X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FColour.java;h=38f77400c14cd84c1937a16aaf0e94a45af118bb;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=2a3423df64b823a5d6c728cbc3d51c0d83b36cbd;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git
diff --git a/src/jalview/binding/Colour.java b/src/jalview/binding/Colour.java
old mode 100755
new mode 100644
index 2a3423d..38f7740
--- a/src/jalview/binding/Colour.java
+++ b/src/jalview/binding/Colour.java
@@ -1,192 +1,500 @@
-/*
- * This class was automatically generated with
- * Castor 0.9.6, using an XML
- * Schema.
- * $Id$
- */
-
-/*
-* Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
-*
-* This program 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 2
-* of the License, or (at your option) any later version.
-*
-* This program 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 this program; if not, write to the Free Software
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-*/
-
-package jalview.binding;
-
- //---------------------------------/
- //- 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 Colour.
- *
- * @version $Revision$ $Date$
- */
-public class Colour implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _name
- */
- private java.lang.String _name;
-
- /**
- * Field _RGB
- */
- private java.lang.String _RGB;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Colour() {
- super();
- } //-- jalview.binding.Colour()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Returns the value of field 'name'.
- *
- * @return String
- * @return the value of field 'name'.
- */
- public java.lang.String getName()
- {
- return this._name;
- } //-- java.lang.String getName()
-
- /**
- * Returns the value of field 'RGB'.
- *
- * @return String
- * @return the value of field 'RGB'.
- */
- public java.lang.String getRGB()
- {
- return this._RGB;
- } //-- java.lang.String getRGB()
-
- /**
- * 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 'name'.
- *
- * @param name the value of field 'name'.
- */
- public void setName(java.lang.String name)
- {
- this._name = name;
- } //-- void setName(java.lang.String)
-
- /**
- * Sets the value of field 'RGB'.
- *
- * @param RGB the value of field 'RGB'.
- */
- public void setRGB(java.lang.String RGB)
- {
- this._RGB = RGB;
- } //-- void setRGB(java.lang.String)
-
- /**
- * 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.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.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, 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.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Colour.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Colour implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _name.
+ */
+ private java.lang.String _name;
+
+ /**
+ * Field _RGB.
+ */
+ private java.lang.String _RGB;
+
+ /**
+ * Field _minRGB.
+ */
+ private java.lang.String _minRGB;
+
+ /**
+ * loosely specified enumeration: NONE,ABOVE, or BELOW
+ */
+ private java.lang.String _threshType;
+
+ /**
+ * Field _threshold.
+ */
+ private float _threshold;
+
+ /**
+ * keeps track of state for field: _threshold
+ */
+ private boolean _has_threshold;
+
+ /**
+ * Field _max.
+ */
+ private float _max;
+
+ /**
+ * keeps track of state for field: _max
+ */
+ private boolean _has_max;
+
+ /**
+ * Field _min.
+ */
+ private float _min;
+
+ /**
+ * keeps track of state for field: _min
+ */
+ private boolean _has_min;
+
+ /**
+ * Field _colourByLabel.
+ */
+ private boolean _colourByLabel;
+
+ /**
+ * keeps track of state for field: _colourByLabel
+ */
+ private boolean _has_colourByLabel;
+
+ /**
+ * Field _autoScale.
+ */
+ private boolean _autoScale;
+
+ /**
+ * keeps track of state for field: _autoScale
+ */
+ private boolean _has_autoScale;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Colour() {
+ super();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ */
+ public void deleteAutoScale(
+ ) {
+ this._has_autoScale= false;
+ }
+
+ /**
+ */
+ public void deleteColourByLabel(
+ ) {
+ this._has_colourByLabel= false;
+ }
+
+ /**
+ */
+ public void deleteMax(
+ ) {
+ this._has_max= false;
+ }
+
+ /**
+ */
+ public void deleteMin(
+ ) {
+ this._has_min= false;
+ }
+
+ /**
+ */
+ public void deleteThreshold(
+ ) {
+ this._has_threshold= false;
+ }
+
+ /**
+ * Returns the value of field 'autoScale'.
+ *
+ * @return the value of field 'AutoScale'.
+ */
+ public boolean getAutoScale(
+ ) {
+ return this._autoScale;
+ }
+
+ /**
+ * Returns the value of field 'colourByLabel'.
+ *
+ * @return the value of field 'ColourByLabel'.
+ */
+ public boolean getColourByLabel(
+ ) {
+ return this._colourByLabel;
+ }
+
+ /**
+ * Returns the value of field 'max'.
+ *
+ * @return the value of field 'Max'.
+ */
+ public float getMax(
+ ) {
+ return this._max;
+ }
+
+ /**
+ * Returns the value of field 'min'.
+ *
+ * @return the value of field 'Min'.
+ */
+ public float getMin(
+ ) {
+ return this._min;
+ }
+
+ /**
+ * Returns the value of field 'minRGB'.
+ *
+ * @return the value of field 'MinRGB'.
+ */
+ public java.lang.String getMinRGB(
+ ) {
+ return this._minRGB;
+ }
+
+ /**
+ * Returns the value of field 'name'.
+ *
+ * @return the value of field 'Name'.
+ */
+ public java.lang.String getName(
+ ) {
+ return this._name;
+ }
+
+ /**
+ * Returns the value of field 'RGB'.
+ *
+ * @return the value of field 'RGB'.
+ */
+ public java.lang.String getRGB(
+ ) {
+ return this._RGB;
+ }
+
+ /**
+ * Returns the value of field 'threshType'. The field
+ * 'threshType' has the following description: loosely
+ * specified enumeration: NONE,ABOVE, or BELOW
+ *
+ * @return the value of field 'ThreshType'.
+ */
+ public java.lang.String getThreshType(
+ ) {
+ return this._threshType;
+ }
+
+ /**
+ * Returns the value of field 'threshold'.
+ *
+ * @return the value of field 'Threshold'.
+ */
+ public float getThreshold(
+ ) {
+ return this._threshold;
+ }
+
+ /**
+ * Method hasAutoScale.
+ *
+ * @return true if at least one AutoScale has been added
+ */
+ public boolean hasAutoScale(
+ ) {
+ return this._has_autoScale;
+ }
+
+ /**
+ * Method hasColourByLabel.
+ *
+ * @return true if at least one ColourByLabel has been added
+ */
+ public boolean hasColourByLabel(
+ ) {
+ return this._has_colourByLabel;
+ }
+
+ /**
+ * Method hasMax.
+ *
+ * @return true if at least one Max has been added
+ */
+ public boolean hasMax(
+ ) {
+ return this._has_max;
+ }
+
+ /**
+ * Method hasMin.
+ *
+ * @return true if at least one Min has been added
+ */
+ public boolean hasMin(
+ ) {
+ return this._has_min;
+ }
+
+ /**
+ * Method hasThreshold.
+ *
+ * @return true if at least one Threshold has been added
+ */
+ public boolean hasThreshold(
+ ) {
+ return this._has_threshold;
+ }
+
+ /**
+ * Returns the value of field 'autoScale'.
+ *
+ * @return the value of field 'AutoScale'.
+ */
+ public boolean isAutoScale(
+ ) {
+ return this._autoScale;
+ }
+
+ /**
+ * Returns the value of field 'colourByLabel'.
+ *
+ * @return the value of field 'ColourByLabel'.
+ */
+ public boolean isColourByLabel(
+ ) {
+ return this._colourByLabel;
+ }
+
+ /**
+ * 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 'autoScale'.
+ *
+ * @param autoScale the value of field 'autoScale'.
+ */
+ public void setAutoScale(
+ final boolean autoScale) {
+ this._autoScale = autoScale;
+ this._has_autoScale = true;
+ }
+
+ /**
+ * Sets the value of field 'colourByLabel'.
+ *
+ * @param colourByLabel the value of field 'colourByLabel'.
+ */
+ public void setColourByLabel(
+ final boolean colourByLabel) {
+ this._colourByLabel = colourByLabel;
+ this._has_colourByLabel = true;
+ }
+
+ /**
+ * Sets the value of field 'max'.
+ *
+ * @param max the value of field 'max'.
+ */
+ public void setMax(
+ final float max) {
+ this._max = max;
+ this._has_max = true;
+ }
+
+ /**
+ * Sets the value of field 'min'.
+ *
+ * @param min the value of field 'min'.
+ */
+ public void setMin(
+ final float min) {
+ this._min = min;
+ this._has_min = true;
+ }
+
+ /**
+ * Sets the value of field 'minRGB'.
+ *
+ * @param minRGB the value of field 'minRGB'.
+ */
+ public void setMinRGB(
+ final java.lang.String minRGB) {
+ this._minRGB = minRGB;
+ }
+
+ /**
+ * Sets the value of field 'name'.
+ *
+ * @param name the value of field 'name'.
+ */
+ public void setName(
+ final java.lang.String name) {
+ this._name = name;
+ }
+
+ /**
+ * Sets the value of field 'RGB'.
+ *
+ * @param RGB the value of field 'RGB'.
+ */
+ public void setRGB(
+ final java.lang.String RGB) {
+ this._RGB = RGB;
+ }
+
+ /**
+ * Sets the value of field 'threshType'. The field 'threshType'
+ * has the following description: loosely specified
+ * enumeration: NONE,ABOVE, or BELOW
+ *
+ * @param threshType the value of field 'threshType'.
+ */
+ public void setThreshType(
+ final java.lang.String threshType) {
+ this._threshType = threshType;
+ }
+
+ /**
+ * 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.binding.Colour
+ */
+ public static jalview.binding.Colour unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.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);
+ }
+
+}