From: Jim Procter Date: Thu, 17 Oct 2013 10:13:02 +0000 (+0100) Subject: JAL-1397 store colour by sequence and originalColour flags for AnnotationColourScheme X-Git-Tag: Jalview_2_9~218^2~3 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f2ae865457eea8f0bd3bf3dd0be853c56583544a;hp=81f6049003ae41d3ce3950fa1e80599c7bb39896;p=jalview.git JAL-1397 store colour by sequence and originalColour flags for AnnotationColourScheme --- diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd index 03c5728..0138f63 100755 --- a/schemas/jalview.xsd +++ b/schemas/jalview.xsd @@ -292,6 +292,12 @@ type="xs:string" /> + + . + * 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 +19,461 @@ 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; - } - 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); - } +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; + + /** + * Field _perSequence. + */ + private boolean _perSequence; + + /** + * keeps track of state for field: _perSequence + */ + private boolean _has_perSequence; + + /** + * Field _predefinedColours. + */ + private boolean _predefinedColours; + + /** + * keeps track of state for field: _predefinedColours + */ + private boolean _has_predefinedColours; + + + //----------------/ + //- 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 deletePerSequence( + ) { + this._has_perSequence= false; + } + + /** + */ + public void deletePredefinedColours( + ) { + this._has_predefinedColours= 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 'perSequence'. + * + * @return the value of field 'PerSequence'. + */ + public boolean getPerSequence( + ) { + return this._perSequence; + } + + /** + * Returns the value of field 'predefinedColours'. + * + * @return the value of field 'PredefinedColours'. + */ + public boolean getPredefinedColours( + ) { + return this._predefinedColours; + } + + /** + * 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 hasPerSequence. + * + * @return true if at least one PerSequence has been added + */ + public boolean hasPerSequence( + ) { + return this._has_perSequence; + } + + /** + * Method hasPredefinedColours. + * + * @return true if at least one PredefinedColours has been added + */ + public boolean hasPredefinedColours( + ) { + return this._has_predefinedColours; + } + + /** + * Method hasThreshold. + * + * @return true if at least one Threshold has been added + */ + public boolean hasThreshold( + ) { + return this._has_threshold; + } + + /** + * Returns the value of field 'perSequence'. + * + * @return the value of field 'PerSequence'. + */ + public boolean isPerSequence( + ) { + return this._perSequence; + } + + /** + * Returns the value of field 'predefinedColours'. + * + * @return the value of field 'PredefinedColours'. + */ + public boolean isPredefinedColours( + ) { + return this._predefinedColours; + } + + /** + * 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 'perSequence'. + * + * @param perSequence the value of field 'perSequence'. + */ + public void setPerSequence( + final boolean perSequence) { + this._perSequence = perSequence; + this._has_perSequence = true; + } + + /** + * Sets the value of field 'predefinedColours'. + * + * @param predefinedColours the value of field + * 'predefinedColours'. + */ + public void setPredefinedColours( + final boolean predefinedColours) { + this._predefinedColours = predefinedColours; + this._has_predefinedColours = 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/descriptors/AnnotationColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java index 876e928..196ad60 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 2.8) - * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 +18,468 @@ 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; + 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); } - 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); + //-- _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"); } - } - - 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); + //-- _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); } - 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); + //-- _perSequence + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_perSequence", "perSequence", 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.hasPerSequence()) { return null; } + return (target.getPerSequence() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + 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.deletePerSequence(); + return; + } + target.setPerSequence( ((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: _perSequence + 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: _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); - // -- _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()); + desc.setValidator(fieldValidator); + //-- _predefinedColours + desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_predefinedColours", "predefinedColours", 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.hasPredefinedColours()) { return null; } + return (target.getPredefinedColours() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE); + } + 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.deletePredefinedColours(); + return; + } + target.setPredefinedColours( ((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: _predefinedColours + 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: _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); + //-- initialize element descriptors + } - 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); + //-----------/ + //- Methods -/ + //-----------/ - // -- 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); + /** + * 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.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; + } }