X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FAnnotationColours.java;h=83c330f9db6b1796996db639a41be95dc053f61f;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=b2af2c44febcaada5dda1ed272bceac3d34d30e5;hpb=224791537adfcd1d6efff3e24fa7c653d042b222;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..83c330f
--- a/src/jalview/schemabinding/version2/AnnotationColours.java
+++ b/src/jalview/schemabinding/version2/AnnotationColours.java
@@ -1,385 +1,141 @@
-/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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.
+ */
+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 extends AnnotationColourScheme implements
+ java.io.Serializable
+{
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public AnnotationColours()
+ {
+ super();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ * 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);
+ }
+
+ /**
+ * 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.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);
+ }
+
+}