X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FAnnotationColours.java;h=5f1b1c72d0756ae0d4cf08fa6f5d1baa6f2cf376;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=b2af2c44febcaada5dda1ed272bceac3d34d30e5;hpb=48df59aa393e03aa7269b2df662ac1b8d58cbb25;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 b2af2c4..5f1b1c7
--- a/src/jalview/schemabinding/version2/AnnotationColours.java
+++ b/src/jalview/schemabinding/version2/AnnotationColours.java
@@ -1,385 +1,379 @@
-/*
- * This class was automatically generated with
- * Castor 0.9.6, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.schemabinding.version2;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * 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();
- } //-- jalview.schemabinding.version2.AnnotationColours()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method deleteAboveThreshold
- *
- */
- public void deleteAboveThreshold()
- {
- this._has_aboveThreshold= false;
- } //-- void deleteAboveThreshold()
-
- /**
- * Method deleteMaxColour
- *
- */
- public void deleteMaxColour()
- {
- this._has_maxColour= false;
- } //-- void deleteMaxColour()
-
- /**
- * Method deleteMinColour
- *
- */
- public void deleteMinColour()
- {
- this._has_minColour= false;
- } //-- void deleteMinColour()
-
- /**
- * Method deleteThreshold
- *
- */
- public void deleteThreshold()
- {
- this._has_threshold= false;
- } //-- void deleteThreshold()
-
- /**
- * Returns the value of field 'aboveThreshold'.
- *
- * @return int
- * @return the value of field 'aboveThreshold'.
- */
- public int getAboveThreshold()
- {
- return this._aboveThreshold;
- } //-- int getAboveThreshold()
-
- /**
- * Returns the value of field 'annotation'.
- *
- * @return String
- * @return the value of field 'annotation'.
- */
- public java.lang.String getAnnotation()
- {
- return this._annotation;
- } //-- java.lang.String getAnnotation()
-
- /**
- * Returns the value of field 'colourScheme'.
- *
- * @return String
- * @return the value of field 'colourScheme'.
- */
- public java.lang.String getColourScheme()
- {
- return this._colourScheme;
- } //-- java.lang.String getColourScheme()
-
- /**
- * Returns the value of field 'maxColour'.
- *
- * @return int
- * @return the value of field 'maxColour'.
- */
- public int getMaxColour()
- {
- return this._maxColour;
- } //-- int getMaxColour()
-
- /**
- * Returns the value of field 'minColour'.
- *
- * @return int
- * @return the value of field 'minColour'.
- */
- public int getMinColour()
- {
- return this._minColour;
- } //-- int getMinColour()
-
- /**
- * Returns the value of field 'threshold'.
- *
- * @return float
- * @return the value of field 'threshold'.
- */
- public float getThreshold()
- {
- return this._threshold;
- } //-- float getThreshold()
-
- /**
- * Method hasAboveThreshold
- *
- *
- *
- * @return boolean
- */
- public boolean hasAboveThreshold()
- {
- return this._has_aboveThreshold;
- } //-- boolean hasAboveThreshold()
-
- /**
- * Method hasMaxColour
- *
- *
- *
- * @return boolean
- */
- public boolean hasMaxColour()
- {
- return this._has_maxColour;
- } //-- boolean hasMaxColour()
-
- /**
- * Method hasMinColour
- *
- *
- *
- * @return boolean
- */
- public boolean hasMinColour()
- {
- return this._has_minColour;
- } //-- boolean hasMinColour()
-
- /**
- * Method hasThreshold
- *
- *
- *
- * @return boolean
- */
- public boolean hasThreshold()
- {
- return this._has_threshold;
- } //-- boolean hasThreshold()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid()
- {
- try {
- validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- } //-- boolean isValid()
-
- /**
- * Method marshal
- *
- *
- *
- * @param out
- */
- public void marshal(java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, out);
- } //-- void marshal(java.io.Writer)
-
- /**
- * Method marshal
- *
- *
- *
- * @param handler
- */
- public void marshal(org.xml.sax.ContentHandler handler)
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
- {
-
- Marshaller.marshal(this, handler);
- } //-- void marshal(org.xml.sax.ContentHandler)
-
- /**
- * Sets the value of field 'aboveThreshold'.
- *
- * @param aboveThreshold the value of field 'aboveThreshold'.
- */
- public void setAboveThreshold(int aboveThreshold)
- {
- this._aboveThreshold = aboveThreshold;
- this._has_aboveThreshold = true;
- } //-- void setAboveThreshold(int)
-
- /**
- * Sets the value of field 'annotation'.
- *
- * @param annotation the value of field 'annotation'.
- */
- public void setAnnotation(java.lang.String annotation)
- {
- this._annotation = annotation;
- } //-- void setAnnotation(java.lang.String)
-
- /**
- * Sets the value of field 'colourScheme'.
- *
- * @param colourScheme the value of field 'colourScheme'.
- */
- public void setColourScheme(java.lang.String colourScheme)
- {
- this._colourScheme = colourScheme;
- } //-- void setColourScheme(java.lang.String)
-
- /**
- * Sets the value of field 'maxColour'.
- *
- * @param maxColour the value of field 'maxColour'.
- */
- public void setMaxColour(int maxColour)
- {
- this._maxColour = maxColour;
- this._has_maxColour = true;
- } //-- void setMaxColour(int)
-
- /**
- * Sets the value of field 'minColour'.
- *
- * @param minColour the value of field 'minColour'.
- */
- public void setMinColour(int minColour)
- {
- this._minColour = minColour;
- this._has_minColour = true;
- } //-- void setMinColour(int)
-
- /**
- * Sets the value of field 'threshold'.
- *
- * @param threshold the value of field 'threshold'.
- */
- public void setThreshold(float threshold)
- {
- this._threshold = threshold;
- this._has_threshold = true;
- } //-- void setThreshold(float)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Object
- */
- public static java.lang.Object unmarshal(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);
- } //-- java.lang.Object unmarshal(java.io.Reader)
-
- /**
- * Method validate
- *
- */
- public void validate()
- throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- } //-- void validate()
-
-}
+/*******************************************************************************
+ * 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);
+ }
+
+}