From 0331d7bcf7f93c0becc000ac93638fdc640ad389 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Fri, 2 May 2014 10:27:38 +0100 Subject: [PATCH] JAL-1233 JAL-1066 fix for JAL-1397 test: allow per group colour by annotation to be stored/recovered in Jalview projects (version compatibility will be 2.8.1 and after) --- schemas/jalview.xsd | 43 +- src/jalview/schemabinding/version2/.castor.cdr | 3 +- .../version2/AnnotationColourScheme.java | 516 +++++++++++++++++ .../schemabinding/version2/AnnotationColours.java | 380 +------------ src/jalview/schemabinding/version2/JGroup.java | 27 + .../AnnotationColourSchemeDescriptor.java | 592 ++++++++++++++++++++ .../descriptors/AnnotationColoursDescriptor.java | 432 +------------- .../version2/descriptors/JGroupDescriptor.java | 42 ++ 8 files changed, 1207 insertions(+), 828 deletions(-) create mode 100644 src/jalview/schemabinding/version2/AnnotationColourScheme.java create mode 100644 src/jalview/schemabinding/version2/descriptors/AnnotationColourSchemeDescriptor.java diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd index eb10ae1..ab893bd 100755 --- a/schemas/jalview.xsd +++ b/schemas/jalview.xsd @@ -230,9 +230,10 @@ - - + + + @@ -278,28 +279,8 @@ - - - - - - - - - - - + @@ -573,4 +554,16 @@ + + + + + + + + + + + diff --git a/src/jalview/schemabinding/version2/.castor.cdr b/src/jalview/schemabinding/version2/.castor.cdr index f307b15..425a30a 100644 --- a/src/jalview/schemabinding/version2/.castor.cdr +++ b/src/jalview/schemabinding/version2/.castor.cdr @@ -1,4 +1,4 @@ -#Fri Apr 25 13:56:18 BST 2014 +#Thu May 01 17:34:18 BST 2014 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 @@ -25,6 +25,7 @@ jalview.schemabinding.version2.WebServiceParameterSet=jalview.schemabinding.vers jalview.schemabinding.version2.Alcodon=jalview.schemabinding.version2.descriptors.AlcodonDescriptor jalview.schemabinding.version2.AnnotationColours=jalview.schemabinding.version2.descriptors.AnnotationColoursDescriptor jalview.schemabinding.version2.Pdbids=jalview.schemabinding.version2.descriptors.PdbidsDescriptor +jalview.schemabinding.version2.AnnotationColourScheme=jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor jalview.schemabinding.version2.Mapping=jalview.schemabinding.version2.descriptors.MappingDescriptor jalview.schemabinding.version2.MappingChoice=jalview.schemabinding.version2.descriptors.MappingChoiceDescriptor jalview.schemabinding.version2.Group=jalview.schemabinding.version2.descriptors.GroupDescriptor diff --git a/src/jalview/schemabinding/version2/AnnotationColourScheme.java b/src/jalview/schemabinding/version2/AnnotationColourScheme.java new file mode 100644 index 0000000..8bf97d5 --- /dev/null +++ b/src/jalview/schemabinding/version2/AnnotationColourScheme.java @@ -0,0 +1,516 @@ +/******************************************************************************* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + ******************************************************************************/ +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2; + +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class AnnotationColourScheme. + * + * @version $Revision$ $Date$ + */ +public class AnnotationColourScheme 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 AnnotationColourScheme() + { + 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.AnnotationColourScheme + */ + public static jalview.schemabinding.version2.AnnotationColourScheme unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException + { + return (jalview.schemabinding.version2.AnnotationColourScheme) Unmarshaller + .unmarshal( + jalview.schemabinding.version2.AnnotationColourScheme.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 e20bbc4..cbda218 100644 --- a/src/jalview/schemabinding/version2/AnnotationColours.java +++ b/src/jalview/schemabinding/version2/AnnotationColours.java @@ -38,83 +38,10 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class AnnotationColours implements java.io.Serializable +public class AnnotationColours extends AnnotationColourScheme 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 -/ // ----------------/ @@ -129,208 +56,6 @@ public class AnnotationColours implements java.io.Serializable // -----------/ /** - */ - 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 @@ -385,100 +110,6 @@ public class AnnotationColours implements java.io.Serializable } /** - * 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 @@ -487,14 +118,15 @@ public class AnnotationColours implements java.io.Serializable * 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 + * @return the unmarshaled + * jalview.schemabinding.version2.AnnotationColourScheme */ - public static jalview.schemabinding.version2.AnnotationColours unmarshal( + public static jalview.schemabinding.version2.AnnotationColourScheme unmarshal( final java.io.Reader reader) throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.AnnotationColours) Unmarshaller + return (jalview.schemabinding.version2.AnnotationColourScheme) Unmarshaller .unmarshal( jalview.schemabinding.version2.AnnotationColours.class, reader); diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java index 56e43b7..44e8739 100644 --- a/src/jalview/schemabinding/version2/JGroup.java +++ b/src/jalview/schemabinding/version2/JGroup.java @@ -226,6 +226,11 @@ public class JGroup implements java.io.Serializable */ private java.util.Vector _seqList; + /** + * Field _annotationColours. + */ + private jalview.schemabinding.version2.AnnotationColours _annotationColours; + // ----------------/ // - Constructors -/ // ----------------/ @@ -390,6 +395,16 @@ public class JGroup implements java.io.Serializable } /** + * 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 'colour'. * * @return the value of field 'Colour'. @@ -954,6 +969,18 @@ public class JGroup implements java.io.Serializable } /** + * 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 'colour'. * * @param colour diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationColourSchemeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationColourSchemeDescriptor.java new file mode 100644 index 0000000..98f2855 --- /dev/null +++ b/src/jalview/schemabinding/version2/descriptors/AnnotationColourSchemeDescriptor.java @@ -0,0 +1,592 @@ +/******************************************************************************* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) + * Copyright (C) 2014 The Jalview Authors + * + * 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 . + * The Jalview Authors are detailed in the 'AUTHORS' file. + ******************************************************************************/ +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2.descriptors; + +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ + +import jalview.schemabinding.version2.AnnotationColourScheme; + +/** + * Class AnnotationColourSchemeDescriptor. + * + * @version $Revision$ $Date$ + */ +public class AnnotationColourSchemeDescriptor 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 AnnotationColourSchemeDescriptor() + { + super(); + _nsURI = "www.jalview.org"; + _xmlName = "AnnotationColourScheme"; + _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 + + // -- _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 + { + AnnotationColourScheme target = (AnnotationColourScheme) 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 + { + AnnotationColourScheme target = (AnnotationColourScheme) 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); + } + 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 + { + AnnotationColourScheme target = (AnnotationColourScheme) object; + return target.getAnnotation(); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + AnnotationColourScheme target = (AnnotationColourScheme) 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"); + } + 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 + { + AnnotationColourScheme target = (AnnotationColourScheme) 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 + { + AnnotationColourScheme target = (AnnotationColourScheme) 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); + } + 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 + { + AnnotationColourScheme target = (AnnotationColourScheme) 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 + { + AnnotationColourScheme target = (AnnotationColourScheme) 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); + } + 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 + { + AnnotationColourScheme target = (AnnotationColourScheme) object; + return target.getColourScheme(); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + AnnotationColourScheme target = (AnnotationColourScheme) 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 + { + AnnotationColourScheme target = (AnnotationColourScheme) 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 + { + AnnotationColourScheme target = (AnnotationColourScheme) 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); + } + 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 + { + AnnotationColourScheme target = (AnnotationColourScheme) 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 + { + AnnotationColourScheme target = (AnnotationColourScheme) 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); + } + 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 + { + AnnotationColourScheme target = (AnnotationColourScheme) 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 + { + AnnotationColourScheme target = (AnnotationColourScheme) 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); + } + 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.AnnotationColourScheme.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/AnnotationColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java index 954e3e5..5eb3939 100644 --- a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java @@ -37,8 +37,9 @@ import jalview.schemabinding.version2.AnnotationColours; * * @version $Revision$ $Date$ */ -public class AnnotationColoursDescriptor extends - org.exolab.castor.xml.util.XMLClassDescriptorImpl +public class AnnotationColoursDescriptor + extends + jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor { // --------------------------/ @@ -72,435 +73,10 @@ public class AnnotationColoursDescriptor extends public AnnotationColoursDescriptor() { super(); + setExtendsWithoutFlatten(new jalview.schemabinding.version2.descriptors.AnnotationColourSchemeDescriptor()); _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); - } - 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"); - } - 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); - } - 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); - } - 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()); - } - } - - 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); - // -- _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); - } - 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); - } - desc.setValidator(fieldValidator); - // -- initialize element descriptors - } // -----------/ diff --git a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java index 4082f2c..aec96ef 100644 --- a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java +++ b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java @@ -1161,6 +1161,48 @@ public class JGroupDescriptor extends typeValidator.setWhiteSpace("preserve"); } desc.setValidator(fieldValidator); + // -- _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 + { + JGroup target = (JGroup) object; + return target.getAnnotationColours(); + } + + public void setValue(java.lang.Object object, java.lang.Object value) + throws IllegalStateException, IllegalArgumentException + { + try + { + JGroup target = (JGroup) 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); } // -----------/ -- 1.7.10.2