinding.version2.Group - * elements - */ - public java.util.Enumeration enumerateGroup() - { - return this._groupList.elements(); - } - - /** - * Method enumerateSetting. - * - * @return an Enumeration over all jalview.schemabinding.version2.Setting - * elements - */ - public java.util.Enumeration enumerateSetting() - { - return this._settingList.elements(); - } - - /** - * Method getGroup. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.Group at the given - * index - */ - public jalview.schemabinding.version2.Group getGroup(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._groupList.size()) - { - throw new IndexOutOfBoundsException("getGroup: Index value '" + index - + "' not in range [0.." + (this._groupList.size() - 1) + "]"); +public class FeatureSettings implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _settingList. + */ + private java.util.Vector _settingList; + + /** + * Field _groupList. + */ + private java.util.Vector _groupList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public FeatureSettings() { + super(); + this._settingList = new java.util.Vector(); + this._groupList = new java.util.Vector(); } - return (jalview.schemabinding.version2.Group) _groupList.get(index); - } - - /** - * Method getGroup.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.schemabinding.version2.Group[] getGroup() - { - jalview.schemabinding.version2.Group[] array = new jalview.schemabinding.version2.Group[0]; - return (jalview.schemabinding.version2.Group[]) this._groupList - .toArray(array); - } - - /** - * Method getGroupCount. - * - * @return the size of this collection - */ - public int getGroupCount() - { - return this._groupList.size(); - } - - /** - * 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.schemabinding.version2.Setting at the - * given index - */ - public jalview.schemabinding.version2.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) + "]"); + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vGroup + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addGroup( + final jalview.schemabinding.version2.Group vGroup) + throws java.lang.IndexOutOfBoundsException { + this._groupList.addElement(vGroup); } - return (jalview.schemabinding.version2.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.schemabinding.version2.Setting[] getSetting() - { - jalview.schemabinding.version2.Setting[] array = new jalview.schemabinding.version2.Setting[0]; - return (jalview.schemabinding.version2.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; + /** + * + * + * @param index + * @param vGroup + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addGroup( + final int index, + final jalview.schemabinding.version2.Group vGroup) + throws java.lang.IndexOutOfBoundsException { + this._groupList.add(index, vGroup); } - 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); - } - - /** + + /** + * + * + * @param vSetting + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection */ - public void removeAllGroup() - { - this._groupList.clear(); - } + public void addSetting( + final jalview.schemabinding.version2.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 removeAllSetting() - { - this._settingList.clear(); - } - - /** - * Method removeGroup. - * - * @param vGroup - * @return true if the object was removed from the collection. - */ - public boolean removeGroup( - final jalview.schemabinding.version2.Group vGroup) - { - boolean removed = _groupList.remove(vGroup); - return removed; - } - - /** - * Method removeGroupAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Group removeGroupAt(final int index) - { - java.lang.Object obj = this._groupList.remove(index); - return (jalview.schemabinding.version2.Group) obj; - } - - /** - * Method removeSetting. - * - * @param vSetting - * @return true if the object was removed from the collection. - */ - public boolean removeSetting( - final jalview.schemabinding.version2.Setting vSetting) - { - boolean removed = _settingList.remove(vSetting); - return removed; - } - - /** - * Method removeSettingAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Setting removeSettingAt( - final int index) - { - java.lang.Object obj = this._settingList.remove(index); - return (jalview.schemabinding.version2.Setting) obj; - } - - /** - * - * - * @param index - * @param vGroup - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setGroup(final int index, - final jalview.schemabinding.version2.Group vGroup) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._groupList.size()) - { - throw new IndexOutOfBoundsException("setGroup: Index value '" + index - + "' not in range [0.." + (this._groupList.size() - 1) + "]"); + public void addSetting( + final int index, + final jalview.schemabinding.version2.Setting vSetting) + throws java.lang.IndexOutOfBoundsException { + this._settingList.add(index, vSetting); } - this._groupList.set(index, vGroup); - } - - /** - * - * - * @param vGroupArray - */ - public void setGroup( - final jalview.schemabinding.version2.Group[] vGroupArray) - { - // -- copy array - _groupList.clear(); - - for (int i = 0; i < vGroupArray.length; i++) - { - this._groupList.add(vGroupArray[i]); + /** + * Method enumerateGroup. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.Group elements + */ + public java.util.Enumeration enumerateGroup( + ) { + return this._groupList.elements(); } - } - - /** - * - * - * @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.schemabinding.version2.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) + "]"); + + /** + * Method enumerateSetting. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.Setting elements + */ + public java.util.Enumeration enumerateSetting( + ) { + return this._settingList.elements(); + } + + /** + * Method getGroup. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.Group at the given index + */ + public jalview.schemabinding.version2.Group getGroup( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._groupList.size()) { + throw new IndexOutOfBoundsException("getGroup: Index value '" + index + "' not in range [0.." + (this._groupList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.Group) _groupList.get(index); + } + + /** + * Method getGroup.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.schemabinding.version2.Group[] getGroup( + ) { + jalview.schemabinding.version2.Group[] array = new jalview.schemabinding.version2.Group[0]; + return (jalview.schemabinding.version2.Group[]) this._groupList.toArray(array); + } + + /** + * Method getGroupCount. + * + * @return the size of this collection + */ + public int getGroupCount( + ) { + return this._groupList.size(); } - this._settingList.set(index, vSetting); - } - - /** - * - * - * @param vSettingArray - */ - public void setSetting( - final jalview.schemabinding.version2.Setting[] vSettingArray) - { - // -- copy array - _settingList.clear(); - - for (int i = 0; i < vSettingArray.length; i++) - { - this._settingList.add(vSettingArray[i]); + /** + * 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.schemabinding.version2.Setting at the given index + */ + public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Setting[] getSetting( + ) { + jalview.schemabinding.version2.Setting[] array = new jalview.schemabinding.version2.Setting[0]; + return (jalview.schemabinding.version2.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 removeAllGroup( + ) { + this._groupList.clear(); + } + + /** + */ + public void removeAllSetting( + ) { + this._settingList.clear(); + } + + /** + * Method removeGroup. + * + * @param vGroup + * @return true if the object was removed from the collection. + */ + public boolean removeGroup( + final jalview.schemabinding.version2.Group vGroup) { + boolean removed = _groupList.remove(vGroup); + return removed; + } + + /** + * Method removeGroupAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Group removeGroupAt( + final int index) { + java.lang.Object obj = this._groupList.remove(index); + return (jalview.schemabinding.version2.Group) obj; + } + + /** + * Method removeSetting. + * + * @param vSetting + * @return true if the object was removed from the collection. + */ + public boolean removeSetting( + final jalview.schemabinding.version2.Setting vSetting) { + boolean removed = _settingList.remove(vSetting); + return removed; + } + + /** + * Method removeSettingAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Setting removeSettingAt( + final int index) { + java.lang.Object obj = this._settingList.remove(index); + return (jalview.schemabinding.version2.Setting) obj; + } + + /** + * + * + * @param index + * @param vGroup + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setGroup( + final int index, + final jalview.schemabinding.version2.Group vGroup) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._groupList.size()) { + throw new IndexOutOfBoundsException("setGroup: Index value '" + index + "' not in range [0.." + (this._groupList.size() - 1) + "]"); + } + + this._groupList.set(index, vGroup); + } + + /** + * + * + * @param vGroupArray + */ + public void setGroup( + final jalview.schemabinding.version2.Group[] vGroupArray) { + //-- copy array + _groupList.clear(); + + for (int i = 0; i < vGroupArray.length; i++) { + this._groupList.add(vGroupArray[i]); + } + } + + /** + * + * + * @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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.FeatureSettings + */ + public static jalview.schemabinding.version2.FeatureSettings unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller.unmarshal(jalview.schemabinding.version2.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); } - } - - /** - * 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.schemabinding.version2.FeatureSettings - */ - public static jalview.schemabinding.version2.FeatureSettings unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.FeatureSettings) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.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/schemabinding/version2/Features.java b/src/jalview/schemabinding/version2/Features.java index 790ecfa..47b28a3 100755 --- a/src/jalview/schemabinding/version2/Features.java +++ b/src/jalview/schemabinding/version2/Features.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,106 +19,98 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class Features extends Feature implements java.io.Serializable +public class Features extends Feature +implements java.io.Serializable { - // ----------------/ - // - Constructors -/ - // ----------------/ - public Features() - { - super(); - } + //----------------/ + //- Constructors -/ + //----------------/ - // -----------/ - // - Methods -/ - // -----------/ + public Features() { + super(); + } - /** - * 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; + + //-----------/ + //- 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; } - 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 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); - } + /** + * + * + * @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.schemabinding.version2.Featur - */ - public static jalview.schemabinding.version2.Feature unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal( - jalview.schemabinding.version2.Features.class, reader); - } + /** + * 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.schemabinding.version2.Featur + */ + public static jalview.schemabinding.version2.Feature unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Feature) Unmarshaller.unmarshal(jalview.schemabinding.version2.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); - } + /** + * + * + * @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/schemabinding/version2/Group.java b/src/jalview/schemabinding/version2/Group.java index e446cb2..826667e 100644 --- a/src/jalview/schemabinding/version2/Group.java +++ b/src/jalview/schemabinding/version2/Group.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,195 +19,184 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class Group implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _name. - */ - private java.lang.String _name; - - /** - * Field _display. - */ - private boolean _display; - - /** - * keeps track of state for field: _display - */ - private boolean _has_display; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Group() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** +public class Group implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _name. + */ + private java.lang.String _name; + + /** + * Field _display. + */ + private boolean _display; + + /** + * keeps track of state for field: _display + */ + private boolean _has_display; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Group() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteDisplay( + ) { + this._has_display= false; + } + + /** + * Returns the value of field 'display'. + * + * @return the value of field 'Display'. + */ + public boolean getDisplay( + ) { + return this._display; + } + + /** + * Returns the value of field 'name'. + * + * @return the value of field 'Name'. + */ + public java.lang.String getName( + ) { + return this._name; + } + + /** + * 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 '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 'name'. + * + * @param name the value of field 'name'. + */ + public void setName( + final java.lang.String name) { + this._name = name; + } + + /** + * 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.schemabinding.version2.Group + */ + public static jalview.schemabinding.version2.Group unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Group) Unmarshaller.unmarshal(jalview.schemabinding.version2.Group.class, reader); + } + + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema */ - public void deleteDisplay() - { - this._has_display = false; - } - - /** - * Returns the value of field 'display'. - * - * @return the value of field 'Display'. - */ - public boolean getDisplay() - { - return this._display; - } - - /** - * Returns the value of field 'name'. - * - * @return the value of field 'Name'. - */ - public java.lang.String getName() - { - return this._name; - } - - /** - * 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; + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); } - 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 '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 'name'. - * - * @param name - * the value of field 'name'. - */ - public void setName(final java.lang.String name) - { - this._name = name; - } - - /** - * 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.schemabinding.version2.Group - */ - public static jalview.schemabinding.version2.Group unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Group) Unmarshaller.unmarshal( - jalview.schemabinding.version2.Group.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/schemabinding/version2/HiddenColumns.java b/src/jalview/schemabinding/version2/HiddenColumns.java index ea6f422..716bfbc 100644 --- a/src/jalview/schemabinding/version2/HiddenColumns.java +++ b/src/jalview/schemabinding/version2/HiddenColumns.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,209 +19,198 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class HiddenColumns 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; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public HiddenColumns() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteEnd() - { - this._has_end = false; - } - - /** - */ - public void deleteStart() - { - this._has_start = false; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd() - { - return this._end; - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart() - { - return this._start; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd() - { - return this._has_end; - } - - /** - * 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; +public class HiddenColumns 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; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public HiddenColumns() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteEnd( + ) { + this._has_end= false; + } + + /** + */ + public void deleteStart( + ) { + this._has_start= false; + } + + /** + * Returns the value of field 'end'. + * + * @return the value of field 'End'. + */ + public int getEnd( + ) { + return this._end; + } + + /** + * Returns the value of field 'start'. + * + * @return the value of field 'Start'. + */ + public int getStart( + ) { + return this._start; + } + + /** + * Method hasEnd. + * + * @return true if at least one End has been added + */ + public boolean hasEnd( + ) { + return this._has_end; + } + + /** + * 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); + } + + /** + * 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 '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.schemabinding.version2.HiddenColumns + */ + public static jalview.schemabinding.version2.HiddenColumns unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller.unmarshal(jalview.schemabinding.version2.HiddenColumns.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); } - 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 '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 '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.schemabinding.version2.HiddenColumns - */ - public static jalview.schemabinding.version2.HiddenColumns unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller - .unmarshal(jalview.schemabinding.version2.HiddenColumns.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/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java index 4da0f75..309e704 100755 --- a/src/jalview/schemabinding/version2/JGroup.java +++ b/src/jalview/schemabinding/version2/JGroup.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,1156 +19,1132 @@ import org.exolab.castor.xml.Unmarshaller; * * @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 _textCol1. - */ - private int _textCol1; - - /** - * keeps track of state for field: _textCol1 - */ - private boolean _has_textCol1; - - /** - * Field _textCol2. - */ - private int _textCol2; - - /** - * keeps track of state for field: _textCol2 - */ - private boolean _has_textCol2; - - /** - * Field _textColThreshold. - */ - private int _textColThreshold; - - /** - * keeps track of state for field: _textColThreshold - */ - private boolean _has_textColThreshold; - - /** - * Field _showUnconserved. - */ - private boolean _showUnconserved; - - /** - * keeps track of state for field: _showUnconserved - */ - private boolean _has_showUnconserved; - - /** - * Field _ignoreGapsinConsensus. - */ - private boolean _ignoreGapsinConsensus = true; - - /** - * keeps track of state for field: _ignoreGapsinConsensus - */ - private boolean _has_ignoreGapsinConsensus; - - /** - * Field _showConsensusHistogram. - */ - private boolean _showConsensusHistogram = true; - - /** - * keeps track of state for field: _showConsensusHistogram - */ - private boolean _has_showConsensusHistogram; - - /** - * Field _showSequenceLogo. - */ - private boolean _showSequenceLogo = false; - - /** - * keeps track of state for field: _showSequenceLogo - */ - private boolean _has_showSequenceLogo; - - /** - * Optional sequence group ID (only needs to be unique for this alignment) - * - */ - private java.lang.String _id; - - /** - * 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 java.lang.String vSeq) - throws java.lang.IndexOutOfBoundsException - { - this._seqList.addElement(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 java.lang.String vSeq) - throws java.lang.IndexOutOfBoundsException - { - this._seqList.add(index, 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 deleteIgnoreGapsinConsensus() - { - this._has_ignoreGapsinConsensus = false; - } - - /** - */ - public void deleteOutlineColour() - { - this._has_outlineColour = false; - } - - /** - */ - public void deletePidThreshold() - { - this._has_pidThreshold = false; - } - - /** - */ - public void deleteShowConsensusHistogram() - { - this._has_showConsensusHistogram = false; - } - - /** - */ - public void deleteShowSequenceLogo() - { - this._has_showSequenceLogo = false; - } - - /** - */ - public void deleteShowUnconserved() - { - this._has_showUnconserved = false; - } - - /** - */ - public void deleteStart() - { - this._has_start = false; - } - - /** - */ - public void deleteTextCol1() - { - this._has_textCol1 = false; - } - - /** - */ - public void deleteTextCol2() - { - this._has_textCol2 = false; - } - - /** - */ - public void deleteTextColThreshold() - { - this._has_textColThreshold = false; - } - - /** - * Method enumerateSeq. - * - * @return an Enumeration over all java.lang.String 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 'id'. The field 'id' has the following - * description: Optional sequence group ID (only needs to be unique for this - * alignment) - * - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * Returns the value of field 'ignoreGapsinConsensus'. - * - * @return the value of field 'IgnoreGapsinConsensus'. - */ - public boolean getIgnoreGapsinConsensus() - { - return this._ignoreGapsinConsensus; - } - - /** - * 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 java.lang.String at the given index - */ - public java.lang.String 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.String) _seqList.get(index); - } - - /** - * Method getSeq.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[] getSeq() - { - java.lang.String[] array = new java.lang.String[0]; - return (java.lang.String[]) this._seqList.toArray(array); - } - - /** - * Method getSeqCount. - * - * @return the size of this collection - */ - public int getSeqCount() - { - return this._seqList.size(); - } - - /** - * Returns the value of field 'showConsensusHistogram'. - * - * @return the value of field 'ShowConsensusHistogram'. - */ - public boolean getShowConsensusHistogram() - { - return this._showConsensusHistogram; - } - - /** - * Returns the value of field 'showSequenceLogo'. - * - * @return the value of field 'ShowSequenceLogo'. - */ - public boolean getShowSequenceLogo() - { - return this._showSequenceLogo; - } - - /** - * Returns the value of field 'showUnconserved'. - * - * @return the value of field 'ShowUnconserved'. - */ - public boolean getShowUnconserved() - { - return this._showUnconserved; - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart() - { - return this._start; - } - - /** - * Returns the value of field 'textCol1'. - * - * @return the value of field 'TextCol1'. - */ - public int getTextCol1() - { - return this._textCol1; - } - - /** - * Returns the value of field 'textCol2'. - * - * @return the value of field 'TextCol2'. - */ - public int getTextCol2() - { - return this._textCol2; - } - - /** - * Returns the value of field 'textColThreshold'. - * - * @return the value of field 'TextColThreshold'. - */ - public int getTextColThreshold() - { - return this._textColThreshold; - } - - /** - * 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 hasIgnoreGapsinConsensus. - * - * @return true if at least one IgnoreGapsinConsensus has been added - */ - public boolean hasIgnoreGapsinConsensus() - { - return this._has_ignoreGapsinConsensus; - } - - /** - * 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 hasShowConsensusHistogram. - * - * @return true if at least one ShowConsensusHistogram has been added - */ - public boolean hasShowConsensusHistogram() - { - return this._has_showConsensusHistogram; - } - - /** - * Method hasShowSequenceLogo. - * - * @return true if at least one ShowSequenceLogo has been added - */ - public boolean hasShowSequenceLogo() - { - return this._has_showSequenceLogo; - } - - /** - * Method hasShowUnconserved. - * - * @return true if at least one ShowUnconserved has been added - */ - public boolean hasShowUnconserved() - { - return this._has_showUnconserved; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart() - { - return this._has_start; - } - - /** - * Method hasTextCol1. - * - * @return true if at least one TextCol1 has been added - */ - public boolean hasTextCol1() - { - return this._has_textCol1; - } - - /** - * Method hasTextCol2. - * - * @return true if at least one TextCol2 has been added - */ - public boolean hasTextCol2() - { - return this._has_textCol2; - } - - /** - * Method hasTextColThreshold. - * - * @return true if at least one TextColThreshold has been added - */ - public boolean hasTextColThreshold() - { - return this._has_textColThreshold; - } - - /** - * 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; - } - - /** - * Returns the value of field 'ignoreGapsinConsensus'. - * - * @return the value of field 'IgnoreGapsinConsensus'. - */ - public boolean isIgnoreGapsinConsensus() - { - return this._ignoreGapsinConsensus; - } - - /** - * Returns the value of field 'showConsensusHistogram'. - * - * @return the value of field 'ShowConsensusHistogram'. - */ - public boolean isShowConsensusHistogram() - { - return this._showConsensusHistogram; - } - - /** - * Returns the value of field 'showSequenceLogo'. - * - * @return the value of field 'ShowSequenceLogo'. - */ - public boolean isShowSequenceLogo() - { - return this._showSequenceLogo; - } - - /** - * Returns the value of field 'showUnconserved'. - * - * @return the value of field 'ShowUnconserved'. - */ - public boolean isShowUnconserved() - { - return this._showUnconserved; - } - - /** - * 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 java.lang.String vSeq) - { - boolean removed = _seqList.remove(vSeq); - return removed; - } - - /** - * Method removeSeqAt. - * - * @param index - * @return the element removed from the collection - */ - public java.lang.String removeSeqAt(final int index) - { - java.lang.Object obj = this._seqList.remove(index); - return (java.lang.String) obj; - } - - /** - * 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 'id'. The field 'id' has the following description: - * Optional sequence group ID (only needs to be unique for this alignment) - * - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * Sets the value of field 'ignoreGapsinConsensus'. - * - * @param ignoreGapsinConsensus - * the value of field 'ignoreGapsinConsensus'. - */ - public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus) - { - this._ignoreGapsinConsensus = ignoreGapsinConsensus; - this._has_ignoreGapsinConsensus = 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 java.lang.String 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, vSeq); - } - - /** - * - * - * @param vSeqArray - */ - public void setSeq(final java.lang.String[] vSeqArray) - { - // -- copy array - _seqList.clear(); - - for (int i = 0; i < vSeqArray.length; i++) - { - this._seqList.add(vSeqArray[i]); - } - } - - /** - * Sets the value of field 'showConsensusHistogram'. - * - * @param showConsensusHistogram - * the value of field 'showConsensusHistogram'. - */ - public void setShowConsensusHistogram(final boolean showConsensusHistogram) - { - this._showConsensusHistogram = showConsensusHistogram; - this._has_showConsensusHistogram = true; - } - - /** - * Sets the value of field 'showSequenceLogo'. - * - * @param showSequenceLogo - * the value of field 'showSequenceLogo' - */ - public void setShowSequenceLogo(final boolean showSequenceLogo) - { - this._showSequenceLogo = showSequenceLogo; - this._has_showSequenceLogo = true; - } - - /** - * Sets the value of field 'showUnconserved'. - * - * @param showUnconserved - * the value of field 'showUnconserved'. - */ - public void setShowUnconserved(final boolean showUnconserved) - { - this._showUnconserved = showUnconserved; - this._has_showUnconserved = true; - } - - /** - * 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; - } - - /** - * Sets the value of field 'textCol1'. - * - * @param textCol1 - * the value of field 'textCol1'. - */ - public void setTextCol1(final int textCol1) - { - this._textCol1 = textCol1; - this._has_textCol1 = true; - } - - /** - * Sets the value of field 'textCol2'. - * - * @param textCol2 - * the value of field 'textCol2'. - */ - public void setTextCol2(final int textCol2) - { - this._textCol2 = textCol2; - this._has_textCol2 = true; - } - - /** - * Sets the value of field 'textColThreshold'. - * - * @param textColThreshold - * the value of field 'textColThreshold' - */ - public void setTextColThreshold(final int textColThreshold) - { - this._textColThreshold = textColThreshold; - this._has_textColThreshold = 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.schemabinding.version2.JGroup - */ - public static jalview.schemabinding.version2.JGroup unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal( - jalview.schemabinding.version2.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); - } +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 _textCol1. + */ + private int _textCol1; + + /** + * keeps track of state for field: _textCol1 + */ + private boolean _has_textCol1; + + /** + * Field _textCol2. + */ + private int _textCol2; + + /** + * keeps track of state for field: _textCol2 + */ + private boolean _has_textCol2; + + /** + * Field _textColThreshold. + */ + private int _textColThreshold; + + /** + * keeps track of state for field: _textColThreshold + */ + private boolean _has_textColThreshold; + + /** + * Field _showUnconserved. + */ + private boolean _showUnconserved; + + /** + * keeps track of state for field: _showUnconserved + */ + private boolean _has_showUnconserved; + + /** + * Field _ignoreGapsinConsensus. + */ + private boolean _ignoreGapsinConsensus = true; + + /** + * keeps track of state for field: _ignoreGapsinConsensus + */ + private boolean _has_ignoreGapsinConsensus; + + /** + * Field _showConsensusHistogram. + */ + private boolean _showConsensusHistogram = true; + + /** + * keeps track of state for field: _showConsensusHistogram + */ + private boolean _has_showConsensusHistogram; + + /** + * Field _showSequenceLogo. + */ + private boolean _showSequenceLogo = false; + + /** + * keeps track of state for field: _showSequenceLogo + */ + private boolean _has_showSequenceLogo; + + /** + * Optional sequence group ID (only needs to be unique for this + * alignment) + * + */ + private java.lang.String _id; + + /** + * 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 java.lang.String vSeq) + throws java.lang.IndexOutOfBoundsException { + this._seqList.addElement(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 java.lang.String vSeq) + throws java.lang.IndexOutOfBoundsException { + this._seqList.add(index, 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 deleteIgnoreGapsinConsensus( + ) { + this._has_ignoreGapsinConsensus= false; + } + + /** + */ + public void deleteOutlineColour( + ) { + this._has_outlineColour= false; + } + + /** + */ + public void deletePidThreshold( + ) { + this._has_pidThreshold= false; + } + + /** + */ + public void deleteShowConsensusHistogram( + ) { + this._has_showConsensusHistogram= false; + } + + /** + */ + public void deleteShowSequenceLogo( + ) { + this._has_showSequenceLogo= false; + } + + /** + */ + public void deleteShowUnconserved( + ) { + this._has_showUnconserved= false; + } + + /** + */ + public void deleteStart( + ) { + this._has_start= false; + } + + /** + */ + public void deleteTextCol1( + ) { + this._has_textCol1= false; + } + + /** + */ + public void deleteTextCol2( + ) { + this._has_textCol2= false; + } + + /** + */ + public void deleteTextColThreshold( + ) { + this._has_textColThreshold= false; + } + + /** + * Method enumerateSeq. + * + * @return an Enumeration over all java.lang.String 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 'id'. The field 'id' has the + * following description: Optional sequence group ID (only + * needs to be unique for this alignment) + * + * + * @return the value of field 'Id'. + */ + public java.lang.String getId( + ) { + return this._id; + } + + /** + * Returns the value of field 'ignoreGapsinConsensus'. + * + * @return the value of field 'IgnoreGapsinConsensus'. + */ + public boolean getIgnoreGapsinConsensus( + ) { + return this._ignoreGapsinConsensus; + } + + /** + * 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 java.lang.String at the given index + */ + public java.lang.String 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.String) _seqList.get(index); + } + + /** + * Method getSeq.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[] getSeq( + ) { + java.lang.String[] array = new java.lang.String[0]; + return (java.lang.String[]) this._seqList.toArray(array); + } + + /** + * Method getSeqCount. + * + * @return the size of this collection + */ + public int getSeqCount( + ) { + return this._seqList.size(); + } + + /** + * Returns the value of field 'showConsensusHistogram'. + * + * @return the value of field 'ShowConsensusHistogram'. + */ + public boolean getShowConsensusHistogram( + ) { + return this._showConsensusHistogram; + } + + /** + * Returns the value of field 'showSequenceLogo'. + * + * @return the value of field 'ShowSequenceLogo'. + */ + public boolean getShowSequenceLogo( + ) { + return this._showSequenceLogo; + } + + /** + * Returns the value of field 'showUnconserved'. + * + * @return the value of field 'ShowUnconserved'. + */ + public boolean getShowUnconserved( + ) { + return this._showUnconserved; + } + + /** + * Returns the value of field 'start'. + * + * @return the value of field 'Start'. + */ + public int getStart( + ) { + return this._start; + } + + /** + * Returns the value of field 'textCol1'. + * + * @return the value of field 'TextCol1'. + */ + public int getTextCol1( + ) { + return this._textCol1; + } + + /** + * Returns the value of field 'textCol2'. + * + * @return the value of field 'TextCol2'. + */ + public int getTextCol2( + ) { + return this._textCol2; + } + + /** + * Returns the value of field 'textColThreshold'. + * + * @return the value of field 'TextColThreshold'. + */ + public int getTextColThreshold( + ) { + return this._textColThreshold; + } + + /** + * 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 hasIgnoreGapsinConsensus. + * + * @return true if at least one IgnoreGapsinConsensus has been + * added + */ + public boolean hasIgnoreGapsinConsensus( + ) { + return this._has_ignoreGapsinConsensus; + } + + /** + * 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 hasShowConsensusHistogram. + * + * @return true if at least one ShowConsensusHistogram has been + * added + */ + public boolean hasShowConsensusHistogram( + ) { + return this._has_showConsensusHistogram; + } + + /** + * Method hasShowSequenceLogo. + * + * @return true if at least one ShowSequenceLogo has been added + */ + public boolean hasShowSequenceLogo( + ) { + return this._has_showSequenceLogo; + } + + /** + * Method hasShowUnconserved. + * + * @return true if at least one ShowUnconserved has been added + */ + public boolean hasShowUnconserved( + ) { + return this._has_showUnconserved; + } + + /** + * Method hasStart. + * + * @return true if at least one Start has been added + */ + public boolean hasStart( + ) { + return this._has_start; + } + + /** + * Method hasTextCol1. + * + * @return true if at least one TextCol1 has been added + */ + public boolean hasTextCol1( + ) { + return this._has_textCol1; + } + + /** + * Method hasTextCol2. + * + * @return true if at least one TextCol2 has been added + */ + public boolean hasTextCol2( + ) { + return this._has_textCol2; + } + + /** + * Method hasTextColThreshold. + * + * @return true if at least one TextColThreshold has been added + */ + public boolean hasTextColThreshold( + ) { + return this._has_textColThreshold; + } + + /** + * 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; + } + + /** + * Returns the value of field 'ignoreGapsinConsensus'. + * + * @return the value of field 'IgnoreGapsinConsensus'. + */ + public boolean isIgnoreGapsinConsensus( + ) { + return this._ignoreGapsinConsensus; + } + + /** + * Returns the value of field 'showConsensusHistogram'. + * + * @return the value of field 'ShowConsensusHistogram'. + */ + public boolean isShowConsensusHistogram( + ) { + return this._showConsensusHistogram; + } + + /** + * Returns the value of field 'showSequenceLogo'. + * + * @return the value of field 'ShowSequenceLogo'. + */ + public boolean isShowSequenceLogo( + ) { + return this._showSequenceLogo; + } + + /** + * Returns the value of field 'showUnconserved'. + * + * @return the value of field 'ShowUnconserved'. + */ + public boolean isShowUnconserved( + ) { + return this._showUnconserved; + } + + /** + * 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 java.lang.String vSeq) { + boolean removed = _seqList.remove(vSeq); + return removed; + } + + /** + * Method removeSeqAt. + * + * @param index + * @return the element removed from the collection + */ + public java.lang.String removeSeqAt( + final int index) { + java.lang.Object obj = this._seqList.remove(index); + return (java.lang.String) obj; + } + + /** + * 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 'id'. The field 'id' has the + * following description: Optional sequence group ID (only + * needs to be unique for this alignment) + * + * + * @param id the value of field 'id'. + */ + public void setId( + final java.lang.String id) { + this._id = id; + } + + /** + * Sets the value of field 'ignoreGapsinConsensus'. + * + * @param ignoreGapsinConsensus the value of field + * 'ignoreGapsinConsensus'. + */ + public void setIgnoreGapsinConsensus( + final boolean ignoreGapsinConsensus) { + this._ignoreGapsinConsensus = ignoreGapsinConsensus; + this._has_ignoreGapsinConsensus = 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 java.lang.String 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, vSeq); + } + + /** + * + * + * @param vSeqArray + */ + public void setSeq( + final java.lang.String[] vSeqArray) { + //-- copy array + _seqList.clear(); + + for (int i = 0; i < vSeqArray.length; i++) { + this._seqList.add(vSeqArray[i]); + } + } + + /** + * Sets the value of field 'showConsensusHistogram'. + * + * @param showConsensusHistogram the value of field + * 'showConsensusHistogram'. + */ + public void setShowConsensusHistogram( + final boolean showConsensusHistogram) { + this._showConsensusHistogram = showConsensusHistogram; + this._has_showConsensusHistogram = true; + } + + /** + * Sets the value of field 'showSequenceLogo'. + * + * @param showSequenceLogo the value of field 'showSequenceLogo' + */ + public void setShowSequenceLogo( + final boolean showSequenceLogo) { + this._showSequenceLogo = showSequenceLogo; + this._has_showSequenceLogo = true; + } + + /** + * Sets the value of field 'showUnconserved'. + * + * @param showUnconserved the value of field 'showUnconserved'. + */ + public void setShowUnconserved( + final boolean showUnconserved) { + this._showUnconserved = showUnconserved; + this._has_showUnconserved = true; + } + + /** + * 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; + } + + /** + * Sets the value of field 'textCol1'. + * + * @param textCol1 the value of field 'textCol1'. + */ + public void setTextCol1( + final int textCol1) { + this._textCol1 = textCol1; + this._has_textCol1 = true; + } + + /** + * Sets the value of field 'textCol2'. + * + * @param textCol2 the value of field 'textCol2'. + */ + public void setTextCol2( + final int textCol2) { + this._textCol2 = textCol2; + this._has_textCol2 = true; + } + + /** + * Sets the value of field 'textColThreshold'. + * + * @param textColThreshold the value of field 'textColThreshold' + */ + public void setTextColThreshold( + final int textColThreshold) { + this._textColThreshold = textColThreshold; + this._has_textColThreshold = 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.schemabinding.version2.JGroup + */ + public static jalview.schemabinding.version2.JGroup unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.JGroup) Unmarshaller.unmarshal(jalview.schemabinding.version2.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/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java index cad210a..a5dc2f7 100755 --- a/src/jalview/schemabinding/version2/JSeq.java +++ b/src/jalview/schemabinding/version2/JSeq.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,847 +19,796 @@ import org.exolab.castor.xml.Unmarshaller; * * @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 java.lang.String _id; - - /** - * Field _hidden. - */ - private boolean _hidden; - - /** - * keeps track of state for field: _hidden - */ - private boolean _has_hidden; - - /** - * Field _featuresList. - */ - private java.util.Vector _featuresList; - - /** - * Field _pdbidsList. - */ - private java.util.Vector _pdbidsList; - - /** - * Field _hiddenSequencesList. - */ - private java.util.Vector _hiddenSequencesList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JSeq() - { - super(); - this._featuresList = new java.util.Vector(); - this._pdbidsList = new java.util.Vector(); - this._hiddenSequencesList = 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.schemabinding.version2.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.schemabinding.version2.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - this._featuresList.add(index, vFeatures); - } - - /** - * - * - * @param vHiddenSequences - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addHiddenSequences(final int vHiddenSequences) - throws java.lang.IndexOutOfBoundsException - { - this._hiddenSequencesList.addElement(new java.lang.Integer( - vHiddenSequences)); - } - - /** - * - * - * @param index - * @param vHiddenSequences - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addHiddenSequences(final int index, final int vHiddenSequences) - throws java.lang.IndexOutOfBoundsException - { - this._hiddenSequencesList.add(index, new java.lang.Integer( - vHiddenSequences)); - } - - /** - * - * - * @param vPdbids - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addPdbids(final jalview.schemabinding.version2.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.schemabinding.version2.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 deleteHidden() - { - this._has_hidden = false; - } - - /** - */ - public void deleteStart() - { - this._has_start = false; - } - - /** - * Method enumerateFeatures. - * - * @return an Enumeration over all jalview.schemabinding.version2.Features - * elements - */ - public java.util.Enumeration enumerateFeatures() - { - return this._featuresList.elements(); - } - - /** - * Method enumerateHiddenSequences. - * - * @return an Enumeration over all int elements - */ - public java.util.Enumeration enumerateHiddenSequences() - { - return this._hiddenSequencesList.elements(); - } - - /** - * Method enumeratePdbids. - * - * @return an Enumeration over all jalview.schemabinding.version2.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.schemabinding.version2.Features at the - * given index - */ - public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Features[] getFeatures() - { - jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0]; - return (jalview.schemabinding.version2.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 'hidden'. - * - * @return the value of field 'Hidden'. - */ - public boolean getHidden() - { - return this._hidden; - } - - /** - * Method getHiddenSequences. - * - * @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 getHiddenSequences(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._hiddenSequencesList.size()) - { - throw new IndexOutOfBoundsException( - "getHiddenSequences: Index value '" + index - + "' not in range [0.." - + (this._hiddenSequencesList.size() - 1) + "]"); - } - - return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue(); - } - - /** - * Method getHiddenSequences.Returns the contents of the collection in an - * Array. - * - * @return this collection as an Array - */ - public int[] getHiddenSequences() - { - int size = this._hiddenSequencesList.size(); - int[] array = new int[size]; - java.util.Iterator iter = _hiddenSequencesList.iterator(); - for (int index = 0; index < size; index++) - { - array[index] = ((java.lang.Integer) iter.next()).intValue(); - } - return array; - } - - /** - * Method getHiddenSequencesCount. - * - * @return the size of this collection - */ - public int getHiddenSequencesCount() - { - return this._hiddenSequencesList.size(); - } - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String 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.schemabinding.version2.Pdbids at the given - * index - */ - public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Pdbids[] getPdbids() - { - jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0]; - return (jalview.schemabinding.version2.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 hasHidden. - * - * @return true if at least one Hidden has been added - */ - public boolean hasHidden() - { - return this._has_hidden; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart() - { - return this._has_start; - } - - /** - * Returns the value of field 'hidden'. - * - * @return the value of field 'Hidden'. - */ - public boolean isHidden() - { - return this._hidden; - } - - /** - * 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 removeAllHiddenSequences() - { - this._hiddenSequencesList.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.schemabinding.version2.Features vFeatures) - { - boolean removed = _featuresList.remove(vFeatures); - return removed; - } - - /** - * Method removeFeaturesAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Features removeFeaturesAt( - final int index) - { - java.lang.Object obj = this._featuresList.remove(index); - return (jalview.schemabinding.version2.Features) obj; - } - - /** - * Method removeHiddenSequences. - * - * @param vHiddenSequences - * @return true if the object was removed from the collection. - */ - public boolean removeHiddenSequences(final int vHiddenSequences) - { - boolean removed = _hiddenSequencesList.remove(new java.lang.Integer( - vHiddenSequences)); - return removed; - } - - /** - * Method removeHiddenSequencesAt. - * - * @param index - * @return the element removed from the collection - */ - public int removeHiddenSequencesAt(final int index) - { - java.lang.Object obj = this._hiddenSequencesList.remove(index); - return ((java.lang.Integer) obj).intValue(); - } - - /** - * Method removePdbids. - * - * @param vPdbids - * @return true if the object was removed from the collection. - */ - public boolean removePdbids( - final jalview.schemabinding.version2.Pdbids vPdbids) - { - boolean removed = _pdbidsList.remove(vPdbids); - return removed; - } - - /** - * Method removePdbidsAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Pdbids removePdbidsAt( - final int index) - { - java.lang.Object obj = this._pdbidsList.remove(index); - return (jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Features[] vFeaturesArray) - { - // -- copy array - _featuresList.clear(); - - for (int i = 0; i < vFeaturesArray.length; i++) - { - this._featuresList.add(vFeaturesArray[i]); - } - } - - /** - * Sets the value of field 'hidden'. - * - * @param hidden - * the value of field 'hidden'. - */ - public void setHidden(final boolean hidden) - { - this._hidden = hidden; - this._has_hidden = true; - } - - /** - * - * - * @param index - * @param vHiddenSequences - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setHiddenSequences(final int index, final int vHiddenSequences) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._hiddenSequencesList.size()) - { - throw new IndexOutOfBoundsException( - "setHiddenSequences: Index value '" + index - + "' not in range [0.." - + (this._hiddenSequencesList.size() - 1) + "]"); - } - - this._hiddenSequencesList.set(index, new java.lang.Integer( - vHiddenSequences)); - } - - /** - * - * - * @param vHiddenSequencesArray - */ - public void setHiddenSequences(final int[] vHiddenSequencesArray) - { - // -- copy array - _hiddenSequencesList.clear(); - - for (int i = 0; i < vHiddenSequencesArray.length; i++) - { - this._hiddenSequencesList.add(new java.lang.Integer( - vHiddenSequencesArray[i])); - } - } - - /** - * 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 vPdbids - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setPdbids(final int index, - final jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.JSeq - */ - public static jalview.schemabinding.version2.JSeq unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal( - jalview.schemabinding.version2.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); - } +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 java.lang.String _id; + + /** + * Field _hidden. + */ + private boolean _hidden; + + /** + * keeps track of state for field: _hidden + */ + private boolean _has_hidden; + + /** + * Field _featuresList. + */ + private java.util.Vector _featuresList; + + /** + * Field _pdbidsList. + */ + private java.util.Vector _pdbidsList; + + /** + * Field _hiddenSequencesList. + */ + private java.util.Vector _hiddenSequencesList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JSeq() { + super(); + this._featuresList = new java.util.Vector(); + this._pdbidsList = new java.util.Vector(); + this._hiddenSequencesList = 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.schemabinding.version2.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.schemabinding.version2.Features vFeatures) + throws java.lang.IndexOutOfBoundsException { + this._featuresList.add(index, vFeatures); + } + + /** + * + * + * @param vHiddenSequences + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addHiddenSequences( + final int vHiddenSequences) + throws java.lang.IndexOutOfBoundsException { + this._hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences)); + } + + /** + * + * + * @param index + * @param vHiddenSequences + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addHiddenSequences( + final int index, + final int vHiddenSequences) + throws java.lang.IndexOutOfBoundsException { + this._hiddenSequencesList.add(index, new java.lang.Integer(vHiddenSequences)); + } + + /** + * + * + * @param vPdbids + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addPdbids( + final jalview.schemabinding.version2.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.schemabinding.version2.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 deleteHidden( + ) { + this._has_hidden= false; + } + + /** + */ + public void deleteStart( + ) { + this._has_start= false; + } + + /** + * Method enumerateFeatures. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.Features elements + */ + public java.util.Enumeration enumerateFeatures( + ) { + return this._featuresList.elements(); + } + + /** + * Method enumerateHiddenSequences. + * + * @return an Enumeration over all int elements + */ + public java.util.Enumeration enumerateHiddenSequences( + ) { + return this._hiddenSequencesList.elements(); + } + + /** + * Method enumeratePdbids. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.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.schemabinding.version2.Features at the given index + */ + public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Features[] getFeatures( + ) { + jalview.schemabinding.version2.Features[] array = new jalview.schemabinding.version2.Features[0]; + return (jalview.schemabinding.version2.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 'hidden'. + * + * @return the value of field 'Hidden'. + */ + public boolean getHidden( + ) { + return this._hidden; + } + + /** + * Method getHiddenSequences. + * + * @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 getHiddenSequences( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._hiddenSequencesList.size()) { + throw new IndexOutOfBoundsException("getHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]"); + } + + return ((java.lang.Integer) _hiddenSequencesList.get(index)).intValue(); + } + + /** + * Method getHiddenSequences.Returns the contents of the + * collection in an Array. + * + * @return this collection as an Array + */ + public int[] getHiddenSequences( + ) { + int size = this._hiddenSequencesList.size(); + int[] array = new int[size]; + java.util.Iterator iter = _hiddenSequencesList.iterator(); + for (int index = 0; index < size; index++) { + array[index] = ((java.lang.Integer) iter.next()).intValue(); + } + return array; + } + + /** + * Method getHiddenSequencesCount. + * + * @return the size of this collection + */ + public int getHiddenSequencesCount( + ) { + return this._hiddenSequencesList.size(); + } + + /** + * Returns the value of field 'id'. + * + * @return the value of field 'Id'. + */ + public java.lang.String 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.schemabinding.version2.Pdbids at the given index + */ + public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Pdbids[] getPdbids( + ) { + jalview.schemabinding.version2.Pdbids[] array = new jalview.schemabinding.version2.Pdbids[0]; + return (jalview.schemabinding.version2.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 hasHidden. + * + * @return true if at least one Hidden has been added + */ + public boolean hasHidden( + ) { + return this._has_hidden; + } + + /** + * Method hasStart. + * + * @return true if at least one Start has been added + */ + public boolean hasStart( + ) { + return this._has_start; + } + + /** + * Returns the value of field 'hidden'. + * + * @return the value of field 'Hidden'. + */ + public boolean isHidden( + ) { + return this._hidden; + } + + /** + * 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 removeAllHiddenSequences( + ) { + this._hiddenSequencesList.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.schemabinding.version2.Features vFeatures) { + boolean removed = _featuresList.remove(vFeatures); + return removed; + } + + /** + * Method removeFeaturesAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Features removeFeaturesAt( + final int index) { + java.lang.Object obj = this._featuresList.remove(index); + return (jalview.schemabinding.version2.Features) obj; + } + + /** + * Method removeHiddenSequences. + * + * @param vHiddenSequences + * @return true if the object was removed from the collection. + */ + public boolean removeHiddenSequences( + final int vHiddenSequences) { + boolean removed = _hiddenSequencesList.remove(new java.lang.Integer(vHiddenSequences)); + return removed; + } + + /** + * Method removeHiddenSequencesAt. + * + * @param index + * @return the element removed from the collection + */ + public int removeHiddenSequencesAt( + final int index) { + java.lang.Object obj = this._hiddenSequencesList.remove(index); + return ((java.lang.Integer) obj).intValue(); + } + + /** + * Method removePdbids. + * + * @param vPdbids + * @return true if the object was removed from the collection. + */ + public boolean removePdbids( + final jalview.schemabinding.version2.Pdbids vPdbids) { + boolean removed = _pdbidsList.remove(vPdbids); + return removed; + } + + /** + * Method removePdbidsAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Pdbids removePdbidsAt( + final int index) { + java.lang.Object obj = this._pdbidsList.remove(index); + return (jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Features[] vFeaturesArray) { + //-- copy array + _featuresList.clear(); + + for (int i = 0; i < vFeaturesArray.length; i++) { + this._featuresList.add(vFeaturesArray[i]); + } + } + + /** + * Sets the value of field 'hidden'. + * + * @param hidden the value of field 'hidden'. + */ + public void setHidden( + final boolean hidden) { + this._hidden = hidden; + this._has_hidden = true; + } + + /** + * + * + * @param index + * @param vHiddenSequences + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setHiddenSequences( + final int index, + final int vHiddenSequences) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._hiddenSequencesList.size()) { + throw new IndexOutOfBoundsException("setHiddenSequences: Index value '" + index + "' not in range [0.." + (this._hiddenSequencesList.size() - 1) + "]"); + } + + this._hiddenSequencesList.set(index, new java.lang.Integer(vHiddenSequences)); + } + + /** + * + * + * @param vHiddenSequencesArray + */ + public void setHiddenSequences( + final int[] vHiddenSequencesArray) { + //-- copy array + _hiddenSequencesList.clear(); + + for (int i = 0; i < vHiddenSequencesArray.length; i++) { + this._hiddenSequencesList.add(new java.lang.Integer(vHiddenSequencesArray[i])); + } + } + + /** + * 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 vPdbids + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setPdbids( + final int index, + final jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.JSeq + */ + public static jalview.schemabinding.version2.JSeq unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.JSeq) Unmarshaller.unmarshal(jalview.schemabinding.version2.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/schemabinding/version2/JalviewModel.java b/src/jalview/schemabinding/version2/JalviewModel.java index ba483e6..f7e049a 100755 --- a/src/jalview/schemabinding/version2/JalviewModel.java +++ b/src/jalview/schemabinding/version2/JalviewModel.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,217 +19,203 @@ import org.exolab.castor.xml.Unmarshaller; * * @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.schemabinding.version2.VamsasModel _vamsasModel; - - /** - * Field _jalviewModelSequence. - */ - private jalview.schemabinding.version2.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.schemabinding.version2.JalviewModelSequence getJalviewModelSequence() - { - return this._jalviewModelSequence; - } - - /** - * Returns the value of field 'vamsasModel'. - * - * @return the value of field 'VamsasModel'. - */ - public jalview.schemabinding.version2.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; +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.schemabinding.version2.VamsasModel _vamsasModel; + + /** + * Field _jalviewModelSequence. + */ + private jalview.schemabinding.version2.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.schemabinding.version2.JalviewModelSequence getJalviewModelSequence( + ) { + return this._jalviewModelSequence; + } + + /** + * Returns the value of field 'vamsasModel'. + * + * @return the value of field 'VamsasModel'. + */ + public jalview.schemabinding.version2.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.schemabinding.version2.JalviewModelSequence jalviewModelSequence) { + this._jalviewModelSequence = jalviewModelSequence; + } + + /** + * Sets the value of field 'vamsasModel'. + * + * @param vamsasModel the value of field 'vamsasModel'. + */ + public void setVamsasModel( + final jalview.schemabinding.version2.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.schemabinding.version2.JalviewModel + */ + public static jalview.schemabinding.version2.JalviewModel unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.JalviewModel) Unmarshaller.unmarshal(jalview.schemabinding.version2.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); } - 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.schemabinding.version2.JalviewModelSequence jalviewModelSequence) - { - this._jalviewModelSequence = jalviewModelSequence; - } - - /** - * Sets the value of field 'vamsasModel'. - * - * @param vamsasModel - * the value of field 'vamsasModel'. - */ - public void setVamsasModel( - final jalview.schemabinding.version2.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.schemabinding.version2.JalviewModel - */ - public static jalview.schemabinding.version2.JalviewModel unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.JalviewModel) Unmarshaller - .unmarshal(jalview.schemabinding.version2.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/schemabinding/version2/JalviewModelSequence.java b/src/jalview/schemabinding/version2/JalviewModelSequence.java index 61a74ff..cb66b37 100755 --- a/src/jalview/schemabinding/version2/JalviewModelSequence.java +++ b/src/jalview/schemabinding/version2/JalviewModelSequence.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,968 +19,907 @@ import org.exolab.castor.xml.Unmarshaller; * * @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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - this._viewportList.add(index, vViewport); - } - - /** - * Method enumerateJGroup. - * - * @return an Enumeration over all jalview.schemabinding.version2.JGroup - * elements - */ - public java.util.Enumeration enumerateJGroup() - { - return this._JGroupList.elements(); - } - - /** - * Method enumerateJSeq. - * - * @return an Enumeration over all jalview.schemabinding.version2.JSeq - * elements - */ - public java.util.Enumeration enumerateJSeq() - { - return this._JSeqList.elements(); - } - - /** - * Method enumerateTree. - * - * @return an Enumeration over all jalview.schemabinding.version2.Tree - * elements - */ - public java.util.Enumeration enumerateTree() - { - return this._treeList.elements(); - } - - /** - * Method enumerateUserColours. - * - * @return an Enumeration over all jalview.schemabinding.version2.UserColours - * elements - */ - public java.util.Enumeration enumerateUserColours() - { - return this._userColoursList.elements(); - } - - /** - * Method enumerateViewport. - * - * @return an Enumeration over all jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.JGroup at the given - * index - */ - public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.JGroup[] getJGroup() - { - jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0]; - return (jalview.schemabinding.version2.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.schemabinding.version2.JSeq at the given - * index - */ - public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.JSeq[] getJSeq() - { - jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0]; - return (jalview.schemabinding.version2.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.schemabinding.version2.Tree at the given - * index - */ - public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Tree[] getTree() - { - jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0]; - return (jalview.schemabinding.version2.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.schemabinding.version2.UserColours at the - * given index - */ - public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.UserColours[] getUserColours() - { - jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0]; - return (jalview.schemabinding.version2.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.schemabinding.version2.Viewport at the - * given index - */ - public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Viewport[] getViewport() - { - jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0]; - return (jalview.schemabinding.version2.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.schemabinding.version2.JGroup vJGroup) - { - boolean removed = _JGroupList.remove(vJGroup); - return removed; - } - - /** - * Method removeJGroupAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.JGroup removeJGroupAt( - final int index) - { - java.lang.Object obj = this._JGroupList.remove(index); - return (jalview.schemabinding.version2.JGroup) obj; - } - - /** - * Method removeJSeq. - * - * @param vJSeq - * @return true if the object was removed from the collection. - */ - public boolean removeJSeq(final jalview.schemabinding.version2.JSeq vJSeq) - { - boolean removed = _JSeqList.remove(vJSeq); - return removed; - } - - /** - * Method removeJSeqAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.JSeq removeJSeqAt(final int index) - { - java.lang.Object obj = this._JSeqList.remove(index); - return (jalview.schemabinding.version2.JSeq) obj; - } - - /** - * Method removeTree. - * - * @param vTree - * @return true if the object was removed from the collection. - */ - public boolean removeTree(final jalview.schemabinding.version2.Tree vTree) - { - boolean removed = _treeList.remove(vTree); - return removed; - } - - /** - * Method removeTreeAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Tree removeTreeAt(final int index) - { - java.lang.Object obj = this._treeList.remove(index); - return (jalview.schemabinding.version2.Tree) obj; - } - - /** - * Method removeUserColours. - * - * @param vUserColours - * @return true if the object was removed from the collection. - */ - public boolean removeUserColours( - final jalview.schemabinding.version2.UserColours vUserColours) - { - boolean removed = _userColoursList.remove(vUserColours); - return removed; - } - - /** - * Method removeUserColoursAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.UserColours removeUserColoursAt( - final int index) - { - java.lang.Object obj = this._userColoursList.remove(index); - return (jalview.schemabinding.version2.UserColours) obj; - } - - /** - * Method removeViewport. - * - * @param vViewport - * @return true if the object was removed from the collection. - */ - public boolean removeViewport( - final jalview.schemabinding.version2.Viewport vViewport) - { - boolean removed = _viewportList.remove(vViewport); - return removed; - } - - /** - * Method removeViewportAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Viewport removeViewportAt( - final int index) - { - java.lang.Object obj = this._viewportList.remove(index); - return (jalview.schemabinding.version2.Viewport) obj; - } - - /** - * Sets the value of field 'featureSettings'. - * - * @param featureSettings - * the value of field 'featureSettings'. - */ - public void setFeatureSettings( - final jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.JalviewModelSequence - */ - public static jalview.schemabinding.version2.JalviewModelSequence unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.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); - } +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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Viewport vViewport) + throws java.lang.IndexOutOfBoundsException { + this._viewportList.add(index, vViewport); + } + + /** + * Method enumerateJGroup. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.JGroup elements + */ + public java.util.Enumeration enumerateJGroup( + ) { + return this._JGroupList.elements(); + } + + /** + * Method enumerateJSeq. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.JSeq elements + */ + public java.util.Enumeration enumerateJSeq( + ) { + return this._JSeqList.elements(); + } + + /** + * Method enumerateTree. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.Tree elements + */ + public java.util.Enumeration enumerateTree( + ) { + return this._treeList.elements(); + } + + /** + * Method enumerateUserColours. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.UserColours elements + */ + public java.util.Enumeration enumerateUserColours( + ) { + return this._userColoursList.elements(); + } + + /** + * Method enumerateViewport. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.JGroup at the given index + */ + public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.JGroup[] getJGroup( + ) { + jalview.schemabinding.version2.JGroup[] array = new jalview.schemabinding.version2.JGroup[0]; + return (jalview.schemabinding.version2.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.schemabinding.version2.JSeq + * at the given index + */ + public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.JSeq[] getJSeq( + ) { + jalview.schemabinding.version2.JSeq[] array = new jalview.schemabinding.version2.JSeq[0]; + return (jalview.schemabinding.version2.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.schemabinding.version2.Tree + * at the given index + */ + public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Tree[] getTree( + ) { + jalview.schemabinding.version2.Tree[] array = new jalview.schemabinding.version2.Tree[0]; + return (jalview.schemabinding.version2.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.schemabinding.version2.UserColours at the given index + */ + public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.UserColours[] getUserColours( + ) { + jalview.schemabinding.version2.UserColours[] array = new jalview.schemabinding.version2.UserColours[0]; + return (jalview.schemabinding.version2.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.schemabinding.version2.Viewport at the given index + */ + public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Viewport[] getViewport( + ) { + jalview.schemabinding.version2.Viewport[] array = new jalview.schemabinding.version2.Viewport[0]; + return (jalview.schemabinding.version2.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.schemabinding.version2.JGroup vJGroup) { + boolean removed = _JGroupList.remove(vJGroup); + return removed; + } + + /** + * Method removeJGroupAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.JGroup removeJGroupAt( + final int index) { + java.lang.Object obj = this._JGroupList.remove(index); + return (jalview.schemabinding.version2.JGroup) obj; + } + + /** + * Method removeJSeq. + * + * @param vJSeq + * @return true if the object was removed from the collection. + */ + public boolean removeJSeq( + final jalview.schemabinding.version2.JSeq vJSeq) { + boolean removed = _JSeqList.remove(vJSeq); + return removed; + } + + /** + * Method removeJSeqAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.JSeq removeJSeqAt( + final int index) { + java.lang.Object obj = this._JSeqList.remove(index); + return (jalview.schemabinding.version2.JSeq) obj; + } + + /** + * Method removeTree. + * + * @param vTree + * @return true if the object was removed from the collection. + */ + public boolean removeTree( + final jalview.schemabinding.version2.Tree vTree) { + boolean removed = _treeList.remove(vTree); + return removed; + } + + /** + * Method removeTreeAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Tree removeTreeAt( + final int index) { + java.lang.Object obj = this._treeList.remove(index); + return (jalview.schemabinding.version2.Tree) obj; + } + + /** + * Method removeUserColours. + * + * @param vUserColours + * @return true if the object was removed from the collection. + */ + public boolean removeUserColours( + final jalview.schemabinding.version2.UserColours vUserColours) { + boolean removed = _userColoursList.remove(vUserColours); + return removed; + } + + /** + * Method removeUserColoursAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.UserColours removeUserColoursAt( + final int index) { + java.lang.Object obj = this._userColoursList.remove(index); + return (jalview.schemabinding.version2.UserColours) obj; + } + + /** + * Method removeViewport. + * + * @param vViewport + * @return true if the object was removed from the collection. + */ + public boolean removeViewport( + final jalview.schemabinding.version2.Viewport vViewport) { + boolean removed = _viewportList.remove(vViewport); + return removed; + } + + /** + * Method removeViewportAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Viewport removeViewportAt( + final int index) { + java.lang.Object obj = this._viewportList.remove(index); + return (jalview.schemabinding.version2.Viewport) obj; + } + + /** + * Sets the value of field 'featureSettings'. + * + * @param featureSettings the value of field 'featureSettings'. + */ + public void setFeatureSettings( + final jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.JalviewModelSequence + */ + public static jalview.schemabinding.version2.JalviewModelSequence unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.JalviewModelSequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.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/schemabinding/version2/JalviewUserColours.java b/src/jalview/schemabinding/version2/JalviewUserColours.java index 36e09f1..28541e7 100755 --- a/src/jalview/schemabinding/version2/JalviewUserColours.java +++ b/src/jalview/schemabinding/version2/JalviewUserColours.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,328 +19,313 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class JalviewUserColours implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _schemeName. - */ - private java.lang.String _schemeName; - - /** - * Jalview colour scheme document version. - * - */ - private java.lang.String _version; - - /** - * 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) + "]"); +public class JalviewUserColours implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _schemeName. + */ + private java.lang.String _schemeName; + + /** + * Jalview colour scheme document version. + * + */ + private java.lang.String _version; + + /** + * Field _colourList. + */ + private java.util.Vector _colourList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JalviewUserColours() { + super(); + this._colourList = new java.util.Vector(); } - 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; - } - - /** - * Returns the value of field 'version'. The field 'version' has the following - * description: Jalview colour scheme document 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; + + //-----------/ + //- 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); } - 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 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 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) + "]"); + public int getColourCount( + ) { + return this._colourList.size(); } - 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]); + /** + * Returns the value of field 'schemeName'. + * + * @return the value of field 'SchemeName'. + */ + public java.lang.String getSchemeName( + ) { + return this._schemeName; + } + + /** + * Returns the value of field 'version'. The field 'version' + * has the following description: Jalview colour scheme + * document 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); + } + + /** + */ + 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; + } + + /** + * Sets the value of field 'version'. The field 'version' has + * the following description: Jalview colour scheme document + * 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.schemabinding.version2.JalviewUserColours + */ + public static jalview.schemabinding.version2.JalviewUserColours unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.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); } - } - - /** - * Sets the value of field 'schemeName'. - * - * @param schemeName - * the value of field 'schemeName'. - */ - public void setSchemeName(final java.lang.String schemeName) - { - this._schemeName = schemeName; - } - - /** - * Sets the value of field 'version'. The field 'version' has the following - * description: Jalview colour scheme document 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.schemabinding.version2.JalviewUserColours - */ - public static jalview.schemabinding.version2.JalviewUserColours unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.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/schemabinding/version2/MapListFrom.java b/src/jalview/schemabinding/version2/MapListFrom.java index 34714b6..acfe18e 100644 --- a/src/jalview/schemabinding/version2/MapListFrom.java +++ b/src/jalview/schemabinding/version2/MapListFrom.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,209 +19,198 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class MapListFrom 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; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MapListFrom() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteEnd() - { - this._has_end = false; - } - - /** - */ - public void deleteStart() - { - this._has_start = false; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd() - { - return this._end; - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart() - { - return this._start; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd() - { - return this._has_end; - } - - /** - * 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; +public class MapListFrom 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; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public MapListFrom() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteEnd( + ) { + this._has_end= false; + } + + /** + */ + public void deleteStart( + ) { + this._has_start= false; + } + + /** + * Returns the value of field 'end'. + * + * @return the value of field 'End'. + */ + public int getEnd( + ) { + return this._end; + } + + /** + * Returns the value of field 'start'. + * + * @return the value of field 'Start'. + */ + public int getStart( + ) { + return this._start; + } + + /** + * Method hasEnd. + * + * @return true if at least one End has been added + */ + public boolean hasEnd( + ) { + return this._has_end; + } + + /** + * 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); + } + + /** + * 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 '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.schemabinding.version2.MapListFrom + */ + public static jalview.schemabinding.version2.MapListFrom unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.MapListFrom) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListFrom.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); } - 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 '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 '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.schemabinding.version2.MapListFrom - */ - public static jalview.schemabinding.version2.MapListFrom unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.MapListFrom) Unmarshaller - .unmarshal(jalview.schemabinding.version2.MapListFrom.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/schemabinding/version2/MapListTo.java b/src/jalview/schemabinding/version2/MapListTo.java index 5b547ee..8c3a7e0 100644 --- a/src/jalview/schemabinding/version2/MapListTo.java +++ b/src/jalview/schemabinding/version2/MapListTo.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,209 +19,198 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class MapListTo 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; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MapListTo() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteEnd() - { - this._has_end = false; - } - - /** - */ - public void deleteStart() - { - this._has_start = false; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd() - { - return this._end; - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart() - { - return this._start; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd() - { - return this._has_end; - } - - /** - * 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; +public class MapListTo 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; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public MapListTo() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteEnd( + ) { + this._has_end= false; + } + + /** + */ + public void deleteStart( + ) { + this._has_start= false; + } + + /** + * Returns the value of field 'end'. + * + * @return the value of field 'End'. + */ + public int getEnd( + ) { + return this._end; + } + + /** + * Returns the value of field 'start'. + * + * @return the value of field 'Start'. + */ + public int getStart( + ) { + return this._start; + } + + /** + * Method hasEnd. + * + * @return true if at least one End has been added + */ + public boolean hasEnd( + ) { + return this._has_end; + } + + /** + * 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); + } + + /** + * 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 '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.schemabinding.version2.MapListTo + */ + public static jalview.schemabinding.version2.MapListTo unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.MapListTo) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListTo.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); } - 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 '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 '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.schemabinding.version2.MapListTo - */ - public static jalview.schemabinding.version2.MapListTo unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.MapListTo) Unmarshaller - .unmarshal(jalview.schemabinding.version2.MapListTo.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/schemabinding/version2/MapListType.java b/src/jalview/schemabinding/version2/MapListType.java index a4097a5..21d56e7 100644 --- a/src/jalview/schemabinding/version2/MapListType.java +++ b/src/jalview/schemabinding/version2/MapListType.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -27,581 +17,566 @@ import org.exolab.castor.xml.Unmarshaller; /** * developed after mapRangeType from * http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes - * - * This effectively represents a java.util.MapList object - * + * + * This effectively represents a java.util.MapList object + * * * @version $Revision$ $Date$ */ -public class MapListType implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * number of dictionary symbol widths involved in each mapped position on this - * sequence (for example, 3 for a dna sequence exon region that is being - * mapped to a protein sequence). This is optional, since the unit can be - * usually be inferred from the dictionary type of each sequence involved in - * the mapping. - */ - private long _mapFromUnit; - - /** - * keeps track of state for field: _mapFromUnit - */ - private boolean _has_mapFromUnit; - - /** - * number of dictionary symbol widths involved in each mapped position on this - * sequence (for example, 3 for a dna sequence exon region that is being - * mapped to a protein sequence). This is optional, since the unit can be - * usually be inferred from the dictionary type of each sequence involved in - * the mapping. - */ - private long _mapToUnit; - - /** - * keeps track of state for field: _mapToUnit - */ - private boolean _has_mapToUnit; - - /** - * a region from start to end inclusive - */ - private java.util.Vector _mapListFromList; - - /** - * a region from start to end inclusive - */ - private java.util.Vector _mapListToList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MapListType() - { - super(); - this._mapListFromList = new java.util.Vector(); - this._mapListToList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vMapListFrom - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addMapListFrom( - final jalview.schemabinding.version2.MapListFrom vMapListFrom) - throws java.lang.IndexOutOfBoundsException - { - this._mapListFromList.addElement(vMapListFrom); - } - - /** - * - * - * @param index - * @param vMapListFrom - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addMapListFrom(final int index, - final jalview.schemabinding.version2.MapListFrom vMapListFrom) - throws java.lang.IndexOutOfBoundsException - { - this._mapListFromList.add(index, vMapListFrom); - } - - /** - * - * - * @param vMapListTo - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addMapListTo( - final jalview.schemabinding.version2.MapListTo vMapListTo) - throws java.lang.IndexOutOfBoundsException - { - this._mapListToList.addElement(vMapListTo); - } - - /** - * - * - * @param index - * @param vMapListTo - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addMapListTo(final int index, - final jalview.schemabinding.version2.MapListTo vMapListTo) - throws java.lang.IndexOutOfBoundsException - { - this._mapListToList.add(index, vMapListTo); - } - - /** - */ - public void deleteMapFromUnit() - { - this._has_mapFromUnit = false; - } - - /** - */ - public void deleteMapToUnit() - { - this._has_mapToUnit = false; - } - - /** - * Method enumerateMapListFrom. - * - * @return an Enumeration over all jalview.schemabinding.version2.MapListFrom - * elements - */ - public java.util.Enumeration enumerateMapListFrom() - { - return this._mapListFromList.elements(); - } - - /** - * Method enumerateMapListTo. - * - * @return an Enumeration over all jalview.schemabinding.version2.MapListTo - * elements - */ - public java.util.Enumeration enumerateMapListTo() - { - return this._mapListToList.elements(); - } - - /** - * Returns the value of field 'mapFromUnit'. The field 'mapFromUnit' has the - * following description: number of dictionary symbol widths involved in each - * mapped position on this sequence (for example, 3 for a dna sequence exon - * region that is being mapped to a protein sequence). This is optional, since - * the unit can be usually be inferred from the dictionary type of each - * sequence involved in the mapping. - * - * @return the value of field 'MapFromUnit'. - */ - public long getMapFromUnit() - { - return this._mapFromUnit; - } - - /** - * Method getMapListFrom. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.MapListFrom at the - * given index - */ - public jalview.schemabinding.version2.MapListFrom getMapListFrom( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._mapListFromList.size()) - { - throw new IndexOutOfBoundsException("getMapListFrom: Index value '" - + index + "' not in range [0.." - + (this._mapListFromList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.MapListFrom) _mapListFromList - .get(index); - } - - /** - * Method getMapListFrom.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.schemabinding.version2.MapListFrom[] getMapListFrom() - { - jalview.schemabinding.version2.MapListFrom[] array = new jalview.schemabinding.version2.MapListFrom[0]; - return (jalview.schemabinding.version2.MapListFrom[]) this._mapListFromList - .toArray(array); - } - - /** - * Method getMapListFromCount. - * - * @return the size of this collection - */ - public int getMapListFromCount() - { - return this._mapListFromList.size(); - } - - /** - * Method getMapListTo. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.MapListTo at the - * given index - */ - public jalview.schemabinding.version2.MapListTo getMapListTo( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._mapListToList.size()) - { - throw new IndexOutOfBoundsException("getMapListTo: Index value '" - + index + "' not in range [0.." - + (this._mapListToList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.MapListTo) _mapListToList - .get(index); - } - - /** - * Method getMapListTo.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.schemabinding.version2.MapListTo[] getMapListTo() - { - jalview.schemabinding.version2.MapListTo[] array = new jalview.schemabinding.version2.MapListTo[0]; - return (jalview.schemabinding.version2.MapListTo[]) this._mapListToList - .toArray(array); - } - - /** - * Method getMapListToCount. - * - * @return the size of this collection - */ - public int getMapListToCount() - { - return this._mapListToList.size(); - } - - /** - * Returns the value of field 'mapToUnit'. The field 'mapToUnit' has the - * following description: number of dictionary symbol widths involved in each - * mapped position on this sequence (for example, 3 for a dna sequence exon - * region that is being mapped to a protein sequence). This is optional, since - * the unit can be usually be inferred from the dictionary type of each - * sequence involved in the mapping. - * - * @return the value of field 'MapToUnit'. - */ - public long getMapToUnit() - { - return this._mapToUnit; - } - - /** - * Method hasMapFromUnit. - * - * @return true if at least one MapFromUnit has been added - */ - public boolean hasMapFromUnit() - { - return this._has_mapFromUnit; - } - - /** - * Method hasMapToUnit. - * - * @return true if at least one MapToUnit has been added - */ - public boolean hasMapToUnit() - { - return this._has_mapToUnit; - } - - /** - * 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 removeAllMapListFrom() - { - this._mapListFromList.clear(); - } - - /** - */ - public void removeAllMapListTo() - { - this._mapListToList.clear(); - } - - /** - * Method removeMapListFrom. - * - * @param vMapListFrom - * @return true if the object was removed from the collection. - */ - public boolean removeMapListFrom( - final jalview.schemabinding.version2.MapListFrom vMapListFrom) - { - boolean removed = _mapListFromList.remove(vMapListFrom); - return removed; - } - - /** - * Method removeMapListFromAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.MapListFrom removeMapListFromAt( - final int index) - { - java.lang.Object obj = this._mapListFromList.remove(index); - return (jalview.schemabinding.version2.MapListFrom) obj; - } - - /** - * Method removeMapListTo. - * - * @param vMapListTo - * @return true if the object was removed from the collection. - */ - public boolean removeMapListTo( - final jalview.schemabinding.version2.MapListTo vMapListTo) - { - boolean removed = _mapListToList.remove(vMapListTo); - return removed; - } - - /** - * Method removeMapListToAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.MapListTo removeMapListToAt( - final int index) - { - java.lang.Object obj = this._mapListToList.remove(index); - return (jalview.schemabinding.version2.MapListTo) obj; - } - - /** - * Sets the value of field 'mapFromUnit'. The field 'mapFromUnit' has the - * following description: number of dictionary symbol widths involved in each - * mapped position on this sequence (for example, 3 for a dna sequence exon - * region that is being mapped to a protein sequence). This is optional, since - * the unit can be usually be inferred from the dictionary type of each - * sequence involved in the mapping. - * - * @param mapFromUnit - * the value of field 'mapFromUnit'. - */ - public void setMapFromUnit(final long mapFromUnit) - { - this._mapFromUnit = mapFromUnit; - this._has_mapFromUnit = true; - } - - /** - * - * - * @param index - * @param vMapListFrom - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setMapListFrom(final int index, - final jalview.schemabinding.version2.MapListFrom vMapListFrom) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._mapListFromList.size()) - { - throw new IndexOutOfBoundsException("setMapListFrom: Index value '" - + index + "' not in range [0.." - + (this._mapListFromList.size() - 1) + "]"); - } - - this._mapListFromList.set(index, vMapListFrom); - } - - /** - * - * - * @param vMapListFromArray - */ - public void setMapListFrom( - final jalview.schemabinding.version2.MapListFrom[] vMapListFromArray) - { - // -- copy array - _mapListFromList.clear(); - - for (int i = 0; i < vMapListFromArray.length; i++) - { - this._mapListFromList.add(vMapListFromArray[i]); - } - } - - /** - * - * - * @param index - * @param vMapListTo - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setMapListTo(final int index, - final jalview.schemabinding.version2.MapListTo vMapListTo) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._mapListToList.size()) - { - throw new IndexOutOfBoundsException("setMapListTo: Index value '" - + index + "' not in range [0.." - + (this._mapListToList.size() - 1) + "]"); - } - - this._mapListToList.set(index, vMapListTo); - } - - /** - * - * - * @param vMapListToArray - */ - public void setMapListTo( - final jalview.schemabinding.version2.MapListTo[] vMapListToArray) - { - // -- copy array - _mapListToList.clear(); - - for (int i = 0; i < vMapListToArray.length; i++) - { - this._mapListToList.add(vMapListToArray[i]); - } - } - - /** - * Sets the value of field 'mapToUnit'. The field 'mapToUnit' has the - * following description: number of dictionary symbol widths involved in each - * mapped position on this sequence (for example, 3 for a dna sequence exon - * region that is being mapped to a protein sequence). This is optional, since - * the unit can be usually be inferred from the dictionary type of each - * sequence involved in the mapping. - * - * @param mapToUnit - * the value of field 'mapToUnit'. - */ - public void setMapToUnit(final long mapToUnit) - { - this._mapToUnit = mapToUnit; - this._has_mapToUnit = 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.schemabinding.version2.MapListType - */ - public static jalview.schemabinding.version2.MapListType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.MapListType) Unmarshaller - .unmarshal(jalview.schemabinding.version2.MapListType.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); - } +public class MapListType implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * number of dictionary symbol widths involved in each + * mapped position on this sequence (for example, 3 for a dna + * sequence exon + * region that is being mapped to a protein sequence). This is + * optional, + * since the unit can be usually be inferred from the + * dictionary type of + * each sequence involved in the mapping. + */ + private long _mapFromUnit; + + /** + * keeps track of state for field: _mapFromUnit + */ + private boolean _has_mapFromUnit; + + /** + * number of dictionary symbol widths involved in each + * mapped position on this sequence (for example, 3 for a dna + * sequence exon + * region that is being mapped to a protein sequence). This is + * optional, + * since the unit can be usually be inferred from the + * dictionary type of + * each sequence involved in the mapping. + */ + private long _mapToUnit; + + /** + * keeps track of state for field: _mapToUnit + */ + private boolean _has_mapToUnit; + + /** + * a region from start to end inclusive + */ + private java.util.Vector _mapListFromList; + + /** + * a region from start to end inclusive + */ + private java.util.Vector _mapListToList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public MapListType() { + super(); + this._mapListFromList = new java.util.Vector(); + this._mapListToList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vMapListFrom + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addMapListFrom( + final jalview.schemabinding.version2.MapListFrom vMapListFrom) + throws java.lang.IndexOutOfBoundsException { + this._mapListFromList.addElement(vMapListFrom); + } + + /** + * + * + * @param index + * @param vMapListFrom + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addMapListFrom( + final int index, + final jalview.schemabinding.version2.MapListFrom vMapListFrom) + throws java.lang.IndexOutOfBoundsException { + this._mapListFromList.add(index, vMapListFrom); + } + + /** + * + * + * @param vMapListTo + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addMapListTo( + final jalview.schemabinding.version2.MapListTo vMapListTo) + throws java.lang.IndexOutOfBoundsException { + this._mapListToList.addElement(vMapListTo); + } + + /** + * + * + * @param index + * @param vMapListTo + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addMapListTo( + final int index, + final jalview.schemabinding.version2.MapListTo vMapListTo) + throws java.lang.IndexOutOfBoundsException { + this._mapListToList.add(index, vMapListTo); + } + + /** + */ + public void deleteMapFromUnit( + ) { + this._has_mapFromUnit= false; + } + + /** + */ + public void deleteMapToUnit( + ) { + this._has_mapToUnit= false; + } + + /** + * Method enumerateMapListFrom. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.MapListFrom elements + */ + public java.util.Enumeration enumerateMapListFrom( + ) { + return this._mapListFromList.elements(); + } + + /** + * Method enumerateMapListTo. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.MapListTo elements + */ + public java.util.Enumeration enumerateMapListTo( + ) { + return this._mapListToList.elements(); + } + + /** + * Returns the value of field 'mapFromUnit'. The field + * 'mapFromUnit' has the following description: number of + * dictionary symbol widths involved in each + * mapped position on this sequence (for example, 3 for a dna + * sequence exon + * region that is being mapped to a protein sequence). This is + * optional, + * since the unit can be usually be inferred from the + * dictionary type of + * each sequence involved in the mapping. + * + * @return the value of field 'MapFromUnit'. + */ + public long getMapFromUnit( + ) { + return this._mapFromUnit; + } + + /** + * Method getMapListFrom. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.MapListFrom at the given index + */ + public jalview.schemabinding.version2.MapListFrom getMapListFrom( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._mapListFromList.size()) { + throw new IndexOutOfBoundsException("getMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.MapListFrom) _mapListFromList.get(index); + } + + /** + * Method getMapListFrom.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.schemabinding.version2.MapListFrom[] getMapListFrom( + ) { + jalview.schemabinding.version2.MapListFrom[] array = new jalview.schemabinding.version2.MapListFrom[0]; + return (jalview.schemabinding.version2.MapListFrom[]) this._mapListFromList.toArray(array); + } + + /** + * Method getMapListFromCount. + * + * @return the size of this collection + */ + public int getMapListFromCount( + ) { + return this._mapListFromList.size(); + } + + /** + * Method getMapListTo. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.MapListTo at the given index + */ + public jalview.schemabinding.version2.MapListTo getMapListTo( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._mapListToList.size()) { + throw new IndexOutOfBoundsException("getMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.MapListTo) _mapListToList.get(index); + } + + /** + * Method getMapListTo.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.schemabinding.version2.MapListTo[] getMapListTo( + ) { + jalview.schemabinding.version2.MapListTo[] array = new jalview.schemabinding.version2.MapListTo[0]; + return (jalview.schemabinding.version2.MapListTo[]) this._mapListToList.toArray(array); + } + + /** + * Method getMapListToCount. + * + * @return the size of this collection + */ + public int getMapListToCount( + ) { + return this._mapListToList.size(); + } + + /** + * Returns the value of field 'mapToUnit'. The field + * 'mapToUnit' has the following description: number of + * dictionary symbol widths involved in each + * mapped position on this sequence (for example, 3 for a dna + * sequence exon + * region that is being mapped to a protein sequence). This is + * optional, + * since the unit can be usually be inferred from the + * dictionary type of + * each sequence involved in the mapping. + * + * @return the value of field 'MapToUnit'. + */ + public long getMapToUnit( + ) { + return this._mapToUnit; + } + + /** + * Method hasMapFromUnit. + * + * @return true if at least one MapFromUnit has been added + */ + public boolean hasMapFromUnit( + ) { + return this._has_mapFromUnit; + } + + /** + * Method hasMapToUnit. + * + * @return true if at least one MapToUnit has been added + */ + public boolean hasMapToUnit( + ) { + return this._has_mapToUnit; + } + + /** + * 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 removeAllMapListFrom( + ) { + this._mapListFromList.clear(); + } + + /** + */ + public void removeAllMapListTo( + ) { + this._mapListToList.clear(); + } + + /** + * Method removeMapListFrom. + * + * @param vMapListFrom + * @return true if the object was removed from the collection. + */ + public boolean removeMapListFrom( + final jalview.schemabinding.version2.MapListFrom vMapListFrom) { + boolean removed = _mapListFromList.remove(vMapListFrom); + return removed; + } + + /** + * Method removeMapListFromAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.MapListFrom removeMapListFromAt( + final int index) { + java.lang.Object obj = this._mapListFromList.remove(index); + return (jalview.schemabinding.version2.MapListFrom) obj; + } + + /** + * Method removeMapListTo. + * + * @param vMapListTo + * @return true if the object was removed from the collection. + */ + public boolean removeMapListTo( + final jalview.schemabinding.version2.MapListTo vMapListTo) { + boolean removed = _mapListToList.remove(vMapListTo); + return removed; + } + + /** + * Method removeMapListToAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.MapListTo removeMapListToAt( + final int index) { + java.lang.Object obj = this._mapListToList.remove(index); + return (jalview.schemabinding.version2.MapListTo) obj; + } + + /** + * Sets the value of field 'mapFromUnit'. The field + * 'mapFromUnit' has the following description: number of + * dictionary symbol widths involved in each + * mapped position on this sequence (for example, 3 for a dna + * sequence exon + * region that is being mapped to a protein sequence). This is + * optional, + * since the unit can be usually be inferred from the + * dictionary type of + * each sequence involved in the mapping. + * + * @param mapFromUnit the value of field 'mapFromUnit'. + */ + public void setMapFromUnit( + final long mapFromUnit) { + this._mapFromUnit = mapFromUnit; + this._has_mapFromUnit = true; + } + + /** + * + * + * @param index + * @param vMapListFrom + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setMapListFrom( + final int index, + final jalview.schemabinding.version2.MapListFrom vMapListFrom) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._mapListFromList.size()) { + throw new IndexOutOfBoundsException("setMapListFrom: Index value '" + index + "' not in range [0.." + (this._mapListFromList.size() - 1) + "]"); + } + + this._mapListFromList.set(index, vMapListFrom); + } + + /** + * + * + * @param vMapListFromArray + */ + public void setMapListFrom( + final jalview.schemabinding.version2.MapListFrom[] vMapListFromArray) { + //-- copy array + _mapListFromList.clear(); + + for (int i = 0; i < vMapListFromArray.length; i++) { + this._mapListFromList.add(vMapListFromArray[i]); + } + } + + /** + * + * + * @param index + * @param vMapListTo + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setMapListTo( + final int index, + final jalview.schemabinding.version2.MapListTo vMapListTo) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._mapListToList.size()) { + throw new IndexOutOfBoundsException("setMapListTo: Index value '" + index + "' not in range [0.." + (this._mapListToList.size() - 1) + "]"); + } + + this._mapListToList.set(index, vMapListTo); + } + + /** + * + * + * @param vMapListToArray + */ + public void setMapListTo( + final jalview.schemabinding.version2.MapListTo[] vMapListToArray) { + //-- copy array + _mapListToList.clear(); + + for (int i = 0; i < vMapListToArray.length; i++) { + this._mapListToList.add(vMapListToArray[i]); + } + } + + /** + * Sets the value of field 'mapToUnit'. The field 'mapToUnit' + * has the following description: number of dictionary symbol + * widths involved in each + * mapped position on this sequence (for example, 3 for a dna + * sequence exon + * region that is being mapped to a protein sequence). This is + * optional, + * since the unit can be usually be inferred from the + * dictionary type of + * each sequence involved in the mapping. + * + * @param mapToUnit the value of field 'mapToUnit'. + */ + public void setMapToUnit( + final long mapToUnit) { + this._mapToUnit = mapToUnit; + this._has_mapToUnit = 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.schemabinding.version2.MapListType + */ + public static jalview.schemabinding.version2.MapListType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.MapListType) Unmarshaller.unmarshal(jalview.schemabinding.version2.MapListType.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/schemabinding/version2/Mapping.java b/src/jalview/schemabinding/version2/Mapping.java index 5ae5031..8dbc12f 100644 --- a/src/jalview/schemabinding/version2/Mapping.java +++ b/src/jalview/schemabinding/version2/Mapping.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,155 +19,147 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class Mapping extends jalview.schemabinding.version2.MapListType - implements java.io.Serializable +public class Mapping extends jalview.schemabinding.version2.MapListType +implements java.io.Serializable { - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Internal choice value storage - */ - private java.lang.Object _choiceValue; - - /** - * Field _mappingChoice. - */ - private jalview.schemabinding.version2.MappingChoice _mappingChoice; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Mapping() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'choiceValue'. The field 'choiceValue' has the - * following description: Internal choice value storage - * - * @return the value of field 'ChoiceValue'. - */ - public java.lang.Object getChoiceValue() - { - return this._choiceValue; - } - - /** - * Returns the value of field 'mappingChoice'. - * - * @return the value of field 'MappingChoice'. - */ - public jalview.schemabinding.version2.MappingChoice getMappingChoice() - { - return this._mappingChoice; - } - - /** - * 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; + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Internal choice value storage + */ + private java.lang.Object _choiceValue; + + /** + * Field _mappingChoice. + */ + private jalview.schemabinding.version2.MappingChoice _mappingChoice; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Mapping() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'choiceValue'. The field + * 'choiceValue' has the following description: Internal choice + * value storage + * + * @return the value of field 'ChoiceValue'. + */ + public java.lang.Object getChoiceValue( + ) { + return this._choiceValue; + } + + /** + * Returns the value of field 'mappingChoice'. + * + * @return the value of field 'MappingChoice'. + */ + public jalview.schemabinding.version2.MappingChoice getMappingChoice( + ) { + return this._mappingChoice; + } + + /** + * 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 'mappingChoice'. + * + * @param mappingChoice the value of field 'mappingChoice'. + */ + public void setMappingChoice( + final jalview.schemabinding.version2.MappingChoice mappingChoice) { + this._mappingChoice = mappingChoice; + this._choiceValue = mappingChoice; + } + + /** + * 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.schemabinding.version2.MapListType + */ + public static jalview.schemabinding.version2.MapListType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.MapListType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Mapping.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); } - 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 'mappingChoice'. - * - * @param mappingChoice - * the value of field 'mappingChoice'. - */ - public void setMappingChoice( - final jalview.schemabinding.version2.MappingChoice mappingChoice) - { - this._mappingChoice = mappingChoice; - this._choiceValue = mappingChoice; - } - - /** - * 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.schemabinding.version2.MapListType - */ - public static jalview.schemabinding.version2.MapListType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.MapListType) Unmarshaller - .unmarshal(jalview.schemabinding.version2.Mapping.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/schemabinding/version2/MappingChoice.java b/src/jalview/schemabinding/version2/MappingChoice.java index db41f09..5f1930d 100644 --- a/src/jalview/schemabinding/version2/MappingChoice.java +++ b/src/jalview/schemabinding/version2/MappingChoice.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,164 +19,152 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class MappingChoice implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _sequence. - */ - private jalview.schemabinding.version2.Sequence _sequence; - - /** - * Field _dseqFor. - */ - private java.lang.String _dseqFor; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MappingChoice() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'dseqFor'. - * - * @return the value of field 'DseqFor'. - */ - public java.lang.String getDseqFor() - { - return this._dseqFor; - } - - /** - * Returns the value of field 'sequence'. - * - * @return the value of field 'Sequence'. - */ - public jalview.schemabinding.version2.Sequence 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; +public class MappingChoice implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _sequence. + */ + private jalview.schemabinding.version2.Sequence _sequence; + + /** + * Field _dseqFor. + */ + private java.lang.String _dseqFor; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public MappingChoice() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'dseqFor'. + * + * @return the value of field 'DseqFor'. + */ + public java.lang.String getDseqFor( + ) { + return this._dseqFor; + } + + /** + * Returns the value of field 'sequence'. + * + * @return the value of field 'Sequence'. + */ + public jalview.schemabinding.version2.Sequence 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 'dseqFor'. + * + * @param dseqFor the value of field 'dseqFor'. + */ + public void setDseqFor( + final java.lang.String dseqFor) { + this._dseqFor = dseqFor; + } + + /** + * Sets the value of field 'sequence'. + * + * @param sequence the value of field 'sequence'. + */ + public void setSequence( + final jalview.schemabinding.version2.Sequence 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.schemabinding.version2.MappingChoice + */ + public static jalview.schemabinding.version2.MappingChoice unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.MappingChoice) Unmarshaller.unmarshal(jalview.schemabinding.version2.MappingChoice.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); } - 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 'dseqFor'. - * - * @param dseqFor - * the value of field 'dseqFor'. - */ - public void setDseqFor(final java.lang.String dseqFor) - { - this._dseqFor = dseqFor; - } - - /** - * Sets the value of field 'sequence'. - * - * @param sequence - * the value of field 'sequence'. - */ - public void setSequence( - final jalview.schemabinding.version2.Sequence 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.schemabinding.version2.MappingChoice - */ - public static jalview.schemabinding.version2.MappingChoice unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.MappingChoice) Unmarshaller - .unmarshal(jalview.schemabinding.version2.MappingChoice.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/schemabinding/version2/OtherData.java b/src/jalview/schemabinding/version2/OtherData.java index 85301fa..94a5566 100644 --- a/src/jalview/schemabinding/version2/OtherData.java +++ b/src/jalview/schemabinding/version2/OtherData.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,163 +19,152 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class OtherData implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _key. - */ - private java.lang.String _key; - - /** - * Field _value. - */ - private java.lang.String _value; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public OtherData() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'key'. - * - * @return the value of field 'Key'. - */ - public java.lang.String getKey() - { - return this._key; - } - - /** - * 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; +public class OtherData implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _key. + */ + private java.lang.String _key; + + /** + * Field _value. + */ + private java.lang.String _value; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public OtherData() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'key'. + * + * @return the value of field 'Key'. + */ + public java.lang.String getKey( + ) { + return this._key; + } + + /** + * 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 'key'. + * + * @param key the value of field 'key'. + */ + public void setKey( + final java.lang.String key) { + this._key = key; + } + + /** + * 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.schemabinding.version2.OtherData + */ + public static jalview.schemabinding.version2.OtherData unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.OtherData) Unmarshaller.unmarshal(jalview.schemabinding.version2.OtherData.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); } - 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 'key'. - * - * @param key - * the value of field 'key'. - */ - public void setKey(final java.lang.String key) - { - this._key = key; - } - - /** - * 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.schemabinding.version2.OtherData - */ - public static jalview.schemabinding.version2.OtherData unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.OtherData) Unmarshaller - .unmarshal(jalview.schemabinding.version2.OtherData.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/schemabinding/version2/Pdbentry.java b/src/jalview/schemabinding/version2/Pdbentry.java index 6721c5b..6ff1819 100755 --- a/src/jalview/schemabinding/version2/Pdbentry.java +++ b/src/jalview/schemabinding/version2/Pdbentry.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,357 +19,334 @@ import org.exolab.castor.xml.Unmarshaller; * * @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 _file. - */ - private java.lang.String _file; - - /** - * 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.schemabinding.version2.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.schemabinding.version2.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - this._items.add(index, vPdbentryItem); - } - - /** - * Method enumeratePdbentryItem. - * - * @return an Enumeration over all jalview.schemabinding.version2.PdbentryItem - * elements - */ - public java.util.Enumeration enumeratePdbentryItem() - { - return this._items.elements(); - } - - /** - * Returns the value of field 'file'. - * - * @return the value of field 'File'. - */ - public java.lang.String getFile() - { - return this._file; - } - - /** - * 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.schemabinding.version2.PdbentryItem at the - * given inde - */ - public jalview.schemabinding.version2.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) - + "]"); +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 _file. + */ + private java.lang.String _file; + + /** + * Field _items. + */ + private java.util.Vector _items; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Pdbentry() { + super(); + this._items = new java.util.Vector(); } - return (jalview.schemabinding.version2.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.schemabinding.version2.PdbentryItem[] getPdbentryItem() - { - jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0]; - return (jalview.schemabinding.version2.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; + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vPdbentryItem + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addPdbentryItem( + final jalview.schemabinding.version2.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.schemabinding.version2.PdbentryItem vPdbentryItem) + throws java.lang.IndexOutOfBoundsException { + this._items.add(index, vPdbentryItem); + } + + /** + * Method enumeratePdbentryItem. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.PdbentryItem elements + */ + public java.util.Enumeration enumeratePdbentryItem( + ) { + return this._items.elements(); + } + + /** + * Returns the value of field 'file'. + * + * @return the value of field 'File'. + */ + public java.lang.String getFile( + ) { + return this._file; } - 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); - } - - /** + + /** + * 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.schemabinding.version2.PdbentryItem at the given inde + */ + public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.PdbentryItem[] getPdbentryItem( + ) { + jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0]; + return (jalview.schemabinding.version2.PdbentryItem[]) this._items.toArray(array); + } + + /** + * Method getPdbentryItemCount. + * + * @return the size of this collection */ - 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.schemabinding.version2.PdbentryItem vPdbentryItem) - { - boolean removed = _items.remove(vPdbentryItem); - return removed; - } - - /** - * Method removePdbentryItemAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt( - final int index) - { - java.lang.Object obj = this._items.remove(index); - return (jalview.schemabinding.version2.PdbentryItem) obj; - } - - /** - * Sets the value of field 'file'. - * - * @param file - * the value of field 'file'. - */ - public void setFile(final java.lang.String file) - { - this._file = file; - } - - /** - * 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.schemabinding.version2.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) - + "]"); + public int getPdbentryItemCount( + ) { + return this._items.size(); } - this._items.set(index, vPdbentryItem); - } - - /** - * - * - * @param vPdbentryItemArray - */ - public void setPdbentryItem( - final jalview.schemabinding.version2.PdbentryItem[] vPdbentryItemArray) - { - // -- copy array - _items.clear(); - - for (int i = 0; i < vPdbentryItemArray.length; i++) - { - this._items.add(vPdbentryItemArray[i]); + /** + * 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.schemabinding.version2.PdbentryItem vPdbentryItem) { + boolean removed = _items.remove(vPdbentryItem); + return removed; + } + + /** + * Method removePdbentryItemAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt( + final int index) { + java.lang.Object obj = this._items.remove(index); + return (jalview.schemabinding.version2.PdbentryItem) obj; + } + + /** + * Sets the value of field 'file'. + * + * @param file the value of field 'file'. + */ + public void setFile( + final java.lang.String file) { + this._file = file; + } + + /** + * 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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Pdbentry + */ + public static jalview.schemabinding.version2.Pdbentry unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.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); } - } - - /** - * 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.schemabinding.version2.Pdbentry - */ - public static jalview.schemabinding.version2.Pdbentry unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Pdbentry) Unmarshaller - .unmarshal(jalview.schemabinding.version2.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/schemabinding/version2/PdbentryItem.java b/src/jalview/schemabinding/version2/PdbentryItem.java index 9cd3c47..3dbc99c 100755 --- a/src/jalview/schemabinding/version2/PdbentryItem.java +++ b/src/jalview/schemabinding/version2/PdbentryItem.java @@ -1,20 +1,10 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; /** @@ -22,193 +12,181 @@ package jalview.schemabinding.version2; * * @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.schemabinding.version2.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.schemabinding.version2.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - this._propertyList.add(index, vProperty); - } - - /** - * Method enumerateProperty. - * - * @return an Enumeration over all jalview.schemabinding.version2.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.schemabinding.version2.Property at the - * given index - */ - public jalview.schemabinding.version2.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) + "]"); +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.schemabinding.version2.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.schemabinding.version2.Property vProperty) + throws java.lang.IndexOutOfBoundsException { + this._propertyList.add(index, vProperty); + } + + /** + * Method enumerateProperty. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.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.schemabinding.version2.Property at the given index + */ + public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Property[] getProperty( + ) { + jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0]; + return (jalview.schemabinding.version2.Property[]) this._propertyList.toArray(array); + } + + /** + * Method getPropertyCount. + * + * @return the size of this collection + */ + public int getPropertyCount( + ) { + return this._propertyList.size(); } - return (jalview.schemabinding.version2.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.schemabinding.version2.Property[] getProperty() - { - jalview.schemabinding.version2.Property[] array = new jalview.schemabinding.version2.Property[0]; - return (jalview.schemabinding.version2.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.schemabinding.version2.Property vProperty) - { - boolean removed = _propertyList.remove(vProperty); - return removed; - } - - /** - * Method removePropertyAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Property removePropertyAt( - final int index) - { - java.lang.Object obj = this._propertyList.remove(index); - return (jalview.schemabinding.version2.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.schemabinding.version2.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) + "]"); + public void removeAllProperty( + ) { + this._propertyList.clear(); } - this._propertyList.set(index, vProperty); - } - - /** - * - * - * @param vPropertyArray - */ - public void setProperty( - final jalview.schemabinding.version2.Property[] vPropertyArray) - { - // -- copy array - _propertyList.clear(); - - for (int i = 0; i < vPropertyArray.length; i++) - { - this._propertyList.add(vPropertyArray[i]); + /** + * Method removeProperty. + * + * @param vProperty + * @return true if the object was removed from the collection. + */ + public boolean removeProperty( + final jalview.schemabinding.version2.Property vProperty) { + boolean removed = _propertyList.remove(vProperty); + return removed; + } + + /** + * Method removePropertyAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Property removePropertyAt( + final int index) { + java.lang.Object obj = this._propertyList.remove(index); + return (jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Property[] vPropertyArray) { + //-- copy array + _propertyList.clear(); + + for (int i = 0; i < vPropertyArray.length; i++) { + this._propertyList.add(vPropertyArray[i]); + } } - } } diff --git a/src/jalview/schemabinding/version2/Pdbids.java b/src/jalview/schemabinding/version2/Pdbids.java index 944bcfe..04685b9 100755 --- a/src/jalview/schemabinding/version2/Pdbids.java +++ b/src/jalview/schemabinding/version2/Pdbids.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,285 +19,262 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class Pdbids extends jalview.schemabinding.version2.Pdbentry - implements java.io.Serializable +public class Pdbids extends jalview.schemabinding.version2.Pdbentry +implements java.io.Serializable { - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - /** - * Field _structureStateList. - */ - private java.util.Vector _structureStateList; + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ - // ----------------/ - // - Constructors -/ - // ----------------/ + /** + * Field _structureStateList. + */ + private java.util.Vector _structureStateList; - public Pdbids() - { - super(); - this._structureStateList = new java.util.Vector(); - } - // -----------/ - // - Methods -/ - // -----------/ + //----------------/ + //- Constructors -/ + //----------------/ - /** - * - * - * @param vStructureState - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addStructureState( - final jalview.schemabinding.version2.StructureState vStructureState) - throws java.lang.IndexOutOfBoundsException - { - this._structureStateList.addElement(vStructureState); - } + public Pdbids() { + super(); + this._structureStateList = new java.util.Vector(); + } - /** - * - * - * @param index - * @param vStructureState - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addStructureState( - final int index, - final jalview.schemabinding.version2.StructureState vStructureState) - throws java.lang.IndexOutOfBoundsException - { - this._structureStateList.add(index, vStructureState); - } - /** - * Method enumerateStructureState. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.StructureState elements - */ - public java.util.Enumeration enumerateStructureState() - { - return this._structureStateList.elements(); - } + //-----------/ + //- Methods -/ + //-----------/ - /** - * Method getStructureState. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.StructureState at - * the given index - */ - public jalview.schemabinding.version2.StructureState getStructureState( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._structureStateList.size()) - { - throw new IndexOutOfBoundsException( - "getStructureState: Index value '" + index - + "' not in range [0.." - + (this._structureStateList.size() - 1) + "]"); + /** + * + * + * @param vStructureState + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addStructureState( + final jalview.schemabinding.version2.StructureState vStructureState) + throws java.lang.IndexOutOfBoundsException { + this._structureStateList.addElement(vStructureState); } - return (jalview.schemabinding.version2.StructureState) _structureStateList - .get(index); - } + /** + * + * + * @param index + * @param vStructureState + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addStructureState( + final int index, + final jalview.schemabinding.version2.StructureState vStructureState) + throws java.lang.IndexOutOfBoundsException { + this._structureStateList.add(index, vStructureState); + } - /** - * Method getStructureState.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.schemabinding.version2.StructureState[] getStructureState() - { - jalview.schemabinding.version2.StructureState[] array = new jalview.schemabinding.version2.StructureState[0]; - return (jalview.schemabinding.version2.StructureState[]) this._structureStateList - .toArray(array); - } + /** + * Method enumerateStructureState. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.StructureState elements + */ + public java.util.Enumeration enumerateStructureState( + ) { + return this._structureStateList.elements(); + } - /** - * Method getStructureStateCount. - * - * @return the size of this collection - */ - public int getStructureStateCount() - { - return this._structureStateList.size(); - } + /** + * Method getStructureState. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.StructureState at the given + * index + */ + public jalview.schemabinding.version2.StructureState getStructureState( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._structureStateList.size()) { + throw new IndexOutOfBoundsException("getStructureState: Index value '" + index + "' not in range [0.." + (this._structureStateList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.StructureState) _structureStateList.get(index); + } - /** - * 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; + /** + * Method getStructureState.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.schemabinding.version2.StructureState[] getStructureState( + ) { + jalview.schemabinding.version2.StructureState[] array = new jalview.schemabinding.version2.StructureState[0]; + return (jalview.schemabinding.version2.StructureState[]) this._structureStateList.toArray(array); } - 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); - } + /** + * Method getStructureStateCount. + * + * @return the size of this collection + */ + public int getStructureStateCount( + ) { + return this._structureStateList.size(); + } - /** - * - * - * @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 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 removeAllStructureState() - { - this._structureStateList.clear(); - } + public void marshal( + final java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + Marshaller.marshal(this, out); + } - /** - * Method removeStructureState. - * - * @param vStructureState - * @return true if the object was removed from the collection. - */ - public boolean removeStructureState( - final jalview.schemabinding.version2.StructureState vStructureState) - { - boolean removed = _structureStateList.remove(vStructureState); - return removed; - } + /** + * + * + * @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 removeStructureStateAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.StructureState removeStructureStateAt( - final int index) - { - java.lang.Object obj = this._structureStateList.remove(index); - return (jalview.schemabinding.version2.StructureState) obj; - } + /** + */ + public void removeAllStructureState( + ) { + this._structureStateList.clear(); + } - /** - * - * - * @param index - * @param vStructureState - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setStructureState( - final int index, - final jalview.schemabinding.version2.StructureState vStructureState) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._structureStateList.size()) - { - throw new IndexOutOfBoundsException( - "setStructureState: Index value '" + index - + "' not in range [0.." - + (this._structureStateList.size() - 1) + "]"); + /** + * Method removeStructureState. + * + * @param vStructureState + * @return true if the object was removed from the collection. + */ + public boolean removeStructureState( + final jalview.schemabinding.version2.StructureState vStructureState) { + boolean removed = _structureStateList.remove(vStructureState); + return removed; } - this._structureStateList.set(index, vStructureState); - } + /** + * Method removeStructureStateAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.StructureState removeStructureStateAt( + final int index) { + java.lang.Object obj = this._structureStateList.remove(index); + return (jalview.schemabinding.version2.StructureState) obj; + } - /** - * - * - * @param vStructureStateArray - */ - public void setStructureState( - final jalview.schemabinding.version2.StructureState[] vStructureStateArray) - { - // -- copy array - _structureStateList.clear(); + /** + * + * + * @param index + * @param vStructureState + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setStructureState( + final int index, + final jalview.schemabinding.version2.StructureState vStructureState) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._structureStateList.size()) { + throw new IndexOutOfBoundsException("setStructureState: Index value '" + index + "' not in range [0.." + (this._structureStateList.size() - 1) + "]"); + } + + this._structureStateList.set(index, vStructureState); + } - for (int i = 0; i < vStructureStateArray.length; i++) - { - this._structureStateList.add(vStructureStateArray[i]); + /** + * + * + * @param vStructureStateArray + */ + public void setStructureState( + final jalview.schemabinding.version2.StructureState[] vStructureStateArray) { + //-- copy array + _structureStateList.clear(); + + for (int i = 0; i < vStructureStateArray.length; i++) { + this._structureStateList.add(vStructureStateArray[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.schemabinding.version2.Pdbentry - */ - public static jalview.schemabinding.version2.Pdbentry unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Pdbentry) Unmarshaller - .unmarshal(jalview.schemabinding.version2.Pdbids.class, reader); - } + /** + * 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.schemabinding.version2.Pdbentry + */ + public static jalview.schemabinding.version2.Pdbentry unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.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); - } + /** + * + * + * @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/schemabinding/version2/Property.java b/src/jalview/schemabinding/version2/Property.java index 13905ec..bfc4dde 100755 --- a/src/jalview/schemabinding/version2/Property.java +++ b/src/jalview/schemabinding/version2/Property.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,163 +19,152 @@ import org.exolab.castor.xml.Unmarshaller; * * @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; +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.schemabinding.version2.Property + */ + public static jalview.schemabinding.version2.Property unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Property) Unmarshaller.unmarshal(jalview.schemabinding.version2.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); } - 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.schemabinding.version2.Property - */ - public static jalview.schemabinding.version2.Property unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Property) Unmarshaller - .unmarshal(jalview.schemabinding.version2.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/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java index 4ec2aaf..e606eeb 100755 --- a/src/jalview/schemabinding/version2/Sequence.java +++ b/src/jalview/schemabinding/version2/Sequence.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,310 +19,293 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class Sequence extends jalview.schemabinding.version2.SequenceType - implements java.io.Serializable +public class Sequence extends jalview.schemabinding.version2.SequenceType +implements java.io.Serializable { - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * dataset sequence id for this sequence. Will be created as union of - * sequences. - * - */ - private java.lang.String _dsseqid; - - /** - * Field _DBRefList. - */ - private java.util.Vector _DBRefList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Sequence() - { - super(); - this._DBRefList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vDBRef - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addDBRef(final jalview.schemabinding.version2.DBRef vDBRef) - throws java.lang.IndexOutOfBoundsException - { - this._DBRefList.addElement(vDBRef); - } - - /** - * - * - * @param index - * @param vDBRef - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addDBRef(final int index, - final jalview.schemabinding.version2.DBRef vDBRef) - throws java.lang.IndexOutOfBoundsException - { - this._DBRefList.add(index, vDBRef); - } - - /** - * Method enumerateDBRef. - * - * @return an Enumeration over all jalview.schemabinding.version2.DBRef - * elements - */ - public java.util.Enumeration enumerateDBRef() - { - return this._DBRefList.elements(); - } - - /** - * Method getDBRef. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.DBRef at the given - * index - */ - public jalview.schemabinding.version2.DBRef getDBRef(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._DBRefList.size()) - { - throw new IndexOutOfBoundsException("getDBRef: Index value '" + index - + "' not in range [0.." + (this._DBRefList.size() - 1) + "]"); + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * dataset sequence id for this sequence. Will be created as + * union of sequences. + * + */ + private java.lang.String _dsseqid; + + /** + * Field _DBRefList. + */ + private java.util.Vector _DBRefList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Sequence() { + super(); + this._DBRefList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vDBRef + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addDBRef( + final jalview.schemabinding.version2.DBRef vDBRef) + throws java.lang.IndexOutOfBoundsException { + this._DBRefList.addElement(vDBRef); + } + + /** + * + * + * @param index + * @param vDBRef + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addDBRef( + final int index, + final jalview.schemabinding.version2.DBRef vDBRef) + throws java.lang.IndexOutOfBoundsException { + this._DBRefList.add(index, vDBRef); + } + + /** + * Method enumerateDBRef. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.DBRef elements + */ + public java.util.Enumeration enumerateDBRef( + ) { + return this._DBRefList.elements(); + } + + /** + * Method getDBRef. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.DBRef at the given index + */ + public jalview.schemabinding.version2.DBRef getDBRef( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._DBRefList.size()) { + throw new IndexOutOfBoundsException("getDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index); + } + + /** + * Method getDBRef.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.schemabinding.version2.DBRef[] getDBRef( + ) { + jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0]; + return (jalview.schemabinding.version2.DBRef[]) this._DBRefList.toArray(array); + } + + /** + * Method getDBRefCount. + * + * @return the size of this collection + */ + public int getDBRefCount( + ) { + return this._DBRefList.size(); + } + + /** + * Returns the value of field 'dsseqid'. The field 'dsseqid' + * has the following description: dataset sequence id for this + * sequence. Will be created as union of sequences. + * + * + * @return the value of field 'Dsseqid'. + */ + public java.lang.String getDsseqid( + ) { + return this._dsseqid; + } + + /** + * 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 removeAllDBRef( + ) { + this._DBRefList.clear(); + } + + /** + * Method removeDBRef. + * + * @param vDBRef + * @return true if the object was removed from the collection. + */ + public boolean removeDBRef( + final jalview.schemabinding.version2.DBRef vDBRef) { + boolean removed = _DBRefList.remove(vDBRef); + return removed; + } + + /** + * Method removeDBRefAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.DBRef removeDBRefAt( + final int index) { + java.lang.Object obj = this._DBRefList.remove(index); + return (jalview.schemabinding.version2.DBRef) obj; + } + + /** + * + * + * @param index + * @param vDBRef + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setDBRef( + final int index, + final jalview.schemabinding.version2.DBRef vDBRef) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._DBRefList.size()) { + throw new IndexOutOfBoundsException("setDBRef: Index value '" + index + "' not in range [0.." + (this._DBRefList.size() - 1) + "]"); + } + + this._DBRefList.set(index, vDBRef); + } + + /** + * + * + * @param vDBRefArray + */ + public void setDBRef( + final jalview.schemabinding.version2.DBRef[] vDBRefArray) { + //-- copy array + _DBRefList.clear(); + + for (int i = 0; i < vDBRefArray.length; i++) { + this._DBRefList.add(vDBRefArray[i]); + } } - return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index); - } - - /** - * Method getDBRef.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.schemabinding.version2.DBRef[] getDBRef() - { - jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0]; - return (jalview.schemabinding.version2.DBRef[]) this._DBRefList - .toArray(array); - } - - /** - * Method getDBRefCount. - * - * @return the size of this collection - */ - public int getDBRefCount() - { - return this._DBRefList.size(); - } - - /** - * Returns the value of field 'dsseqid'. The field 'dsseqid' has the following - * description: dataset sequence id for this sequence. Will be created as - * union of sequences. - * - * - * @return the value of field 'Dsseqid'. - */ - public java.lang.String getDsseqid() - { - return this._dsseqid; - } - - /** - * 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; + /** + * Sets the value of field 'dsseqid'. The field 'dsseqid' has + * the following description: dataset sequence id for this + * sequence. Will be created as union of sequences. + * + * + * @param dsseqid the value of field 'dsseqid'. + */ + public void setDsseqid( + final java.lang.String dsseqid) { + this._dsseqid = dsseqid; } - 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.schemabinding.version2.SequenceType */ - public void removeAllDBRef() - { - this._DBRefList.clear(); - } - - /** - * Method removeDBRef. - * - * @param vDBRef - * @return true if the object was removed from the collection. - */ - public boolean removeDBRef( - final jalview.schemabinding.version2.DBRef vDBRef) - { - boolean removed = _DBRefList.remove(vDBRef); - return removed; - } - - /** - * Method removeDBRefAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.DBRef removeDBRefAt(final int index) - { - java.lang.Object obj = this._DBRefList.remove(index); - return (jalview.schemabinding.version2.DBRef) obj; - } - - /** - * - * - * @param index - * @param vDBRef - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setDBRef(final int index, - final jalview.schemabinding.version2.DBRef vDBRef) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._DBRefList.size()) - { - throw new IndexOutOfBoundsException("setDBRef: Index value '" + index - + "' not in range [0.." + (this._DBRefList.size() - 1) + "]"); + public static jalview.schemabinding.version2.SequenceType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.class, reader); } - this._DBRefList.set(index, vDBRef); - } - - /** - * - * - * @param vDBRefArray - */ - public void setDBRef( - final jalview.schemabinding.version2.DBRef[] vDBRefArray) - { - // -- copy array - _DBRefList.clear(); - - for (int i = 0; i < vDBRefArray.length; i++) - { - this._DBRefList.add(vDBRefArray[i]); + /** + * + * + * @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); } - } - - /** - * Sets the value of field 'dsseqid'. The field 'dsseqid' has the following - * description: dataset sequence id for this sequence. Will be created as - * union of sequences. - * - * - * @param dsseqid - * the value of field 'dsseqid'. - */ - public void setDsseqid(final java.lang.String dsseqid) - { - this._dsseqid = dsseqid; - } - - /** - * 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.schemabinding.version2.SequenceType - */ - public static jalview.schemabinding.version2.SequenceType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.SequenceType) Unmarshaller - .unmarshal(jalview.schemabinding.version2.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/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java index bd5efa9..481c37f 100755 --- a/src/jalview/schemabinding/version2/SequenceSet.java +++ b/src/jalview/schemabinding/version2/SequenceSet.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,854 +19,789 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class SequenceSet implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _gapChar. - */ - private java.lang.String _gapChar; - - /** - * reference to set where jalview will gather the dataset sequences for all - * sequences in the set. - * - */ - private java.lang.String _datasetId; - - /** - * Field _sequenceList. - */ - private java.util.Vector _sequenceList; - - /** - * Field _annotationList. - */ - private java.util.Vector _annotationList; - - /** - * Field _sequenceSetPropertiesList. - */ - private java.util.Vector _sequenceSetPropertiesList; - - /** - * Field _alcodonFrameList. - */ - private java.util.Vector _alcodonFrameList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SequenceSet() - { - super(); - this._sequenceList = new java.util.Vector(); - this._annotationList = new java.util.Vector(); - this._sequenceSetPropertiesList = new java.util.Vector(); - this._alcodonFrameList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vAlcodonFrame - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlcodonFrame( - final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) - throws java.lang.IndexOutOfBoundsException - { - this._alcodonFrameList.addElement(vAlcodonFrame); - } - - /** - * - * - * @param index - * @param vAlcodonFrame - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlcodonFrame(final int index, - final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) - throws java.lang.IndexOutOfBoundsException - { - this._alcodonFrameList.add(index, vAlcodonFrame); - } - - /** - * - * - * @param vAnnotation - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAnnotation( - final jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - this._sequenceList.add(index, vSequence); - } - - /** - * - * - * @param vSequenceSetProperties - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSequenceSetProperties( - final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) - throws java.lang.IndexOutOfBoundsException - { - this._sequenceSetPropertiesList.addElement(vSequenceSetProperties); - } - - /** - * - * - * @param index - * @param vSequenceSetProperties - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSequenceSetProperties( - final int index, - final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) - throws java.lang.IndexOutOfBoundsException - { - this._sequenceSetPropertiesList.add(index, vSequenceSetProperties); - } - - /** - * Method enumerateAlcodonFrame. - * - * @return an Enumeration over all jalview.schemabinding.version2.AlcodonFrame - * elements - */ - public java.util.Enumeration enumerateAlcodonFrame() - { - return this._alcodonFrameList.elements(); - } - - /** - * Method enumerateAnnotation. - * - * @return an Enumeration over all jalview.schemabinding.version2.Annotation - * elements - */ - public java.util.Enumeration enumerateAnnotation() - { - return this._annotationList.elements(); - } - - /** - * Method enumerateSequence. - * - * @return an Enumeration over all jalview.schemabinding.version2.Sequence - * elements - */ - public java.util.Enumeration enumerateSequence() - { - return this._sequenceList.elements(); - } - - /** - * Method enumerateSequenceSetProperties. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.SequenceSetProperties elements - */ - public java.util.Enumeration enumerateSequenceSetProperties() - { - return this._sequenceSetPropertiesList.elements(); - } - - /** - * Method getAlcodonFrame. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.AlcodonFrame at the - * given inde - */ - public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alcodonFrameList.size()) - { - throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '" - + index + "' not in range [0.." - + (this._alcodonFrameList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList - .get(index); - } - - /** - * Method getAlcodonFrame.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.schemabinding.version2.AlcodonFrame[] getAlcodonFrame() - { - jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0]; - return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList - .toArray(array); - } - - /** - * Method getAlcodonFrameCount. - * - * @return the size of this collection - */ - public int getAlcodonFrameCount() - { - return this._alcodonFrameList.size(); - } - - /** - * 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.schemabinding.version2.Annotation at the - * given index - */ - public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Annotation[] getAnnotation() - { - jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0]; - return (jalview.schemabinding.version2.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 'datasetId'. The field 'datasetId' has the - * following description: reference to set where jalview will gather the - * dataset sequences for all sequences in the set. - * - * - * @return the value of field 'DatasetId'. - */ - public java.lang.String getDatasetId() - { - return this._datasetId; - } - - /** - * 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.schemabinding.version2.Sequence at the - * given index - */ - public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Sequence[] getSequence() - { - jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0]; - return (jalview.schemabinding.version2.Sequence[]) this._sequenceList - .toArray(array); - } - - /** - * Method getSequenceCount. - * - * @return the size of this collection - */ - public int getSequenceCount() - { - return this._sequenceList.size(); - } - - /** - * Method getSequenceSetProperties. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the - * jalview.schemabinding.version2.SequenceSetProperties at the given - * index - */ - public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._sequenceSetPropertiesList.size()) - { - throw new IndexOutOfBoundsException( - "getSequenceSetProperties: Index value '" + index - + "' not in range [0.." - + (this._sequenceSetPropertiesList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList - .get(index); - } - - /** - * Method getSequenceSetProperties.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.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties() - { - jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0]; - return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList - .toArray(array); - } - - /** - * Method getSequenceSetPropertiesCount. - * - * @return the size of this collection - */ - public int getSequenceSetPropertiesCount() - { - return this._sequenceSetPropertiesList.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 removeAlcodonFrame. - * - * @param vAlcodonFrame - * @return true if the object was removed from the collection. - */ - public boolean removeAlcodonFrame( - final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) - { - boolean removed = _alcodonFrameList.remove(vAlcodonFrame); - return removed; - } - - /** - * Method removeAlcodonFrameAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt( - final int index) - { - java.lang.Object obj = this._alcodonFrameList.remove(index); - return (jalview.schemabinding.version2.AlcodonFrame) obj; - } - - /** - */ - public void removeAllAlcodonFrame() - { - this._alcodonFrameList.clear(); - } - - /** - */ - public void removeAllAnnotation() - { - this._annotationList.clear(); - } - - /** - */ - public void removeAllSequence() - { - this._sequenceList.clear(); - } - - /** - */ - public void removeAllSequenceSetProperties() - { - this._sequenceSetPropertiesList.clear(); - } - - /** - * Method removeAnnotation. - * - * @param vAnnotation - * @return true if the object was removed from the collection. - */ - public boolean removeAnnotation( - final jalview.schemabinding.version2.Annotation vAnnotation) - { - boolean removed = _annotationList.remove(vAnnotation); - return removed; - } - - /** - * Method removeAnnotationAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Annotation removeAnnotationAt( - final int index) - { - java.lang.Object obj = this._annotationList.remove(index); - return (jalview.schemabinding.version2.Annotation) obj; - } - - /** - * Method removeSequence. - * - * @param vSequence - * @return true if the object was removed from the collection. - */ - public boolean removeSequence( - final jalview.schemabinding.version2.Sequence vSequence) - { - boolean removed = _sequenceList.remove(vSequence); - return removed; - } - - /** - * Method removeSequenceAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Sequence removeSequenceAt( - final int index) - { - java.lang.Object obj = this._sequenceList.remove(index); - return (jalview.schemabinding.version2.Sequence) obj; - } - - /** - * Method removeSequenceSetProperties. - * - * @param vSequenceSetProperties - * @return true if the object was removed from the collection. - */ - public boolean removeSequenceSetProperties( - final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) - { - boolean removed = _sequenceSetPropertiesList - .remove(vSequenceSetProperties); - return removed; - } - - /** - * Method removeSequenceSetPropertiesAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt( - final int index) - { - java.lang.Object obj = this._sequenceSetPropertiesList.remove(index); - return (jalview.schemabinding.version2.SequenceSetProperties) obj; - } - - /** - * - * - * @param index - * @param vAlcodonFrame - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAlcodonFrame(final int index, - final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alcodonFrameList.size()) - { - throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '" - + index + "' not in range [0.." - + (this._alcodonFrameList.size() - 1) + "]"); - } - - this._alcodonFrameList.set(index, vAlcodonFrame); - } - - /** - * - * - * @param vAlcodonFrameArray - */ - public void setAlcodonFrame( - final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray) - { - // -- copy array - _alcodonFrameList.clear(); - - for (int i = 0; i < vAlcodonFrameArray.length; i++) - { - this._alcodonFrameList.add(vAlcodonFrameArray[i]); - } - } - - /** - * - * - * @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.schemabinding.version2.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.schemabinding.version2.Annotation[] vAnnotationArray) - { - // -- copy array - _annotationList.clear(); - - for (int i = 0; i < vAnnotationArray.length; i++) - { - this._annotationList.add(vAnnotationArray[i]); - } - } - - /** - * Sets the value of field 'datasetId'. The field 'datasetId' has the - * following description: reference to set where jalview will gather the - * dataset sequences for all sequences in the set. - * - * - * @param datasetId - * the value of field 'datasetId'. - */ - public void setDatasetId(final java.lang.String datasetId) - { - this._datasetId = datasetId; - } - - /** - * 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.schemabinding.version2.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.schemabinding.version2.Sequence[] vSequenceArray) - { - // -- copy array - _sequenceList.clear(); - - for (int i = 0; i < vSequenceArray.length; i++) - { - this._sequenceList.add(vSequenceArray[i]); - } - } - - /** - * - * - * @param index - * @param vSequenceSetProperties - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setSequenceSetProperties( - final int index, - final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._sequenceSetPropertiesList.size()) - { - throw new IndexOutOfBoundsException( - "setSequenceSetProperties: Index value '" + index - + "' not in range [0.." - + (this._sequenceSetPropertiesList.size() - 1) + "]"); - } - - this._sequenceSetPropertiesList.set(index, vSequenceSetProperties); - } - - /** - * - * - * @param vSequenceSetPropertiesArray - */ - public void setSequenceSetProperties( - final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray) - { - // -- copy array - _sequenceSetPropertiesList.clear(); - - for (int i = 0; i < vSequenceSetPropertiesArray.length; i++) - { - this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[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.schemabinding.version2.SequenceSet - */ - public static jalview.schemabinding.version2.SequenceSet unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.SequenceSet) Unmarshaller - .unmarshal(jalview.schemabinding.version2.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); - } +public class SequenceSet implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _gapChar. + */ + private java.lang.String _gapChar; + + /** + * reference to set where jalview will gather the dataset + * sequences for all sequences in the set. + * + */ + private java.lang.String _datasetId; + + /** + * Field _sequenceList. + */ + private java.util.Vector _sequenceList; + + /** + * Field _annotationList. + */ + private java.util.Vector _annotationList; + + /** + * Field _sequenceSetPropertiesList. + */ + private java.util.Vector _sequenceSetPropertiesList; + + /** + * Field _alcodonFrameList. + */ + private java.util.Vector _alcodonFrameList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceSet() { + super(); + this._sequenceList = new java.util.Vector(); + this._annotationList = new java.util.Vector(); + this._sequenceSetPropertiesList = new java.util.Vector(); + this._alcodonFrameList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vAlcodonFrame + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAlcodonFrame( + final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) + throws java.lang.IndexOutOfBoundsException { + this._alcodonFrameList.addElement(vAlcodonFrame); + } + + /** + * + * + * @param index + * @param vAlcodonFrame + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAlcodonFrame( + final int index, + final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) + throws java.lang.IndexOutOfBoundsException { + this._alcodonFrameList.add(index, vAlcodonFrame); + } + + /** + * + * + * @param vAnnotation + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addAnnotation( + final jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Sequence vSequence) + throws java.lang.IndexOutOfBoundsException { + this._sequenceList.add(index, vSequence); + } + + /** + * + * + * @param vSequenceSetProperties + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSequenceSetProperties( + final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) + throws java.lang.IndexOutOfBoundsException { + this._sequenceSetPropertiesList.addElement(vSequenceSetProperties); + } + + /** + * + * + * @param index + * @param vSequenceSetProperties + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSequenceSetProperties( + final int index, + final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) + throws java.lang.IndexOutOfBoundsException { + this._sequenceSetPropertiesList.add(index, vSequenceSetProperties); + } + + /** + * Method enumerateAlcodonFrame. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.AlcodonFrame elements + */ + public java.util.Enumeration enumerateAlcodonFrame( + ) { + return this._alcodonFrameList.elements(); + } + + /** + * Method enumerateAnnotation. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.Annotation elements + */ + public java.util.Enumeration enumerateAnnotation( + ) { + return this._annotationList.elements(); + } + + /** + * Method enumerateSequence. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.Sequence elements + */ + public java.util.Enumeration enumerateSequence( + ) { + return this._sequenceList.elements(); + } + + /** + * Method enumerateSequenceSetProperties. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.SequenceSetProperties elements + */ + public java.util.Enumeration enumerateSequenceSetProperties( + ) { + return this._sequenceSetPropertiesList.elements(); + } + + /** + * Method getAlcodonFrame. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.AlcodonFrame at the given inde + */ + public jalview.schemabinding.version2.AlcodonFrame getAlcodonFrame( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alcodonFrameList.size()) { + throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList.get(index); + } + + /** + * Method getAlcodonFrame.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.schemabinding.version2.AlcodonFrame[] getAlcodonFrame( + ) { + jalview.schemabinding.version2.AlcodonFrame[] array = new jalview.schemabinding.version2.AlcodonFrame[0]; + return (jalview.schemabinding.version2.AlcodonFrame[]) this._alcodonFrameList.toArray(array); + } + + /** + * Method getAlcodonFrameCount. + * + * @return the size of this collection + */ + public int getAlcodonFrameCount( + ) { + return this._alcodonFrameList.size(); + } + + /** + * 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.schemabinding.version2.Annotation at the given index + */ + public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Annotation[] getAnnotation( + ) { + jalview.schemabinding.version2.Annotation[] array = new jalview.schemabinding.version2.Annotation[0]; + return (jalview.schemabinding.version2.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 'datasetId'. The field + * 'datasetId' has the following description: reference to set + * where jalview will gather the dataset sequences for all + * sequences in the set. + * + * + * @return the value of field 'DatasetId'. + */ + public java.lang.String getDatasetId( + ) { + return this._datasetId; + } + + /** + * 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.schemabinding.version2.Sequence at the given index + */ + public jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.Sequence[] getSequence( + ) { + jalview.schemabinding.version2.Sequence[] array = new jalview.schemabinding.version2.Sequence[0]; + return (jalview.schemabinding.version2.Sequence[]) this._sequenceList.toArray(array); + } + + /** + * Method getSequenceCount. + * + * @return the size of this collection + */ + public int getSequenceCount( + ) { + return this._sequenceList.size(); + } + + /** + * Method getSequenceSetProperties. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.SequenceSetProperties at the + * given index + */ + public jalview.schemabinding.version2.SequenceSetProperties getSequenceSetProperties( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._sequenceSetPropertiesList.size()) { + throw new IndexOutOfBoundsException("getSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList.get(index); + } + + /** + * Method getSequenceSetProperties.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.schemabinding.version2.SequenceSetProperties[] getSequenceSetProperties( + ) { + jalview.schemabinding.version2.SequenceSetProperties[] array = new jalview.schemabinding.version2.SequenceSetProperties[0]; + return (jalview.schemabinding.version2.SequenceSetProperties[]) this._sequenceSetPropertiesList.toArray(array); + } + + /** + * Method getSequenceSetPropertiesCount. + * + * @return the size of this collection + */ + public int getSequenceSetPropertiesCount( + ) { + return this._sequenceSetPropertiesList.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 removeAlcodonFrame. + * + * @param vAlcodonFrame + * @return true if the object was removed from the collection. + */ + public boolean removeAlcodonFrame( + final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) { + boolean removed = _alcodonFrameList.remove(vAlcodonFrame); + return removed; + } + + /** + * Method removeAlcodonFrameAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.AlcodonFrame removeAlcodonFrameAt( + final int index) { + java.lang.Object obj = this._alcodonFrameList.remove(index); + return (jalview.schemabinding.version2.AlcodonFrame) obj; + } + + /** + */ + public void removeAllAlcodonFrame( + ) { + this._alcodonFrameList.clear(); + } + + /** + */ + public void removeAllAnnotation( + ) { + this._annotationList.clear(); + } + + /** + */ + public void removeAllSequence( + ) { + this._sequenceList.clear(); + } + + /** + */ + public void removeAllSequenceSetProperties( + ) { + this._sequenceSetPropertiesList.clear(); + } + + /** + * Method removeAnnotation. + * + * @param vAnnotation + * @return true if the object was removed from the collection. + */ + public boolean removeAnnotation( + final jalview.schemabinding.version2.Annotation vAnnotation) { + boolean removed = _annotationList.remove(vAnnotation); + return removed; + } + + /** + * Method removeAnnotationAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Annotation removeAnnotationAt( + final int index) { + java.lang.Object obj = this._annotationList.remove(index); + return (jalview.schemabinding.version2.Annotation) obj; + } + + /** + * Method removeSequence. + * + * @param vSequence + * @return true if the object was removed from the collection. + */ + public boolean removeSequence( + final jalview.schemabinding.version2.Sequence vSequence) { + boolean removed = _sequenceList.remove(vSequence); + return removed; + } + + /** + * Method removeSequenceAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Sequence removeSequenceAt( + final int index) { + java.lang.Object obj = this._sequenceList.remove(index); + return (jalview.schemabinding.version2.Sequence) obj; + } + + /** + * Method removeSequenceSetProperties. + * + * @param vSequenceSetProperties + * @return true if the object was removed from the collection. + */ + public boolean removeSequenceSetProperties( + final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) { + boolean removed = _sequenceSetPropertiesList.remove(vSequenceSetProperties); + return removed; + } + + /** + * Method removeSequenceSetPropertiesAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.SequenceSetProperties removeSequenceSetPropertiesAt( + final int index) { + java.lang.Object obj = this._sequenceSetPropertiesList.remove(index); + return (jalview.schemabinding.version2.SequenceSetProperties) obj; + } + + /** + * + * + * @param index + * @param vAlcodonFrame + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setAlcodonFrame( + final int index, + final jalview.schemabinding.version2.AlcodonFrame vAlcodonFrame) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._alcodonFrameList.size()) { + throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '" + index + "' not in range [0.." + (this._alcodonFrameList.size() - 1) + "]"); + } + + this._alcodonFrameList.set(index, vAlcodonFrame); + } + + /** + * + * + * @param vAlcodonFrameArray + */ + public void setAlcodonFrame( + final jalview.schemabinding.version2.AlcodonFrame[] vAlcodonFrameArray) { + //-- copy array + _alcodonFrameList.clear(); + + for (int i = 0; i < vAlcodonFrameArray.length; i++) { + this._alcodonFrameList.add(vAlcodonFrameArray[i]); + } + } + + /** + * + * + * @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.schemabinding.version2.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.schemabinding.version2.Annotation[] vAnnotationArray) { + //-- copy array + _annotationList.clear(); + + for (int i = 0; i < vAnnotationArray.length; i++) { + this._annotationList.add(vAnnotationArray[i]); + } + } + + /** + * Sets the value of field 'datasetId'. The field 'datasetId' + * has the following description: reference to set where + * jalview will gather the dataset sequences for all sequences + * in the set. + * + * + * @param datasetId the value of field 'datasetId'. + */ + public void setDatasetId( + final java.lang.String datasetId) { + this._datasetId = datasetId; + } + + /** + * 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.schemabinding.version2.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.schemabinding.version2.Sequence[] vSequenceArray) { + //-- copy array + _sequenceList.clear(); + + for (int i = 0; i < vSequenceArray.length; i++) { + this._sequenceList.add(vSequenceArray[i]); + } + } + + /** + * + * + * @param index + * @param vSequenceSetProperties + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setSequenceSetProperties( + final int index, + final jalview.schemabinding.version2.SequenceSetProperties vSequenceSetProperties) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._sequenceSetPropertiesList.size()) { + throw new IndexOutOfBoundsException("setSequenceSetProperties: Index value '" + index + "' not in range [0.." + (this._sequenceSetPropertiesList.size() - 1) + "]"); + } + + this._sequenceSetPropertiesList.set(index, vSequenceSetProperties); + } + + /** + * + * + * @param vSequenceSetPropertiesArray + */ + public void setSequenceSetProperties( + final jalview.schemabinding.version2.SequenceSetProperties[] vSequenceSetPropertiesArray) { + //-- copy array + _sequenceSetPropertiesList.clear(); + + for (int i = 0; i < vSequenceSetPropertiesArray.length; i++) { + this._sequenceSetPropertiesList.add(vSequenceSetPropertiesArray[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.schemabinding.version2.SequenceSet + */ + public static jalview.schemabinding.version2.SequenceSet unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.SequenceSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.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/schemabinding/version2/SequenceSetProperties.java b/src/jalview/schemabinding/version2/SequenceSetProperties.java index dca7936..a078c78 100644 --- a/src/jalview/schemabinding/version2/SequenceSetProperties.java +++ b/src/jalview/schemabinding/version2/SequenceSetProperties.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,165 +19,152 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class SequenceSetProperties implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _key. - */ - private java.lang.String _key; - - /** - * Field _value. - */ - private java.lang.String _value; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SequenceSetProperties() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'key'. - * - * @return the value of field 'Key'. - */ - public java.lang.String getKey() - { - return this._key; - } - - /** - * 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; +public class SequenceSetProperties implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _key. + */ + private java.lang.String _key; + + /** + * Field _value. + */ + private java.lang.String _value; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceSetProperties() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'key'. + * + * @return the value of field 'Key'. + */ + public java.lang.String getKey( + ) { + return this._key; + } + + /** + * 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 'key'. + * + * @param key the value of field 'key'. + */ + public void setKey( + final java.lang.String key) { + this._key = key; + } + + /** + * 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.schemabinding.version2.SequenceSetProperties + */ + public static jalview.schemabinding.version2.SequenceSetProperties unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.SequenceSetProperties) Unmarshaller.unmarshal(jalview.schemabinding.version2.SequenceSetProperties.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); } - 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 'key'. - * - * @param key - * the value of field 'key'. - */ - public void setKey(final java.lang.String key) - { - this._key = key; - } - - /** - * 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.schemabinding.version2.SequenceSetProperties - */ - public static jalview.schemabinding.version2.SequenceSetProperties unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.SequenceSetProperties) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.SequenceSetProperties.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/schemabinding/version2/SequenceType.java b/src/jalview/schemabinding/version2/SequenceType.java index ce75ece..0d07812 100755 --- a/src/jalview/schemabinding/version2/SequenceType.java +++ b/src/jalview/schemabinding/version2/SequenceType.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,215 +19,202 @@ import org.exolab.castor.xml.Unmarshaller; * * @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(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * 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 '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; +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(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * 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 '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 'description'. + * + * @param description the value of field 'description'. + */ + public void setDescription( + final java.lang.String description) { + this._description = description; + } + + /** + * 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.schemabinding.version2.SequenceType + */ + public static jalview.schemabinding.version2.SequenceType unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.SequenceType) Unmarshaller.unmarshal(jalview.schemabinding.version2.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); } - 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 '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.schemabinding.version2.SequenceType - */ - public static jalview.schemabinding.version2.SequenceType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.SequenceType) Unmarshaller - .unmarshal(jalview.schemabinding.version2.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/schemabinding/version2/Setting.java b/src/jalview/schemabinding/version2/Setting.java index 9a49315..f4e57a9 100755 --- a/src/jalview/schemabinding/version2/Setting.java +++ b/src/jalview/schemabinding/version2/Setting.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,662 +19,648 @@ import org.exolab.castor.xml.Unmarshaller; * * @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; - - /** - * Field _order. - */ - private float _order; - - /** - * keeps track of state for field: _order - */ - private boolean _has_order; - - /** - * Optional minimum colour for graduated feature colour - */ - private int _mincolour; - - /** - * keeps track of state for field: _mincolour - */ - private boolean _has_mincolour; - - /** - * threshold value for graduated feature colour - */ - private float _threshold; - - /** - * keeps track of state for field: _threshold - */ - private boolean _has_threshold; - - /** - * threshold type for graduated feature colour - */ - private int _threshstate; - - /** - * keeps track of state for field: _threshstate - */ - private boolean _has_threshstate; - - /** - * Field _max. - */ - private float _max; - - /** - * keeps track of state for field: _max - */ - private boolean _has_max; - - /** - * Field _min. - */ - private float _min; - - /** - * keeps track of state for field: _min - */ - private boolean _has_min; - - /** - * Field _colourByLabel. - */ - private boolean _colourByLabel; - - /** - * keeps track of state for field: _colourByLabel - */ - private boolean _has_colourByLabel; - - /** - * Field _autoScale. - */ - private boolean _autoScale; - - /** - * keeps track of state for field: _autoScale - */ - private boolean _has_autoScale; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Setting() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteAutoScale() - { - this._has_autoScale = false; - } - - /** - */ - public void deleteColour() - { - this._has_colour = false; - } - - /** - */ - public void deleteColourByLabel() - { - this._has_colourByLabel = false; - } - - /** - */ - public void deleteDisplay() - { - this._has_display = false; - } - - /** - */ - public void deleteMax() - { - this._has_max = false; - } - - /** - */ - public void deleteMin() - { - this._has_min = false; - } - - /** - */ - public void deleteMincolour() - { - this._has_mincolour = false; - } - - /** - */ - public void deleteOrder() - { - this._has_order = false; - } - - /** - */ - public void deleteThreshold() - { - this._has_threshold = false; - } - - /** - */ - public void deleteThreshstate() - { - this._has_threshstate = false; - } - - /** - * Returns the value of field 'autoScale'. - * - * @return the value of field 'AutoScale'. - */ - public boolean getAutoScale() - { - return this._autoScale; - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public int getColour() - { - return this._colour; - } - - /** - * Returns the value of field 'colourByLabel'. - * - * @return the value of field 'ColourByLabel'. - */ - public boolean getColourByLabel() - { - return this._colourByLabel; - } - - /** - * Returns the value of field 'display'. - * - * @return the value of field 'Display'. - */ - public boolean getDisplay() - { - return this._display; - } - - /** - * Returns the value of field 'max'. - * - * @return the value of field 'Max'. - */ - public float getMax() - { - return this._max; - } - - /** - * Returns the value of field 'min'. - * - * @return the value of field 'Min'. - */ - public float getMin() - { - return this._min; - } - - /** - * Returns the value of field 'mincolour'. The field 'mincolour' has the - * following description: Optional minimum colour for graduated feature colour - * - * @return the value of field 'Mincolour'. - */ - public int getMincolour() - { - return this._mincolour; - } - - /** - * Returns the value of field 'order'. - * - * @return the value of field 'Order'. - */ - public float getOrder() - { - return this._order; - } - - /** - * Returns the value of field 'threshold'. The field 'threshold' has the - * following description: threshold value for graduated feature colour - * - * @return the value of field 'Threshold'. - */ - public float getThreshold() - { - return this._threshold; - } - - /** - * Returns the value of field 'threshstate'. The field 'threshstate' has the - * following description: threshold type for graduated feature colour - * - * @return the value of field 'Threshstate'. - */ - public int getThreshstate() - { - return this._threshstate; - } - - /** - * Returns the value of field 'type'. - * - * @return the value of field 'Type'. - */ - public java.lang.String getType() - { - return this._type; - } - - /** - * Method hasAutoScale. - * - * @return true if at least one AutoScale has been added - */ - public boolean hasAutoScale() - { - return this._has_autoScale; - } - - /** - * Method hasColour. - * - * @return true if at least one Colour has been added - */ - public boolean hasColour() - { - return this._has_colour; - } - - /** - * Method hasColourByLabel. - * - * @return true if at least one ColourByLabel has been added - */ - public boolean hasColourByLabel() - { - return this._has_colourByLabel; - } - - /** - * Method hasDisplay. - * - * @return true if at least one Display has been added - */ - public boolean hasDisplay() - { - return this._has_display; - } - - /** - * Method hasMax. - * - * @return true if at least one Max has been added - */ - public boolean hasMax() - { - return this._has_max; - } - - /** - * Method hasMin. - * - * @return true if at least one Min has been added - */ - public boolean hasMin() - { - return this._has_min; - } - - /** - * Method hasMincolour. - * - * @return true if at least one Mincolour has been added - */ - public boolean hasMincolour() - { - return this._has_mincolour; - } - - /** - * Method hasOrder. - * - * @return true if at least one Order has been added - */ - public boolean hasOrder() - { - return this._has_order; - } - - /** - * Method hasThreshold. - * - * @return true if at least one Threshold has been added - */ - public boolean hasThreshold() - { - return this._has_threshold; - } - - /** - * Method hasThreshstate. - * - * @return true if at least one Threshstate has been added - */ - public boolean hasThreshstate() - { - return this._has_threshstate; - } - - /** - * Returns the value of field 'autoScale'. - * - * @return the value of field 'AutoScale'. - */ - public boolean isAutoScale() - { - return this._autoScale; - } - - /** - * Returns the value of field 'colourByLabel'. - * - * @return the value of field 'ColourByLabel'. - */ - public boolean isColourByLabel() - { - return this._colourByLabel; - } - - /** - * 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 'autoScale'. - * - * @param autoScale - * the value of field 'autoScale'. - */ - public void setAutoScale(final boolean autoScale) - { - this._autoScale = autoScale; - this._has_autoScale = true; - } - - /** - * 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 'colourByLabel'. - * - * @param colourByLabel - * the value of field 'colourByLabel'. - */ - public void setColourByLabel(final boolean colourByLabel) - { - this._colourByLabel = colourByLabel; - this._has_colourByLabel = 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 'max'. - * - * @param max - * the value of field 'max'. - */ - public void setMax(final float max) - { - this._max = max; - this._has_max = true; - } - - /** - * Sets the value of field 'min'. - * - * @param min - * the value of field 'min'. - */ - public void setMin(final float min) - { - this._min = min; - this._has_min = true; - } - - /** - * Sets the value of field 'mincolour'. The field 'mincolour' has the - * following description: Optional minimum colour for graduated feature colour - * - * @param mincolour - * the value of field 'mincolour'. - */ - public void setMincolour(final int mincolour) - { - this._mincolour = mincolour; - this._has_mincolour = true; - } - - /** - * Sets the value of field 'order'. - * - * @param order - * the value of field 'order'. - */ - public void setOrder(final float order) - { - this._order = order; - this._has_order = true; - } - - /** - * Sets the value of field 'threshold'. The field 'threshold' has the - * following description: threshold value for graduated feature colour - * - * @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 'threshstate'. The field 'threshstate' has the - * following description: threshold type for graduated feature colour - * - * @param threshstate - * the value of field 'threshstate'. - */ - public void setThreshstate(final int threshstate) - { - this._threshstate = threshstate; - this._has_threshstate = 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.schemabinding.version2.Settin - */ - public static jalview.schemabinding.version2.Setting unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal( - jalview.schemabinding.version2.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); - } +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; + + /** + * Field _order. + */ + private float _order; + + /** + * keeps track of state for field: _order + */ + private boolean _has_order; + + /** + * Optional minimum colour for graduated feature colour + */ + private int _mincolour; + + /** + * keeps track of state for field: _mincolour + */ + private boolean _has_mincolour; + + /** + * threshold value for graduated feature colour + */ + private float _threshold; + + /** + * keeps track of state for field: _threshold + */ + private boolean _has_threshold; + + /** + * threshold type for graduated feature colour + */ + private int _threshstate; + + /** + * keeps track of state for field: _threshstate + */ + private boolean _has_threshstate; + + /** + * Field _max. + */ + private float _max; + + /** + * keeps track of state for field: _max + */ + private boolean _has_max; + + /** + * Field _min. + */ + private float _min; + + /** + * keeps track of state for field: _min + */ + private boolean _has_min; + + /** + * Field _colourByLabel. + */ + private boolean _colourByLabel; + + /** + * keeps track of state for field: _colourByLabel + */ + private boolean _has_colourByLabel; + + /** + * Field _autoScale. + */ + private boolean _autoScale; + + /** + * keeps track of state for field: _autoScale + */ + private boolean _has_autoScale; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Setting() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteAutoScale( + ) { + this._has_autoScale= false; + } + + /** + */ + public void deleteColour( + ) { + this._has_colour= false; + } + + /** + */ + public void deleteColourByLabel( + ) { + this._has_colourByLabel= false; + } + + /** + */ + public void deleteDisplay( + ) { + this._has_display= false; + } + + /** + */ + public void deleteMax( + ) { + this._has_max= false; + } + + /** + */ + public void deleteMin( + ) { + this._has_min= false; + } + + /** + */ + public void deleteMincolour( + ) { + this._has_mincolour= false; + } + + /** + */ + public void deleteOrder( + ) { + this._has_order= false; + } + + /** + */ + public void deleteThreshold( + ) { + this._has_threshold= false; + } + + /** + */ + public void deleteThreshstate( + ) { + this._has_threshstate= false; + } + + /** + * Returns the value of field 'autoScale'. + * + * @return the value of field 'AutoScale'. + */ + public boolean getAutoScale( + ) { + return this._autoScale; + } + + /** + * Returns the value of field 'colour'. + * + * @return the value of field 'Colour'. + */ + public int getColour( + ) { + return this._colour; + } + + /** + * Returns the value of field 'colourByLabel'. + * + * @return the value of field 'ColourByLabel'. + */ + public boolean getColourByLabel( + ) { + return this._colourByLabel; + } + + /** + * Returns the value of field 'display'. + * + * @return the value of field 'Display'. + */ + public boolean getDisplay( + ) { + return this._display; + } + + /** + * Returns the value of field 'max'. + * + * @return the value of field 'Max'. + */ + public float getMax( + ) { + return this._max; + } + + /** + * Returns the value of field 'min'. + * + * @return the value of field 'Min'. + */ + public float getMin( + ) { + return this._min; + } + + /** + * Returns the value of field 'mincolour'. The field + * 'mincolour' has the following description: Optional minimum + * colour for graduated feature colour + * + * @return the value of field 'Mincolour'. + */ + public int getMincolour( + ) { + return this._mincolour; + } + + /** + * Returns the value of field 'order'. + * + * @return the value of field 'Order'. + */ + public float getOrder( + ) { + return this._order; + } + + /** + * Returns the value of field 'threshold'. The field + * 'threshold' has the following description: threshold value + * for graduated feature colour + * + * @return the value of field 'Threshold'. + */ + public float getThreshold( + ) { + return this._threshold; + } + + /** + * Returns the value of field 'threshstate'. The field + * 'threshstate' has the following description: threshold type + * for graduated feature colour + * + * @return the value of field 'Threshstate'. + */ + public int getThreshstate( + ) { + return this._threshstate; + } + + /** + * Returns the value of field 'type'. + * + * @return the value of field 'Type'. + */ + public java.lang.String getType( + ) { + return this._type; + } + + /** + * Method hasAutoScale. + * + * @return true if at least one AutoScale has been added + */ + public boolean hasAutoScale( + ) { + return this._has_autoScale; + } + + /** + * Method hasColour. + * + * @return true if at least one Colour has been added + */ + public boolean hasColour( + ) { + return this._has_colour; + } + + /** + * Method hasColourByLabel. + * + * @return true if at least one ColourByLabel has been added + */ + public boolean hasColourByLabel( + ) { + return this._has_colourByLabel; + } + + /** + * Method hasDisplay. + * + * @return true if at least one Display has been added + */ + public boolean hasDisplay( + ) { + return this._has_display; + } + + /** + * Method hasMax. + * + * @return true if at least one Max has been added + */ + public boolean hasMax( + ) { + return this._has_max; + } + + /** + * Method hasMin. + * + * @return true if at least one Min has been added + */ + public boolean hasMin( + ) { + return this._has_min; + } + + /** + * Method hasMincolour. + * + * @return true if at least one Mincolour has been added + */ + public boolean hasMincolour( + ) { + return this._has_mincolour; + } + + /** + * Method hasOrder. + * + * @return true if at least one Order has been added + */ + public boolean hasOrder( + ) { + return this._has_order; + } + + /** + * Method hasThreshold. + * + * @return true if at least one Threshold has been added + */ + public boolean hasThreshold( + ) { + return this._has_threshold; + } + + /** + * Method hasThreshstate. + * + * @return true if at least one Threshstate has been added + */ + public boolean hasThreshstate( + ) { + return this._has_threshstate; + } + + /** + * Returns the value of field 'autoScale'. + * + * @return the value of field 'AutoScale'. + */ + public boolean isAutoScale( + ) { + return this._autoScale; + } + + /** + * Returns the value of field 'colourByLabel'. + * + * @return the value of field 'ColourByLabel'. + */ + public boolean isColourByLabel( + ) { + return this._colourByLabel; + } + + /** + * 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 'autoScale'. + * + * @param autoScale the value of field 'autoScale'. + */ + public void setAutoScale( + final boolean autoScale) { + this._autoScale = autoScale; + this._has_autoScale = true; + } + + /** + * 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 'colourByLabel'. + * + * @param colourByLabel the value of field 'colourByLabel'. + */ + public void setColourByLabel( + final boolean colourByLabel) { + this._colourByLabel = colourByLabel; + this._has_colourByLabel = 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 'max'. + * + * @param max the value of field 'max'. + */ + public void setMax( + final float max) { + this._max = max; + this._has_max = true; + } + + /** + * Sets the value of field 'min'. + * + * @param min the value of field 'min'. + */ + public void setMin( + final float min) { + this._min = min; + this._has_min = true; + } + + /** + * Sets the value of field 'mincolour'. The field 'mincolour' + * has the following description: Optional minimum colour for + * graduated feature colour + * + * @param mincolour the value of field 'mincolour'. + */ + public void setMincolour( + final int mincolour) { + this._mincolour = mincolour; + this._has_mincolour = true; + } + + /** + * Sets the value of field 'order'. + * + * @param order the value of field 'order'. + */ + public void setOrder( + final float order) { + this._order = order; + this._has_order = true; + } + + /** + * Sets the value of field 'threshold'. The field 'threshold' + * has the following description: threshold value for graduated + * feature colour + * + * @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 'threshstate'. The field + * 'threshstate' has the following description: threshold type + * for graduated feature colour + * + * @param threshstate the value of field 'threshstate'. + */ + public void setThreshstate( + final int threshstate) { + this._threshstate = threshstate; + this._has_threshstate = 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.schemabinding.version2.Settin + */ + public static jalview.schemabinding.version2.Setting unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Setting) Unmarshaller.unmarshal(jalview.schemabinding.version2.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/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java index 4ce6aa7..7a2b076 100644 --- a/src/jalview/schemabinding/version2/StructureState.java +++ b/src/jalview/schemabinding/version2/StructureState.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,435 +19,584 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class StructureState implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * internal content storage - */ - private java.lang.String _content = ""; - - /** - * Field _visible. - */ - private boolean _visible; - - /** - * keeps track of state for field: _visible - */ - private boolean _has_visible; - - /** - * 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; - - /** - * additional identifier which properly disambiguates the structure view from - * any other view with the same attributes. This is not an ID, because it is - * possible to have many references to the same physical structure view from - * different sequences in an alignment. A structureState element citing the - * same viewId will appear for each instance. - */ - private java.lang.String _viewId; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public StructureState() - { - super(); - setContent(""); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteHeight() - { - this._has_height = false; - } - - /** - */ - public void deleteVisible() - { - this._has_visible = 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 'content'. The field 'content' has the following - * description: internal content storage - * - * @return the value of field 'Content'. - */ - public java.lang.String getContent() - { - return this._content; - } - - /** - * Returns the value of field 'height'. - * - * @return the value of field 'Height'. - */ - public int getHeight() - { - return this._height; - } - - /** - * Returns the value of field 'viewId'. The field 'viewId' has the following - * description: additional identifier which properly disambiguates the - * structure view from any other view with the same attributes. This is not an - * ID, because it is possible to have many references to the same physical - * structure view from different sequences in an alignment. A structureState - * element citing the same viewId will appear for each instance. - * - * @return the value of field 'ViewId'. - */ - public java.lang.String getViewId() - { - return this._viewId; - } - - /** - * Returns the value of field 'visible'. - * - * @return the value of field 'Visible'. - */ - public boolean getVisible() - { - return this._visible; - } - - /** - * 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 hasHeight. - * - * @return true if at least one Height has been added - */ - public boolean hasHeight() - { - return this._has_height; - } - - /** - * Method hasVisible. - * - * @return true if at least one Visible has been added - */ - public boolean hasVisible() - { - return this._has_visible; - } - - /** - * 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; - } - - /** - * 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 'visible'. - * - * @return the value of field 'Visible'. - */ - public boolean isVisible() - { - return this._visible; - } - - /** - * - * - * @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 'content'. The field 'content' has the following - * description: internal content storage - * - * @param content - * the value of field 'content'. - */ - public void setContent(final java.lang.String content) - { - this._content = content; - } - - /** - * 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 'viewId'. The field 'viewId' has the following - * description: additional identifier which properly disambiguates the - * structure view from any other view with the same attributes. This is not an - * ID, because it is possible to have many references to the same physical - * structure view from different sequences in an alignment. A structureState - * element citing the same viewId will appear for each instance. - * - * @param viewId - * the value of field 'viewId'. - */ - public void setViewId(final java.lang.String viewId) - { - this._viewId = viewId; - } - - /** - * Sets the value of field 'visible'. - * - * @param visible - * the value of field 'visible'. - */ - public void setVisible(final boolean visible) - { - this._visible = visible; - this._has_visible = true; - } - - /** - * 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.schemabinding.version2.StructureState - */ - public static jalview.schemabinding.version2.StructureState unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.StructureState) Unmarshaller - .unmarshal(jalview.schemabinding.version2.StructureState.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); - } +public class StructureState implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * internal content storage + */ + private java.lang.String _content = ""; + + /** + * Field _visible. + */ + private boolean _visible; + + /** + * keeps track of state for field: _visible + */ + private boolean _has_visible; + + /** + * 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; + + /** + * additional identifier which properly disambiguates + * the structure view from any other view with the same + * attributes. This is not an ID, + * because it is possible to have many references to the same + * physical structure view + * from different sequences in an alignment. A structureState + * element citing the same + * viewId will appear for each instance. + */ + private java.lang.String _viewId; + + /** + * Flag set if the alignment panel containing this JSeq should + * be explicitly linked to the Jmol view referred to/created by + * this structureState (since Jalview 2.7). + * + */ + private boolean _linkAlignPanel = true; + + /** + * keeps track of state for field: _linkAlignPanel + */ + private boolean _has_linkAlignPanel; + + /** + * Flag set if the alignment panel containing this JSeq should + * be included in those used to perform a structure + * superposition (since Jalview 2.7). + * + */ + private boolean _alignwithAlignPanel = true; + + /** + * keeps track of state for field: _alignwithAlignPanel + */ + private boolean _has_alignwithAlignPanel; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public StructureState() { + super(); + setContent(""); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteAlignwithAlignPanel( + ) { + this._has_alignwithAlignPanel= false; + } + + /** + */ + public void deleteHeight( + ) { + this._has_height= false; + } + + /** + */ + public void deleteLinkAlignPanel( + ) { + this._has_linkAlignPanel= false; + } + + /** + */ + public void deleteVisible( + ) { + this._has_visible= 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 'alignwithAlignPanel'. The field + * 'alignwithAlignPanel' has the following description: Flag + * set if the alignment panel containing this JSeq should be + * included in those used to perform a structure superposition + * (since Jalview 2.7). + * + * + * @return the value of field 'AlignwithAlignPanel'. + */ + public boolean getAlignwithAlignPanel( + ) { + return this._alignwithAlignPanel; + } + + /** + * Returns the value of field 'content'. The field 'content' + * has the following description: internal content storage + * + * @return the value of field 'Content'. + */ + public java.lang.String getContent( + ) { + return this._content; + } + + /** + * Returns the value of field 'height'. + * + * @return the value of field 'Height'. + */ + public int getHeight( + ) { + return this._height; + } + + /** + * Returns the value of field 'linkAlignPanel'. The field + * 'linkAlignPanel' has the following description: Flag set if + * the alignment panel containing this JSeq should be + * explicitly linked to the Jmol view referred to/created by + * this structureState (since Jalview 2.7). + * + * + * @return the value of field 'LinkAlignPanel'. + */ + public boolean getLinkAlignPanel( + ) { + return this._linkAlignPanel; + } + + /** + * Returns the value of field 'viewId'. The field 'viewId' has + * the following description: additional identifier which + * properly disambiguates + * the structure view from any other view with the same + * attributes. This is not an ID, + * because it is possible to have many references to the same + * physical structure view + * from different sequences in an alignment. A structureState + * element citing the same + * viewId will appear for each instance. + * + * @return the value of field 'ViewId'. + */ + public java.lang.String getViewId( + ) { + return this._viewId; + } + + /** + * Returns the value of field 'visible'. + * + * @return the value of field 'Visible'. + */ + public boolean getVisible( + ) { + return this._visible; + } + + /** + * 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 hasAlignwithAlignPanel. + * + * @return true if at least one AlignwithAlignPanel has been + * added + */ + public boolean hasAlignwithAlignPanel( + ) { + return this._has_alignwithAlignPanel; + } + + /** + * Method hasHeight. + * + * @return true if at least one Height has been added + */ + public boolean hasHeight( + ) { + return this._has_height; + } + + /** + * Method hasLinkAlignPanel. + * + * @return true if at least one LinkAlignPanel has been added + */ + public boolean hasLinkAlignPanel( + ) { + return this._has_linkAlignPanel; + } + + /** + * Method hasVisible. + * + * @return true if at least one Visible has been added + */ + public boolean hasVisible( + ) { + return this._has_visible; + } + + /** + * 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 'alignwithAlignPanel'. The field + * 'alignwithAlignPanel' has the following description: Flag + * set if the alignment panel containing this JSeq should be + * included in those used to perform a structure superposition + * (since Jalview 2.7). + * + * + * @return the value of field 'AlignwithAlignPanel'. + */ + public boolean isAlignwithAlignPanel( + ) { + return this._alignwithAlignPanel; + } + + /** + * Returns the value of field 'linkAlignPanel'. The field + * 'linkAlignPanel' has the following description: Flag set if + * the alignment panel containing this JSeq should be + * explicitly linked to the Jmol view referred to/created by + * this structureState (since Jalview 2.7). + * + * + * @return the value of field 'LinkAlignPanel'. + */ + public boolean isLinkAlignPanel( + ) { + return this._linkAlignPanel; + } + + /** + * 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 'visible'. + * + * @return the value of field 'Visible'. + */ + public boolean isVisible( + ) { + return this._visible; + } + + /** + * + * + * @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 'alignwithAlignPanel'. The field + * 'alignwithAlignPanel' has the following description: Flag + * set if the alignment panel containing this JSeq should be + * included in those used to perform a structure superposition + * (since Jalview 2.7). + * + * + * @param alignwithAlignPanel the value of field + * 'alignwithAlignPanel'. + */ + public void setAlignwithAlignPanel( + final boolean alignwithAlignPanel) { + this._alignwithAlignPanel = alignwithAlignPanel; + this._has_alignwithAlignPanel = true; + } + + /** + * Sets the value of field 'content'. The field 'content' has + * the following description: internal content storage + * + * @param content the value of field 'content'. + */ + public void setContent( + final java.lang.String content) { + this._content = content; + } + + /** + * 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 'linkAlignPanel'. The field + * 'linkAlignPanel' has the following description: Flag set if + * the alignment panel containing this JSeq should be + * explicitly linked to the Jmol view referred to/created by + * this structureState (since Jalview 2.7). + * + * + * @param linkAlignPanel the value of field 'linkAlignPanel'. + */ + public void setLinkAlignPanel( + final boolean linkAlignPanel) { + this._linkAlignPanel = linkAlignPanel; + this._has_linkAlignPanel = true; + } + + /** + * Sets the value of field 'viewId'. The field 'viewId' has the + * following description: additional identifier which properly + * disambiguates + * the structure view from any other view with the same + * attributes. This is not an ID, + * because it is possible to have many references to the same + * physical structure view + * from different sequences in an alignment. A structureState + * element citing the same + * viewId will appear for each instance. + * + * @param viewId the value of field 'viewId'. + */ + public void setViewId( + final java.lang.String viewId) { + this._viewId = viewId; + } + + /** + * Sets the value of field 'visible'. + * + * @param visible the value of field 'visible'. + */ + public void setVisible( + final boolean visible) { + this._visible = visible; + this._has_visible = true; + } + + /** + * 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.schemabinding.version2.StructureState + */ + public static jalview.schemabinding.version2.StructureState unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.StructureState) Unmarshaller.unmarshal(jalview.schemabinding.version2.StructureState.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/schemabinding/version2/ThresholdLine.java b/src/jalview/schemabinding/version2/ThresholdLine.java index f479c36..4e3f124 100755 --- a/src/jalview/schemabinding/version2/ThresholdLine.java +++ b/src/jalview/schemabinding/version2/ThresholdLine.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,235 +19,223 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class ThresholdLine implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _label. - */ - private java.lang.String _label; - - /** - * Field _value. - */ - private float _value; - - /** - * keeps track of state for field: _value - */ - private boolean _has_value; - - /** - * Field _colour. - */ - private int _colour; - - /** - * keeps track of state for field: _colour - */ - private boolean _has_colour; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public ThresholdLine() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** +public class ThresholdLine implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _label. + */ + private java.lang.String _label; + + /** + * Field _value. + */ + private float _value; + + /** + * keeps track of state for field: _value + */ + private boolean _has_value; + + /** + * Field _colour. + */ + private int _colour; + + /** + * keeps track of state for field: _colour */ - public void deleteColour() - { - this._has_colour = false; - } + private boolean _has_colour; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public ThresholdLine() { + super(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + */ + public void deleteColour( + ) { + this._has_colour= false; + } + + /** + */ + public void deleteValue( + ) { + this._has_value= false; + } + + /** + * Returns the value of field 'colour'. + * + * @return the value of field 'Colour'. + */ + public int getColour( + ) { + return this._colour; + } + + /** + * Returns the value of field 'label'. + * + * @return the value of field 'Label'. + */ + public java.lang.String getLabel( + ) { + return this._label; + } + + /** + * Returns the value of field 'value'. + * + * @return the value of field 'Value'. + */ + public float getValue( + ) { + return this._value; + } + + /** + * Method hasColour. + * + * @return true if at least one Colour has been added + */ + public boolean hasColour( + ) { + return this._has_colour; + } + + /** + * 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 '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 'label'. + * + * @param label the value of field 'label'. + */ + public void setLabel( + final java.lang.String label) { + this._label = label; + } + + /** + * 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.schemabinding.version2.ThresholdLine + */ + public static jalview.schemabinding.version2.ThresholdLine unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.ThresholdLine) Unmarshaller.unmarshal(jalview.schemabinding.version2.ThresholdLine.class, reader); + } - /** + /** + * + * + * @throws org.exolab.castor.xml.ValidationException if this + * object is an invalid instance according to the schema */ - public void deleteValue() - { - this._has_value = false; - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public int getColour() - { - return this._colour; - } - - /** - * Returns the value of field 'label'. - * - * @return the value of field 'Label'. - */ - public java.lang.String getLabel() - { - return this._label; - } - - /** - * Returns the value of field 'value'. - * - * @return the value of field 'Value'. - */ - public float getValue() - { - return this._value; - } - - /** - * Method hasColour. - * - * @return true if at least one Colour has been added - */ - public boolean hasColour() - { - return this._has_colour; - } - - /** - * 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; + public void validate( + ) + throws org.exolab.castor.xml.ValidationException { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); } - 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 'label'. - * - * @param label - * the value of field 'label'. - */ - public void setLabel(final java.lang.String label) - { - this._label = label; - } - - /** - * 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.schemabinding.version2.ThresholdLine - */ - public static jalview.schemabinding.version2.ThresholdLine unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.ThresholdLine) Unmarshaller - .unmarshal(jalview.schemabinding.version2.ThresholdLine.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/schemabinding/version2/Tree.java b/src/jalview/schemabinding/version2/Tree.java index 498e29f..c73cb12 100755 --- a/src/jalview/schemabinding/version2/Tree.java +++ b/src/jalview/schemabinding/version2/Tree.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,857 +19,834 @@ import org.exolab.castor.xml.Unmarshaller; * * @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; - - /** - * Tree ID added for binding tree visualization settings to vamsas document - * trees in jalview 2.4.1 - */ - private java.lang.String _id; - - /** - * 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 'id'. The field 'id' has the following - * description: Tree ID added for binding tree visualization settings to - * vamsas document trees in jalview 2.4.1 - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * 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 'id'. The field 'id' has the following description: - * Tree ID added for binding tree visualization settings to vamsas document - * trees in jalview 2.4.1 - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * 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.schemabinding.version2.Tree - */ - public static jalview.schemabinding.version2.Tree unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal( - jalview.schemabinding.version2.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); - } +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; + + /** + * Tree ID added for binding tree visualization settings to + * vamsas document trees in jalview 2.4.1 + */ + private java.lang.String _id; + + /** + * 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 'id'. The field 'id' has the + * following description: Tree ID added for binding tree + * visualization settings to vamsas document trees in jalview + * 2.4.1 + * + * @return the value of field 'Id'. + */ + public java.lang.String getId( + ) { + return this._id; + } + + /** + * 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 'id'. The field 'id' has the + * following description: Tree ID added for binding tree + * visualization settings to vamsas document trees in jalview + * 2.4.1 + * + * @param id the value of field 'id'. + */ + public void setId( + final java.lang.String id) { + this._id = id; + } + + /** + * 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.schemabinding.version2.Tree + */ + public static jalview.schemabinding.version2.Tree unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Tree) Unmarshaller.unmarshal(jalview.schemabinding.version2.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/schemabinding/version2/UserColourScheme.java b/src/jalview/schemabinding/version2/UserColourScheme.java index 28c415f..3cb65e0 100755 --- a/src/jalview/schemabinding/version2/UserColourScheme.java +++ b/src/jalview/schemabinding/version2/UserColourScheme.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,109 +19,99 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class UserColourScheme extends JalviewUserColours implements - java.io.Serializable +public class UserColourScheme extends JalviewUserColours +implements java.io.Serializable { - // ----------------/ - // - Constructors -/ - // ----------------/ - public UserColourScheme() - { - super(); - } + //----------------/ + //- Constructors -/ + //----------------/ - // -----------/ - // - Methods -/ - // -----------/ + public UserColourScheme() { + super(); + } - /** - * 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; + + //-----------/ + //- 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; } - 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 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); - } + /** + * + * + * @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.schemabinding.version2.JalviewUserColours - */ - public static jalview.schemabinding.version2.JalviewUserColours unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.UserColourScheme.class, - reader); - } + /** + * 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.schemabinding.version2.JalviewUserColours + */ + public static jalview.schemabinding.version2.JalviewUserColours unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.JalviewUserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.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); - } + /** + * + * + * @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/schemabinding/version2/UserColours.java b/src/jalview/schemabinding/version2/UserColours.java index 12356b5..062024f 100755 --- a/src/jalview/schemabinding/version2/UserColours.java +++ b/src/jalview/schemabinding/version2/UserColours.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,164 +19,152 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class UserColours implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _userColourScheme. - */ - private jalview.schemabinding.version2.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.schemabinding.version2.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; +public class UserColours implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _id. + */ + private java.lang.String _id; + + /** + * Field _userColourScheme. + */ + private jalview.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.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.schemabinding.version2.UserColours + */ + public static jalview.schemabinding.version2.UserColours unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.UserColours) Unmarshaller.unmarshal(jalview.schemabinding.version2.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); } - 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.schemabinding.version2.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.schemabinding.version2.UserColours - */ - public static jalview.schemabinding.version2.UserColours unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.UserColours) Unmarshaller - .unmarshal(jalview.schemabinding.version2.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/schemabinding/version2/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java index a0b3460..ae8e17f 100755 --- a/src/jalview/schemabinding/version2/VAMSAS.java +++ b/src/jalview/schemabinding/version2/VAMSAS.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,436 +19,411 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class VAMSAS implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _treeList. - */ - private java.util.Vector _treeList; - - /** - * Field _sequenceSetList. - */ - private java.util.Vector _sequenceSetList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public VAMSAS() - { - super(); - this._treeList = new java.util.Vector(); - this._sequenceSetList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vSequenceSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSequenceSet( - final jalview.schemabinding.version2.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 jalview.schemabinding.version2.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 enumerateSequenceSet. - * - * @return an Enumeration over all jalview.schemabinding.version2.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 getSequenceSet. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.SequenceSet at the - * given index - */ - public jalview.schemabinding.version2.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) + "]"); +public class VAMSAS implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _treeList. + */ + private java.util.Vector _treeList; + + /** + * Field _sequenceSetList. + */ + private java.util.Vector _sequenceSetList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public VAMSAS() { + super(); + this._treeList = new java.util.Vector(); + this._sequenceSetList = new java.util.Vector(); } - return (jalview.schemabinding.version2.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 jalview.schemabinding.version2.SequenceSet[] getSequenceSet() - { - jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0]; - return (jalview.schemabinding.version2.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) + "]"); + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vSequenceSet + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addSequenceSet( + final jalview.schemabinding.version2.SequenceSet vSequenceSet) + throws java.lang.IndexOutOfBoundsException { + this._sequenceSetList.addElement(vSequenceSet); } - 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; + /** + * + * + * @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 jalview.schemabinding.version2.SequenceSet vSequenceSet) + throws java.lang.IndexOutOfBoundsException { + this._sequenceSetList.add(index, vSequenceSet); } - 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); - } - - /** + + /** + * + * + * @param vTree + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection */ - public void removeAllSequenceSet() - { - this._sequenceSetList.clear(); - } + 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 removeAllTree() - { - this._treeList.clear(); - } - - /** - * Method removeSequenceSet. - * - * @param vSequenceSet - * @return true if the object was removed from the collection. - */ - public boolean removeSequenceSet( - final jalview.schemabinding.version2.SequenceSet vSequenceSet) - { - boolean removed = _sequenceSetList.remove(vSequenceSet); - return removed; - } - - /** - * Method removeSequenceSetAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt( - final int index) - { - java.lang.Object obj = this._sequenceSetList.remove(index); - return (jalview.schemabinding.version2.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 vSequenceSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setSequenceSet(final int index, - final jalview.schemabinding.version2.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) + "]"); + public void addTree( + final int index, + final java.lang.String vTree) + throws java.lang.IndexOutOfBoundsException { + this._treeList.add(index, vTree); } - this._sequenceSetList.set(index, vSequenceSet); - } - - /** - * - * - * @param vSequenceSetArray - */ - public void setSequenceSet( - final jalview.schemabinding.version2.SequenceSet[] vSequenceSetArray) - { - // -- copy array - _sequenceSetList.clear(); - - for (int i = 0; i < vSequenceSetArray.length; i++) - { - this._sequenceSetList.add(vSequenceSetArray[i]); + /** + * Method enumerateSequenceSet. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.SequenceSet elements + */ + public java.util.Enumeration enumerateSequenceSet( + ) { + return this._sequenceSetList.elements(); } - } - - /** - * - * - * @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) + "]"); + + /** + * Method enumerateTree. + * + * @return an Enumeration over all java.lang.String elements + */ + public java.util.Enumeration enumerateTree( + ) { + return this._treeList.elements(); + } + + /** + * Method getSequenceSet. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.SequenceSet at the given index + */ + public jalview.schemabinding.version2.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 (jalview.schemabinding.version2.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 jalview.schemabinding.version2.SequenceSet[] getSequenceSet( + ) { + jalview.schemabinding.version2.SequenceSet[] array = new jalview.schemabinding.version2.SequenceSet[0]; + return (jalview.schemabinding.version2.SequenceSet[]) this._sequenceSetList.toArray(array); + } + + /** + * Method getSequenceSetCount. + * + * @return the size of this collection + */ + public int getSequenceSetCount( + ) { + return this._sequenceSetList.size(); } - 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 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); + } + + /** + */ + 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 jalview.schemabinding.version2.SequenceSet vSequenceSet) { + boolean removed = _sequenceSetList.remove(vSequenceSet); + return removed; + } + + /** + * Method removeSequenceSetAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.SequenceSet removeSequenceSetAt( + final int index) { + java.lang.Object obj = this._sequenceSetList.remove(index); + return (jalview.schemabinding.version2.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 vSequenceSet + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setSequenceSet( + final int index, + final jalview.schemabinding.version2.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 jalview.schemabinding.version2.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.schemabinding.version2.VAMSAS + */ + public static jalview.schemabinding.version2.VAMSAS unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.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); } - } - - /** - * 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.schemabinding.version2.VAMSAS - */ - public static jalview.schemabinding.version2.VAMSAS unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal( - jalview.schemabinding.version2.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/schemabinding/version2/VamsasModel.java b/src/jalview/schemabinding/version2/VamsasModel.java index d76cc82..26814dc 100755 --- a/src/jalview/schemabinding/version2/VamsasModel.java +++ b/src/jalview/schemabinding/version2/VamsasModel.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,106 +19,98 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class VamsasModel extends VAMSAS implements java.io.Serializable +public class VamsasModel extends VAMSAS +implements java.io.Serializable { - // ----------------/ - // - Constructors -/ - // ----------------/ - public VamsasModel() - { - super(); - } + //----------------/ + //- Constructors -/ + //----------------/ - // -----------/ - // - Methods -/ - // -----------/ + public VamsasModel() { + super(); + } - /** - * 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; + + //-----------/ + //- 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; } - 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 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); - } + /** + * + * + * @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.schemabinding.version2.VAMSAS - */ - public static jalview.schemabinding.version2.VAMSAS unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal( - jalview.schemabinding.version2.VamsasModel.class, reader); - } + /** + * 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.schemabinding.version2.VAMSAS + */ + public static jalview.schemabinding.version2.VAMSAS unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.VAMSAS) Unmarshaller.unmarshal(jalview.schemabinding.version2.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); - } + /** + * + * + * @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/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java index 3cfdb3e..49b0db2 100755 --- a/src/jalview/schemabinding/version2/Viewport.java +++ b/src/jalview/schemabinding/version2/Viewport.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,2465 +19,2416 @@ import org.exolab.castor.xml.Unmarshaller; * * @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 _rightAlignIds. - */ - private boolean _rightAlignIds; - - /** - * keeps track of state for field: _rightAlignIds - */ - private boolean _has_rightAlignIds; - - /** - * 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 _showUnconserved. - */ - private boolean _showUnconserved = false; - - /** - * keeps track of state for field: _showUnconserved - */ - private boolean _has_showUnconserved; - - /** - * 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 _showNPfeatureTooltip. - */ - private boolean _showNPfeatureTooltip; - - /** - * keeps track of state for field: _showNPfeatureTooltip - */ - private boolean _has_showNPfeatureTooltip; - - /** - * Field _showDbRefTooltip. - */ - private boolean _showDbRefTooltip; - - /** - * keeps track of state for field: _showDbRefTooltip - */ - private boolean _has_showDbRefTooltip; - - /** - * Field _followHighlight. - */ - private boolean _followHighlight = true; - - /** - * keeps track of state for field: _followHighlight - */ - private boolean _has_followHighlight; - - /** - * Field _followSelection. - */ - private boolean _followSelection = true; - - /** - * keeps track of state for field: _followSelection - */ - private boolean _has_followSelection; - - /** - * Field _showAnnotation. - */ - private boolean _showAnnotation; - - /** - * keeps track of state for field: _showAnnotation - */ - private boolean _has_showAnnotation; - - /** - * Field _centreColumnLabels. - */ - private boolean _centreColumnLabels = false; - - /** - * keeps track of state for field: _centreColumnLabels - */ - private boolean _has_centreColumnLabels; - - /** - * Field _showGroupConservation. - */ - private boolean _showGroupConservation = false; - - /** - * keeps track of state for field: _showGroupConservation - */ - private boolean _has_showGroupConservation; - - /** - * Field _showGroupConsensus. - */ - private boolean _showGroupConsensus = false; - - /** - * keeps track of state for field: _showGroupConsensus - */ - private boolean _has_showGroupConsensus; - - /** - * Field _showConsensusHistogram. - */ - private boolean _showConsensusHistogram = true; - - /** - * keeps track of state for field: _showConsensusHistogram - */ - private boolean _has_showConsensusHistogram; - - /** - * Field _showSequenceLogo. - */ - private boolean _showSequenceLogo = false; - - /** - * keeps track of state for field: _showSequenceLogo - */ - private boolean _has_showSequenceLogo; - - /** - * Field _ignoreGapsinConsensus. - */ - private boolean _ignoreGapsinConsensus = true; - - /** - * keeps track of state for field: _ignoreGapsinConsensus - */ - private boolean _has_ignoreGapsinConsensus; - - /** - * 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; - - /** - * Field _viewName. - */ - private java.lang.String _viewName; - - /** - * Field _sequenceSetId. - */ - private java.lang.String _sequenceSetId; - - /** - * Field _gatheredViews. - */ - private boolean _gatheredViews; - - /** - * keeps track of state for field: _gatheredViews - */ - private boolean _has_gatheredViews; - - /** - * Field _textCol1. - */ - private int _textCol1; - - /** - * keeps track of state for field: _textCol1 - */ - private boolean _has_textCol1; - - /** - * Field _textCol2. - */ - private int _textCol2; - - /** - * keeps track of state for field: _textCol2 - */ - private boolean _has_textCol2; - - /** - * Field _textColThreshold. - */ - private int _textColThreshold; - - /** - * keeps track of state for field: _textColThreshold - */ - private boolean _has_textColThreshold; - - /** - * unique id used by jalview to synchronize between stored and instantiated - * views - * - */ - private java.lang.String _id; - - /** - * Field _annotationColours. - */ - private jalview.schemabinding.version2.AnnotationColours _annotationColours; - - /** - * Field _hiddenColumnsList. - */ - private java.util.Vector _hiddenColumnsList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Viewport() - { - super(); - this._hiddenColumnsList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vHiddenColumns - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addHiddenColumns( - final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) - throws java.lang.IndexOutOfBoundsException - { - this._hiddenColumnsList.addElement(vHiddenColumns); - } - - /** - * - * - * @param index - * @param vHiddenColumns - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addHiddenColumns(final int index, - final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) - throws java.lang.IndexOutOfBoundsException - { - this._hiddenColumnsList.add(index, vHiddenColumns); - } - - /** - */ - public void deleteCentreColumnLabels() - { - this._has_centreColumnLabels = false; - } - - /** - */ - public void deleteConsThreshold() - { - this._has_consThreshold = false; - } - - /** - */ - public void deleteConservationSelected() - { - this._has_conservationSelected = false; - } - - /** - */ - public void deleteFollowHighlight() - { - this._has_followHighlight = false; - } - - /** - */ - public void deleteFollowSelection() - { - this._has_followSelection = false; - } - - /** - */ - public void deleteFontSize() - { - this._has_fontSize = false; - } - - /** - */ - public void deleteFontStyle() - { - this._has_fontStyle = false; - } +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 _rightAlignIds. + */ + private boolean _rightAlignIds; + + /** + * keeps track of state for field: _rightAlignIds + */ + private boolean _has_rightAlignIds; + + /** + * 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 _showUnconserved. + */ + private boolean _showUnconserved = false; + + /** + * keeps track of state for field: _showUnconserved + */ + private boolean _has_showUnconserved; + + /** + * 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 _showNPfeatureTooltip. + */ + private boolean _showNPfeatureTooltip; + + /** + * keeps track of state for field: _showNPfeatureTooltip + */ + private boolean _has_showNPfeatureTooltip; + + /** + * Field _showDbRefTooltip. + */ + private boolean _showDbRefTooltip; + + /** + * keeps track of state for field: _showDbRefTooltip + */ + private boolean _has_showDbRefTooltip; + + /** + * Field _followHighlight. + */ + private boolean _followHighlight = true; + + /** + * keeps track of state for field: _followHighlight + */ + private boolean _has_followHighlight; + + /** + * Field _followSelection. + */ + private boolean _followSelection = true; + + /** + * keeps track of state for field: _followSelection + */ + private boolean _has_followSelection; + + /** + * Field _showAnnotation. + */ + private boolean _showAnnotation; + + /** + * keeps track of state for field: _showAnnotation + */ + private boolean _has_showAnnotation; + + /** + * Field _centreColumnLabels. + */ + private boolean _centreColumnLabels = false; + + /** + * keeps track of state for field: _centreColumnLabels + */ + private boolean _has_centreColumnLabels; + + /** + * Field _showGroupConservation. + */ + private boolean _showGroupConservation = false; + + /** + * keeps track of state for field: _showGroupConservation + */ + private boolean _has_showGroupConservation; + + /** + * Field _showGroupConsensus. + */ + private boolean _showGroupConsensus = false; + + /** + * keeps track of state for field: _showGroupConsensus + */ + private boolean _has_showGroupConsensus; + + /** + * Field _showConsensusHistogram. + */ + private boolean _showConsensusHistogram = true; + + /** + * keeps track of state for field: _showConsensusHistogram + */ + private boolean _has_showConsensusHistogram; + + /** + * Field _showSequenceLogo. + */ + private boolean _showSequenceLogo = false; + + /** + * keeps track of state for field: _showSequenceLogo + */ + private boolean _has_showSequenceLogo; + + /** + * Field _ignoreGapsinConsensus. + */ + private boolean _ignoreGapsinConsensus = true; + + /** + * keeps track of state for field: _ignoreGapsinConsensus + */ + private boolean _has_ignoreGapsinConsensus; + + /** + * 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. */ - public void deleteGatheredViews() - { - this._has_gatheredViews = false; - } + private int _startSeq; - /** + /** + * keeps track of state for field: _startSeq */ - public void deleteHeight() - { - this._has_height = false; - } + private boolean _has_startSeq; - /** + /** + * Field _fontName. */ - public void deleteIgnoreGapsinConsensus() - { - this._has_ignoreGapsinConsensus = false; - } + private java.lang.String _fontName; - /** + /** + * Field _fontSize. */ - public void deletePidSelected() - { - this._has_pidSelected = false; - } + private int _fontSize; - /** + /** + * keeps track of state for field: _fontSize */ - public void deletePidThreshold() - { - this._has_pidThreshold = false; - } + private boolean _has_fontSize; - /** + /** + * Field _fontStyle. */ - public void deleteRenderGaps() - { - this._has_renderGaps = false; - } + private int _fontStyle; - /** + /** + * keeps track of state for field: _fontStyle */ - public void deleteRightAlignIds() - { - this._has_rightAlignIds = false; - } + private boolean _has_fontStyle; - /** + /** + * Field _viewName. */ - public void deleteShowAnnotation() - { - this._has_showAnnotation = false; - } + private java.lang.String _viewName; - /** + /** + * Field _sequenceSetId. */ - public void deleteShowBoxes() - { - this._has_showBoxes = false; - } + private java.lang.String _sequenceSetId; - /** + /** + * Field _gatheredViews. */ - public void deleteShowColourText() - { - this._has_showColourText = false; - } + private boolean _gatheredViews; - /** + /** + * keeps track of state for field: _gatheredViews */ - public void deleteShowConsensusHistogram() - { - this._has_showConsensusHistogram = false; - } + private boolean _has_gatheredViews; - /** + /** + * Field _textCol1. */ - public void deleteShowDbRefTooltip() - { - this._has_showDbRefTooltip = false; - } + private int _textCol1; - /** + /** + * keeps track of state for field: _textCol1 */ - public void deleteShowFullId() - { - this._has_showFullId = false; - } + private boolean _has_textCol1; - /** + /** + * Field _textCol2. */ - public void deleteShowGroupConsensus() - { - this._has_showGroupConsensus = false; - } + private int _textCol2; - /** + /** + * keeps track of state for field: _textCol2 */ - public void deleteShowGroupConservation() - { - this._has_showGroupConservation = false; - } + private boolean _has_textCol2; - /** + /** + * Field _textColThreshold. */ - public void deleteShowNPfeatureTooltip() - { - this._has_showNPfeatureTooltip = false; - } + private int _textColThreshold; - /** + /** + * keeps track of state for field: _textColThreshold */ - public void deleteShowSequenceFeatures() - { - this._has_showSequenceFeatures = false; - } + private boolean _has_textColThreshold; - /** + /** + * unique id used by jalview to synchronize between stored and + * instantiated views + * */ - public void deleteShowSequenceLogo() - { - this._has_showSequenceLogo = false; - } + private java.lang.String _id; - /** + /** + * Field _annotationColours. */ - public void deleteShowText() - { - this._has_showText = false; - } + private jalview.schemabinding.version2.AnnotationColours _annotationColours; - /** + /** + * Field _hiddenColumnsList. */ - public void deleteShowUnconserved() - { - this._has_showUnconserved = false; - } + private java.util.Vector _hiddenColumnsList; - /** + + //----------------/ + //- Constructors -/ + //----------------/ + + public Viewport() { + super(); + this._hiddenColumnsList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vHiddenColumns + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addHiddenColumns( + final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) + throws java.lang.IndexOutOfBoundsException { + this._hiddenColumnsList.addElement(vHiddenColumns); + } + + /** + * + * + * @param index + * @param vHiddenColumns + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addHiddenColumns( + final int index, + final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) + throws java.lang.IndexOutOfBoundsException { + this._hiddenColumnsList.add(index, vHiddenColumns); + } + + /** + */ + public void deleteCentreColumnLabels( + ) { + this._has_centreColumnLabels= false; + } + + /** + */ + public void deleteConsThreshold( + ) { + this._has_consThreshold= false; + } + + /** + */ + public void deleteConservationSelected( + ) { + this._has_conservationSelected= false; + } + + /** + */ + public void deleteFollowHighlight( + ) { + this._has_followHighlight= false; + } + + /** + */ + public void deleteFollowSelection( + ) { + this._has_followSelection= false; + } + + /** + */ + public void deleteFontSize( + ) { + this._has_fontSize= false; + } + + /** + */ + public void deleteFontStyle( + ) { + this._has_fontStyle= false; + } + + /** + */ + public void deleteGatheredViews( + ) { + this._has_gatheredViews= false; + } + + /** + */ + public void deleteHeight( + ) { + this._has_height= false; + } + + /** + */ + public void deleteIgnoreGapsinConsensus( + ) { + this._has_ignoreGapsinConsensus= false; + } + + /** + */ + public void deletePidSelected( + ) { + this._has_pidSelected= false; + } + + /** + */ + public void deletePidThreshold( + ) { + this._has_pidThreshold= false; + } + + /** + */ + public void deleteRenderGaps( + ) { + this._has_renderGaps= false; + } + + /** + */ + public void deleteRightAlignIds( + ) { + this._has_rightAlignIds= false; + } + + /** + */ + public void deleteShowAnnotation( + ) { + this._has_showAnnotation= false; + } + + /** + */ + public void deleteShowBoxes( + ) { + this._has_showBoxes= false; + } + + /** + */ + public void deleteShowColourText( + ) { + this._has_showColourText= false; + } + + /** + */ + public void deleteShowConsensusHistogram( + ) { + this._has_showConsensusHistogram= false; + } + + /** + */ + public void deleteShowDbRefTooltip( + ) { + this._has_showDbRefTooltip= false; + } + + /** + */ + public void deleteShowFullId( + ) { + this._has_showFullId= false; + } + + /** + */ + public void deleteShowGroupConsensus( + ) { + this._has_showGroupConsensus= false; + } + + /** + */ + public void deleteShowGroupConservation( + ) { + this._has_showGroupConservation= false; + } + + /** + */ + public void deleteShowNPfeatureTooltip( + ) { + this._has_showNPfeatureTooltip= false; + } + + /** + */ + public void deleteShowSequenceFeatures( + ) { + this._has_showSequenceFeatures= false; + } + + /** + */ + public void deleteShowSequenceLogo( + ) { + this._has_showSequenceLogo= false; + } + + /** + */ + public void deleteShowText( + ) { + this._has_showText= false; + } + + /** + */ + public void deleteShowUnconserved( + ) { + this._has_showUnconserved= false; + } + + /** + */ + public void deleteStartRes( + ) { + this._has_startRes= false; + } + + /** */ - public void deleteStartRes() - { - this._has_startRes = false; - } - - /** - */ - public void deleteStartSeq() - { - this._has_startSeq = false; - } - - /** - */ - public void deleteTextCol1() - { - this._has_textCol1 = false; - } - - /** - */ - public void deleteTextCol2() - { - this._has_textCol2 = false; - } - - /** - */ - public void deleteTextColThreshold() - { - this._has_textColThreshold = 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; - } - - /** - * Method enumerateHiddenColumns. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.HiddenColumns elements - */ - public java.util.Enumeration enumerateHiddenColumns() - { - return this._hiddenColumnsList.elements(); - } - - /** - * Returns the value of field 'annotationColours'. - * - * @return the value of field 'AnnotationColours'. - */ - public jalview.schemabinding.version2.AnnotationColours getAnnotationColours() - { - return this._annotationColours; - } - - /** - * 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 'centreColumnLabels'. - * - * @return the value of field 'CentreColumnLabels'. - */ - public boolean getCentreColumnLabels() - { - return this._centreColumnLabels; - } - - /** - * 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 'followHighlight'. - * - * @return the value of field 'FollowHighlight'. - */ - public boolean getFollowHighlight() - { - return this._followHighlight; - } - - /** - * Returns the value of field 'followSelection'. - * - * @return the value of field 'FollowSelection'. - */ - public boolean getFollowSelection() - { - return this._followSelection; - } - - /** - * 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 'gatheredViews'. - * - * @return the value of field 'GatheredViews'. - */ - public boolean getGatheredViews() - { - return this._gatheredViews; - } - - /** - * Returns the value of field 'height'. - * - * @return the value of field 'Height'. - */ - public int getHeight() - { - return this._height; - } - - /** - * Method getHiddenColumns. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.schemabinding.version2.HiddenColumns at - * the given index - */ - public jalview.schemabinding.version2.HiddenColumns getHiddenColumns( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._hiddenColumnsList.size()) - { - throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" - + index + "' not in range [0.." - + (this._hiddenColumnsList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList - .get(index); - } - - /** - * Method getHiddenColumns.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.schemabinding.version2.HiddenColumns[] getHiddenColumns() - { - jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0]; - return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList - .toArray(array); - } - - /** - * Method getHiddenColumnsCount. - * - * @return the size of this collection - */ - public int getHiddenColumnsCount() - { - return this._hiddenColumnsList.size(); - } - - /** - * Returns the value of field 'id'. The field 'id' has the following - * description: unique id used by jalview to synchronize between stored and - * instantiated views - * - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * Returns the value of field 'ignoreGapsinConsensus'. - * - * @return the value of field 'IgnoreGapsinConsensus'. - */ - public boolean getIgnoreGapsinConsensus() - { - return this._ignoreGapsinConsensus; - } - - /** - * 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 'rightAlignIds'. - * - * @return the value of field 'RightAlignIds'. - */ - public boolean getRightAlignIds() - { - return this._rightAlignIds; - } - - /** - * Returns the value of field 'sequenceSetId'. - * - * @return the value of field 'SequenceSetId'. - */ - public java.lang.String getSequenceSetId() - { - return this._sequenceSetId; - } - - /** - * 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 'showConsensusHistogram'. - * - * @return the value of field 'ShowConsensusHistogram'. - */ - public boolean getShowConsensusHistogram() - { - return this._showConsensusHistogram; - } - - /** - * Returns the value of field 'showDbRefTooltip'. - * - * @return the value of field 'ShowDbRefTooltip'. - */ - public boolean getShowDbRefTooltip() - { - return this._showDbRefTooltip; - } - - /** - * Returns the value of field 'showFullId'. - * - * @return the value of field 'ShowFullId'. - */ - public boolean getShowFullId() - { - return this._showFullId; - } - - /** - * Returns the value of field 'showGroupConsensus'. - * - * @return the value of field 'ShowGroupConsensus'. - */ - public boolean getShowGroupConsensus() - { - return this._showGroupConsensus; - } - - /** - * Returns the value of field 'showGroupConservation'. - * - * @return the value of field 'ShowGroupConservation'. - */ - public boolean getShowGroupConservation() - { - return this._showGroupConservation; - } - - /** - * Returns the value of field 'showNPfeatureTooltip'. - * - * @return the value of field 'ShowNPfeatureTooltip'. - */ - public boolean getShowNPfeatureTooltip() - { - return this._showNPfeatureTooltip; - } - - /** - * Returns the value of field 'showSequenceFeatures'. - * - * @return the value of field 'ShowSequenceFeatures'. - */ - public boolean getShowSequenceFeatures() - { - return this._showSequenceFeatures; - } - - /** - * Returns the value of field 'showSequenceLogo'. - * - * @return the value of field 'ShowSequenceLogo'. - */ - public boolean getShowSequenceLogo() - { - return this._showSequenceLogo; - } - - /** - * Returns the value of field 'showText'. - * - * @return the value of field 'ShowText'. - */ - public boolean getShowText() - { - return this._showText; - } - - /** - * Returns the value of field 'showUnconserved'. - * - * @return the value of field 'ShowUnconserved'. - */ - public boolean getShowUnconserved() - { - return this._showUnconserved; - } - - /** - * 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 'textCol1'. - * - * @return the value of field 'TextCol1'. - */ - public int getTextCol1() - { - return this._textCol1; - } - - /** - * Returns the value of field 'textCol2'. - * - * @return the value of field 'TextCol2'. - */ - public int getTextCol2() - { - return this._textCol2; - } - - /** - * Returns the value of field 'textColThreshold'. - * - * @return the value of field 'TextColThreshold'. - */ - public int getTextColThreshold() - { - return this._textColThreshold; - } - - /** - * 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 'viewName'. - * - * @return the value of field 'ViewName'. - */ - public java.lang.String getViewName() - { - return this._viewName; - } - - /** - * 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 hasCentreColumnLabels. - * - * @return true if at least one CentreColumnLabels has been adde - */ - public boolean hasCentreColumnLabels() - { - return this._has_centreColumnLabels; - } - - /** - * 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 hasFollowHighlight. - * - * @return true if at least one FollowHighlight has been added - */ - public boolean hasFollowHighlight() - { - return this._has_followHighlight; - } - - /** - * Method hasFollowSelection. - * - * @return true if at least one FollowSelection has been added - */ - public boolean hasFollowSelection() - { - return this._has_followSelection; - } - - /** - * 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 hasGatheredViews. - * - * @return true if at least one GatheredViews has been added - */ - public boolean hasGatheredViews() - { - return this._has_gatheredViews; - } - - /** - * Method hasHeight. - * - * @return true if at least one Height has been added - */ - public boolean hasHeight() - { - return this._has_height; - } - - /** - * Method hasIgnoreGapsinConsensus. - * - * @return true if at least one IgnoreGapsinConsensus has been added - */ - public boolean hasIgnoreGapsinConsensus() - { - return this._has_ignoreGapsinConsensus; - } - - /** - * 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 hasRightAlignIds. - * - * @return true if at least one RightAlignIds has been added - */ - public boolean hasRightAlignIds() - { - return this._has_rightAlignIds; - } - - /** - * 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 hasShowConsensusHistogram. - * - * @return true if at least one ShowConsensusHistogram has been added - */ - public boolean hasShowConsensusHistogram() - { - return this._has_showConsensusHistogram; - } - - /** - * Method hasShowDbRefTooltip. - * - * @return true if at least one ShowDbRefTooltip has been added - */ - public boolean hasShowDbRefTooltip() - { - return this._has_showDbRefTooltip; - } - - /** - * Method hasShowFullId. - * - * @return true if at least one ShowFullId has been added - */ - public boolean hasShowFullId() - { - return this._has_showFullId; - } - - /** - * Method hasShowGroupConsensus. - * - * @return true if at least one ShowGroupConsensus has been adde - */ - public boolean hasShowGroupConsensus() - { - return this._has_showGroupConsensus; - } - - /** - * Method hasShowGroupConservation. - * - * @return true if at least one ShowGroupConservation has been added - */ - public boolean hasShowGroupConservation() - { - return this._has_showGroupConservation; - } - - /** - * Method hasShowNPfeatureTooltip. - * - * @return true if at least one ShowNPfeatureTooltip has been added - */ - public boolean hasShowNPfeatureTooltip() - { - return this._has_showNPfeatureTooltip; - } - - /** - * Method hasShowSequenceFeatures. - * - * @return true if at least one ShowSequenceFeatures has been added - */ - public boolean hasShowSequenceFeatures() - { - return this._has_showSequenceFeatures; - } - - /** - * Method hasShowSequenceLogo. - * - * @return true if at least one ShowSequenceLogo has been added - */ - public boolean hasShowSequenceLogo() - { - return this._has_showSequenceLogo; - } - - /** - * Method hasShowText. - * - * @return true if at least one ShowText has been added - */ - public boolean hasShowText() - { - return this._has_showText; - } - - /** - * Method hasShowUnconserved. - * - * @return true if at least one ShowUnconserved has been added - */ - public boolean hasShowUnconserved() - { - return this._has_showUnconserved; - } - - /** - * 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 hasTextCol1. - * - * @return true if at least one TextCol1 has been added - */ - public boolean hasTextCol1() - { - return this._has_textCol1; - } - - /** - * Method hasTextCol2. - * - * @return true if at least one TextCol2 has been added - */ - public boolean hasTextCol2() - { - return this._has_textCol2; - } - - /** - * Method hasTextColThreshold. - * - * @return true if at least one TextColThreshold has been added - */ - public boolean hasTextColThreshold() - { - return this._has_textColThreshold; - } - - /** - * 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 'centreColumnLabels'. - * - * @return the value of field 'CentreColumnLabels'. - */ - public boolean isCentreColumnLabels() - { - return this._centreColumnLabels; - } - - /** - * Returns the value of field 'conservationSelected'. - * - * @return the value of field 'ConservationSelected'. - */ - public boolean isConservationSelected() - { - return this._conservationSelected; - } - - /** - * Returns the value of field 'followHighlight'. - * - * @return the value of field 'FollowHighlight'. - */ - public boolean isFollowHighlight() - { - return this._followHighlight; - } - - /** - * Returns the value of field 'followSelection'. - * - * @return the value of field 'FollowSelection'. - */ - public boolean isFollowSelection() - { - return this._followSelection; - } - - /** - * Returns the value of field 'gatheredViews'. - * - * @return the value of field 'GatheredViews'. - */ - public boolean isGatheredViews() - { - return this._gatheredViews; - } - - /** - * Returns the value of field 'ignoreGapsinConsensus'. - * - * @return the value of field 'IgnoreGapsinConsensus'. - */ - public boolean isIgnoreGapsinConsensus() - { - return this._ignoreGapsinConsensus; - } - - /** - * 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 'rightAlignIds'. - * - * @return the value of field 'RightAlignIds'. - */ - public boolean isRightAlignIds() - { - return this._rightAlignIds; - } - - /** - * 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 'showConsensusHistogram'. - * - * @return the value of field 'ShowConsensusHistogram'. - */ - public boolean isShowConsensusHistogram() - { - return this._showConsensusHistogram; - } - - /** - * Returns the value of field 'showDbRefTooltip'. - * - * @return the value of field 'ShowDbRefTooltip'. - */ - public boolean isShowDbRefTooltip() - { - return this._showDbRefTooltip; - } - - /** - * Returns the value of field 'showFullId'. - * - * @return the value of field 'ShowFullId'. - */ - public boolean isShowFullId() - { - return this._showFullId; - } - - /** - * Returns the value of field 'showGroupConsensus'. - * - * @return the value of field 'ShowGroupConsensus'. - */ - public boolean isShowGroupConsensus() - { - return this._showGroupConsensus; - } - - /** - * Returns the value of field 'showGroupConservation'. - * - * @return the value of field 'ShowGroupConservation'. - */ - public boolean isShowGroupConservation() - { - return this._showGroupConservation; - } - - /** - * Returns the value of field 'showNPfeatureTooltip'. - * - * @return the value of field 'ShowNPfeatureTooltip'. - */ - public boolean isShowNPfeatureTooltip() - { - return this._showNPfeatureTooltip; - } - - /** - * Returns the value of field 'showSequenceFeatures'. - * - * @return the value of field 'ShowSequenceFeatures'. - */ - public boolean isShowSequenceFeatures() - { - return this._showSequenceFeatures; - } - - /** - * Returns the value of field 'showSequenceLogo'. - * - * @return the value of field 'ShowSequenceLogo'. - */ - public boolean isShowSequenceLogo() - { - return this._showSequenceLogo; - } - - /** - * Returns the value of field 'showText'. - * - * @return the value of field 'ShowText'. - */ - public boolean isShowText() - { - return this._showText; - } - - /** - * Returns the value of field 'showUnconserved'. - * - * @return the value of field 'ShowUnconserved'. - */ - public boolean isShowUnconserved() - { - return this._showUnconserved; - } - - /** - * 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); - } - - /** - */ - public void removeAllHiddenColumns() - { - this._hiddenColumnsList.clear(); - } - - /** - * Method removeHiddenColumns. - * - * @param vHiddenColumns - * @return true if the object was removed from the collection. - */ - public boolean removeHiddenColumns( - final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) - { - boolean removed = _hiddenColumnsList.remove(vHiddenColumns); - return removed; - } - - /** - * Method removeHiddenColumnsAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt( - final int index) - { - java.lang.Object obj = this._hiddenColumnsList.remove(index); - return (jalview.schemabinding.version2.HiddenColumns) obj; - } - - /** - * Sets the value of field 'annotationColours'. - * - * @param annotationColours - * the value of field 'annotationColours'. - */ - public void setAnnotationColours( - final jalview.schemabinding.version2.AnnotationColours annotationColours) - { - this._annotationColours = annotationColours; - } - - /** - * 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 'centreColumnLabels'. - * - * @param centreColumnLabels - * the value of field 'centreColumnLabels'. - */ - public void setCentreColumnLabels(final boolean centreColumnLabels) - { - this._centreColumnLabels = centreColumnLabels; - this._has_centreColumnLabels = 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 '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 'followHighlight'. - * - * @param followHighlight - * the value of field 'followHighlight'. - */ - public void setFollowHighlight(final boolean followHighlight) - { - this._followHighlight = followHighlight; - this._has_followHighlight = true; - } - - /** - * Sets the value of field 'followSelection'. - * - * @param followSelection - * the value of field 'followSelection'. - */ - public void setFollowSelection(final boolean followSelection) - { - this._followSelection = followSelection; - this._has_followSelection = 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 'gatheredViews'. - * - * @param gatheredViews - * the value of field 'gatheredViews'. - */ - public void setGatheredViews(final boolean gatheredViews) - { - this._gatheredViews = gatheredViews; - this._has_gatheredViews = 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; - } - - /** - * - * - * @param index - * @param vHiddenColumns - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setHiddenColumns(final int index, - final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._hiddenColumnsList.size()) - { - throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" - + index + "' not in range [0.." - + (this._hiddenColumnsList.size() - 1) + "]"); - } - - this._hiddenColumnsList.set(index, vHiddenColumns); - } - - /** - * - * - * @param vHiddenColumnsArray - */ - public void setHiddenColumns( - final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) - { - // -- copy array - _hiddenColumnsList.clear(); - - for (int i = 0; i < vHiddenColumnsArray.length; i++) - { - this._hiddenColumnsList.add(vHiddenColumnsArray[i]); - } - } - - /** - * Sets the value of field 'id'. The field 'id' has the following description: - * unique id used by jalview to synchronize between stored and instantiated - * views - * - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * Sets the value of field 'ignoreGapsinConsensus'. - * - * @param ignoreGapsinConsensus - * the value of field 'ignoreGapsinConsensus'. - */ - public void setIgnoreGapsinConsensus(final boolean ignoreGapsinConsensus) - { - this._ignoreGapsinConsensus = ignoreGapsinConsensus; - this._has_ignoreGapsinConsensus = 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 'rightAlignIds'. - * - * @param rightAlignIds - * the value of field 'rightAlignIds'. - */ - public void setRightAlignIds(final boolean rightAlignIds) - { - this._rightAlignIds = rightAlignIds; - this._has_rightAlignIds = true; - } - - /** - * Sets the value of field 'sequenceSetId'. - * - * @param sequenceSetId - * the value of field 'sequenceSetId'. - */ - public void setSequenceSetId(final java.lang.String sequenceSetId) - { - this._sequenceSetId = sequenceSetId; - } - - /** - * 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 'showConsensusHistogram'. - * - * @param showConsensusHistogram - * the value of field 'showConsensusHistogram'. - */ - public void setShowConsensusHistogram(final boolean showConsensusHistogram) - { - this._showConsensusHistogram = showConsensusHistogram; - this._has_showConsensusHistogram = true; - } - - /** - * Sets the value of field 'showDbRefTooltip'. - * - * @param showDbRefTooltip - * the value of field 'showDbRefTooltip' - */ - public void setShowDbRefTooltip(final boolean showDbRefTooltip) - { - this._showDbRefTooltip = showDbRefTooltip; - this._has_showDbRefTooltip = 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 'showGroupConsensus'. - * - * @param showGroupConsensus - * the value of field 'showGroupConsensus'. - */ - public void setShowGroupConsensus(final boolean showGroupConsensus) - { - this._showGroupConsensus = showGroupConsensus; - this._has_showGroupConsensus = true; - } - - /** - * Sets the value of field 'showGroupConservation'. - * - * @param showGroupConservation - * the value of field 'showGroupConservation'. - */ - public void setShowGroupConservation(final boolean showGroupConservation) - { - this._showGroupConservation = showGroupConservation; - this._has_showGroupConservation = true; - } - - /** - * Sets the value of field 'showNPfeatureTooltip'. - * - * @param showNPfeatureTooltip - * the value of field 'showNPfeatureTooltip'. - */ - public void setShowNPfeatureTooltip(final boolean showNPfeatureTooltip) - { - this._showNPfeatureTooltip = showNPfeatureTooltip; - this._has_showNPfeatureTooltip = 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 'showSequenceLogo'. - * - * @param showSequenceLogo - * the value of field 'showSequenceLogo' - */ - public void setShowSequenceLogo(final boolean showSequenceLogo) - { - this._showSequenceLogo = showSequenceLogo; - this._has_showSequenceLogo = 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 'showUnconserved'. - * - * @param showUnconserved - * the value of field 'showUnconserved'. - */ - public void setShowUnconserved(final boolean showUnconserved) - { - this._showUnconserved = showUnconserved; - this._has_showUnconserved = 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 'textCol1'. - * - * @param textCol1 - * the value of field 'textCol1'. - */ - public void setTextCol1(final int textCol1) - { - this._textCol1 = textCol1; - this._has_textCol1 = true; - } - - /** - * Sets the value of field 'textCol2'. - * - * @param textCol2 - * the value of field 'textCol2'. - */ - public void setTextCol2(final int textCol2) - { - this._textCol2 = textCol2; - this._has_textCol2 = true; - } - - /** - * Sets the value of field 'textColThreshold'. - * - * @param textColThreshold - * the value of field 'textColThreshold' - */ - public void setTextColThreshold(final int textColThreshold) - { - this._textColThreshold = textColThreshold; - this._has_textColThreshold = 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 'viewName'. - * - * @param viewName - * the value of field 'viewName'. - */ - public void setViewName(final java.lang.String viewName) - { - this._viewName = viewName; - } - - /** - * 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.schemabinding.version2.Viewport - */ - public static jalview.schemabinding.version2.Viewport unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.Viewport) Unmarshaller - .unmarshal(jalview.schemabinding.version2.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); - } + public void deleteStartSeq( + ) { + this._has_startSeq= false; + } + + /** + */ + public void deleteTextCol1( + ) { + this._has_textCol1= false; + } + + /** + */ + public void deleteTextCol2( + ) { + this._has_textCol2= false; + } + + /** + */ + public void deleteTextColThreshold( + ) { + this._has_textColThreshold= 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; + } + + /** + * Method enumerateHiddenColumns. + * + * @return an Enumeration over all + * jalview.schemabinding.version2.HiddenColumns elements + */ + public java.util.Enumeration enumerateHiddenColumns( + ) { + return this._hiddenColumnsList.elements(); + } + + /** + * Returns the value of field 'annotationColours'. + * + * @return the value of field 'AnnotationColours'. + */ + public jalview.schemabinding.version2.AnnotationColours getAnnotationColours( + ) { + return this._annotationColours; + } + + /** + * 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 'centreColumnLabels'. + * + * @return the value of field 'CentreColumnLabels'. + */ + public boolean getCentreColumnLabels( + ) { + return this._centreColumnLabels; + } + + /** + * 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 'followHighlight'. + * + * @return the value of field 'FollowHighlight'. + */ + public boolean getFollowHighlight( + ) { + return this._followHighlight; + } + + /** + * Returns the value of field 'followSelection'. + * + * @return the value of field 'FollowSelection'. + */ + public boolean getFollowSelection( + ) { + return this._followSelection; + } + + /** + * 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 'gatheredViews'. + * + * @return the value of field 'GatheredViews'. + */ + public boolean getGatheredViews( + ) { + return this._gatheredViews; + } + + /** + * Returns the value of field 'height'. + * + * @return the value of field 'Height'. + */ + public int getHeight( + ) { + return this._height; + } + + /** + * Method getHiddenColumns. + * + * @param index + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.HiddenColumns at the given + * index + */ + public jalview.schemabinding.version2.HiddenColumns getHiddenColumns( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._hiddenColumnsList.size()) { + throw new IndexOutOfBoundsException("getHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.get(index); + } + + /** + * Method getHiddenColumns.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.schemabinding.version2.HiddenColumns[] getHiddenColumns( + ) { + jalview.schemabinding.version2.HiddenColumns[] array = new jalview.schemabinding.version2.HiddenColumns[0]; + return (jalview.schemabinding.version2.HiddenColumns[]) this._hiddenColumnsList.toArray(array); + } + + /** + * Method getHiddenColumnsCount. + * + * @return the size of this collection + */ + public int getHiddenColumnsCount( + ) { + return this._hiddenColumnsList.size(); + } + + /** + * Returns the value of field 'id'. The field 'id' has the + * following description: unique id used by jalview to + * synchronize between stored and instantiated views + * + * + * @return the value of field 'Id'. + */ + public java.lang.String getId( + ) { + return this._id; + } + + /** + * Returns the value of field 'ignoreGapsinConsensus'. + * + * @return the value of field 'IgnoreGapsinConsensus'. + */ + public boolean getIgnoreGapsinConsensus( + ) { + return this._ignoreGapsinConsensus; + } + + /** + * 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 'rightAlignIds'. + * + * @return the value of field 'RightAlignIds'. + */ + public boolean getRightAlignIds( + ) { + return this._rightAlignIds; + } + + /** + * Returns the value of field 'sequenceSetId'. + * + * @return the value of field 'SequenceSetId'. + */ + public java.lang.String getSequenceSetId( + ) { + return this._sequenceSetId; + } + + /** + * 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 'showConsensusHistogram'. + * + * @return the value of field 'ShowConsensusHistogram'. + */ + public boolean getShowConsensusHistogram( + ) { + return this._showConsensusHistogram; + } + + /** + * Returns the value of field 'showDbRefTooltip'. + * + * @return the value of field 'ShowDbRefTooltip'. + */ + public boolean getShowDbRefTooltip( + ) { + return this._showDbRefTooltip; + } + + /** + * Returns the value of field 'showFullId'. + * + * @return the value of field 'ShowFullId'. + */ + public boolean getShowFullId( + ) { + return this._showFullId; + } + + /** + * Returns the value of field 'showGroupConsensus'. + * + * @return the value of field 'ShowGroupConsensus'. + */ + public boolean getShowGroupConsensus( + ) { + return this._showGroupConsensus; + } + + /** + * Returns the value of field 'showGroupConservation'. + * + * @return the value of field 'ShowGroupConservation'. + */ + public boolean getShowGroupConservation( + ) { + return this._showGroupConservation; + } + + /** + * Returns the value of field 'showNPfeatureTooltip'. + * + * @return the value of field 'ShowNPfeatureTooltip'. + */ + public boolean getShowNPfeatureTooltip( + ) { + return this._showNPfeatureTooltip; + } + + /** + * Returns the value of field 'showSequenceFeatures'. + * + * @return the value of field 'ShowSequenceFeatures'. + */ + public boolean getShowSequenceFeatures( + ) { + return this._showSequenceFeatures; + } + + /** + * Returns the value of field 'showSequenceLogo'. + * + * @return the value of field 'ShowSequenceLogo'. + */ + public boolean getShowSequenceLogo( + ) { + return this._showSequenceLogo; + } + + /** + * Returns the value of field 'showText'. + * + * @return the value of field 'ShowText'. + */ + public boolean getShowText( + ) { + return this._showText; + } + + /** + * Returns the value of field 'showUnconserved'. + * + * @return the value of field 'ShowUnconserved'. + */ + public boolean getShowUnconserved( + ) { + return this._showUnconserved; + } + + /** + * 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 'textCol1'. + * + * @return the value of field 'TextCol1'. + */ + public int getTextCol1( + ) { + return this._textCol1; + } + + /** + * Returns the value of field 'textCol2'. + * + * @return the value of field 'TextCol2'. + */ + public int getTextCol2( + ) { + return this._textCol2; + } + + /** + * Returns the value of field 'textColThreshold'. + * + * @return the value of field 'TextColThreshold'. + */ + public int getTextColThreshold( + ) { + return this._textColThreshold; + } + + /** + * 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 'viewName'. + * + * @return the value of field 'ViewName'. + */ + public java.lang.String getViewName( + ) { + return this._viewName; + } + + /** + * 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 hasCentreColumnLabels. + * + * @return true if at least one CentreColumnLabels has been adde + */ + public boolean hasCentreColumnLabels( + ) { + return this._has_centreColumnLabels; + } + + /** + * 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 hasFollowHighlight. + * + * @return true if at least one FollowHighlight has been added + */ + public boolean hasFollowHighlight( + ) { + return this._has_followHighlight; + } + + /** + * Method hasFollowSelection. + * + * @return true if at least one FollowSelection has been added + */ + public boolean hasFollowSelection( + ) { + return this._has_followSelection; + } + + /** + * 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 hasGatheredViews. + * + * @return true if at least one GatheredViews has been added + */ + public boolean hasGatheredViews( + ) { + return this._has_gatheredViews; + } + + /** + * Method hasHeight. + * + * @return true if at least one Height has been added + */ + public boolean hasHeight( + ) { + return this._has_height; + } + + /** + * Method hasIgnoreGapsinConsensus. + * + * @return true if at least one IgnoreGapsinConsensus has been + * added + */ + public boolean hasIgnoreGapsinConsensus( + ) { + return this._has_ignoreGapsinConsensus; + } + + /** + * 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 hasRightAlignIds. + * + * @return true if at least one RightAlignIds has been added + */ + public boolean hasRightAlignIds( + ) { + return this._has_rightAlignIds; + } + + /** + * 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 hasShowConsensusHistogram. + * + * @return true if at least one ShowConsensusHistogram has been + * added + */ + public boolean hasShowConsensusHistogram( + ) { + return this._has_showConsensusHistogram; + } + + /** + * Method hasShowDbRefTooltip. + * + * @return true if at least one ShowDbRefTooltip has been added + */ + public boolean hasShowDbRefTooltip( + ) { + return this._has_showDbRefTooltip; + } + + /** + * Method hasShowFullId. + * + * @return true if at least one ShowFullId has been added + */ + public boolean hasShowFullId( + ) { + return this._has_showFullId; + } + + /** + * Method hasShowGroupConsensus. + * + * @return true if at least one ShowGroupConsensus has been adde + */ + public boolean hasShowGroupConsensus( + ) { + return this._has_showGroupConsensus; + } + + /** + * Method hasShowGroupConservation. + * + * @return true if at least one ShowGroupConservation has been + * added + */ + public boolean hasShowGroupConservation( + ) { + return this._has_showGroupConservation; + } + + /** + * Method hasShowNPfeatureTooltip. + * + * @return true if at least one ShowNPfeatureTooltip has been + * added + */ + public boolean hasShowNPfeatureTooltip( + ) { + return this._has_showNPfeatureTooltip; + } + + /** + * Method hasShowSequenceFeatures. + * + * @return true if at least one ShowSequenceFeatures has been + * added + */ + public boolean hasShowSequenceFeatures( + ) { + return this._has_showSequenceFeatures; + } + + /** + * Method hasShowSequenceLogo. + * + * @return true if at least one ShowSequenceLogo has been added + */ + public boolean hasShowSequenceLogo( + ) { + return this._has_showSequenceLogo; + } + + /** + * Method hasShowText. + * + * @return true if at least one ShowText has been added + */ + public boolean hasShowText( + ) { + return this._has_showText; + } + + /** + * Method hasShowUnconserved. + * + * @return true if at least one ShowUnconserved has been added + */ + public boolean hasShowUnconserved( + ) { + return this._has_showUnconserved; + } + + /** + * 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 hasTextCol1. + * + * @return true if at least one TextCol1 has been added + */ + public boolean hasTextCol1( + ) { + return this._has_textCol1; + } + + /** + * Method hasTextCol2. + * + * @return true if at least one TextCol2 has been added + */ + public boolean hasTextCol2( + ) { + return this._has_textCol2; + } + + /** + * Method hasTextColThreshold. + * + * @return true if at least one TextColThreshold has been added + */ + public boolean hasTextColThreshold( + ) { + return this._has_textColThreshold; + } + + /** + * 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 'centreColumnLabels'. + * + * @return the value of field 'CentreColumnLabels'. + */ + public boolean isCentreColumnLabels( + ) { + return this._centreColumnLabels; + } + + /** + * Returns the value of field 'conservationSelected'. + * + * @return the value of field 'ConservationSelected'. + */ + public boolean isConservationSelected( + ) { + return this._conservationSelected; + } + + /** + * Returns the value of field 'followHighlight'. + * + * @return the value of field 'FollowHighlight'. + */ + public boolean isFollowHighlight( + ) { + return this._followHighlight; + } + + /** + * Returns the value of field 'followSelection'. + * + * @return the value of field 'FollowSelection'. + */ + public boolean isFollowSelection( + ) { + return this._followSelection; + } + + /** + * Returns the value of field 'gatheredViews'. + * + * @return the value of field 'GatheredViews'. + */ + public boolean isGatheredViews( + ) { + return this._gatheredViews; + } + + /** + * Returns the value of field 'ignoreGapsinConsensus'. + * + * @return the value of field 'IgnoreGapsinConsensus'. + */ + public boolean isIgnoreGapsinConsensus( + ) { + return this._ignoreGapsinConsensus; + } + + /** + * 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 'rightAlignIds'. + * + * @return the value of field 'RightAlignIds'. + */ + public boolean isRightAlignIds( + ) { + return this._rightAlignIds; + } + + /** + * 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 'showConsensusHistogram'. + * + * @return the value of field 'ShowConsensusHistogram'. + */ + public boolean isShowConsensusHistogram( + ) { + return this._showConsensusHistogram; + } + + /** + * Returns the value of field 'showDbRefTooltip'. + * + * @return the value of field 'ShowDbRefTooltip'. + */ + public boolean isShowDbRefTooltip( + ) { + return this._showDbRefTooltip; + } + + /** + * Returns the value of field 'showFullId'. + * + * @return the value of field 'ShowFullId'. + */ + public boolean isShowFullId( + ) { + return this._showFullId; + } + + /** + * Returns the value of field 'showGroupConsensus'. + * + * @return the value of field 'ShowGroupConsensus'. + */ + public boolean isShowGroupConsensus( + ) { + return this._showGroupConsensus; + } + + /** + * Returns the value of field 'showGroupConservation'. + * + * @return the value of field 'ShowGroupConservation'. + */ + public boolean isShowGroupConservation( + ) { + return this._showGroupConservation; + } + + /** + * Returns the value of field 'showNPfeatureTooltip'. + * + * @return the value of field 'ShowNPfeatureTooltip'. + */ + public boolean isShowNPfeatureTooltip( + ) { + return this._showNPfeatureTooltip; + } + + /** + * Returns the value of field 'showSequenceFeatures'. + * + * @return the value of field 'ShowSequenceFeatures'. + */ + public boolean isShowSequenceFeatures( + ) { + return this._showSequenceFeatures; + } + + /** + * Returns the value of field 'showSequenceLogo'. + * + * @return the value of field 'ShowSequenceLogo'. + */ + public boolean isShowSequenceLogo( + ) { + return this._showSequenceLogo; + } + + /** + * Returns the value of field 'showText'. + * + * @return the value of field 'ShowText'. + */ + public boolean isShowText( + ) { + return this._showText; + } + + /** + * Returns the value of field 'showUnconserved'. + * + * @return the value of field 'ShowUnconserved'. + */ + public boolean isShowUnconserved( + ) { + return this._showUnconserved; + } + + /** + * 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); + } + + /** + */ + public void removeAllHiddenColumns( + ) { + this._hiddenColumnsList.clear(); + } + + /** + * Method removeHiddenColumns. + * + * @param vHiddenColumns + * @return true if the object was removed from the collection. + */ + public boolean removeHiddenColumns( + final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) { + boolean removed = _hiddenColumnsList.remove(vHiddenColumns); + return removed; + } + + /** + * Method removeHiddenColumnsAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.HiddenColumns removeHiddenColumnsAt( + final int index) { + java.lang.Object obj = this._hiddenColumnsList.remove(index); + return (jalview.schemabinding.version2.HiddenColumns) obj; + } + + /** + * Sets the value of field 'annotationColours'. + * + * @param annotationColours the value of field + * 'annotationColours'. + */ + public void setAnnotationColours( + final jalview.schemabinding.version2.AnnotationColours annotationColours) { + this._annotationColours = annotationColours; + } + + /** + * 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 'centreColumnLabels'. + * + * @param centreColumnLabels the value of field + * 'centreColumnLabels'. + */ + public void setCentreColumnLabels( + final boolean centreColumnLabels) { + this._centreColumnLabels = centreColumnLabels; + this._has_centreColumnLabels = 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 '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 'followHighlight'. + * + * @param followHighlight the value of field 'followHighlight'. + */ + public void setFollowHighlight( + final boolean followHighlight) { + this._followHighlight = followHighlight; + this._has_followHighlight = true; + } + + /** + * Sets the value of field 'followSelection'. + * + * @param followSelection the value of field 'followSelection'. + */ + public void setFollowSelection( + final boolean followSelection) { + this._followSelection = followSelection; + this._has_followSelection = 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 'gatheredViews'. + * + * @param gatheredViews the value of field 'gatheredViews'. + */ + public void setGatheredViews( + final boolean gatheredViews) { + this._gatheredViews = gatheredViews; + this._has_gatheredViews = 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; + } + + /** + * + * + * @param index + * @param vHiddenColumns + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setHiddenColumns( + final int index, + final jalview.schemabinding.version2.HiddenColumns vHiddenColumns) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._hiddenColumnsList.size()) { + throw new IndexOutOfBoundsException("setHiddenColumns: Index value '" + index + "' not in range [0.." + (this._hiddenColumnsList.size() - 1) + "]"); + } + + this._hiddenColumnsList.set(index, vHiddenColumns); + } + + /** + * + * + * @param vHiddenColumnsArray + */ + public void setHiddenColumns( + final jalview.schemabinding.version2.HiddenColumns[] vHiddenColumnsArray) { + //-- copy array + _hiddenColumnsList.clear(); + + for (int i = 0; i < vHiddenColumnsArray.length; i++) { + this._hiddenColumnsList.add(vHiddenColumnsArray[i]); + } + } + + /** + * Sets the value of field 'id'. The field 'id' has the + * following description: unique id used by jalview to + * synchronize between stored and instantiated views + * + * + * @param id the value of field 'id'. + */ + public void setId( + final java.lang.String id) { + this._id = id; + } + + /** + * Sets the value of field 'ignoreGapsinConsensus'. + * + * @param ignoreGapsinConsensus the value of field + * 'ignoreGapsinConsensus'. + */ + public void setIgnoreGapsinConsensus( + final boolean ignoreGapsinConsensus) { + this._ignoreGapsinConsensus = ignoreGapsinConsensus; + this._has_ignoreGapsinConsensus = 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 'rightAlignIds'. + * + * @param rightAlignIds the value of field 'rightAlignIds'. + */ + public void setRightAlignIds( + final boolean rightAlignIds) { + this._rightAlignIds = rightAlignIds; + this._has_rightAlignIds = true; + } + + /** + * Sets the value of field 'sequenceSetId'. + * + * @param sequenceSetId the value of field 'sequenceSetId'. + */ + public void setSequenceSetId( + final java.lang.String sequenceSetId) { + this._sequenceSetId = sequenceSetId; + } + + /** + * 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 'showConsensusHistogram'. + * + * @param showConsensusHistogram the value of field + * 'showConsensusHistogram'. + */ + public void setShowConsensusHistogram( + final boolean showConsensusHistogram) { + this._showConsensusHistogram = showConsensusHistogram; + this._has_showConsensusHistogram = true; + } + + /** + * Sets the value of field 'showDbRefTooltip'. + * + * @param showDbRefTooltip the value of field 'showDbRefTooltip' + */ + public void setShowDbRefTooltip( + final boolean showDbRefTooltip) { + this._showDbRefTooltip = showDbRefTooltip; + this._has_showDbRefTooltip = 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 'showGroupConsensus'. + * + * @param showGroupConsensus the value of field + * 'showGroupConsensus'. + */ + public void setShowGroupConsensus( + final boolean showGroupConsensus) { + this._showGroupConsensus = showGroupConsensus; + this._has_showGroupConsensus = true; + } + + /** + * Sets the value of field 'showGroupConservation'. + * + * @param showGroupConservation the value of field + * 'showGroupConservation'. + */ + public void setShowGroupConservation( + final boolean showGroupConservation) { + this._showGroupConservation = showGroupConservation; + this._has_showGroupConservation = true; + } + + /** + * Sets the value of field 'showNPfeatureTooltip'. + * + * @param showNPfeatureTooltip the value of field + * 'showNPfeatureTooltip'. + */ + public void setShowNPfeatureTooltip( + final boolean showNPfeatureTooltip) { + this._showNPfeatureTooltip = showNPfeatureTooltip; + this._has_showNPfeatureTooltip = 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 'showSequenceLogo'. + * + * @param showSequenceLogo the value of field 'showSequenceLogo' + */ + public void setShowSequenceLogo( + final boolean showSequenceLogo) { + this._showSequenceLogo = showSequenceLogo; + this._has_showSequenceLogo = 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 'showUnconserved'. + * + * @param showUnconserved the value of field 'showUnconserved'. + */ + public void setShowUnconserved( + final boolean showUnconserved) { + this._showUnconserved = showUnconserved; + this._has_showUnconserved = 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 'textCol1'. + * + * @param textCol1 the value of field 'textCol1'. + */ + public void setTextCol1( + final int textCol1) { + this._textCol1 = textCol1; + this._has_textCol1 = true; + } + + /** + * Sets the value of field 'textCol2'. + * + * @param textCol2 the value of field 'textCol2'. + */ + public void setTextCol2( + final int textCol2) { + this._textCol2 = textCol2; + this._has_textCol2 = true; + } + + /** + * Sets the value of field 'textColThreshold'. + * + * @param textColThreshold the value of field 'textColThreshold' + */ + public void setTextColThreshold( + final int textColThreshold) { + this._textColThreshold = textColThreshold; + this._has_textColThreshold = 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 'viewName'. + * + * @param viewName the value of field 'viewName'. + */ + public void setViewName( + final java.lang.String viewName) { + this._viewName = viewName; + } + + /** + * 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.schemabinding.version2.Viewport + */ + public static jalview.schemabinding.version2.Viewport unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.Viewport) Unmarshaller.unmarshal(jalview.schemabinding.version2.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); + } } diff --git a/src/jalview/schemabinding/version2/WebServiceParameterSet.java b/src/jalview/schemabinding/version2/WebServiceParameterSet.java index 6c7c211..611c981 100644 --- a/src/jalview/schemabinding/version2/WebServiceParameterSet.java +++ b/src/jalview/schemabinding/version2/WebServiceParameterSet.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,418 +19,421 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class WebServiceParameterSet implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * The short name for the parameter set. This will be shown amongst the other - * presets for the web service. - * - */ - private java.lang.String _name; - - /** - * A Jalview Web Service Parameter Set container version number. Version 1 - * created for storing Jaba user presets. - * - */ - private java.lang.String _version; - - /** - * Short description - as utf8 encoded text. This is usually displayed in the - * body of an HTML capable tooltip, so HTML tags may be embedded using - * standard UTF8 encoding. - * - */ - private java.lang.String _description; - - /** - * URL for which the parameter set is valid. Jalview will use it to match up - * parameter sets to service instances that can parse the parameter set - * payload. - * - */ - private java.util.Vector _serviceURLList; - - /** - * UTF8 encoded string to be processed into a specific web services' parameter - * set. Note - newlines may be important to the structure of this file. - * - */ - private java.lang.String _parameters; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public WebServiceParameterSet() - { - super(); - this._serviceURLList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vServiceURL - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addServiceURL(final java.lang.String vServiceURL) - throws java.lang.IndexOutOfBoundsException - { - this._serviceURLList.addElement(vServiceURL); - } - - /** - * - * - * @param index - * @param vServiceURL - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addServiceURL(final int index, - final java.lang.String vServiceURL) - throws java.lang.IndexOutOfBoundsException - { - this._serviceURLList.add(index, vServiceURL); - } - - /** - * Method enumerateServiceURL. - * - * @return an Enumeration over all java.lang.String elements - */ - public java.util.Enumeration enumerateServiceURL() - { - return this._serviceURLList.elements(); - } - - /** - * Returns the value of field 'description'. The field 'description' has the - * following description: Short description - as utf8 encoded text. This is - * usually displayed in the body of an HTML capable tooltip, so HTML tags may - * be embedded using standard UTF8 encoding. - * - * - * @return the value of field 'Description'. - */ - public java.lang.String getDescription() - { - return this._description; - } - - /** - * Returns the value of field 'name'. The field 'name' has the following - * description: The short name for the parameter set. This will be shown - * amongst the other presets for the web service. - * - * - * @return the value of field 'Name'. - */ - public java.lang.String getName() - { - return this._name; - } - - /** - * Returns the value of field 'parameters'. The field 'parameters' has the - * following description: UTF8 encoded string to be processed into a specific - * web services' parameter set. Note - newlines may be important to the - * structure of this file. - * - * - * @return the value of field 'Parameters'. - */ - public java.lang.String getParameters() - { - return this._parameters; - } - - /** - * Method getServiceURL. - * - * @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 getServiceURL(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._serviceURLList.size()) - { - throw new IndexOutOfBoundsException("getServiceURL: Index value '" - + index + "' not in range [0.." - + (this._serviceURLList.size() - 1) + "]"); +public class WebServiceParameterSet implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * The short name for the parameter set. This will be shown + * amongst the + * other presets for the web service. + * + */ + private java.lang.String _name; + + /** + * A Jalview Web Service Parameter Set container + * version number. + * Version 1 created for storing Jaba user presets. + * + */ + private java.lang.String _version; + + /** + * Short description - as utf8 encoded text. This is + * usually displayed + * in the body of an HTML capable tooltip, so HTML tags may be + * embedded + * using standard UTF8 encoding. + * + */ + private java.lang.String _description; + + /** + * URL for which the parameter set is valid. Jalview will use + * it to + * match up parameter sets to service instances that can parse + * the + * parameter set payload. + * + */ + private java.util.Vector _serviceURLList; + + /** + * UTF8 encoded string to be processed into a specific web + * services' + * parameter set. Note - newlines may be important to the + * structure + * of this file. + * + */ + private java.lang.String _parameters; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public WebServiceParameterSet() { + super(); + this._serviceURLList = new java.util.Vector(); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * + * + * @param vServiceURL + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addServiceURL( + final java.lang.String vServiceURL) + throws java.lang.IndexOutOfBoundsException { + this._serviceURLList.addElement(vServiceURL); + } + + /** + * + * + * @param index + * @param vServiceURL + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void addServiceURL( + final int index, + final java.lang.String vServiceURL) + throws java.lang.IndexOutOfBoundsException { + this._serviceURLList.add(index, vServiceURL); + } + + /** + * Method enumerateServiceURL. + * + * @return an Enumeration over all java.lang.String elements + */ + public java.util.Enumeration enumerateServiceURL( + ) { + return this._serviceURLList.elements(); + } + + /** + * Returns the value of field 'description'. The field + * 'description' has the following description: Short + * description - as utf8 encoded text. This is + * usually displayed + * in the body of an HTML capable tooltip, so HTML tags may be + * embedded + * using standard UTF8 encoding. + * + * + * @return the value of field 'Description'. + */ + public java.lang.String getDescription( + ) { + return this._description; + } + + /** + * Returns the value of field 'name'. The field 'name' has the + * following description: The short name for the parameter set. + * This will be shown amongst the + * other presets for the web service. + * + * + * @return the value of field 'Name'. + */ + public java.lang.String getName( + ) { + return this._name; + } + + /** + * Returns the value of field 'parameters'. The field + * 'parameters' has the following description: UTF8 encoded + * string to be processed into a specific web services' + * parameter set. Note - newlines may be important to the + * structure + * of this file. + * + * + * @return the value of field 'Parameters'. + */ + public java.lang.String getParameters( + ) { + return this._parameters; + } + + /** + * Method getServiceURL. + * + * @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 getServiceURL( + final int index) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._serviceURLList.size()) { + throw new IndexOutOfBoundsException("getServiceURL: Index value '" + index + "' not in range [0.." + (this._serviceURLList.size() - 1) + "]"); + } + + return (java.lang.String) _serviceURLList.get(index); + } + + /** + * Method getServiceURL.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[] getServiceURL( + ) { + java.lang.String[] array = new java.lang.String[0]; + return (java.lang.String[]) this._serviceURLList.toArray(array); + } + + /** + * Method getServiceURLCount. + * + * @return the size of this collection + */ + public int getServiceURLCount( + ) { + return this._serviceURLList.size(); + } + + /** + * Returns the value of field 'version'. The field 'version' + * has the following description: A Jalview Web Service + * Parameter Set container + * version number. + * Version 1 created for storing Jaba user presets. + * + * + * @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); } - return (java.lang.String) _serviceURLList.get(index); - } - - /** - * Method getServiceURL.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[] getServiceURL() - { - java.lang.String[] array = new java.lang.String[0]; - return (java.lang.String[]) this._serviceURLList.toArray(array); - } - - /** - * Method getServiceURLCount. - * - * @return the size of this collection - */ - public int getServiceURLCount() - { - return this._serviceURLList.size(); - } - - /** - * Returns the value of field 'version'. The field 'version' has the following - * description: A Jalview Web Service Parameter Set container version number. - * Version 1 created for storing Jaba user presets. - * - * - * @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; + /** + * + * + * @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); } - 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 removeAllServiceURL() - { - this._serviceURLList.clear(); - } - - /** - * Method removeServiceURL. - * - * @param vServiceURL - * @return true if the object was removed from the collection. - */ - public boolean removeServiceURL(final java.lang.String vServiceURL) - { - boolean removed = _serviceURLList.remove(vServiceURL); - return removed; - } - - /** - * Method removeServiceURLAt. - * - * @param index - * @return the element removed from the collection - */ - public java.lang.String removeServiceURLAt(final int index) - { - java.lang.Object obj = this._serviceURLList.remove(index); - return (java.lang.String) obj; - } - - /** - * Sets the value of field 'description'. The field 'description' has the - * following description: Short description - as utf8 encoded text. This is - * usually displayed in the body of an HTML capable tooltip, so HTML tags may - * be embedded using standard UTF8 encoding. - * - * - * @param description - * the value of field 'description'. - */ - public void setDescription(final java.lang.String description) - { - this._description = description; - } - - /** - * Sets the value of field 'name'. The field 'name' has the following - * description: The short name for the parameter set. This will be shown - * amongst the other presets for the web service. - * - * - * @param name - * the value of field 'name'. - */ - public void setName(final java.lang.String name) - { - this._name = name; - } - - /** - * Sets the value of field 'parameters'. The field 'parameters' has the - * following description: UTF8 encoded string to be processed into a specific - * web services' parameter set. Note - newlines may be important to the - * structure of this file. - * - * - * @param parameters - * the value of field 'parameters'. - */ - public void setParameters(final java.lang.String parameters) - { - this._parameters = parameters; - } - - /** - * - * - * @param index - * @param vServiceURL - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setServiceURL(final int index, - final java.lang.String vServiceURL) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._serviceURLList.size()) - { - throw new IndexOutOfBoundsException("setServiceURL: Index value '" - + index + "' not in range [0.." - + (this._serviceURLList.size() - 1) + "]"); + public void removeAllServiceURL( + ) { + this._serviceURLList.clear(); } - this._serviceURLList.set(index, vServiceURL); - } - - /** - * - * - * @param vServiceURLArray - */ - public void setServiceURL(final java.lang.String[] vServiceURLArray) - { - // -- copy array - _serviceURLList.clear(); - - for (int i = 0; i < vServiceURLArray.length; i++) - { - this._serviceURLList.add(vServiceURLArray[i]); + /** + * Method removeServiceURL. + * + * @param vServiceURL + * @return true if the object was removed from the collection. + */ + public boolean removeServiceURL( + final java.lang.String vServiceURL) { + boolean removed = _serviceURLList.remove(vServiceURL); + return removed; + } + + /** + * Method removeServiceURLAt. + * + * @param index + * @return the element removed from the collection + */ + public java.lang.String removeServiceURLAt( + final int index) { + java.lang.Object obj = this._serviceURLList.remove(index); + return (java.lang.String) obj; + } + + /** + * Sets the value of field 'description'. The field + * 'description' has the following description: Short + * description - as utf8 encoded text. This is + * usually displayed + * in the body of an HTML capable tooltip, so HTML tags may be + * embedded + * using standard UTF8 encoding. + * + * + * @param description the value of field 'description'. + */ + public void setDescription( + final java.lang.String description) { + this._description = description; + } + + /** + * Sets the value of field 'name'. The field 'name' has the + * following description: The short name for the parameter set. + * This will be shown amongst the + * other presets for the web service. + * + * + * @param name the value of field 'name'. + */ + public void setName( + final java.lang.String name) { + this._name = name; + } + + /** + * Sets the value of field 'parameters'. The field 'parameters' + * has the following description: UTF8 encoded string to be + * processed into a specific web services' + * parameter set. Note - newlines may be important to the + * structure + * of this file. + * + * + * @param parameters the value of field 'parameters'. + */ + public void setParameters( + final java.lang.String parameters) { + this._parameters = parameters; + } + + /** + * + * + * @param index + * @param vServiceURL + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setServiceURL( + final int index, + final java.lang.String vServiceURL) + throws java.lang.IndexOutOfBoundsException { + // check bounds for index + if (index < 0 || index >= this._serviceURLList.size()) { + throw new IndexOutOfBoundsException("setServiceURL: Index value '" + index + "' not in range [0.." + (this._serviceURLList.size() - 1) + "]"); + } + + this._serviceURLList.set(index, vServiceURL); + } + + /** + * + * + * @param vServiceURLArray + */ + public void setServiceURL( + final java.lang.String[] vServiceURLArray) { + //-- copy array + _serviceURLList.clear(); + + for (int i = 0; i < vServiceURLArray.length; i++) { + this._serviceURLList.add(vServiceURLArray[i]); + } + } + + /** + * Sets the value of field 'version'. The field 'version' has + * the following description: A Jalview Web Service Parameter + * Set container + * version number. + * Version 1 created for storing Jaba user presets. + * + * + * @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.schemabinding.version2.WebServiceParameterSet + */ + public static jalview.schemabinding.version2.WebServiceParameterSet unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { + return (jalview.schemabinding.version2.WebServiceParameterSet) Unmarshaller.unmarshal(jalview.schemabinding.version2.WebServiceParameterSet.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); } - } - - /** - * Sets the value of field 'version'. The field 'version' has the following - * description: A Jalview Web Service Parameter Set container version number. - * Version 1 created for storing Jaba user presets. - * - * - * @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.schemabinding.version2.WebServiceParameterSet - */ - public static jalview.schemabinding.version2.WebServiceParameterSet unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.WebServiceParameterSet) Unmarshaller - .unmarshal( - jalview.schemabinding.version2.WebServiceParameterSet.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/schemabinding/version2/descriptors/AlcodMapDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java index 23cf8cb..fbc56a3 100644 --- a/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AlcodMapDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.AlcodMap; @@ -28,230 +18,217 @@ import jalview.schemabinding.version2.AlcodMap; * * @version $Revision$ $Date$ */ -public class AlcodMapDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AlcodMapDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "alcodMap"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _dnasq - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_dnasq", "dnasq", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AlcodMap target = (AlcodMap) object; - return target.getDnasq(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AlcodMap target = (AlcodMap) object; - target.setDnasq((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class AlcodMapDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AlcodMapDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "alcodMap"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _dnasq + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dnasq", "dnasq", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AlcodMap target = (AlcodMap) object; + return target.getDnasq(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AlcodMap target = (AlcodMap) object; + target.setDnasq( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _dnasq + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _dnasq - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _mapping + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Mapping.class, "_mapping", "Mapping", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AlcodMap target = (AlcodMap) object; + return target.getMapping(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AlcodMap target = (AlcodMap) object; + target.setMapping( (jalview.schemabinding.version2.Mapping) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Mapping(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _mapping + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - // -- _mapping - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Mapping.class, "_mapping", - "Mapping", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AlcodMap target = (AlcodMap) object; - return target.getMapping(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AlcodMap target = (AlcodMap) object; - target.setMapping((jalview.schemabinding.version2.Mapping) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Mapping(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); + //-----------/ + //- Methods -/ + //-----------/ - // -- validation code for: _mapping - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.AlcodMap.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.AlcodMap.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java index f3b49b8..cd87309 100644 --- a/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AlcodonDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.Alcodon; @@ -28,296 +18,263 @@ import jalview.schemabinding.version2.Alcodon; * * @version $Revision$ $Date$ */ -public class AlcodonDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ +public class AlcodonDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; - // ----------------/ - // - Constructors -/ - // ----------------/ + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; - public AlcodonDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "alcodon"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - // -- _pos1 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Long.TYPE, "_pos1", "pos1", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Alcodon target = (Alcodon) object; - if (!target.hasPos1()) - { - return null; - } - return new java.lang.Long(target.getPos1()); - } + //----------------/ + //- Constructors -/ + //----------------/ - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Alcodon target = (Alcodon) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deletePos1(); - return; - } - target.setPos1(((java.lang.Long) value).longValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + public AlcodonDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "alcodon"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _pos1 + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos1", "pos1", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Alcodon target = (Alcodon) object; + if (!target.hasPos1()) { return null; } + return new java.lang.Long(target.getPos1()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Alcodon target = (Alcodon) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deletePos1(); + return; + } + target.setPos1( ((java.lang.Long) value).longValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _pos1 + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.LongValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.LongValidator(); + fieldValidator.setValidator(typeValidator); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _pos1 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.LongValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.LongValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _pos2 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Long.TYPE, "_pos2", "pos2", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Alcodon target = (Alcodon) object; - if (!target.hasPos2()) - { - return null; + desc.setValidator(fieldValidator); + //-- _pos2 + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos2", "pos2", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Alcodon target = (Alcodon) object; + if (!target.hasPos2()) { return null; } + return new java.lang.Long(target.getPos2()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Alcodon target = (Alcodon) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deletePos2(); + return; + } + target.setPos2( ((java.lang.Long) value).longValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _pos2 + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.LongValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.LongValidator(); + fieldValidator.setValidator(typeValidator); } - return new java.lang.Long(target.getPos2()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Alcodon target = (Alcodon) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deletePos2(); - return; - } - target.setPos2(((java.lang.Long) value).longValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _pos3 + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_pos3", "pos3", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Alcodon target = (Alcodon) object; + if (!target.hasPos3()) { return null; } + return new java.lang.Long(target.getPos3()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Alcodon target = (Alcodon) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deletePos3(); + return; + } + target.setPos3( ((java.lang.Long) value).longValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _pos3 + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.LongValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.LongValidator(); + fieldValidator.setValidator(typeValidator); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _pos2 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.LongValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.LongValidator(); - fieldValidator.setValidator(typeValidator); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + } - desc.setValidator(fieldValidator); - // -- _pos3 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Long.TYPE, "_pos3", "pos3", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Alcodon target = (Alcodon) object; - if (!target.hasPos3()) - { - return null; - } - return new java.lang.Long(target.getPos3()); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Alcodon target = (Alcodon) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deletePos3(); - return; - } - target.setPos3(((java.lang.Long) value).longValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); + //-----------/ + //- Methods -/ + //-----------/ - // -- validation code for: _pos3 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.LongValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.LongValidator(); - fieldValidator.setValidator(typeValidator); + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Alcodon.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Alcodon.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java index 5c646ca..5341376 100644 --- a/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AlcodonFrameDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.AlcodonFrame; @@ -28,250 +18,227 @@ import jalview.schemabinding.version2.AlcodonFrame; * * @version $Revision$ $Date$ */ -public class AlcodonFrameDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AlcodonFrameDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "AlcodonFrame"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _alcodonList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Alcodon.class, "_alcodonList", - "alcodon", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AlcodonFrame target = (AlcodonFrame) object; - return target.getAlcodon(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AlcodonFrame target = (AlcodonFrame) object; - target.addAlcodon((jalview.schemabinding.version2.Alcodon) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class AlcodonFrameDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AlcodonFrameDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "AlcodonFrame"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _alcodonList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Alcodon.class, "_alcodonList", "alcodon", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AlcodonFrame target = (AlcodonFrame) object; + return target.getAlcodon(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AlcodonFrame target = (AlcodonFrame) object; + target.addAlcodon( (jalview.schemabinding.version2.Alcodon) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + AlcodonFrame target = (AlcodonFrame) object; + target.removeAllAlcodon(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Alcodon(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _alcodonList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - AlcodonFrame target = (AlcodonFrame) object; - target.removeAllAlcodon(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _alcodMapList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AlcodMap.class, "_alcodMapList", "alcodMap", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AlcodonFrame target = (AlcodonFrame) object; + return target.getAlcodMap(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AlcodonFrame target = (AlcodonFrame) object; + target.addAlcodMap( (jalview.schemabinding.version2.AlcodMap) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + AlcodonFrame target = (AlcodonFrame) object; + target.removeAllAlcodMap(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.AlcodMap(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _alcodMapList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Alcodon(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _alcodonList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- _alcodMapList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.AlcodMap.class, "_alcodMapList", - "alcodMap", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AlcodonFrame target = (AlcodonFrame) object; - return target.getAlcodMap(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AlcodonFrame target = (AlcodonFrame) object; - target.addAlcodMap((jalview.schemabinding.version2.AlcodMap) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - AlcodonFrame target = (AlcodonFrame) object; - target.removeAllAlcodMap(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.AlcodMap(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); + //-----------/ + //- Methods -/ + //-----------/ - // -- validation code for: _alcodMapList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.AlcodonFrame.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.AlcodonFrame.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java index 5a703c3..3d32ff6 100644 --- a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.AnnotationColours; @@ -28,447 +18,386 @@ import jalview.schemabinding.version2.AnnotationColours; * * @version $Revision$ $Date$ */ -public class AnnotationColoursDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AnnotationColoursDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "AnnotationColours"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _aboveThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationColours target = (AnnotationColours) object; - if (!target.hasAboveThreshold()) - { - return null; +public class AnnotationColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AnnotationColoursDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "AnnotationColours"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _aboveThreshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_aboveThreshold", "aboveThreshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationColours target = (AnnotationColours) object; + if (!target.hasAboveThreshold()) { return null; } + return new java.lang.Integer(target.getAboveThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationColours target = (AnnotationColours) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteAboveThreshold(); + return; + } + target.setAboveThreshold( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _aboveThreshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - return new java.lang.Integer(target.getAboveThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationColours target = (AnnotationColours) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteAboveThreshold(); - return; - } - target.setAboveThreshold(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _annotation + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_annotation", "annotation", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationColours target = (AnnotationColours) object; + return target.getAnnotation(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationColours target = (AnnotationColours) object; + target.setAnnotation( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _annotation + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _aboveThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _annotation - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_annotation", "annotation", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationColours target = (AnnotationColours) object; - return target.getAnnotation(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationColours target = (AnnotationColours) object; - target.setAnnotation((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _minColour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_minColour", "minColour", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationColours target = (AnnotationColours) object; + if (!target.hasMinColour()) { return null; } + return new java.lang.Integer(target.getMinColour()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationColours target = (AnnotationColours) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteMinColour(); + return; + } + target.setMinColour( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _minColour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _annotation - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _minColour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_minColour", "minColour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationColours target = (AnnotationColours) object; - if (!target.hasMinColour()) - { - return null; - } - return new java.lang.Integer(target.getMinColour()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationColours target = (AnnotationColours) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteMinColour(); - return; - } - target.setMinColour(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _maxColour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_maxColour", "maxColour", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationColours target = (AnnotationColours) object; + if (!target.hasMaxColour()) { return null; } + return new java.lang.Integer(target.getMaxColour()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationColours target = (AnnotationColours) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteMaxColour(); + return; + } + target.setMaxColour( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _maxColour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _minColour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _maxColour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_maxColour", "maxColour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationColours target = (AnnotationColours) object; - if (!target.hasMaxColour()) - { - return null; + desc.setValidator(fieldValidator); + //-- _colourScheme + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colourScheme", "colourScheme", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationColours target = (AnnotationColours) object; + return target.getColourScheme(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationColours target = (AnnotationColours) object; + target.setColourScheme( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colourScheme + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - return new java.lang.Integer(target.getMaxColour()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationColours target = (AnnotationColours) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteMaxColour(); - return; - } - target.setMaxColour(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _threshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationColours target = (AnnotationColours) object; + if (!target.hasThreshold()) { return null; } + return new java.lang.Float(target.getThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationColours target = (AnnotationColours) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteThreshold(); + return; + } + target.setThreshold( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _threshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _maxColour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + } - desc.setValidator(fieldValidator); - // -- _colourScheme - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_colourScheme", "colourScheme", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationColours target = (AnnotationColours) object; - return target.getColourScheme(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationColours target = (AnnotationColours) object; - target.setColourScheme((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _colourScheme - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _threshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_threshold", "threshold", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationColours target = (AnnotationColours) object; - if (!target.hasThreshold()) - { - return null; - } - return new java.lang.Float(target.getThreshold()); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationColours target = (AnnotationColours) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteThreshold(); - return; - } - target.setThreshold(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } + //-----------/ + //- Methods -/ + //-----------/ - public java.lang.Object newInstance(java.lang.Object parent) - { + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _threshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.AnnotationColours.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.AnnotationColours.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java index c30ef18..c1910ee 100644 --- a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.Annotation; @@ -28,1071 +18,866 @@ import jalview.schemabinding.version2.Annotation; * * @version $Revision$ $Date$ */ -public class AnnotationDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AnnotationDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "Annotation"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _graph - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_graph", "graph", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasGraph()) - { - return null; +public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AnnotationDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "Annotation"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _graph + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasGraph()) { return null; } + return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setGraph( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _graph + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - return (target.getGraph() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setGraph(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _graphType + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphType", "graphType", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasGraphType()) { return null; } + return new java.lang.Integer(target.getGraphType()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteGraphType(); + return; + } + target.setGraphType( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _graphType + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _graph - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _graphType - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_graphType", "graphType", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasGraphType()) - { - return null; + desc.setValidator(fieldValidator); + //-- _sequenceRef + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceRef", "sequenceRef", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + return target.getSequenceRef(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + target.setSequenceRef( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _sequenceRef + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - return new java.lang.Integer(target.getGraphType()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteGraphType(); - return; - } - target.setGraphType(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _groupRef + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_groupRef", "groupRef", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + return target.getGroupRef(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + target.setGroupRef( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _groupRef + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _graphType - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _sequenceRef - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_sequenceRef", "sequenceRef", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getSequenceRef(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.setSequenceRef((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _graphColour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphColour", "graphColour", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasGraphColour()) { return null; } + return new java.lang.Integer(target.getGraphColour()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteGraphColour(); + return; + } + target.setGraphColour( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _graphColour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _sequenceRef - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _groupRef - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_groupRef", "groupRef", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getGroupRef(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.setGroupRef((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _graphGroup + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphGroup", "graphGroup", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasGraphGroup()) { return null; } + return new java.lang.Integer(target.getGraphGroup()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteGraphGroup(); + return; + } + target.setGraphGroup( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _graphGroup + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _groupRef - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _graphColour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_graphColour", "graphColour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasGraphColour()) - { - return null; + desc.setValidator(fieldValidator); + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + target.setId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - return new java.lang.Integer(target.getGraphColour()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteGraphColour(); - return; - } - target.setGraphColour(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _scoreOnly + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scoreOnly", "scoreOnly", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasScoreOnly()) { return null; } + return (target.getScoreOnly() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteScoreOnly(); + return; + } + target.setScoreOnly( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _scoreOnly + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _graphColour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _graphGroup - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_graphGroup", "graphGroup", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasGraphGroup()) - { - return null; + desc.setValidator(fieldValidator); + //-- _score + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Double.TYPE, "_score", "score", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasScore()) { return null; } + return new java.lang.Double(target.getScore()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteScore(); + return; + } + target.setScore( ((java.lang.Double) value).doubleValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _score + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.DoubleValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.DoubleValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-1.7976931348623157E308); + typeValidator.setMaxInclusive(1.7976931348623157E308); } - return new java.lang.Integer(target.getGraphGroup()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteGraphGroup(); - return; - } - target.setGraphGroup(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _visible + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasVisible()) { return null; } + return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteVisible(); + return; + } + target.setVisible( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _visible + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _graphGroup - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_id", "id", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.setId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _centreColLabels + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_centreColLabels", "centreColLabels", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasCentreColLabels()) { return null; } + return (target.getCentreColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteCentreColLabels(); + return; + } + target.setCentreColLabels( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _centreColLabels + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _scoreOnly - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_scoreOnly", "scoreOnly", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasScoreOnly()) - { - return null; + desc.setValidator(fieldValidator); + //-- _scaleColLabels + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scaleColLabels", "scaleColLabels", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasScaleColLabels()) { return null; } + return (target.getScaleColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteScaleColLabels(); + return; + } + target.setScaleColLabels( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _scaleColLabels + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - return (target.getScoreOnly() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteScoreOnly(); - return; - } - target.setScoreOnly(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _showAllColLabels + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAllColLabels", "showAllColLabels", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasShowAllColLabels()) { return null; } + return (target.getShowAllColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowAllColLabels(); + return; + } + target.setShowAllColLabels( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showAllColLabels + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _scoreOnly - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _score - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Double.TYPE, "_score", "score", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasScore()) - { - return null; + desc.setValidator(fieldValidator); + //-- _autoCalculated + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoCalculated", "autoCalculated", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + if (!target.hasAutoCalculated()) { return null; } + return (target.getAutoCalculated() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteAutoCalculated(); + return; + } + target.setAutoCalculated( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _autoCalculated + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - return new java.lang.Double(target.getScore()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteScore(); - return; - } - target.setScore(((java.lang.Double) value).doubleValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _annotationElementList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + return target.getAnnotationElement(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + target.addAnnotationElement( (jalview.schemabinding.version2.AnnotationElement) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + Annotation target = (Annotation) object; + target.removeAllAnnotationElement(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.AnnotationElement(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _annotationElementList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _score - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.DoubleValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.DoubleValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-1.7976931348623157E308); - typeValidator.setMaxInclusive(1.7976931348623157E308); - } - desc.setValidator(fieldValidator); - // -- _visible - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_visible", "visible", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasVisible()) - { - return null; - } - return (target.getVisible() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteVisible(); - return; - } - target.setVisible(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _label + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + return target.getLabel(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + target.setLabel( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _label + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _visible - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _centreColLabels - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_centreColLabels", "centreColLabels", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasCentreColLabels()) - { - return null; + desc.setValidator(fieldValidator); + //-- _description + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + return target.getDescription(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + target.setDescription( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _description + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - return (target.getCentreColLabels() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteCentreColLabels(); - return; - } - target.setCentreColLabels(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _thresholdLine + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.ThresholdLine.class, "_thresholdLine", "thresholdLine", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Annotation target = (Annotation) object; + return target.getThresholdLine(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Annotation target = (Annotation) object; + target.setThresholdLine( (jalview.schemabinding.version2.ThresholdLine) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.ThresholdLine(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _thresholdLine + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _centreColLabels - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- _scaleColLabels - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_scaleColLabels", "scaleColLabels", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasScaleColLabels()) - { - return null; - } - return (target.getScaleColLabels() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteScaleColLabels(); - return; - } - target.setScaleColLabels(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _scaleColLabels - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showAllColLabels - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showAllColLabels", - "showAllColLabels", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasShowAllColLabels()) - { - return null; - } - return (target.getShowAllColLabels() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowAllColLabels(); - return; - } - target.setShowAllColLabels(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } + //-----------/ + //- Methods -/ + //-----------/ - public java.lang.Object newInstance(java.lang.Object parent) - { + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showAllColLabels - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); } - desc.setValidator(fieldValidator); - // -- _autoCalculated - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_autoCalculated", "autoCalculated", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - if (!target.hasAutoCalculated()) - { - return null; - } - return (target.getAutoCalculated() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteAutoCalculated(); - return; - } - target.setAutoCalculated(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _autoCalculated - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _annotationElementList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.AnnotationElement.class, - "_annotationElementList", "annotationElement", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getAnnotationElement(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.addAnnotationElement((jalview.schemabinding.version2.AnnotationElement) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.removeAllAnnotationElement(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.AnnotationElement(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - // -- validation code for: _annotationElementList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Annotation.class; } - desc.setValidator(fieldValidator); - // -- _label - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_label", "label", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getLabel(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.setLabel((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _label - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; } - desc.setValidator(fieldValidator); - // -- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_description", "description", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getDescription(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.setDescription((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; } - desc.setValidator(fieldValidator); - // -- _thresholdLine - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.ThresholdLine.class, - "_thresholdLine", "thresholdLine", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Annotation target = (Annotation) object; - return target.getThresholdLine(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Annotation target = (Annotation) object; - target.setThresholdLine((jalview.schemabinding.version2.ThresholdLine) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.ThresholdLine(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - // -- validation code for: _thresholdLine - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Annotation.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java index 2c3343b..61221a1 100644 --- a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.AnnotationElement; @@ -28,447 +18,388 @@ import jalview.schemabinding.version2.AnnotationElement; * * @version $Revision$ $Date$ */ -public class AnnotationElementDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public AnnotationElementDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "annotationElement"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _position - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_position", "position", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - if (!target.hasPosition()) - { - return null; +public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AnnotationElementDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "annotationElement"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _position + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_position", "position", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationElement target = (AnnotationElement) object; + if (!target.hasPosition()) { return null; } + return new java.lang.Integer(target.getPosition()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationElement target = (AnnotationElement) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setPosition( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _position + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - return new java.lang.Integer(target.getPosition()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationElement target = (AnnotationElement) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setPosition(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _colour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationElement target = (AnnotationElement) object; + if (!target.hasColour()) { return null; } + return new java.lang.Integer(target.getColour()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationElement target = (AnnotationElement) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteColour(); + return; + } + target.setColour( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _position - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _colour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_colour", "colour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - if (!target.hasColour()) - { - return null; + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _displayCharacter + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_displayCharacter", "displayCharacter", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationElement target = (AnnotationElement) object; + return target.getDisplayCharacter(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationElement target = (AnnotationElement) object; + target.setDisplayCharacter( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _displayCharacter + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - return new java.lang.Integer(target.getColour()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationElement target = (AnnotationElement) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteColour(); - return; - } - target.setColour(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _description + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationElement target = (AnnotationElement) object; + return target.getDescription(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationElement target = (AnnotationElement) object; + target.setDescription( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _description + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _colour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); + desc.setValidator(fieldValidator); + //-- _secondaryStructure + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_secondaryStructure", "secondaryStructure", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationElement target = (AnnotationElement) object; + return target.getSecondaryStructure(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationElement target = (AnnotationElement) object; + target.setSecondaryStructure( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _secondaryStructure + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + typeValidator.setLength(1); + } + desc.setValidator(fieldValidator); + //-- _value + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_value", "value", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + AnnotationElement target = (AnnotationElement) object; + if (!target.hasValue()) { return null; } + return new java.lang.Float(target.getValue()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + AnnotationElement target = (AnnotationElement) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteValue(); + return; + } + target.setValue( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _value + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); + } + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - // -- _displayCharacter - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_displayCharacter", - "displayCharacter", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - return target.getDisplayCharacter(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationElement target = (AnnotationElement) object; - target.setDisplayCharacter((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } + //-----------/ + //- Methods -/ + //-----------/ - public java.lang.Object newInstance(java.lang.Object parent) - { + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _displayCharacter - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); } - desc.setValidator(fieldValidator); - // -- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_description", "description", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - return target.getDescription(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationElement target = (AnnotationElement) object; - target.setDescription((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - // -- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); } - desc.setValidator(fieldValidator); - // -- _secondaryStructure - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_secondaryStructure", - "secondaryStructure", org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - return target.getSecondaryStructure(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationElement target = (AnnotationElement) object; - target.setSecondaryStructure((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _secondaryStructure - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - typeValidator.setLength(1); + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.AnnotationElement.class; } - desc.setValidator(fieldValidator); - // -- _value - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_value", "value", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - AnnotationElement target = (AnnotationElement) object; - if (!target.hasValue()) - { - return null; - } - return new java.lang.Float(target.getValue()); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - AnnotationElement target = (AnnotationElement) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteValue(); - return; - } - target.setValue(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _value - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.AnnotationElement.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java index bd14d09..40cc7a5 100644 --- a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.Colour; @@ -28,592 +18,500 @@ import jalview.schemabinding.version2.Colour; * * @version $Revision$ $Date$ */ -public class ColourDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public ColourDescriptor() - { - super(); - _xmlName = "colour"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_name", "Name", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Colour target = (Colour) object; - return target.getName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - target.setName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _RGB - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_RGB", "RGB", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Colour target = (Colour) object; - return target.getRGB(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - target.setRGB((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class ColourDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public ColourDescriptor() { + super(); + _xmlName = "colour"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _name + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "Name", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + return target.getName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + target.setName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _name + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _RGB - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _minRGB - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_minRGB", "minRGB", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Colour target = (Colour) object; - return target.getMinRGB(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - target.setMinRGB((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _RGB + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_RGB", "RGB", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + return target.getRGB(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + target.setRGB( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _RGB + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _minRGB - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _threshType - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_threshType", "threshType", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Colour target = (Colour) object; - return target.getThreshType(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - target.setThreshType((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _minRGB + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_minRGB", "minRGB", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + return target.getMinRGB(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + target.setMinRGB( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _minRGB + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _threshType - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _threshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_threshold", "threshold", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Colour target = (Colour) object; - if (!target.hasThreshold()) - { - return null; + desc.setValidator(fieldValidator); + //-- _threshType + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_threshType", "threshType", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + return target.getThreshType(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + target.setThreshType( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _threshType + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - return new java.lang.Float(target.getThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteThreshold(); - return; - } - target.setThreshold(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _threshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + if (!target.hasThreshold()) { return null; } + return new java.lang.Float(target.getThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteThreshold(); + return; + } + target.setThreshold( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _threshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _threshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - // -- _max - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_max", "max", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Colour target = (Colour) object; - if (!target.hasMax()) - { - return null; + desc.setValidator(fieldValidator); + //-- _max + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_max", "max", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + if (!target.hasMax()) { return null; } + return new java.lang.Float(target.getMax()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteMax(); + return; + } + target.setMax( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _max + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); } - return new java.lang.Float(target.getMax()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteMax(); - return; - } - target.setMax(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _min + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_min", "min", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + if (!target.hasMin()) { return null; } + return new java.lang.Float(target.getMin()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteMin(); + return; + } + target.setMin( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _min + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _max - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - // -- _min - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_min", "min", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Colour target = (Colour) object; - if (!target.hasMin()) - { - return null; + desc.setValidator(fieldValidator); + //-- _colourByLabel + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + if (!target.hasColourByLabel()) { return null; } + return (target.getColourByLabel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteColourByLabel(); + return; + } + target.setColourByLabel( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colourByLabel + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - return new java.lang.Float(target.getMin()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteMin(); - return; - } - target.setMin(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _autoScale + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoScale", "autoScale", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Colour target = (Colour) object; + if (!target.hasAutoScale()) { return null; } + return (target.getAutoScale() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Colour target = (Colour) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteAutoScale(); + return; + } + target.setAutoScale( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _autoScale + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _min - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + } - desc.setValidator(fieldValidator); - // -- _colourByLabel - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Colour target = (Colour) object; - if (!target.hasColourByLabel()) - { - return null; - } - return (target.getColourByLabel() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteColourByLabel(); - return; - } - target.setColourByLabel(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - // -- validation code for: _colourByLabel - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _autoScale - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_autoScale", "autoScale", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Colour target = (Colour) object; - if (!target.hasAutoScale()) - { - return null; - } - return (target.getAutoScale() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } + //-----------/ + //- Methods -/ + //-----------/ - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Colour target = (Colour) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteAutoScale(); - return; - } - target.setAutoScale(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _autoScale - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Colour.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Colour.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java index 58c088b..1a55978 100644 --- a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.DBRef; @@ -28,316 +18,287 @@ import jalview.schemabinding.version2.DBRef; * * @version $Revision$ $Date$ */ -public class DBRefDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public DBRefDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "DBRef"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _source - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_source", "source", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - DBRef target = (DBRef) object; - return target.getSource(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - DBRef target = (DBRef) object; - target.setSource((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class DBRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public DBRefDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "DBRef"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _source + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + DBRef target = (DBRef) object; + return target.getSource(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + DBRef target = (DBRef) object; + target.setSource( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _source + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _source - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_version", "version", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - DBRef target = (DBRef) object; - return target.getVersion(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - DBRef target = (DBRef) object; - target.setVersion((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _version + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + DBRef target = (DBRef) object; + return target.getVersion(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + DBRef target = (DBRef) object; + target.setVersion( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _version + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _version - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _accessionId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_accessionId", "accessionId", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - DBRef target = (DBRef) object; - return target.getAccessionId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - DBRef target = (DBRef) object; - target.setAccessionId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _accessionId + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + DBRef target = (DBRef) object; + return target.getAccessionId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + DBRef target = (DBRef) object; + target.setAccessionId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _accessionId + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _accessionId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _mapping + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Mapping.class, "_mapping", "Mapping", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + DBRef target = (DBRef) object; + return target.getMapping(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + DBRef target = (DBRef) object; + target.setMapping( (jalview.schemabinding.version2.Mapping) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Mapping(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _mapping + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - // -- _mapping - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Mapping.class, "_mapping", - "Mapping", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - DBRef target = (DBRef) object; - return target.getMapping(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - DBRef target = (DBRef) object; - target.setMapping((jalview.schemabinding.version2.Mapping) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Mapping(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); + //-----------/ + //- Methods -/ + //-----------/ - // -- validation code for: _mapping - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.DBRef.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.DBRef.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java index e50fc8c..92c919e 100644 --- a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.Feature; @@ -28,547 +18,464 @@ import jalview.schemabinding.version2.Feature; * * @version $Revision$ $Date$ */ -public class FeatureDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FeatureDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "feature"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _begin - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_begin", "begin", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Feature target = (Feature) object; - if (!target.hasBegin()) - { - return null; +public class FeatureDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public FeatureDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "feature"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _begin + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Feature target = (Feature) object; + if (!target.hasBegin()) { return null; } + return new java.lang.Integer(target.getBegin()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Feature target = (Feature) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setBegin( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _begin + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - return new java.lang.Integer(target.getBegin()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Feature target = (Feature) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setBegin(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _end + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Feature target = (Feature) object; + if (!target.hasEnd()) { return null; } + return new java.lang.Integer(target.getEnd()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Feature target = (Feature) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setEnd( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _end + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _begin - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_end", "end", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Feature target = (Feature) object; - if (!target.hasEnd()) - { - return null; + desc.setValidator(fieldValidator); + //-- _type + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Feature target = (Feature) object; + return target.getType(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Feature target = (Feature) object; + target.setType( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _type + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - return new java.lang.Integer(target.getEnd()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Feature target = (Feature) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setEnd(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _description + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Feature target = (Feature) object; + return target.getDescription(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Feature target = (Feature) object; + target.setDescription( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _description + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _end - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _type - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_type", "type", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Feature target = (Feature) object; - return target.getType(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Feature target = (Feature) object; - target.setType((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _status + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Feature target = (Feature) object; + return target.getStatus(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Feature target = (Feature) object; + target.setStatus( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _status + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _type - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_description", "description", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Feature target = (Feature) object; - return target.getDescription(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Feature target = (Feature) object; - target.setDescription((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _featureGroup + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_featureGroup", "featureGroup", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Feature target = (Feature) object; + return target.getFeatureGroup(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Feature target = (Feature) object; + target.setFeatureGroup( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _featureGroup + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _status - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_status", "status", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Feature target = (Feature) object; - return target.getStatus(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Feature target = (Feature) object; - target.setStatus((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _score + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_score", "score", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Feature target = (Feature) object; + if (!target.hasScore()) { return null; } + return new java.lang.Float(target.getScore()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Feature target = (Feature) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteScore(); + return; + } + target.setScore( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _score + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _status - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _featureGroup - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_featureGroup", "featureGroup", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Feature target = (Feature) object; - return target.getFeatureGroup(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Feature target = (Feature) object; - target.setFeatureGroup((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _otherDataList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.OtherData.class, "_otherDataList", "otherData", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Feature target = (Feature) object; + return target.getOtherData(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Feature target = (Feature) object; + target.addOtherData( (jalview.schemabinding.version2.OtherData) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + Feature target = (Feature) object; + target.removeAllOtherData(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.OtherData(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _otherDataList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _featureGroup - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- _score - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_score", "score", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Feature target = (Feature) object; - if (!target.hasScore()) - { - return null; - } - return new java.lang.Float(target.getScore()); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Feature target = (Feature) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteScore(); - return; - } - target.setScore(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); + //-----------/ + //- Methods -/ + //-----------/ - // -- validation code for: _score - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _otherDataList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.OtherData.class, - "_otherDataList", "otherData", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Feature target = (Feature) object; - return target.getOtherData(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Feature target = (Feature) object; - target.addOtherData((jalview.schemabinding.version2.OtherData) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - Feature target = (Feature) object; - target.removeAllOtherData(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.OtherData(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _otherDataList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Feature.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Feature.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java index 8111b37..930aac9 100644 --- a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.FeatureSettings; @@ -28,250 +18,227 @@ import jalview.schemabinding.version2.FeatureSettings; * * @version $Revision$ $Date$ */ -public class FeatureSettingsDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FeatureSettingsDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "FeatureSettings"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _settingList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Setting.class, "_settingList", - "setting", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - FeatureSettings target = (FeatureSettings) object; - return target.getSetting(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - FeatureSettings target = (FeatureSettings) object; - target.addSetting((jalview.schemabinding.version2.Setting) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class FeatureSettingsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public FeatureSettingsDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "FeatureSettings"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _settingList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Setting.class, "_settingList", "setting", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + FeatureSettings target = (FeatureSettings) object; + return target.getSetting(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + FeatureSettings target = (FeatureSettings) object; + target.addSetting( (jalview.schemabinding.version2.Setting) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + FeatureSettings target = (FeatureSettings) object; + target.removeAllSetting(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Setting(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _settingList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - FeatureSettings target = (FeatureSettings) object; - target.removeAllSetting(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _groupList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Group.class, "_groupList", "group", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + FeatureSettings target = (FeatureSettings) object; + return target.getGroup(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + FeatureSettings target = (FeatureSettings) object; + target.addGroup( (jalview.schemabinding.version2.Group) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + FeatureSettings target = (FeatureSettings) object; + target.removeAllGroup(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Group(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _groupList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Setting(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _settingList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- _groupList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Group.class, "_groupList", - "group", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - FeatureSettings target = (FeatureSettings) object; - return target.getGroup(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - FeatureSettings target = (FeatureSettings) object; - target.addGroup((jalview.schemabinding.version2.Group) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - FeatureSettings target = (FeatureSettings) object; - target.removeAllGroup(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Group(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); + //-----------/ + //- Methods -/ + //-----------/ - // -- validation code for: _groupList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.FeatureSettings.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.FeatureSettings.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java index c6d3ee2..380d46e 100644 --- a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.Features; @@ -28,131 +18,134 @@ import jalview.schemabinding.version2.Features; * * @version $Revision$ $Date$ */ -public class FeaturesDescriptor extends - jalview.schemabinding.version2.descriptors.FeatureDescriptor -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FeaturesDescriptor() - { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.FeatureDescriptor()); - _nsURI = "www.jalview.org"; - _xmlName = "features"; - _elementDefinition = true; - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Features.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } +public class FeaturesDescriptor extends jalview.schemabinding.version2.descriptors.FeatureDescriptor { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public FeaturesDescriptor() { + super(); + setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.FeatureDescriptor()); + _nsURI = "www.jalview.org"; + _xmlName = "features"; + _elementDefinition = true; + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Features.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java index a4a74e2..417dbbb 100644 --- a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.Group; @@ -28,240 +18,220 @@ import jalview.schemabinding.version2.Group; * * @version $Revision$ $Date$ */ -public class GroupDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public GroupDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "group"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_name", "name", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Group target = (Group) object; - return target.getName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Group target = (Group) object; - target.setName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class GroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public GroupDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "group"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _name + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Group target = (Group) object; + return target.getName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Group target = (Group) object; + target.setName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _name + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _display - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_display", "display", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Group target = (Group) object; - if (!target.hasDisplay()) - { - return null; + desc.setValidator(fieldValidator); + //-- _display + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_display", "display", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Group target = (Group) object; + if (!target.hasDisplay()) { return null; } + return (target.getDisplay() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Group target = (Group) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setDisplay( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _display + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - return (target.getDisplay() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Group target = (Group) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - target.setDisplay(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } + //-----------/ + //- Methods -/ + //-----------/ - public java.lang.Object newInstance(java.lang.Object parent) - { + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _display - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Group.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Group.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java index 1b4933b..f307ee4 100644 --- a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.HiddenColumns; @@ -28,247 +18,226 @@ import jalview.schemabinding.version2.HiddenColumns; * * @version $Revision$ $Date$ */ -public class HiddenColumnsDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public HiddenColumnsDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "hiddenColumns"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_start", "start", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - HiddenColumns target = (HiddenColumns) object; - if (!target.hasStart()) - { - return null; +public class HiddenColumnsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public HiddenColumnsDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "hiddenColumns"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _start + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + HiddenColumns target = (HiddenColumns) object; + if (!target.hasStart()) { return null; } + return new java.lang.Integer(target.getStart()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + HiddenColumns target = (HiddenColumns) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteStart(); + return; + } + target.setStart( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _start + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - return new java.lang.Integer(target.getStart()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - HiddenColumns target = (HiddenColumns) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteStart(); - return; - } - target.setStart(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _end + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + HiddenColumns target = (HiddenColumns) object; + if (!target.hasEnd()) { return null; } + return new java.lang.Integer(target.getEnd()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + HiddenColumns target = (HiddenColumns) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteEnd(); + return; + } + target.setEnd( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _end + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _start - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + } - desc.setValidator(fieldValidator); - // -- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_end", "end", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - HiddenColumns target = (HiddenColumns) object; - if (!target.hasEnd()) - { - return null; - } - return new java.lang.Integer(target.getEnd()); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - HiddenColumns target = (HiddenColumns) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteEnd(); - return; - } - target.setEnd(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); + //-----------/ + //- Methods -/ + //-----------/ - // -- validation code for: _end - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.HiddenColumns.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.HiddenColumns.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java index 08b9aea..10965c3 100644 --- a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.JGroup; @@ -28,1160 +18,933 @@ import jalview.schemabinding.version2.JGroup; * * @version $Revision$ $Date$ */ -public class JGroupDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JGroupDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "JGroup"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_start", "start", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasStart()) - { - return null; - } - return new java.lang.Integer(target.getStart()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteStart(); - return; - } - target.setStart(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _start - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_end", "end", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasEnd()) - { - return null; - } - return new java.lang.Integer(target.getEnd()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteEnd(); - return; - } - target.setEnd(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _end - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_name", "name", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - return target.getName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - target.setName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _colour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_colour", "colour", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - return target.getColour(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - target.setColour((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _colour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _consThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_consThreshold", "consThreshold", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasConsThreshold()) - { - return null; - } - return new java.lang.Integer(target.getConsThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteConsThreshold(); - return; - } - target.setConsThreshold(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _consThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _pidThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasPidThreshold()) - { - return null; - } - return new java.lang.Integer(target.getPidThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deletePidThreshold(); - return; - } - target.setPidThreshold(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _pidThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _outlineColour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_outlineColour", "outlineColour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasOutlineColour()) - { - return null; - } - return new java.lang.Integer(target.getOutlineColour()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteOutlineColour(); - return; - } - target.setOutlineColour(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _outlineColour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _displayBoxes - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_displayBoxes", "displayBoxes", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasDisplayBoxes()) - { - return null; - } - return (target.getDisplayBoxes() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteDisplayBoxes(); - return; - } - target.setDisplayBoxes(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _displayBoxes - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); +public class JGroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JGroupDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "JGroup"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _start + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasStart()) { return null; } + return new java.lang.Integer(target.getStart()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteStart(); + return; + } + target.setStart( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _start + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _end + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasEnd()) { return null; } + return new java.lang.Integer(target.getEnd()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteEnd(); + return; + } + target.setEnd( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _end + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _name + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + return target.getName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + target.setName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _name + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _colour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + return target.getColour(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + target.setColour( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _consThreshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasConsThreshold()) { return null; } + return new java.lang.Integer(target.getConsThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteConsThreshold(); + return; + } + target.setConsThreshold( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _consThreshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _pidThreshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasPidThreshold()) { return null; } + return new java.lang.Integer(target.getPidThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deletePidThreshold(); + return; + } + target.setPidThreshold( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _pidThreshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _outlineColour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_outlineColour", "outlineColour", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasOutlineColour()) { return null; } + return new java.lang.Integer(target.getOutlineColour()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteOutlineColour(); + return; + } + target.setOutlineColour( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _outlineColour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _displayBoxes + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayBoxes", "displayBoxes", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasDisplayBoxes()) { return null; } + return (target.getDisplayBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteDisplayBoxes(); + return; + } + target.setDisplayBoxes( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _displayBoxes + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _displayText + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_displayText", "displayText", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasDisplayText()) { return null; } + return (target.getDisplayText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteDisplayText(); + return; + } + target.setDisplayText( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _displayText + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _colourText + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourText", "colourText", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasColourText()) { return null; } + return (target.getColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteColourText(); + return; + } + target.setColourText( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colourText + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _textCol1 + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasTextCol1()) { return null; } + return new java.lang.Integer(target.getTextCol1()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteTextCol1(); + return; + } + target.setTextCol1( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _textCol1 + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _textCol2 + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasTextCol2()) { return null; } + return new java.lang.Integer(target.getTextCol2()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteTextCol2(); + return; + } + target.setTextCol2( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _textCol2 + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _textColThreshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasTextColThreshold()) { return null; } + return new java.lang.Integer(target.getTextColThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteTextColThreshold(); + return; + } + target.setTextColThreshold( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _textColThreshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _showUnconserved + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasShowUnconserved()) { return null; } + return (target.getShowUnconserved() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowUnconserved(); + return; + } + target.setShowUnconserved( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showUnconserved + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _ignoreGapsinConsensus + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", "ignoreGapsinConsensus", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasIgnoreGapsinConsensus()) { return null; } + return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteIgnoreGapsinConsensus(); + return; + } + target.setIgnoreGapsinConsensus( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _ignoreGapsinConsensus + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showConsensusHistogram + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusHistogram", "showConsensusHistogram", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasShowConsensusHistogram()) { return null; } + return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowConsensusHistogram(); + return; + } + target.setShowConsensusHistogram( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showConsensusHistogram + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showSequenceLogo + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceLogo", "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + if (!target.hasShowSequenceLogo()) { return null; } + return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowSequenceLogo(); + return; + } + target.setShowSequenceLogo( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showSequenceLogo + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + target.setId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _seqList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_seqList", "seq", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JGroup target = (JGroup) object; + return target.getSeq(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JGroup target = (JGroup) object; + target.addSeq( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JGroup target = (JGroup) object; + target.removeAllSeq(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setRequired(true); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _seqList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- _displayText - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_displayText", "displayText", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasDisplayText()) - { - return null; - } - return (target.getDisplayText() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteDisplayText(); - return; - } - target.setDisplayText(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _displayText - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _colourText - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_colourText", "colourText", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasColourText()) - { - return null; - } - return (target.getColourText() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteColourText(); - return; - } - target.setColourText(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _colourText - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _textCol1 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_textCol1", "textCol1", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasTextCol1()) - { - return null; - } - return new java.lang.Integer(target.getTextCol1()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteTextCol1(); - return; - } - target.setTextCol1(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - // -- validation code for: _textCol1 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _textCol2 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_textCol2", "textCol2", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasTextCol2()) - { - return null; - } - return new java.lang.Integer(target.getTextCol2()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteTextCol2(); - return; - } - target.setTextCol2(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } + //-----------/ + //- Methods -/ + //-----------/ - public java.lang.Object newInstance(java.lang.Object parent) - { + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _textCol2 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); } - desc.setValidator(fieldValidator); - // -- _textColThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_textColThreshold", - "textColThreshold", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasTextColThreshold()) - { - return null; - } - return new java.lang.Integer(target.getTextColThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteTextColThreshold(); - return; - } - target.setTextColThreshold(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _textColThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); } - desc.setValidator(fieldValidator); - // -- _showUnconserved - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasShowUnconserved()) - { - return null; - } - return (target.getShowUnconserved() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowUnconserved(); - return; - } - target.setShowUnconserved(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - // -- validation code for: _showUnconserved - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.JGroup.class; } - desc.setValidator(fieldValidator); - // -- _ignoreGapsinConsensus - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", - "ignoreGapsinConsensus", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasIgnoreGapsinConsensus()) - { - return null; - } - return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteIgnoreGapsinConsensus(); - return; - } - target.setIgnoreGapsinConsensus(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _ignoreGapsinConsensus - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; } - desc.setValidator(fieldValidator); - // -- _showConsensusHistogram - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showConsensusHistogram", - "showConsensusHistogram", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasShowConsensusHistogram()) - { - return null; - } - return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowConsensusHistogram(); - return; - } - target.setShowConsensusHistogram(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - // -- validation code for: _showConsensusHistogram - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; } - desc.setValidator(fieldValidator); - // -- _showSequenceLogo - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showSequenceLogo", - "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - if (!target.hasShowSequenceLogo()) - { - return null; - } - return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowSequenceLogo(); - return; - } - target.setShowSequenceLogo(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - // -- validation code for: _showSequenceLogo - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; } - desc.setValidator(fieldValidator); - // -- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_id", "id", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - return target.getId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - target.setId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - // -- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _seqList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_seqList", "seq", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JGroup target = (JGroup) object; - return target.getSeq(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - target.addSeq((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JGroup target = (JGroup) object; - target.removeAllSeq(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _seqList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.JGroup.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } } diff --git a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java index b33eda7..427702d 100644 --- a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.JSeq; @@ -28,586 +18,486 @@ import jalview.schemabinding.version2.JSeq; * * @version $Revision$ $Date$ */ -public class JSeqDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JSeqDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "JSeq"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _colour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_colour", "colour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JSeq target = (JSeq) object; - if (!target.hasColour()) - { - return null; - } - return new java.lang.Integer(target.getColour()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteColour(); - return; - } - target.setColour(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JSeqDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "JSeq"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _colour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JSeq target = (JSeq) object; + if (!target.hasColour()) { return null; } + return new java.lang.Integer(target.getColour()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JSeq target = (JSeq) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteColour(); + return; + } + target.setColour( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _colour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_start", "start", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JSeq target = (JSeq) object; - if (!target.hasStart()) - { - return null; + desc.setValidator(fieldValidator); + //-- _start + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JSeq target = (JSeq) object; + if (!target.hasStart()) { return null; } + return new java.lang.Integer(target.getStart()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JSeq target = (JSeq) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setStart( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _start + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - return new java.lang.Integer(target.getStart()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setStart(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _end + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JSeq target = (JSeq) object; + if (!target.hasEnd()) { return null; } + return new java.lang.Integer(target.getEnd()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JSeq target = (JSeq) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setEnd( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _end + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _start - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_end", "end", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JSeq target = (JSeq) object; - if (!target.hasEnd()) - { - return null; + desc.setValidator(fieldValidator); + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JSeq target = (JSeq) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JSeq target = (JSeq) object; + target.setId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - return new java.lang.Integer(target.getEnd()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setEnd(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _hidden + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_hidden", "hidden", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JSeq target = (JSeq) object; + if (!target.hasHidden()) { return null; } + return (target.getHidden() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JSeq target = (JSeq) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteHidden(); + return; + } + target.setHidden( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _hidden + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _end - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_id", "id", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JSeq target = (JSeq) object; - return target.getId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - target.setId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _featuresList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Features.class, "_featuresList", "features", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JSeq target = (JSeq) object; + return target.getFeatures(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JSeq target = (JSeq) object; + target.addFeatures( (jalview.schemabinding.version2.Features) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JSeq target = (JSeq) object; + target.removeAllFeatures(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Features(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _featuresList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _hidden - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_hidden", "hidden", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JSeq target = (JSeq) object; - if (!target.hasHidden()) - { - return null; + desc.setValidator(fieldValidator); + //-- _pdbidsList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Pdbids.class, "_pdbidsList", "pdbids", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JSeq target = (JSeq) object; + return target.getPdbids(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JSeq target = (JSeq) object; + target.addPdbids( (jalview.schemabinding.version2.Pdbids) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JSeq target = (JSeq) object; + target.removeAllPdbids(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Pdbids(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _pdbidsList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - return (target.getHidden() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteHidden(); - return; - } - target.setHidden(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _hiddenSequencesList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_hiddenSequencesList", "hiddenSequences", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JSeq target = (JSeq) object; + return target.getHiddenSequences(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JSeq target = (JSeq) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.addHiddenSequences( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JSeq target = (JSeq) object; + target.removeAllHiddenSequences(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _hiddenSequencesList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _hidden - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - // -- _featuresList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Features.class, "_featuresList", - "features", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JSeq target = (JSeq) object; - return target.getFeatures(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - target.addFeatures((jalview.schemabinding.version2.Features) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } + //-----------/ + //- Methods -/ + //-----------/ - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - target.removeAllFeatures(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Features(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _featuresList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; } - desc.setValidator(fieldValidator); - // -- _pdbidsList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Pdbids.class, "_pdbidsList", - "pdbids", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JSeq target = (JSeq) object; - return target.getPdbids(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - target.addPdbids((jalview.schemabinding.version2.Pdbids) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - target.removeAllPdbids(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Pdbids(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _pdbidsList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); } - desc.setValidator(fieldValidator); - // -- _hiddenSequencesList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_hiddenSequencesList", - "hiddenSequences", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JSeq target = (JSeq) object; - return target.getHiddenSequences(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - target.addHiddenSequences(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JSeq target = (JSeq) object; - target.removeAllHiddenSequences(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _hiddenSequencesList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.JSeq.class; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.JSeq.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java index 4480ea9..9aad95c 100644 --- a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.JalviewModel; @@ -28,326 +18,295 @@ import jalview.schemabinding.version2.JalviewModel; * * @version $Revision$ $Date$ */ -public class JalviewModelDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JalviewModelDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "JalviewModel"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _creationDate - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.util.Date.class, "_creationDate", "creationDate", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModel target = (JalviewModel) object; - return target.getCreationDate(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModel target = (JalviewModel) object; - target.setCreationDate((java.util.Date) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class JalviewModelDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JalviewModelDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "JalviewModel"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _creationDate + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.util.Date.class, "_creationDate", "creationDate", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModel target = (JalviewModel) object; + return target.getCreationDate(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModel target = (JalviewModel) object; + target.setCreationDate( (java.util.Date) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new java.util.Date(); + } + }; + handler = new org.exolab.castor.xml.handlers.DateFieldHandler(handler); + desc.setImmutable(true); + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _creationDate + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.DateTimeValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.DateTimeValidator(); + fieldValidator.setValidator(typeValidator); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new java.util.Date(); - } - }; - handler = new org.exolab.castor.xml.handlers.DateFieldHandler(handler); - desc.setImmutable(true); - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _creationDate - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.DateTimeValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.DateTimeValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_version", "version", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModel target = (JalviewModel) object; - return target.getVersion(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModel target = (JalviewModel) object; - target.setVersion((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _version + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModel target = (JalviewModel) object; + return target.getVersion(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModel target = (JalviewModel) object; + target.setVersion( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _version + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _version - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _vamsasModel - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.VamsasModel.class, - "_vamsasModel", "vamsasModel", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModel target = (JalviewModel) object; - return target.getVamsasModel(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModel target = (JalviewModel) object; - target.setVamsasModel((jalview.schemabinding.version2.VamsasModel) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _vamsasModel + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.VamsasModel.class, "_vamsasModel", "vamsasModel", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModel target = (JalviewModel) object; + return target.getVamsasModel(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModel target = (JalviewModel) object; + target.setVamsasModel( (jalview.schemabinding.version2.VamsasModel) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.VamsasModel(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _vamsasModel + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.VamsasModel(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _vamsasModel - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope + desc.setValidator(fieldValidator); + //-- _jalviewModelSequence + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JalviewModelSequence.class, "_jalviewModelSequence", "-error-if-this-is-used-", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModel target = (JalviewModel) object; + return target.getJalviewModelSequence(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModel target = (JalviewModel) object; + target.setJalviewModelSequence( (jalview.schemabinding.version2.JalviewModelSequence) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.JalviewModelSequence(); + } + }; + desc.setHandler(handler); + desc.setContainer(true); + desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor()); + desc.setNameSpaceURI("www.jalview.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _jalviewModelSequence + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- _jalviewModelSequence - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.JalviewModelSequence.class, - "_jalviewModelSequence", "-error-if-this-is-used-", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModel target = (JalviewModel) object; - return target.getJalviewModelSequence(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModel target = (JalviewModel) object; - target.setJalviewModelSequence((jalview.schemabinding.version2.JalviewModelSequence) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.JalviewModelSequence(); - } - }; - desc.setHandler(handler); - desc.setContainer(true); - desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.JalviewModelSequenceDescriptor()); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); + //-----------/ + //- Methods -/ + //-----------/ - // -- validation code for: _jalviewModelSequence - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.JalviewModel.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.JalviewModel.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java index 4ea81bc..d6fd0ba 100644 --- a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.JalviewModelSequence; @@ -28,459 +18,387 @@ import jalview.schemabinding.version2.JalviewModelSequence; * * @version $Revision$ $Date$ */ -public class JalviewModelSequenceDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JalviewModelSequenceDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _JSeqList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.JSeq.class, "_JSeqList", "JSeq", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModelSequence target = (JalviewModelSequence) object; - return target.getJSeq(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.addJSeq((jalview.schemabinding.version2.JSeq) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class JalviewModelSequenceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JalviewModelSequenceDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _JSeqList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JSeq.class, "_JSeqList", "JSeq", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModelSequence target = (JalviewModelSequence) object; + return target.getJSeq(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.addJSeq( (jalview.schemabinding.version2.JSeq) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.removeAllJSeq(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.JSeq(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setRequired(true); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _JSeqList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.removeAllJSeq(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _JGroupList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.JGroup.class, "_JGroupList", "JGroup", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModelSequence target = (JalviewModelSequence) object; + return target.getJGroup(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.addJGroup( (jalview.schemabinding.version2.JGroup) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.removeAllJGroup(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.JGroup(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _JGroupList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.JSeq(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _JSeqList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _JGroupList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.JGroup.class, "_JGroupList", - "JGroup", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModelSequence target = (JalviewModelSequence) object; - return target.getJGroup(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.addJGroup((jalview.schemabinding.version2.JGroup) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _viewportList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Viewport.class, "_viewportList", "Viewport", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModelSequence target = (JalviewModelSequence) object; + return target.getViewport(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.addViewport( (jalview.schemabinding.version2.Viewport) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.removeAllViewport(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Viewport(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setRequired(true); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _viewportList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.removeAllJGroup(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _userColoursList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColours.class, "_userColoursList", "UserColours", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModelSequence target = (JalviewModelSequence) object; + return target.getUserColours(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.addUserColours( (jalview.schemabinding.version2.UserColours) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.removeAllUserColours(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.UserColours(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _userColoursList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.JGroup(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _JGroupList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _viewportList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Viewport.class, "_viewportList", - "Viewport", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModelSequence target = (JalviewModelSequence) object; - return target.getViewport(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.addViewport((jalview.schemabinding.version2.Viewport) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _treeList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Tree.class, "_treeList", "tree", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModelSequence target = (JalviewModelSequence) object; + return target.getTree(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.addTree( (jalview.schemabinding.version2.Tree) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.removeAllTree(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Tree(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _treeList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.removeAllViewport(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _featureSettings + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.FeatureSettings.class, "_featureSettings", "FeatureSettings", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewModelSequence target = (JalviewModelSequence) object; + return target.getFeatureSettings(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewModelSequence target = (JalviewModelSequence) object; + target.setFeatureSettings( (jalview.schemabinding.version2.FeatureSettings) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.FeatureSettings(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _featureSettings + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Viewport(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _viewportList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- _userColoursList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.UserColours.class, - "_userColoursList", "UserColours", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModelSequence target = (JalviewModelSequence) object; - return target.getUserColours(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.addUserColours((jalview.schemabinding.version2.UserColours) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.removeAllUserColours(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } + //-----------/ + //- Methods -/ + //-----------/ - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.UserColours(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _userColoursList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; } - desc.setValidator(fieldValidator); - // -- _treeList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Tree.class, "_treeList", "tree", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModelSequence target = (JalviewModelSequence) object; - return target.getTree(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.addTree((jalview.schemabinding.version2.Tree) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.removeAllTree(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Tree(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - // -- validation code for: _treeList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); } - desc.setValidator(fieldValidator); - // -- _featureSettings - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.FeatureSettings.class, - "_featureSettings", "FeatureSettings", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewModelSequence target = (JalviewModelSequence) object; - return target.getFeatureSettings(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewModelSequence target = (JalviewModelSequence) object; - target.setFeatureSettings((jalview.schemabinding.version2.FeatureSettings) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.FeatureSettings(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _featureSettings - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.JalviewModelSequence.class; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.JalviewModelSequence.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java index 92537b5..d4b4d05 100644 --- a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java @@ -1,312 +1,276 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -import jalview.schemabinding.version2.JalviewUserColours; import jalview.schemabinding.version2.Colour; +import jalview.schemabinding.version2.JalviewUserColours; /** * Class JalviewUserColoursDescriptor. * * @version $Revision$ $Date$ */ -public class JalviewUserColoursDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JalviewUserColoursDescriptor() - { - super(); - _nsURI = "www.jalview.org/colours"; - _xmlName = "JalviewUserColours"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _schemeName - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_schemeName", "schemeName", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewUserColours target = (JalviewUserColours) object; - return target.getSchemeName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewUserColours target = (JalviewUserColours) object; - target.setSchemeName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class JalviewUserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JalviewUserColoursDescriptor() { + super(); + _nsURI = "www.jalview.org/colours"; + _xmlName = "JalviewUserColours"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _schemeName + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_schemeName", "schemeName", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewUserColours target = (JalviewUserColours) object; + return target.getSchemeName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewUserColours target = (JalviewUserColours) object; + target.setSchemeName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _schemeName + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _schemeName - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _version + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "Version", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewUserColours target = (JalviewUserColours) object; + return target.getVersion(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewUserColours target = (JalviewUserColours) object; + target.setVersion( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _version + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _colourList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(Colour.class, "_colourList", "colour", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + JalviewUserColours target = (JalviewUserColours) object; + return target.getColour(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + JalviewUserColours target = (JalviewUserColours) object; + target.addColour( (Colour) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + JalviewUserColours target = (JalviewUserColours) object; + target.removeAllColour(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new Colour(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _colourList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - // -- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_version", "Version", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewUserColours target = (JalviewUserColours) object; - return target.getVersion(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewUserColours target = (JalviewUserColours) object; - target.setVersion((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } + //-----------/ + //- Methods -/ + //-----------/ - public java.lang.Object newInstance(java.lang.Object parent) - { + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _version - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); } - desc.setValidator(fieldValidator); - // -- _colourList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - Colour.class, "_colourList", "colour", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - JalviewUserColours target = (JalviewUserColours) object; - return target.getColour(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - JalviewUserColours target = (JalviewUserColours) object; - target.addColour((Colour) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - JalviewUserColours target = (JalviewUserColours) object; - target.removeAllColour(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new Colour(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(true); - addFieldDescriptor(desc); - // -- validation code for: _colourList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); } - desc.setValidator(fieldValidator); - } - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.JalviewUserColours.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.JalviewUserColours.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java index d83357c..f39b18f 100644 --- a/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MapListFromDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.MapListFrom; @@ -28,251 +18,226 @@ import jalview.schemabinding.version2.MapListFrom; * * @version $Revision$ $Date$ */ -public class MapListFromDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MapListFromDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "mapListFrom"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_start", "start", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MapListFrom target = (MapListFrom) object; - if (!target.hasStart()) - { - return null; +public class MapListFromDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public MapListFromDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "mapListFrom"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _start + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MapListFrom target = (MapListFrom) object; + if (!target.hasStart()) { return null; } + return new java.lang.Integer(target.getStart()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MapListFrom target = (MapListFrom) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setStart( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _start + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - return new java.lang.Integer(target.getStart()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MapListFrom target = (MapListFrom) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setStart(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _end + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MapListFrom target = (MapListFrom) object; + if (!target.hasEnd()) { return null; } + return new java.lang.Integer(target.getEnd()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MapListFrom target = (MapListFrom) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setEnd( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _end + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _start - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + } - desc.setValidator(fieldValidator); - // -- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_end", "end", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MapListFrom target = (MapListFrom) object; - if (!target.hasEnd()) - { - return null; - } - return new java.lang.Integer(target.getEnd()); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MapListFrom target = (MapListFrom) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - target.setEnd(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } + //-----------/ + //- Methods -/ + //-----------/ - public java.lang.Object newInstance(java.lang.Object parent) - { + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _end - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.MapListFrom.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.MapListFrom.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java index 70ce324..4de1738 100644 --- a/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MapListToDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.MapListTo; @@ -28,251 +18,226 @@ import jalview.schemabinding.version2.MapListTo; * * @version $Revision$ $Date$ */ -public class MapListToDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MapListToDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "mapListTo"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _start - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_start", "start", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MapListTo target = (MapListTo) object; - if (!target.hasStart()) - { - return null; +public class MapListToDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public MapListToDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "mapListTo"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _start + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MapListTo target = (MapListTo) object; + if (!target.hasStart()) { return null; } + return new java.lang.Integer(target.getStart()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MapListTo target = (MapListTo) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setStart( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _start + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - return new java.lang.Integer(target.getStart()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MapListTo target = (MapListTo) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setStart(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _end + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MapListTo target = (MapListTo) object; + if (!target.hasEnd()) { return null; } + return new java.lang.Integer(target.getEnd()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MapListTo target = (MapListTo) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setEnd( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _end + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _start - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + } - desc.setValidator(fieldValidator); - // -- _end - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_end", "end", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MapListTo target = (MapListTo) object; - if (!target.hasEnd()) - { - return null; - } - return new java.lang.Integer(target.getEnd()); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MapListTo target = (MapListTo) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - target.setEnd(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } + //-----------/ + //- Methods -/ + //-----------/ - public java.lang.Object newInstance(java.lang.Object parent) - { + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _end - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.MapListTo.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.MapListTo.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java index 858753f..7dc7bc5 100644 --- a/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MapListTypeDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.MapListType; @@ -28,364 +18,311 @@ import jalview.schemabinding.version2.MapListType; * * @version $Revision$ $Date$ */ -public class MapListTypeDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MapListTypeDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "mapListType"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _mapFromUnit - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Long.TYPE, "_mapFromUnit", "mapFromUnit", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MapListType target = (MapListType) object; - if (!target.hasMapFromUnit()) - { - return null; +public class MapListTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public MapListTypeDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "mapListType"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _mapFromUnit + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_mapFromUnit", "mapFromUnit", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MapListType target = (MapListType) object; + if (!target.hasMapFromUnit()) { return null; } + return new java.lang.Long(target.getMapFromUnit()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MapListType target = (MapListType) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setMapFromUnit( ((java.lang.Long) value).longValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _mapFromUnit + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.LongValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.LongValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(1L); } - return new java.lang.Long(target.getMapFromUnit()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MapListType target = (MapListType) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setMapFromUnit(((java.lang.Long) value).longValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _mapToUnit + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Long.TYPE, "_mapToUnit", "mapToUnit", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MapListType target = (MapListType) object; + if (!target.hasMapToUnit()) { return null; } + return new java.lang.Long(target.getMapToUnit()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MapListType target = (MapListType) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setMapToUnit( ((java.lang.Long) value).longValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _mapToUnit + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.LongValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.LongValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(1L); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _mapFromUnit - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.LongValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.LongValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(1L); - } - desc.setValidator(fieldValidator); - // -- _mapToUnit - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Long.TYPE, "_mapToUnit", "mapToUnit", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MapListType target = (MapListType) object; - if (!target.hasMapToUnit()) - { - return null; + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _mapListFromList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MapListFrom.class, "_mapListFromList", "mapListFrom", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MapListType target = (MapListType) object; + return target.getMapListFrom(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MapListType target = (MapListType) object; + target.addMapListFrom( (jalview.schemabinding.version2.MapListFrom) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + MapListType target = (MapListType) object; + target.removeAllMapListFrom(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.MapListFrom(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _mapListFromList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - return new java.lang.Long(target.getMapToUnit()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MapListType target = (MapListType) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setMapToUnit(((java.lang.Long) value).longValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _mapListToList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MapListTo.class, "_mapListToList", "mapListTo", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MapListType target = (MapListType) object; + return target.getMapListTo(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MapListType target = (MapListType) object; + target.addMapListTo( (jalview.schemabinding.version2.MapListTo) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + MapListType target = (MapListType) object; + target.removeAllMapListTo(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.MapListTo(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _mapListToList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _mapToUnit - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.LongValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.LongValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(1L); + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - // -- _mapListFromList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.MapListFrom.class, - "_mapListFromList", "mapListFrom", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MapListType target = (MapListType) object; - return target.getMapListFrom(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MapListType target = (MapListType) object; - target.addMapListFrom((jalview.schemabinding.version2.MapListFrom) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - MapListType target = (MapListType) object; - target.removeAllMapListFrom(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } + //-----------/ + //- Methods -/ + //-----------/ - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.MapListFrom(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _mapListFromList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; } - desc.setValidator(fieldValidator); - // -- _mapListToList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.MapListTo.class, - "_mapListToList", "mapListTo", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MapListType target = (MapListType) object; - return target.getMapListTo(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MapListType target = (MapListType) object; - target.addMapListTo((jalview.schemabinding.version2.MapListTo) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - MapListType target = (MapListType) object; - target.removeAllMapListTo(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.MapListTo(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - // -- validation code for: _mapListToList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.MapListType.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.MapListType.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java index 92aac5e..63543d7 100644 --- a/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MappingChoiceDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.MappingChoice; @@ -28,226 +18,213 @@ import jalview.schemabinding.version2.MappingChoice; * * @version $Revision$ $Date$ */ -public class MappingChoiceDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MappingChoiceDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsChoice(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _sequence - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Sequence.class, "_sequence", - "Sequence", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MappingChoice target = (MappingChoice) object; - return target.getSequence(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MappingChoice target = (MappingChoice) object; - target.setSequence((jalview.schemabinding.version2.Sequence) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class MappingChoiceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public MappingChoiceDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsChoice(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _sequence + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequence", "Sequence", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MappingChoice target = (MappingChoice) object; + return target.getSequence(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MappingChoice target = (MappingChoice) object; + target.setSequence( (jalview.schemabinding.version2.Sequence) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Sequence(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _sequence + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Sequence(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _sequence - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _dseqFor - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_dseqFor", "dseqFor", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - MappingChoice target = (MappingChoice) object; - return target.getDseqFor(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - MappingChoice target = (MappingChoice) object; - target.setDseqFor((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _dseqFor + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dseqFor", "dseqFor", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + MappingChoice target = (MappingChoice) object; + return target.getDseqFor(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + MappingChoice target = (MappingChoice) object; + target.setDseqFor( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _dseqFor + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } + desc.setValidator(fieldValidator); + } + - public java.lang.Object newInstance(java.lang.Object parent) - { + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _dseqFor - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.MappingChoice.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.MappingChoice.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java index 9c748cf..95e1a87 100644 --- a/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/MappingDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.Mapping; @@ -28,185 +18,179 @@ import jalview.schemabinding.version2.Mapping; * * @version $Revision$ $Date$ */ -public class MappingDescriptor extends - jalview.schemabinding.version2.descriptors.MapListTypeDescriptor -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MappingDescriptor() - { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.MapListTypeDescriptor()); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "Mapping"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsChoice(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _mappingChoice - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.MappingChoice.class, - "_mappingChoice", "-error-if-this-is-used-", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Mapping target = (Mapping) object; - return target.getMappingChoice(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Mapping target = (Mapping) object; - target.setMappingChoice((jalview.schemabinding.version2.MappingChoice) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class MappingDescriptor extends jalview.schemabinding.version2.descriptors.MapListTypeDescriptor { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public MappingDescriptor() { + super(); + setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.MapListTypeDescriptor()); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "Mapping"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsChoice(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _mappingChoice + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.MappingChoice.class, "_mappingChoice", "-error-if-this-is-used-", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Mapping target = (Mapping) object; + return target.getMappingChoice(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Mapping target = (Mapping) object; + target.setMappingChoice( (jalview.schemabinding.version2.MappingChoice) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.MappingChoice(); + } + }; + desc.setHandler(handler); + desc.setContainer(true); + desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor()); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _mappingChoice + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.MappingChoice(); - } - }; - desc.setHandler(handler); - desc.setContainer(true); - desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor()); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _mappingChoice - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Mapping.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Mapping.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } } diff --git a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java index 4e49c36..46f6682 100644 --- a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.OtherData; @@ -28,231 +18,218 @@ import jalview.schemabinding.version2.OtherData; * * @version $Revision$ $Date$ */ -public class OtherDataDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public OtherDataDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "otherData"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _key - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_key", "key", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - OtherData target = (OtherData) object; - return target.getKey(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - OtherData target = (OtherData) object; - target.setKey((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class OtherDataDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public OtherDataDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "otherData"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _key + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + OtherData target = (OtherData) object; + return target.getKey(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + OtherData target = (OtherData) object; + target.setKey( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _key + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _key - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _value - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_value", "value", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - OtherData target = (OtherData) object; - return target.getValue(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - OtherData target = (OtherData) object; - target.setValue((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _value + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + OtherData target = (OtherData) object; + return target.getValue(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + OtherData target = (OtherData) object; + target.setValue( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _value + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _value - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - } - // -----------/ - // - Methods -/ - // -----------/ + //-----------/ + //- Methods -/ + //-----------/ - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.OtherData.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.OtherData.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java index f892f79..dbf0c3a 100644 --- a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.Pdbentry; @@ -28,329 +18,295 @@ import jalview.schemabinding.version2.Pdbentry; * * @version $Revision$ $Date$ */ -public class PdbentryDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public PdbentryDescriptor() - { - super(); - _xmlName = "pdbentry"; - _elementDefinition = false; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_id", "id", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Pdbentry target = (Pdbentry) object; - return target.getId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Pdbentry target = (Pdbentry) object; - target.setId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class PdbentryDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public PdbentryDescriptor() { + super(); + _xmlName = "pdbentry"; + _elementDefinition = false; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Pdbentry target = (Pdbentry) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Pdbentry target = (Pdbentry) object; + target.setId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _type - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_type", "type", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Pdbentry target = (Pdbentry) object; - return target.getType(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Pdbentry target = (Pdbentry) object; - target.setType((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _type + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Pdbentry target = (Pdbentry) object; + return target.getType(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Pdbentry target = (Pdbentry) object; + target.setType( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _type + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _type - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _file - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_file", "file", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Pdbentry target = (Pdbentry) object; - return target.getFile(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Pdbentry target = (Pdbentry) object; - target.setFile((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _file + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_file", "file", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Pdbentry target = (Pdbentry) object; + return target.getFile(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Pdbentry target = (Pdbentry) object; + target.setFile( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _file + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _file - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _items - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.PdbentryItem.class, "_items", - (java.lang.String) null, org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Pdbentry target = (Pdbentry) object; - return target.getPdbentryItem(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Pdbentry target = (Pdbentry) object; - target.addPdbentryItem((jalview.schemabinding.version2.PdbentryItem) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _items + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.PdbentryItem.class, "_items", (java.lang.String) null, org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Pdbentry target = (Pdbentry) object; + return target.getPdbentryItem(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Pdbentry target = (Pdbentry) object; + target.addPdbentryItem( (jalview.schemabinding.version2.PdbentryItem) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + Pdbentry target = (Pdbentry) object; + target.removeAllPdbentryItem(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.PdbentryItem(); + } + }; + desc.setHandler(handler); + desc.setContainer(true); + desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor()); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _items + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } + desc.setValidator(fieldValidator); + } - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - Pdbentry target = (Pdbentry) object; - target.removeAllPdbentryItem(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.PdbentryItem(); - } - }; - desc.setHandler(handler); - desc.setContainer(true); - desc.setClassDescriptor(new jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor()); - desc.setMultivalued(true); - addFieldDescriptor(desc); + //-----------/ + //- Methods -/ + //-----------/ - // -- validation code for: _items - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Pdbentry.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Pdbentry.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java index 0a043d7..693ad61 100644 --- a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.PdbentryItem; @@ -28,195 +18,185 @@ import jalview.schemabinding.version2.PdbentryItem; * * @version $Revision$ $Date$ */ -public class PdbentryItemDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public PdbentryItemDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "pdbentry"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _propertyList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Property.class, "_propertyList", - "property", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - PdbentryItem target = (PdbentryItem) object; - return target.getProperty(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - PdbentryItem target = (PdbentryItem) object; - target.addProperty((jalview.schemabinding.version2.Property) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - PdbentryItem target = (PdbentryItem) object; - target.removeAllProperty(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class PdbentryItemDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public PdbentryItemDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "pdbentry"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _propertyList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Property.class, "_propertyList", "property", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + PdbentryItem target = (PdbentryItem) object; + return target.getProperty(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + PdbentryItem target = (PdbentryItem) object; + target.addProperty( (jalview.schemabinding.version2.Property) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + PdbentryItem target = (PdbentryItem) object; + target.removeAllProperty(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Property(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _propertyList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Property(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _propertyList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.PdbentryItem.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.PdbentryItem.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } } diff --git a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java index cf746cd..2547f1d 100644 --- a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.Pdbids; @@ -28,197 +18,186 @@ import jalview.schemabinding.version2.Pdbids; * * @version $Revision$ $Date$ */ -public class PdbidsDescriptor extends - jalview.schemabinding.version2.descriptors.PdbentryDescriptor -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public PdbidsDescriptor() - { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.PdbentryDescriptor()); - _nsURI = "www.jalview.org"; - _xmlName = "pdbids"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _structureStateList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.StructureState.class, - "_structureStateList", "structureState", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Pdbids target = (Pdbids) object; - return target.getStructureState(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Pdbids target = (Pdbids) object; - target.addStructureState((jalview.schemabinding.version2.StructureState) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - Pdbids target = (Pdbids) object; - target.removeAllStructureState(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class PdbidsDescriptor extends jalview.schemabinding.version2.descriptors.PdbentryDescriptor { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public PdbidsDescriptor() { + super(); + setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.PdbentryDescriptor()); + _nsURI = "www.jalview.org"; + _xmlName = "pdbids"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _structureStateList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.StructureState.class, "_structureStateList", "structureState", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Pdbids target = (Pdbids) object; + return target.getStructureState(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Pdbids target = (Pdbids) object; + target.addStructureState( (jalview.schemabinding.version2.StructureState) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + Pdbids target = (Pdbids) object; + target.removeAllStructureState(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.StructureState(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _structureStateList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.StructureState(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _structureStateList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + desc.setValidator(fieldValidator); + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Pdbids.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Pdbids.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } } diff --git a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java index 0e27e21..15f2e37 100644 --- a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.Property; @@ -28,231 +18,218 @@ import jalview.schemabinding.version2.Property; * * @version $Revision$ $Date$ */ -public class PropertyDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public PropertyDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "property"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_name", "name", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Property target = (Property) object; - return target.getName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Property target = (Property) object; - target.setName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class PropertyDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public PropertyDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "property"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _name + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Property target = (Property) object; + return target.getName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Property target = (Property) object; + target.setName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _name + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _value - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_value", "value", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Property target = (Property) object; - return target.getValue(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Property target = (Property) object; - target.setValue((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _value + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Property target = (Property) object; + return target.getValue(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Property target = (Property) object; + target.setValue( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _value + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _value - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - } - // -----------/ - // - Methods -/ - // -----------/ + //-----------/ + //- Methods -/ + //-----------/ - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Property.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Property.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java index 07a6181..4dfd168 100644 --- a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.Sequence; @@ -28,241 +18,223 @@ import jalview.schemabinding.version2.Sequence; * * @version $Revision$ $Date$ */ -public class SequenceDescriptor extends - jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SequenceDescriptor() - { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor()); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "Sequence"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _dsseqid - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_dsseqid", "dsseqid", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Sequence target = (Sequence) object; - return target.getDsseqid(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Sequence target = (Sequence) object; - target.setDsseqid((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class SequenceDescriptor extends jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceDescriptor() { + super(); + setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor()); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "Sequence"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _dsseqid + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dsseqid", "dsseqid", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Sequence target = (Sequence) object; + return target.getDsseqid(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Sequence target = (Sequence) object; + target.setDsseqid( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _dsseqid + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _dsseqid - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _DBRefList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.DBRef.class, "_DBRefList", - "DBRef", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Sequence target = (Sequence) object; - return target.getDBRef(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Sequence target = (Sequence) object; - target.addDBRef((jalview.schemabinding.version2.DBRef) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _DBRefList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.DBRef.class, "_DBRefList", "DBRef", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Sequence target = (Sequence) object; + return target.getDBRef(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Sequence target = (Sequence) object; + target.addDBRef( (jalview.schemabinding.version2.DBRef) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + Sequence target = (Sequence) object; + target.removeAllDBRef(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.DBRef(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _DBRefList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } + desc.setValidator(fieldValidator); + } - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - Sequence target = (Sequence) object; - target.removeAllDBRef(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.DBRef(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); + //-----------/ + //- Methods -/ + //-----------/ - // -- validation code for: _DBRefList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Sequence.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Sequence.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java index ab0d2b8..aa0c798 100644 --- a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.SequenceSet; @@ -28,455 +18,387 @@ import jalview.schemabinding.version2.SequenceSet; * * @version $Revision$ $Date$ */ -public class SequenceSetDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SequenceSetDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "SequenceSet"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _gapChar - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_gapChar", "gapChar", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getGapChar(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.setGapChar((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceSetDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "SequenceSet"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _gapChar + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getGapChar(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.setGapChar( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _gapChar + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _gapChar - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _datasetId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_datasetId", "datasetId", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getDatasetId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.setDatasetId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _datasetId + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_datasetId", "datasetId", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getDatasetId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.setDatasetId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _datasetId + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _datasetId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _sequenceList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Sequence.class, "_sequenceList", - "Sequence", org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getSequence(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.addSequence((jalview.schemabinding.version2.Sequence) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _sequenceList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getSequence(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.addSequence( (jalview.schemabinding.version2.Sequence) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + SequenceSet target = (SequenceSet) object; + target.removeAllSequence(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Sequence(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _sequenceList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.removeAllSequence(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _annotationList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotationList", "Annotation", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getAnnotation(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.addAnnotation( (jalview.schemabinding.version2.Annotation) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + SequenceSet target = (SequenceSet) object; + target.removeAllAnnotation(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.Annotation(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _annotationList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Sequence(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _sequenceList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - } - desc.setValidator(fieldValidator); - // -- _annotationList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.Annotation.class, - "_annotationList", "Annotation", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getAnnotation(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.addAnnotation((jalview.schemabinding.version2.Annotation) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _sequenceSetPropertiesList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSetProperties.class, "_sequenceSetPropertiesList", "sequenceSetProperties", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getSequenceSetProperties(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.addSequenceSetProperties( (jalview.schemabinding.version2.SequenceSetProperties) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + SequenceSet target = (SequenceSet) object; + target.removeAllSequenceSetProperties(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.SequenceSetProperties(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _sequenceSetPropertiesList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.removeAllAnnotation(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _alcodonFrameList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AlcodonFrame.class, "_alcodonFrameList", "AlcodonFrame", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSet target = (SequenceSet) object; + return target.getAlcodonFrame(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSet target = (SequenceSet) object; + target.addAlcodonFrame( (jalview.schemabinding.version2.AlcodonFrame) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + SequenceSet target = (SequenceSet) object; + target.removeAllAlcodonFrame(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.AlcodonFrame(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _alcodonFrameList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.Annotation(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _annotationList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- _sequenceSetPropertiesList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.SequenceSetProperties.class, - "_sequenceSetPropertiesList", "sequenceSetProperties", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getSequenceSetProperties(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.addSequenceSetProperties((jalview.schemabinding.version2.SequenceSetProperties) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.removeAllSequenceSetProperties(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.SequenceSetProperties(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); + //-----------/ + //- Methods -/ + //-----------/ - // -- validation code for: _sequenceSetPropertiesList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; } - desc.setValidator(fieldValidator); - // -- _alcodonFrameList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.AlcodonFrame.class, - "_alcodonFrameList", "AlcodonFrame", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SequenceSet target = (SequenceSet) object; - return target.getAlcodonFrame(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.addAlcodonFrame((jalview.schemabinding.version2.AlcodonFrame) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - SequenceSet target = (SequenceSet) object; - target.removeAllAlcodonFrame(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.AlcodonFrame(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - // -- validation code for: _alcodonFrameList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.SequenceSet.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.SequenceSet.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java index 11a25fb..9c3c578 100644 --- a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.SequenceSetProperties; @@ -28,227 +18,214 @@ import jalview.schemabinding.version2.SequenceSetProperties; * * @version $Revision$ $Date$ */ -public class SequenceSetPropertiesDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SequenceSetPropertiesDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "sequenceSetProperties"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _key - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_key", "key", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SequenceSetProperties target = (SequenceSetProperties) object; - return target.getKey(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceSetProperties target = (SequenceSetProperties) object; - target.setKey((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class SequenceSetPropertiesDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceSetPropertiesDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "sequenceSetProperties"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _key + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSetProperties target = (SequenceSetProperties) object; + return target.getKey(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSetProperties target = (SequenceSetProperties) object; + target.setKey( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _key + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } + desc.setValidator(fieldValidator); + //-- _value + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceSetProperties target = (SequenceSetProperties) object; + return target.getValue(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceSetProperties target = (SequenceSetProperties) object; + target.setValue( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _value + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + } + - public java.lang.Object newInstance(java.lang.Object parent) - { + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _key - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); } - desc.setValidator(fieldValidator); - // -- _value - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_value", "value", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SequenceSetProperties target = (SequenceSetProperties) object; - return target.getValue(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceSetProperties target = (SequenceSetProperties) object; - target.setValue((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _value - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.SequenceSetProperties.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.SequenceSetProperties.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } } diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java index 5554046..fa73621 100644 --- a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.SequenceType; @@ -28,322 +18,293 @@ import jalview.schemabinding.version2.SequenceType; * * @version $Revision$ $Date$ */ -public class SequenceTypeDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SequenceTypeDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "SequenceType"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_id", "id", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceType target = (SequenceType) object; - target.setId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceTypeDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "SequenceType"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceType target = (SequenceType) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceType target = (SequenceType) object; + target.setId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_description", "description", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getDescription(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceType target = (SequenceType) object; - target.setDescription((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _description + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceType target = (SequenceType) object; + return target.getDescription(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceType target = (SequenceType) object; + target.setDescription( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _description + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _sequence + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequence", "sequence", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceType target = (SequenceType) object; + return target.getSequence(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceType target = (SequenceType) object; + target.setSequence( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _sequence + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _name + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + SequenceType target = (SequenceType) object; + return target.getName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + SequenceType target = (SequenceType) object; + target.setName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _name + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - // -- _sequence - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_sequence", "sequence", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getSequence(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceType target = (SequenceType) object; - target.setSequence((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } + //-----------/ + //- Methods -/ + //-----------/ - public java.lang.Object newInstance(java.lang.Object parent) - { + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _sequence - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); } - desc.setValidator(fieldValidator); - // -- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_name", "name", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - SequenceType target = (SequenceType) object; - return target.getName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - SequenceType target = (SequenceType) object; - target.setName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - // -- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.SequenceType.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.SequenceType.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java index ca375af..772e9bc 100644 --- a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.Setting; @@ -28,736 +18,603 @@ import jalview.schemabinding.version2.Setting; * * @version $Revision$ $Date$ */ -public class SettingDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public SettingDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "setting"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _type - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_type", "type", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - return target.getType(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - target.setType((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class SettingDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SettingDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "setting"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _type + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + return target.getType(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + target.setType( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _type + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _type - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _colour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_colour", "colour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasColour()) - { - return null; + desc.setValidator(fieldValidator); + //-- _colour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasColour()) { return null; } + return new java.lang.Integer(target.getColour()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setColour( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - return new java.lang.Integer(target.getColour()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setColour(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _display + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_display", "display", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasDisplay()) { return null; } + return (target.getDisplay() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // ignore null values for non optional primitives + if (value == null) { return; } + + target.setDisplay( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _display + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _colour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _display - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_display", "display", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasDisplay()) - { - return null; + desc.setValidator(fieldValidator); + //-- _order + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_order", "order", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasOrder()) { return null; } + return new java.lang.Float(target.getOrder()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteOrder(); + return; + } + target.setOrder( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _order + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); } - return (target.getDisplay() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // ignore null values for non optional primitives - if (value == null) - { - return; - } - - target.setDisplay(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _mincolour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_mincolour", "mincolour", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasMincolour()) { return null; } + return new java.lang.Integer(target.getMincolour()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteMincolour(); + return; + } + target.setMincolour( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _mincolour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _display - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _order - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_order", "order", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasOrder()) - { - return null; + desc.setValidator(fieldValidator); + //-- _threshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasThreshold()) { return null; } + return new java.lang.Float(target.getThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteThreshold(); + return; + } + target.setThreshold( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _threshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); } - return new java.lang.Float(target.getOrder()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteOrder(); - return; - } - target.setOrder(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _threshstate + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_threshstate", "threshstate", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasThreshstate()) { return null; } + return new java.lang.Integer(target.getThreshstate()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteThreshstate(); + return; + } + target.setThreshstate( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _threshstate + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _order - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - // -- _mincolour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_mincolour", "mincolour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasMincolour()) - { - return null; + desc.setValidator(fieldValidator); + //-- _max + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_max", "max", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasMax()) { return null; } + return new java.lang.Float(target.getMax()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteMax(); + return; + } + target.setMax( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _max + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); } - return new java.lang.Integer(target.getMincolour()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteMincolour(); - return; - } - target.setMincolour(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _min + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_min", "min", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasMin()) { return null; } + return new java.lang.Float(target.getMin()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteMin(); + return; + } + target.setMin( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _min + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _mincolour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _threshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_threshold", "threshold", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasThreshold()) - { - return null; + desc.setValidator(fieldValidator); + //-- _colourByLabel + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasColourByLabel()) { return null; } + return (target.getColourByLabel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteColourByLabel(); + return; + } + target.setColourByLabel( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colourByLabel + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - return new java.lang.Float(target.getThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteThreshold(); - return; - } - target.setThreshold(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _autoScale + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoScale", "autoScale", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Setting target = (Setting) object; + if (!target.hasAutoScale()) { return null; } + return (target.getAutoScale() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Setting target = (Setting) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteAutoScale(); + return; + } + target.setAutoScale( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _autoScale + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _threshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + } - desc.setValidator(fieldValidator); - // -- _threshstate - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_threshstate", "threshstate", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasThreshstate()) - { - return null; - } - return new java.lang.Integer(target.getThreshstate()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteThreshstate(); - return; - } - target.setThreshstate(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - // -- validation code for: _threshstate - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _max - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_max", "max", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasMax()) - { - return null; - } - return new java.lang.Float(target.getMax()); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteMax(); - return; - } - target.setMax(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } + //-----------/ + //- Methods -/ + //-----------/ - public java.lang.Object newInstance(java.lang.Object parent) - { + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _max - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); } - desc.setValidator(fieldValidator); - // -- _min - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_min", "min", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasMin()) - { - return null; - } - return new java.lang.Float(target.getMin()); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteMin(); - return; - } - target.setMin(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _min - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); } - desc.setValidator(fieldValidator); - // -- _colourByLabel - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_colourByLabel", "colourByLabel", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasColourByLabel()) - { - return null; - } - return (target.getColourByLabel() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteColourByLabel(); - return; - } - target.setColourByLabel(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _colourByLabel - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Setting.class; } - desc.setValidator(fieldValidator); - // -- _autoScale - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_autoScale", "autoScale", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Setting target = (Setting) object; - if (!target.hasAutoScale()) - { - return null; - } - return (target.getAutoScale() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Setting target = (Setting) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteAutoScale(); - return; - } - target.setAutoScale(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _autoScale - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Setting.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java index 09171ea..3db3b4c 100644 --- a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.StructureState; @@ -28,500 +18,508 @@ import jalview.schemabinding.version2.StructureState; * * @version $Revision$ $Date$ */ -public class StructureStateDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public StructureStateDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "structureState"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- _content - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_content", "PCDATA", - org.exolab.castor.xml.NodeType.Text); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - StructureState target = (StructureState) object; - return target.getContent(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - StructureState target = (StructureState) object; - target.setContent((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public StructureStateDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "structureState"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- _content + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + StructureState target = (StructureState) object; + return target.getContent(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + StructureState target = (StructureState) object; + target.setContent( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + addFieldDescriptor(desc); + + //-- validation code for: _content + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - addFieldDescriptor(desc); - - // -- validation code for: _content - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize attribute descriptors - - // -- _visible - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_visible", "visible", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasVisible()) - { - return null; + desc.setValidator(fieldValidator); + //-- initialize attribute descriptors + + //-- _visible + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_visible", "visible", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + StructureState target = (StructureState) object; + if (!target.hasVisible()) { return null; } + return (target.getVisible() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + StructureState target = (StructureState) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteVisible(); + return; + } + target.setVisible( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _visible + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - return (target.getVisible() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteVisible(); - return; - } - target.setVisible(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _xpos + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + StructureState target = (StructureState) object; + if (!target.hasXpos()) { return null; } + return new java.lang.Integer(target.getXpos()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + StructureState target = (StructureState) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteXpos(); + return; + } + target.setXpos( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _xpos + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _visible - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _xpos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_xpos", "xpos", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasXpos()) - { - return null; + desc.setValidator(fieldValidator); + //-- _ypos + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + StructureState target = (StructureState) object; + if (!target.hasYpos()) { return null; } + return new java.lang.Integer(target.getYpos()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + StructureState target = (StructureState) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteYpos(); + return; + } + target.setYpos( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _ypos + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - return new java.lang.Integer(target.getXpos()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteXpos(); - return; - } - target.setXpos(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _width + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + StructureState target = (StructureState) object; + if (!target.hasWidth()) { return null; } + return new java.lang.Integer(target.getWidth()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + StructureState target = (StructureState) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteWidth(); + return; + } + target.setWidth( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _width + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _xpos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _ypos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_ypos", "ypos", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasYpos()) - { - return null; + desc.setValidator(fieldValidator); + //-- _height + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + StructureState target = (StructureState) object; + if (!target.hasHeight()) { return null; } + return new java.lang.Integer(target.getHeight()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + StructureState target = (StructureState) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteHeight(); + return; + } + target.setHeight( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _height + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - return new java.lang.Integer(target.getYpos()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteYpos(); - return; - } - target.setYpos(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _viewId + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewId", "viewId", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + StructureState target = (StructureState) object; + return target.getViewId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + StructureState target = (StructureState) object; + target.setViewId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _viewId + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _ypos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _width - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_width", "width", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasWidth()) - { - return null; + desc.setValidator(fieldValidator); + //-- _linkAlignPanel + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_linkAlignPanel", "linkAlignPanel", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + StructureState target = (StructureState) object; + if (!target.hasLinkAlignPanel()) { return null; } + return (target.getLinkAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + StructureState target = (StructureState) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteLinkAlignPanel(); + return; + } + target.setLinkAlignPanel( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _linkAlignPanel + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - return new java.lang.Integer(target.getWidth()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteWidth(); - return; - } - target.setWidth(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _alignwithAlignPanel + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_alignwithAlignPanel", "alignwithAlignPanel", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + StructureState target = (StructureState) object; + if (!target.hasAlignwithAlignPanel()) { return null; } + return (target.getAlignwithAlignPanel() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + StructureState target = (StructureState) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteAlignwithAlignPanel(); + return; + } + target.setAlignwithAlignPanel( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _alignwithAlignPanel + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _width - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + } - desc.setValidator(fieldValidator); - // -- _height - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_height", "height", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - StructureState target = (StructureState) object; - if (!target.hasHeight()) - { - return null; - } - return new java.lang.Integer(target.getHeight()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - StructureState target = (StructureState) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteHeight(); - return; - } - target.setHeight(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - // -- validation code for: _height - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _viewId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_viewId", "viewId", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - StructureState target = (StructureState) object; - return target.getViewId(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - StructureState target = (StructureState) object; - target.setViewId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } + //-----------/ + //- Methods -/ + //-----------/ - public java.lang.Object newInstance(java.lang.Object parent) - { + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _viewId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.StructureState.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.StructureState.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java index c683978..951e7ca 100644 --- a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.ThresholdLine; @@ -28,292 +18,263 @@ import jalview.schemabinding.version2.ThresholdLine; * * @version $Revision$ $Date$ */ -public class ThresholdLineDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ +public class ThresholdLineDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; - // ----------------/ - // - Constructors -/ - // ----------------/ + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; - public ThresholdLineDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "thresholdLine"; - _elementDefinition = true; - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - // -- _label - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_label", "label", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - ThresholdLine target = (ThresholdLine) object; - return target.getLabel(); - } + //----------------/ + //- Constructors -/ + //----------------/ - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - ThresholdLine target = (ThresholdLine) object; - target.setLabel((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + public ThresholdLineDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "thresholdLine"; + _elementDefinition = true; + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _label + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + ThresholdLine target = (ThresholdLine) object; + return target.getLabel(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + ThresholdLine target = (ThresholdLine) object; + target.setLabel( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _label + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _label - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _value - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_value", "value", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - ThresholdLine target = (ThresholdLine) object; - if (!target.hasValue()) - { - return null; + desc.setValidator(fieldValidator); + //-- _value + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_value", "value", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + ThresholdLine target = (ThresholdLine) object; + if (!target.hasValue()) { return null; } + return new java.lang.Float(target.getValue()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + ThresholdLine target = (ThresholdLine) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteValue(); + return; + } + target.setValue( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _value + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); } - return new java.lang.Float(target.getValue()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - ThresholdLine target = (ThresholdLine) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteValue(); - return; - } - target.setValue(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _colour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_colour", "colour", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + ThresholdLine target = (ThresholdLine) object; + if (!target.hasColour()) { return null; } + return new java.lang.Integer(target.getColour()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + ThresholdLine target = (ThresholdLine) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteColour(); + return; + } + target.setColour( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _colour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _value - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + } - desc.setValidator(fieldValidator); - // -- _colour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_colour", "colour", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - ThresholdLine target = (ThresholdLine) object; - if (!target.hasColour()) - { - return null; - } - return new java.lang.Integer(target.getColour()); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - ThresholdLine target = (ThresholdLine) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteColour(); - return; - } - target.setColour(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); + //-----------/ + //- Methods -/ + //-----------/ - // -- validation code for: _colour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.ThresholdLine.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.ThresholdLine.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java index 9d70d62..f4741a2 100644 --- a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.Tree; @@ -28,978 +18,798 @@ import jalview.schemabinding.version2.Tree; * * @version $Revision$ $Date$ */ -public class TreeDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public TreeDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "tree"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _width - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_width", "width", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasWidth()) - { - return null; - } - return new java.lang.Integer(target.getWidth()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteWidth(); - return; - } - target.setWidth(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public TreeDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "tree"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _width + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasWidth()) { return null; } + return new java.lang.Integer(target.getWidth()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteWidth(); + return; + } + target.setWidth( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _width + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _width - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _height - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_height", "height", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasHeight()) - { - return null; + desc.setValidator(fieldValidator); + //-- _height + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasHeight()) { return null; } + return new java.lang.Integer(target.getHeight()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteHeight(); + return; + } + target.setHeight( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _height + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - return new java.lang.Integer(target.getHeight()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteHeight(); - return; - } - target.setHeight(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _xpos + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasXpos()) { return null; } + return new java.lang.Integer(target.getXpos()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteXpos(); + return; + } + target.setXpos( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _xpos + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _height - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _xpos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_xpos", "xpos", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasXpos()) - { - return null; + desc.setValidator(fieldValidator); + //-- _ypos + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasYpos()) { return null; } + return new java.lang.Integer(target.getYpos()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteYpos(); + return; + } + target.setYpos( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _ypos + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - return new java.lang.Integer(target.getXpos()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteXpos(); - return; - } - target.setXpos(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _fontName + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + return target.getFontName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + target.setFontName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _fontName + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _xpos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _ypos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_ypos", "ypos", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasYpos()) - { - return null; + desc.setValidator(fieldValidator); + //-- _fontSize + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasFontSize()) { return null; } + return new java.lang.Integer(target.getFontSize()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteFontSize(); + return; + } + target.setFontSize( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _fontSize + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - return new java.lang.Integer(target.getYpos()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteYpos(); - return; - } - target.setYpos(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _fontStyle + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasFontStyle()) { return null; } + return new java.lang.Integer(target.getFontStyle()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteFontStyle(); + return; + } + target.setFontStyle( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _fontStyle + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _ypos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _fontName - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_fontName", "fontName", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getFontName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - target.setFontName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _threshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Float.TYPE, "_threshold", "threshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasThreshold()) { return null; } + return new java.lang.Float(target.getThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteThreshold(); + return; + } + target.setThreshold( ((java.lang.Float) value).floatValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _threshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.FloatValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive((float) -3.4028235E38); + typeValidator.setMaxInclusive((float) 3.4028235E38); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _fontName - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _fontSize - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_fontSize", "fontSize", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasFontSize()) - { - return null; + desc.setValidator(fieldValidator); + //-- _showBootstrap + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasShowBootstrap()) { return null; } + return (target.getShowBootstrap() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowBootstrap(); + return; + } + target.setShowBootstrap( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showBootstrap + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - return new java.lang.Integer(target.getFontSize()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteFontSize(); - return; - } - target.setFontSize(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _showDistances + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDistances", "showDistances", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasShowDistances()) { return null; } + return (target.getShowDistances() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowDistances(); + return; + } + target.setShowDistances( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showDistances + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _fontSize - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _fontStyle - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_fontStyle", "fontStyle", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasFontStyle()) - { - return null; + desc.setValidator(fieldValidator); + //-- _markUnlinked + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasMarkUnlinked()) { return null; } + return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteMarkUnlinked(); + return; + } + target.setMarkUnlinked( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _markUnlinked + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - return new java.lang.Integer(target.getFontStyle()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteFontStyle(); - return; - } - target.setFontStyle(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _fitToWindow + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasFitToWindow()) { return null; } + return (target.getFitToWindow() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteFitToWindow(); + return; + } + target.setFitToWindow( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _fitToWindow + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _fontStyle - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _threshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Float.TYPE, "_threshold", "threshold", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasThreshold()) - { - return null; + desc.setValidator(fieldValidator); + //-- _currentTree + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_currentTree", "currentTree", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + if (!target.hasCurrentTree()) { return null; } + return (target.getCurrentTree() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteCurrentTree(); + return; + } + target.setCurrentTree( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _currentTree + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); } - return new java.lang.Float(target.getThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteThreshold(); - return; - } - target.setThreshold(((java.lang.Float) value).floatValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + super.setIdentity(desc); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + target.setId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IdValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IdValidator(); + fieldValidator.setValidator(typeValidator); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _threshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.FloatValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.FloatValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive((float) -3.4028235E38); - typeValidator.setMaxInclusive((float) 3.4028235E38); - } - desc.setValidator(fieldValidator); - // -- _showBootstrap - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showBootstrap", "showBootstrap", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasShowBootstrap()) - { - return null; + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _title + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + return target.getTitle(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + target.setTitle( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _title + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - return (target.getShowBootstrap() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowBootstrap(); - return; - } - target.setShowBootstrap(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _newick + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newick", "newick", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Tree target = (Tree) object; + return target.getNewick(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Tree target = (Tree) object; + target.setNewick( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _newick + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showBootstrap - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- _showDistances - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showDistances", "showDistances", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasShowDistances()) - { - return null; - } - return (target.getShowDistances() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowDistances(); - return; - } - target.setShowDistances(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); + //-----------/ + //- Methods -/ + //-----------/ - // -- validation code for: _showDistances - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _markUnlinked - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_markUnlinked", "markUnlinked", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasMarkUnlinked()) - { - return null; - } - return (target.getMarkUnlinked() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteMarkUnlinked(); - return; - } - target.setMarkUnlinked(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _markUnlinked - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); } - desc.setValidator(fieldValidator); - // -- _fitToWindow - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_fitToWindow", "fitToWindow", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasFitToWindow()) - { - return null; - } - return (target.getFitToWindow() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteFitToWindow(); - return; - } - target.setFitToWindow(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _fitToWindow - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); } - desc.setValidator(fieldValidator); - // -- _currentTree - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_currentTree", "currentTree", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - if (!target.hasCurrentTree()) - { - return null; - } - return (target.getCurrentTree() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteCurrentTree(); - return; - } - target.setCurrentTree(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _currentTree - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Tree.class; } - desc.setValidator(fieldValidator); - // -- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_id", "id", - org.exolab.castor.xml.NodeType.Attribute); - super.setIdentity(desc); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - target.setId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - // -- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IdValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IdValidator(); - fieldValidator.setValidator(typeValidator); + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - // -- _title - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_title", "title", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getTitle(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - target.setTitle((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _title - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; } - desc.setValidator(fieldValidator); - // -- _newick - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_newick", "newick", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Tree target = (Tree) object; - return target.getNewick(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Tree target = (Tree) object; - target.setNewick((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _newick - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Tree.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java index eb93e57..be7012a 100644 --- a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.UserColourScheme; @@ -28,132 +18,134 @@ import jalview.schemabinding.version2.UserColourScheme; * * @version $Revision$ $Date$ */ -public class UserColourSchemeDescriptor - extends - jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public UserColourSchemeDescriptor() - { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor()); - _nsURI = "www.jalview.org"; - _xmlName = "UserColourScheme"; - _elementDefinition = true; - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.UserColourScheme.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } +public class UserColourSchemeDescriptor extends jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public UserColourSchemeDescriptor() { + super(); + setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor()); + _nsURI = "www.jalview.org"; + _xmlName = "UserColourScheme"; + _elementDefinition = true; + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.UserColourScheme.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java index e98dffb..bda1c5e 100644 --- a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.UserColours; @@ -28,229 +18,215 @@ import jalview.schemabinding.version2.UserColours; * * @version $Revision$ $Date$ */ -public class UserColoursDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public UserColoursDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "UserColours"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_id", "id", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - UserColours target = (UserColours) object; - return target.getId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - UserColours target = (UserColours) object; - target.setId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class UserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public UserColoursDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "UserColours"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + UserColours target = (UserColours) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + UserColours target = (UserColours) object; + target.setId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _userColourScheme + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.UserColourScheme.class, "_userColourScheme", "UserColourScheme", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + UserColours target = (UserColours) object; + return target.getUserColourScheme(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + UserColours target = (UserColours) object; + target.setUserColourScheme( (jalview.schemabinding.version2.UserColourScheme) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.UserColourScheme(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _userColourScheme + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + } + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - // -- _userColourScheme - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.UserColourScheme.class, - "_userColourScheme", "UserColourScheme", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - UserColours target = (UserColours) object; - return target.getUserColourScheme(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - UserColours target = (UserColours) object; - target.setUserColourScheme((jalview.schemabinding.version2.UserColourScheme) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.UserColourScheme(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); + //-----------/ + //- Methods -/ + //-----------/ - // -- validation code for: _userColourScheme - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.UserColours.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.UserColours.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java index b46ab62..375f435 100644 --- a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.VAMSAS; @@ -28,256 +18,232 @@ import jalview.schemabinding.version2.VAMSAS; * * @version $Revision$ $Date$ */ -public class VAMSASDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public VAMSASDescriptor() - { - super(); - _nsURI = "www.vamsas.ac.uk/jalview/version2"; - _xmlName = "VAMSAS"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- initialize element descriptors - - // -- _treeList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_treeList", "Tree", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - VAMSAS target = (VAMSAS) object; - return target.getTree(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - VAMSAS target = (VAMSAS) object; - target.addTree((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public VAMSASDescriptor() { + super(); + _nsURI = "www.vamsas.ac.uk/jalview/version2"; + _xmlName = "VAMSAS"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- initialize element descriptors + + //-- _treeList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + VAMSAS target = (VAMSAS) object; + return target.getTree(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + VAMSAS target = (VAMSAS) object; + target.addTree( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + VAMSAS target = (VAMSAS) object; + target.removeAllTree(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _treeList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - VAMSAS target = (VAMSAS) object; - target.removeAllTree(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _sequenceSetList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSet.class, "_sequenceSetList", "SequenceSet", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + VAMSAS target = (VAMSAS) object; + return target.getSequenceSet(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + VAMSAS target = (VAMSAS) object; + target.addSequenceSet( (jalview.schemabinding.version2.SequenceSet) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + VAMSAS target = (VAMSAS) object; + target.removeAllSequenceSet(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.SequenceSet(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _sequenceSetList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _treeList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- _sequenceSetList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.SequenceSet.class, - "_sequenceSetList", "SequenceSet", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - VAMSAS target = (VAMSAS) object; - return target.getSequenceSet(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - VAMSAS target = (VAMSAS) object; - target.addSequenceSet((jalview.schemabinding.version2.SequenceSet) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - VAMSAS target = (VAMSAS) object; - target.removeAllSequenceSet(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.SequenceSet(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2"); - desc.setMultivalued(true); - addFieldDescriptor(desc); + //-----------/ + //- Methods -/ + //-----------/ - // -- validation code for: _sequenceSetList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.VAMSAS.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.VAMSAS.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java index 9b25bae..bc14cfd 100644 --- a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.VamsasModel; @@ -28,131 +18,134 @@ import jalview.schemabinding.version2.VamsasModel; * * @version $Revision$ $Date$ */ -public class VamsasModelDescriptor extends - jalview.schemabinding.version2.descriptors.VAMSASDescriptor -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public VamsasModelDescriptor() - { - super(); - setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.VAMSASDescriptor()); - _nsURI = "www.jalview.org"; - _xmlName = "vamsasModel"; - _elementDefinition = true; - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.VamsasModel.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } +public class VamsasModelDescriptor extends jalview.schemabinding.version2.descriptors.VAMSASDescriptor { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public VamsasModelDescriptor() { + super(); + setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.VAMSASDescriptor()); + _nsURI = "www.jalview.org"; + _xmlName = "vamsasModel"; + _elementDefinition = true; + } + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; + } + + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } + + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.VamsasModel.class; + } + + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } + + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } + + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } + + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } + + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } } diff --git a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java index 254b785..21b8cf2 100644 --- a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.Viewport; @@ -28,2488 +18,1941 @@ import jalview.schemabinding.version2.Viewport; * * @version $Revision$ $Date$ */ -public class ViewportDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public ViewportDescriptor() - { - super(); - _nsURI = "www.jalview.org"; - _xmlName = "Viewport"; - _elementDefinition = true; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _conservationSelected - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_conservationSelected", - "conservationSelected", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasConservationSelected()) - { - return null; - } - return (target.getConservationSelected() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteConservationSelected(); - return; - } - target.setConservationSelected(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _conservationSelected - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _pidSelected - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_pidSelected", "pidSelected", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasPidSelected()) - { - return null; - } - return (target.getPidSelected() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deletePidSelected(); - return; - } - target.setPidSelected(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _pidSelected - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _bgColour - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_bgColour", "bgColour", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getBgColour(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.setBgColour((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _bgColour - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _consThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_consThreshold", "consThreshold", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasConsThreshold()) - { - return null; - } - return new java.lang.Integer(target.getConsThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteConsThreshold(); - return; - } - target.setConsThreshold(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _consThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _pidThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasPidThreshold()) - { - return null; - } - return new java.lang.Integer(target.getPidThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deletePidThreshold(); - return; - } - target.setPidThreshold(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _pidThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _title - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_title", "title", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getTitle(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.setTitle((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _title - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _showFullId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showFullId", "showFullId", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowFullId()) - { - return null; - } - return (target.getShowFullId() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowFullId(); - return; - } - target.setShowFullId(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showFullId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _rightAlignIds - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasRightAlignIds()) - { - return null; - } - return (target.getRightAlignIds() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteRightAlignIds(); - return; - } - target.setRightAlignIds(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _rightAlignIds - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showText - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showText", "showText", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowText()) - { - return null; - } - return (target.getShowText() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowText(); - return; - } - target.setShowText(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showText - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showColourText - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showColourText", "showColourText", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowColourText()) - { - return null; - } - return (target.getShowColourText() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowColourText(); - return; - } - target.setShowColourText(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showColourText - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showUnconserved - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowUnconserved()) - { - return null; - } - return (target.getShowUnconserved() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowUnconserved(); - return; - } - target.setShowUnconserved(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showUnconserved - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showBoxes - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showBoxes", "showBoxes", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowBoxes()) - { - return null; - } - return (target.getShowBoxes() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowBoxes(); - return; - } - target.setShowBoxes(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showBoxes - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _wrapAlignment - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasWrapAlignment()) - { - return null; - } - return (target.getWrapAlignment() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteWrapAlignment(); - return; - } - target.setWrapAlignment(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _wrapAlignment - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _renderGaps - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_renderGaps", "renderGaps", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasRenderGaps()) - { - return null; - } - return (target.getRenderGaps() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteRenderGaps(); - return; - } - target.setRenderGaps(((java.lang.Boolean) value).booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _renderGaps - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showSequenceFeatures - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showSequenceFeatures", - "showSequenceFeatures", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowSequenceFeatures()) - { - return null; - } - return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowSequenceFeatures(); - return; - } - target.setShowSequenceFeatures(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showSequenceFeatures - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showNPfeatureTooltip - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showNPfeatureTooltip", - "showNPfeatureTooltip", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowNPfeatureTooltip()) - { - return null; - } - return (target.getShowNPfeatureTooltip() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowNPfeatureTooltip(); - return; - } - target.setShowNPfeatureTooltip(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showNPfeatureTooltip - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showDbRefTooltip - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showDbRefTooltip", - "showDbRefTooltip", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowDbRefTooltip()) - { - return null; - } - return (target.getShowDbRefTooltip() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowDbRefTooltip(); - return; - } - target.setShowDbRefTooltip(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showDbRefTooltip - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _followHighlight - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_followHighlight", "followHighlight", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasFollowHighlight()) - { - return null; - } - return (target.getFollowHighlight() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteFollowHighlight(); - return; - } - target.setFollowHighlight(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _followHighlight - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _followSelection - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_followSelection", "followSelection", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasFollowSelection()) - { - return null; - } - return (target.getFollowSelection() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteFollowSelection(); - return; - } - target.setFollowSelection(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _followSelection - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showAnnotation - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowAnnotation()) - { - return null; - } - return (target.getShowAnnotation() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowAnnotation(); - return; - } - target.setShowAnnotation(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showAnnotation - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); +public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public ViewportDescriptor() { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "Viewport"; + _elementDefinition = true; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _conservationSelected + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_conservationSelected", "conservationSelected", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasConservationSelected()) { return null; } + return (target.getConservationSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteConservationSelected(); + return; + } + target.setConservationSelected( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _conservationSelected + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _pidSelected + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_pidSelected", "pidSelected", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasPidSelected()) { return null; } + return (target.getPidSelected() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deletePidSelected(); + return; + } + target.setPidSelected( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _pidSelected + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _bgColour + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_bgColour", "bgColour", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getBgColour(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + target.setBgColour( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _bgColour + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _consThreshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_consThreshold", "consThreshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasConsThreshold()) { return null; } + return new java.lang.Integer(target.getConsThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteConsThreshold(); + return; + } + target.setConsThreshold( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _consThreshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _pidThreshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_pidThreshold", "pidThreshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasPidThreshold()) { return null; } + return new java.lang.Integer(target.getPidThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deletePidThreshold(); + return; + } + target.setPidThreshold( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _pidThreshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _title + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getTitle(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + target.setTitle( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _title + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _showFullId + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showFullId", "showFullId", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowFullId()) { return null; } + return (target.getShowFullId() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowFullId(); + return; + } + target.setShowFullId( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showFullId + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _rightAlignIds + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasRightAlignIds()) { return null; } + return (target.getRightAlignIds() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteRightAlignIds(); + return; + } + target.setRightAlignIds( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _rightAlignIds + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showText + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showText", "showText", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowText()) { return null; } + return (target.getShowText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowText(); + return; + } + target.setShowText( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showText + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showColourText + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showColourText", "showColourText", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowColourText()) { return null; } + return (target.getShowColourText() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowColourText(); + return; + } + target.setShowColourText( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showColourText + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showUnconserved + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowUnconserved()) { return null; } + return (target.getShowUnconserved() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowUnconserved(); + return; + } + target.setShowUnconserved( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showUnconserved + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showBoxes + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBoxes", "showBoxes", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowBoxes()) { return null; } + return (target.getShowBoxes() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowBoxes(); + return; + } + target.setShowBoxes( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showBoxes + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _wrapAlignment + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_wrapAlignment", "wrapAlignment", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasWrapAlignment()) { return null; } + return (target.getWrapAlignment() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteWrapAlignment(); + return; + } + target.setWrapAlignment( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _wrapAlignment + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _renderGaps + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_renderGaps", "renderGaps", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasRenderGaps()) { return null; } + return (target.getRenderGaps() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteRenderGaps(); + return; + } + target.setRenderGaps( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _renderGaps + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showSequenceFeatures + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceFeatures", "showSequenceFeatures", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowSequenceFeatures()) { return null; } + return (target.getShowSequenceFeatures() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowSequenceFeatures(); + return; + } + target.setShowSequenceFeatures( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showSequenceFeatures + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showNPfeatureTooltip + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showNPfeatureTooltip", "showNPfeatureTooltip", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowNPfeatureTooltip()) { return null; } + return (target.getShowNPfeatureTooltip() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowNPfeatureTooltip(); + return; + } + target.setShowNPfeatureTooltip( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showNPfeatureTooltip + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showDbRefTooltip + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showDbRefTooltip", "showDbRefTooltip", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowDbRefTooltip()) { return null; } + return (target.getShowDbRefTooltip() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowDbRefTooltip(); + return; + } + target.setShowDbRefTooltip( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showDbRefTooltip + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _followHighlight + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_followHighlight", "followHighlight", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasFollowHighlight()) { return null; } + return (target.getFollowHighlight() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteFollowHighlight(); + return; + } + target.setFollowHighlight( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _followHighlight + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _followSelection + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_followSelection", "followSelection", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasFollowSelection()) { return null; } + return (target.getFollowSelection() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteFollowSelection(); + return; + } + target.setFollowSelection( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _followSelection + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showAnnotation + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAnnotation", "showAnnotation", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowAnnotation()) { return null; } + return (target.getShowAnnotation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowAnnotation(); + return; + } + target.setShowAnnotation( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showAnnotation + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _centreColumnLabels + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_centreColumnLabels", "centreColumnLabels", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasCentreColumnLabels()) { return null; } + return (target.getCentreColumnLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteCentreColumnLabels(); + return; + } + target.setCentreColumnLabels( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _centreColumnLabels + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showGroupConservation + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showGroupConservation", "showGroupConservation", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowGroupConservation()) { return null; } + return (target.getShowGroupConservation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowGroupConservation(); + return; + } + target.setShowGroupConservation( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showGroupConservation + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showGroupConsensus + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showGroupConsensus", "showGroupConsensus", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowGroupConsensus()) { return null; } + return (target.getShowGroupConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowGroupConsensus(); + return; + } + target.setShowGroupConsensus( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showGroupConsensus + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showConsensusHistogram + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConsensusHistogram", "showConsensusHistogram", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowConsensusHistogram()) { return null; } + return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowConsensusHistogram(); + return; + } + target.setShowConsensusHistogram( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showConsensusHistogram + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _showSequenceLogo + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showSequenceLogo", "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasShowSequenceLogo()) { return null; } + return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteShowSequenceLogo(); + return; + } + target.setShowSequenceLogo( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _showSequenceLogo + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _ignoreGapsinConsensus + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", "ignoreGapsinConsensus", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasIgnoreGapsinConsensus()) { return null; } + return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteIgnoreGapsinConsensus(); + return; + } + target.setIgnoreGapsinConsensus( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _ignoreGapsinConsensus + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _xpos + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasXpos()) { return null; } + return new java.lang.Integer(target.getXpos()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteXpos(); + return; + } + target.setXpos( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _xpos + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _ypos + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasYpos()) { return null; } + return new java.lang.Integer(target.getYpos()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteYpos(); + return; + } + target.setYpos( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _ypos + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _width + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasWidth()) { return null; } + return new java.lang.Integer(target.getWidth()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteWidth(); + return; + } + target.setWidth( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _width + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _height + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasHeight()) { return null; } + return new java.lang.Integer(target.getHeight()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteHeight(); + return; + } + target.setHeight( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _height + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _startRes + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startRes", "startRes", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasStartRes()) { return null; } + return new java.lang.Integer(target.getStartRes()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteStartRes(); + return; + } + target.setStartRes( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _startRes + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _startSeq + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startSeq", "startSeq", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasStartSeq()) { return null; } + return new java.lang.Integer(target.getStartSeq()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteStartSeq(); + return; + } + target.setStartSeq( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _startSeq + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _fontName + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getFontName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + target.setFontName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _fontName + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _fontSize + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasFontSize()) { return null; } + return new java.lang.Integer(target.getFontSize()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteFontSize(); + return; + } + target.setFontSize( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _fontSize + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _fontStyle + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasFontStyle()) { return null; } + return new java.lang.Integer(target.getFontStyle()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteFontStyle(); + return; + } + target.setFontStyle( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _fontStyle + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _viewName + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewName", "viewName", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getViewName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + target.setViewName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _viewName + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _sequenceSetId + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceSetId", "sequenceSetId", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getSequenceSetId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + target.setSequenceSetId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _sequenceSetId + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); + } + desc.setValidator(fieldValidator); + //-- _gatheredViews + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasGatheredViews()) { return null; } + return (target.getGatheredViews() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteGatheredViews(); + return; + } + target.setGatheredViews( ((java.lang.Boolean) value).booleanValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _gatheredViews + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.BooleanValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- _textCol1 + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasTextCol1()) { return null; } + return new java.lang.Integer(target.getTextCol1()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteTextCol1(); + return; + } + target.setTextCol1( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _textCol1 + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _textCol2 + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasTextCol2()) { return null; } + return new java.lang.Integer(target.getTextCol2()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteTextCol2(); + return; + } + target.setTextCol2( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _textCol2 + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _textColThreshold + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + if (!target.hasTextColThreshold()) { return null; } + return new java.lang.Integer(target.getTextColThreshold()); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + // if null, use delete method for optional primitives + if (value == null) { + target.deleteTextColThreshold(); + return; + } + target.setTextColThreshold( ((java.lang.Integer) value).intValue()); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _textColThreshold + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IntValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IntValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setMinInclusive(-2147483648); + typeValidator.setMaxInclusive(2147483647); + } + desc.setValidator(fieldValidator); + //-- _id + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute); + super.setIdentity(desc); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getId(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + target.setId( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _id + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.IdValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.IdValidator(); + fieldValidator.setValidator(typeValidator); + } + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _annotationColours + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationColours.class, "_annotationColours", "AnnotationColours", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getAnnotationColours(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + target.setAnnotationColours( (jalview.schemabinding.version2.AnnotationColours) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.AnnotationColours(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _annotationColours + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + } + desc.setValidator(fieldValidator); + //-- _hiddenColumnsList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.HiddenColumns.class, "_hiddenColumnsList", "hiddenColumns", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + Viewport target = (Viewport) object; + return target.getHiddenColumns(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + Viewport target = (Viewport) object; + target.addHiddenColumns( (jalview.schemabinding.version2.HiddenColumns) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + Viewport target = (Viewport) object; + target.removeAllHiddenColumns(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new jalview.schemabinding.version2.HiddenColumns(); + } + }; + desc.setHandler(handler); + desc.setNameSpaceURI("www.jalview.org"); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _hiddenColumnsList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(0); + { //-- local scope + } + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- _centreColumnLabels - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_centreColumnLabels", - "centreColumnLabels", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasCentreColumnLabels()) - { - return null; - } - return (target.getCentreColumnLabels() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteCentreColumnLabels(); - return; - } - target.setCentreColumnLabels(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _centreColumnLabels - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showGroupConservation - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showGroupConservation", - "showGroupConservation", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowGroupConservation()) - { - return null; - } - return (target.getShowGroupConservation() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowGroupConservation(); - return; - } - target.setShowGroupConservation(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showGroupConservation - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showGroupConsensus - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showGroupConsensus", - "showGroupConsensus", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowGroupConsensus()) - { - return null; - } - return (target.getShowGroupConsensus() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowGroupConsensus(); - return; - } - target.setShowGroupConsensus(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showGroupConsensus - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showConsensusHistogram - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showConsensusHistogram", - "showConsensusHistogram", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowConsensusHistogram()) - { - return null; - } - return (target.getShowConsensusHistogram() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowConsensusHistogram(); - return; - } - target.setShowConsensusHistogram(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showConsensusHistogram - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _showSequenceLogo - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_showSequenceLogo", - "showSequenceLogo", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasShowSequenceLogo()) - { - return null; - } - return (target.getShowSequenceLogo() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteShowSequenceLogo(); - return; - } - target.setShowSequenceLogo(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _showSequenceLogo - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _ignoreGapsinConsensus - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_ignoreGapsinConsensus", - "ignoreGapsinConsensus", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasIgnoreGapsinConsensus()) - { - return null; - } - return (target.getIgnoreGapsinConsensus() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteIgnoreGapsinConsensus(); - return; - } - target.setIgnoreGapsinConsensus(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _ignoreGapsinConsensus - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); - } - desc.setValidator(fieldValidator); - // -- _xpos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_xpos", "xpos", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasXpos()) - { - return null; - } - return new java.lang.Integer(target.getXpos()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteXpos(); - return; - } - target.setXpos(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _xpos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _ypos - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_ypos", "ypos", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasYpos()) - { - return null; - } - return new java.lang.Integer(target.getYpos()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteYpos(); - return; - } - target.setYpos(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _ypos - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _width - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_width", "width", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasWidth()) - { - return null; - } - return new java.lang.Integer(target.getWidth()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteWidth(); - return; - } - target.setWidth(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _width - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _height - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_height", "height", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasHeight()) - { - return null; - } - return new java.lang.Integer(target.getHeight()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteHeight(); - return; - } - target.setHeight(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _height - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _startRes - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_startRes", "startRes", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasStartRes()) - { - return null; - } - return new java.lang.Integer(target.getStartRes()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteStartRes(); - return; - } - target.setStartRes(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _startRes - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _startSeq - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_startSeq", "startSeq", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasStartSeq()) - { - return null; - } - return new java.lang.Integer(target.getStartSeq()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteStartSeq(); - return; - } - target.setStartSeq(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _startSeq - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _fontName - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_fontName", "fontName", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getFontName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.setFontName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _fontName - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _fontSize - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_fontSize", "fontSize", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasFontSize()) - { - return null; - } - return new java.lang.Integer(target.getFontSize()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteFontSize(); - return; - } - target.setFontSize(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - // -- validation code for: _fontSize - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _fontStyle - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_fontStyle", "fontStyle", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasFontStyle()) - { - return null; - } - return new java.lang.Integer(target.getFontStyle()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteFontStyle(); - return; - } - target.setFontStyle(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - // -- validation code for: _fontStyle - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); - } - desc.setValidator(fieldValidator); - // -- _viewName - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_viewName", "viewName", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getViewName(); - } + //-----------/ + //- Methods -/ + //-----------/ - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.setViewName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _viewName - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); } - desc.setValidator(fieldValidator); - // -- _sequenceSetId - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_sequenceSetId", "sequenceSetId", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getSequenceSetId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.setSequenceSetId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _sequenceSetId - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _gatheredViews - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasGatheredViews()) - { - return null; - } - return (target.getGatheredViews() ? java.lang.Boolean.TRUE - : java.lang.Boolean.FALSE); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteGatheredViews(); - return; - } - target.setGatheredViews(((java.lang.Boolean) value) - .booleanValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _gatheredViews - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.BooleanValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.BooleanValidator(); - fieldValidator.setValidator(typeValidator); + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); } - desc.setValidator(fieldValidator); - // -- _textCol1 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_textCol1", "textCol1", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasTextCol1()) - { - return null; - } - return new java.lang.Integer(target.getTextCol1()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteTextCol1(); - return; - } - target.setTextCol1(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _textCol1 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.Viewport.class; } - desc.setValidator(fieldValidator); - // -- _textCol2 - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_textCol2", "textCol2", - org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasTextCol2()) - { - return null; - } - return new java.lang.Integer(target.getTextCol2()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteTextCol2(); - return; - } - target.setTextCol2(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _textCol2 - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; } - desc.setValidator(fieldValidator); - // -- _textColThreshold - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.Integer.TYPE, "_textColThreshold", - "textColThreshold", org.exolab.castor.xml.NodeType.Attribute); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - if (!target.hasTextColThreshold()) - { - return null; - } - return new java.lang.Integer(target.getTextColThreshold()); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - // if null, use delete method for optional primitives - if (value == null) - { - target.deleteTextColThreshold(); - return; - } - target.setTextColThreshold(((java.lang.Integer) value).intValue()); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _textColThreshold - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IntValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IntValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setMinInclusive(-2147483648); - typeValidator.setMaxInclusive(2147483647); + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; } - desc.setValidator(fieldValidator); - // -- _id - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_id", "id", - org.exolab.castor.xml.NodeType.Attribute); - super.setIdentity(desc); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getId(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.setId((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _id - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.IdValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.IdValidator(); - fieldValidator.setValidator(typeValidator); + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _annotationColours - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.AnnotationColours.class, - "_annotationColours", "AnnotationColours", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getAnnotationColours(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.setAnnotationColours((jalview.schemabinding.version2.AnnotationColours) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.AnnotationColours(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(false); - addFieldDescriptor(desc); - // -- validation code for: _annotationColours - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; } - desc.setValidator(fieldValidator); - // -- _hiddenColumnsList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - jalview.schemabinding.version2.HiddenColumns.class, - "_hiddenColumnsList", "hiddenColumns", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - Viewport target = (Viewport) object; - return target.getHiddenColumns(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.addHiddenColumns((jalview.schemabinding.version2.HiddenColumns) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - Viewport target = (Viewport) object; - target.removeAllHiddenColumns(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new jalview.schemabinding.version2.HiddenColumns(); - } - }; - desc.setHandler(handler); - desc.setNameSpaceURI("www.jalview.org"); - desc.setMultivalued(true); - addFieldDescriptor(desc); - // -- validation code for: _hiddenColumnsList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(0); - { // -- local scope + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } - - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.Viewport.class; - } - - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } - - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } - - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } - - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } - - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } } diff --git a/src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java index bf029a2..8c61a2d 100644 --- a/src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/WebServiceParameterSetDescriptor.java @@ -1,24 +1,14 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.schemabinding.version2.descriptors; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import jalview.schemabinding.version2.WebServiceParameterSet; @@ -28,379 +18,337 @@ import jalview.schemabinding.version2.WebServiceParameterSet; * * @version $Revision$ $Date$ */ -public class WebServiceParameterSetDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _elementDefinition. - */ - private boolean _elementDefinition; - - /** - * Field _nsPrefix. - */ - private java.lang.String _nsPrefix; - - /** - * Field _nsURI. - */ - private java.lang.String _nsURI; - - /** - * Field _xmlName. - */ - private java.lang.String _xmlName; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public WebServiceParameterSetDescriptor() - { - super(); - _nsURI = "www.jalview.org/xml/wsparamset"; - _xmlName = "WebServiceParameterSet"; - _elementDefinition = false; - - // -- set grouping compositor - setCompositorAsSequence(); - org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; - org.exolab.castor.mapping.FieldHandler handler = null; - org.exolab.castor.xml.FieldValidator fieldValidator = null; - // -- initialize attribute descriptors - - // -- _name - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_name", "name", - org.exolab.castor.xml.NodeType.Attribute); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - return target.getName(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - target.setName((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); +public class WebServiceParameterSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _elementDefinition. + */ + private boolean _elementDefinition; + + /** + * Field _nsPrefix. + */ + private java.lang.String _nsPrefix; + + /** + * Field _nsURI. + */ + private java.lang.String _nsURI; + + /** + * Field _xmlName. + */ + private java.lang.String _xmlName; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public WebServiceParameterSetDescriptor() { + super(); + _nsURI = "www.jalview.org/xml/wsparamset"; + _xmlName = "WebServiceParameterSet"; + _elementDefinition = false; + + //-- set grouping compositor + setCompositorAsSequence(); + org.exolab.castor.xml.util.XMLFieldDescriptorImpl desc = null; + org.exolab.castor.mapping.FieldHandler handler = null; + org.exolab.castor.xml.FieldValidator fieldValidator = null; + //-- initialize attribute descriptors + + //-- _name + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + WebServiceParameterSet target = (WebServiceParameterSet) object; + return target.getName(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + WebServiceParameterSet target = (WebServiceParameterSet) object; + target.setName( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _name + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _name - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - - // -- _version - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_version", "Version", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - return target.getVersion(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - target.setVersion((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- initialize element descriptors + + //-- _version + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "Version", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + WebServiceParameterSet target = (WebServiceParameterSet) object; + return target.getVersion(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + WebServiceParameterSet target = (WebServiceParameterSet) object; + target.setVersion( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _version + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _version - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _description - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_description", "description", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - return target.getDescription(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - target.setDescription((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _description + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + WebServiceParameterSet target = (WebServiceParameterSet) object; + return target.getDescription(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + WebServiceParameterSet target = (WebServiceParameterSet) object; + target.setDescription( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _description + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setMultivalued(false); - addFieldDescriptor(desc); - - // -- validation code for: _description - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); - } - desc.setValidator(fieldValidator); - // -- _serviceURLList - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_serviceURLList", "serviceURL", - org.exolab.castor.xml.NodeType.Element); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - return target.getServiceURL(); - } - - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - target.addServiceURL((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _serviceURLList + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_serviceURLList", "serviceURL", org.exolab.castor.xml.NodeType.Element); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + WebServiceParameterSet target = (WebServiceParameterSet) object; + return target.getServiceURL(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + WebServiceParameterSet target = (WebServiceParameterSet) object; + target.addServiceURL( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException { + try { + WebServiceParameterSet target = (WebServiceParameterSet) object; + target.removeAllServiceURL(); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return new java.lang.String(); + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(true); + addFieldDescriptor(desc); + + //-- validation code for: _serviceURLList + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope } - } - - public void resetValue(Object object) throws IllegalStateException, - IllegalArgumentException - { - try - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - target.removeAllServiceURL(); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); + desc.setValidator(fieldValidator); + //-- _parameters + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_parameters", "parameters", org.exolab.castor.xml.NodeType.Element); + desc.setImmutable(true); + handler = new org.exolab.castor.xml.XMLFieldHandler() { + public java.lang.Object getValue( java.lang.Object object ) + throws IllegalStateException + { + WebServiceParameterSet target = (WebServiceParameterSet) object; + return target.getParameters(); + } + public void setValue( java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try { + WebServiceParameterSet target = (WebServiceParameterSet) object; + target.setParameters( (java.lang.String) value); + } catch (java.lang.Exception ex) { + throw new IllegalStateException(ex.toString()); + } + } + public java.lang.Object newInstance(java.lang.Object parent) { + return null; + } + }; + desc.setHandler(handler); + desc.setRequired(true); + desc.setMultivalued(false); + addFieldDescriptor(desc); + + //-- validation code for: _parameters + fieldValidator = new org.exolab.castor.xml.FieldValidator(); + fieldValidator.setMinOccurs(1); + { //-- local scope + org.exolab.castor.xml.validators.StringValidator typeValidator; + typeValidator = new org.exolab.castor.xml.validators.StringValidator(); + fieldValidator.setValidator(typeValidator); + typeValidator.setWhiteSpace("preserve"); } - } - - public java.lang.Object newInstance(java.lang.Object parent) - { - return new java.lang.String(); - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(true); - addFieldDescriptor(desc); - - // -- validation code for: _serviceURLList - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope + desc.setValidator(fieldValidator); } - desc.setValidator(fieldValidator); - // -- _parameters - desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl( - java.lang.String.class, "_parameters", "parameters", - org.exolab.castor.xml.NodeType.Element); - desc.setImmutable(true); - handler = new org.exolab.castor.xml.XMLFieldHandler() - { - public java.lang.Object getValue(java.lang.Object object) - throws IllegalStateException - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - return target.getParameters(); - } - public void setValue(java.lang.Object object, java.lang.Object value) - throws IllegalStateException, IllegalArgumentException - { - try - { - WebServiceParameterSet target = (WebServiceParameterSet) object; - target.setParameters((java.lang.String) value); - } catch (java.lang.Exception ex) - { - throw new IllegalStateException(ex.toString()); - } - } - public java.lang.Object newInstance(java.lang.Object parent) - { - return null; - } - }; - desc.setHandler(handler); - desc.setRequired(true); - desc.setMultivalued(false); - addFieldDescriptor(desc); + //-----------/ + //- Methods -/ + //-----------/ - // -- validation code for: _parameters - fieldValidator = new org.exolab.castor.xml.FieldValidator(); - fieldValidator.setMinOccurs(1); - { // -- local scope - org.exolab.castor.xml.validators.StringValidator typeValidator; - typeValidator = new org.exolab.castor.xml.validators.StringValidator(); - fieldValidator.setValidator(typeValidator); - typeValidator.setWhiteSpace("preserve"); + /** + * Method getAccessMode. + * + * @return the access mode specified for this class. + */ + public org.exolab.castor.mapping.AccessMode getAccessMode( + ) { + return null; } - desc.setValidator(fieldValidator); - } - - // -----------/ - // - Methods -/ - // -----------/ - /** - * Method getAccessMode. - * - * @return the access mode specified for this class. - */ - public org.exolab.castor.mapping.AccessMode getAccessMode() - { - return null; - } - - /** - * Method getIdentity. - * - * @return the identity field, null if this class has no identity. - */ - public org.exolab.castor.mapping.FieldDescriptor getIdentity() - { - return super.getIdentity(); - } + /** + * Method getIdentity. + * + * @return the identity field, null if this class has no + * identity. + */ + public org.exolab.castor.mapping.FieldDescriptor getIdentity( + ) { + return super.getIdentity(); + } - /** - * Method getJavaClass. - * - * @return the Java class represented by this descriptor. - */ - public java.lang.Class getJavaClass() - { - return jalview.schemabinding.version2.WebServiceParameterSet.class; - } + /** + * Method getJavaClass. + * + * @return the Java class represented by this descriptor. + */ + public java.lang.Class getJavaClass( + ) { + return jalview.schemabinding.version2.WebServiceParameterSet.class; + } - /** - * Method getNameSpacePrefix. - * - * @return the namespace prefix to use when marshaling as XML. - */ - public java.lang.String getNameSpacePrefix() - { - return _nsPrefix; - } + /** + * Method getNameSpacePrefix. + * + * @return the namespace prefix to use when marshaling as XML. + */ + public java.lang.String getNameSpacePrefix( + ) { + return _nsPrefix; + } - /** - * Method getNameSpaceURI. - * - * @return the namespace URI used when marshaling and unmarshaling as XML. - */ - public java.lang.String getNameSpaceURI() - { - return _nsURI; - } + /** + * Method getNameSpaceURI. + * + * @return the namespace URI used when marshaling and + * unmarshaling as XML. + */ + public java.lang.String getNameSpaceURI( + ) { + return _nsURI; + } - /** - * Method getValidator. - * - * @return a specific validator for the class described by this - * ClassDescriptor. - */ - public org.exolab.castor.xml.TypeValidator getValidator() - { - return this; - } + /** + * Method getValidator. + * + * @return a specific validator for the class described by this + * ClassDescriptor. + */ + public org.exolab.castor.xml.TypeValidator getValidator( + ) { + return this; + } - /** - * Method getXMLName. - * - * @return the XML Name for the Class being described. - */ - public java.lang.String getXMLName() - { - return _xmlName; - } + /** + * Method getXMLName. + * + * @return the XML Name for the Class being described. + */ + public java.lang.String getXMLName( + ) { + return _xmlName; + } - /** - * Method isElementDefinition. - * - * @return true if XML schema definition of this Class is that of a global - * element or element with anonymous type definition. - */ - public boolean isElementDefinition() - { - return _elementDefinition; - } + /** + * Method isElementDefinition. + * + * @return true if XML schema definition of this Class is that + * of a global + * element or element with anonymous type definition. + */ + public boolean isElementDefinition( + ) { + return _elementDefinition; + } }