X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FAnnotationColours.java;h=5f1b1c72d0756ae0d4cf08fa6f5d1baa6f2cf376;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=2a3b82ce17bffe93a5a0d4c6f3e1cd30b290286c;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/src/jalview/schemabinding/version2/AnnotationColours.java b/src/jalview/schemabinding/version2/AnnotationColours.java old mode 100755 new mode 100644 index 2a3b82c..5f1b1c7 --- a/src/jalview/schemabinding/version2/AnnotationColours.java +++ b/src/jalview/schemabinding/version2/AnnotationColours.java @@ -1,388 +1,379 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * - * This file is part of Jalview. - * - * Jalview is free software: you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. - * - * Jalview is distributed in the hope that it will be useful, but - * WITHOUT ANY WARRANTY; without even the implied warranty - * of MERCHANTABILITY or FITNESS FOR A PARTICULAR - * PURPOSE. See the GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . - */ -package jalview.schemabinding.version2; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class AnnotationColours. - * - * @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); - } - -} +/******************************************************************************* + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7) + * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + *******************************************************************************/ +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class AnnotationColours. + * + * @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); + } + +}