JAL-3120 preserve feature colour/mincolour/maxcolour while modifying,

[jalview.git] / src / jalview / binding / AnnotationElement.java

diff --git a/src/jalview/binding/AnnotationElement.java b/src/jalview/binding/AnnotationElement.java
old mode 100755 (executable)
new mode 100644 (file)
index 160141c..505d91e
--- a/src/jalview/binding/AnnotationElement.java
+++ b/src/jalview/binding/AnnotationElement.java
@@ -1,26 +1,15 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 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
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
  */
+
 package jalview.binding;
 
-// ---------------------------------/
-// - Imported classes and packages -/
-// ---------------------------------/
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -86,14 +75,14 @@ public class AnnotationElement implements java.io.Serializable
   // -----------/
 
   /**
-   */
+     */
   public void deletePosition()
   {
     this._has_position = false;
   }
 
   /**
-   */
+     */
   public void deleteValue()
   {
     this._has_value = false;
@@ -191,11 +180,10 @@ public class AnnotationElement implements java.io.Serializable
    * 
    * @param out
    * @throws org.exolab.castor.xml.MarshalException
-   *                 if object is null or if any SAXException is thrown during
-   *                 marshaling
+   *           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
+   *           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,
@@ -209,13 +197,12 @@ public class AnnotationElement implements java.io.Serializable
    * 
    * @param handler
    * @throws java.io.IOException
-   *                 if an IOException occurs during marshaling
+   *           if an IOException occurs during marshaling
    * @throws org.exolab.castor.xml.ValidationException
-   *                 if this object is an invalid instance according to the
-   *                 schema
+   *           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
+   *           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,
@@ -229,7 +216,7 @@ public class AnnotationElement implements java.io.Serializable
    * Sets the value of field 'description'.
    * 
    * @param description
-   *                the value of field 'description'.
+   *          the value of field 'description'.
    */
   public void setDescription(final java.lang.String description)
   {
@@ -240,7 +227,7 @@ public class AnnotationElement implements java.io.Serializable
    * Sets the value of field 'displayCharacter'.
    * 
    * @param displayCharacter
-   *                the value of field 'displayCharacter'
+   *          the value of field 'displayCharacter'
    */
   public void setDisplayCharacter(final java.lang.String displayCharacter)
   {
@@ -251,7 +238,7 @@ public class AnnotationElement implements java.io.Serializable
    * Sets the value of field 'position'.
    * 
    * @param position
-   *                the value of field 'position'.
+   *          the value of field 'position'.
    */
   public void setPosition(final int position)
   {
@@ -263,7 +250,7 @@ public class AnnotationElement implements java.io.Serializable
    * Sets the value of field 'secondaryStructure'.
    * 
    * @param secondaryStructure
-   *                the value of field 'secondaryStructure'.
+   *          the value of field 'secondaryStructure'.
    */
   public void setSecondaryStructure(
           final java.lang.String secondaryStructure)
@@ -275,7 +262,7 @@ public class AnnotationElement implements java.io.Serializable
    * Sets the value of field 'value'.
    * 
    * @param value
-   *                the value of field 'value'.
+   *          the value of field 'value'.
    */
   public void setValue(final float value)
   {
@@ -288,11 +275,10 @@ public class AnnotationElement implements java.io.Serializable
    * 
    * @param reader
    * @throws org.exolab.castor.xml.MarshalException
-   *                 if object is null or if any SAXException is thrown during
-   *                 marshaling
+   *           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
+   *           if this object is an invalid instance according to the schema
    * @return the unmarshaled jalview.binding.AnnotationElement
    */
   public static jalview.binding.AnnotationElement unmarshal(
@@ -300,16 +286,15 @@ public class AnnotationElement implements java.io.Serializable
           throws org.exolab.castor.xml.MarshalException,
           org.exolab.castor.xml.ValidationException
   {
-    return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(
-            jalview.binding.AnnotationElement.class, reader);
+    return (jalview.binding.AnnotationElement) Unmarshaller
+            .unmarshal(jalview.binding.AnnotationElement.class, reader);
   }
 
   /**
    * 
    * 
    * @throws org.exolab.castor.xml.ValidationException
-   *                 if this object is an invalid instance according to the
-   *                 schema
+   *           if this object is an invalid instance according to the schema
    */
   public void validate() throws org.exolab.castor.xml.ValidationException
   {