X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FAnnotationColourScheme.java;h=2f76e767394239f749f591ac9f0df6e8e9c699ae;hb=d8720fc191cba996c440171ef8e07462ef9f7035;hp=91222f1184d76c3d3887242b75b20c8927ee2adf;hpb=cb7c4a276c52b0bb3e448e6761886fecc0e9d05c;p=jalview.git diff --git a/src/jalview/schemabinding/version2/AnnotationColourScheme.java b/src/jalview/schemabinding/version2/AnnotationColourScheme.java index 91222f1..2f76e76 100644 --- a/src/jalview/schemabinding/version2/AnnotationColourScheme.java +++ b/src/jalview/schemabinding/version2/AnnotationColourScheme.java @@ -7,8 +7,8 @@ package jalview.schemabinding.version2; - //---------------------------------/ - //- Imported classes and packages -/ +//---------------------------------/ +//- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -19,461 +19,479 @@ import org.exolab.castor.xml.Unmarshaller; * * @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); - } +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); + } }