X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FAlignment.java;fp=src%2Fjalview%2Fbinding%2FAlignment.java;h=5b107b5e5d95657935f48a9fdb519715172dfb7e;hb=c9df5bd6e95c23c9b560c0a59003d1f4043f8055;hp=0cc251493ad2ef776c9e70a2128da2c8883c6737;hpb=6296524c4ccada42516aac9a85398170f5a3bc5d;p=jalview.git

diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java
index 0cc2514..5b107b5 100644
--- a/src/jalview/binding/Alignment.java
+++ b/src/jalview/binding/Alignment.java
@@ -1,27 +1,14 @@
 /*
- * 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 <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
+ * 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;
@@ -32,162 +19,151 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Alignment implements java.io.Serializable
-{
-
-  // --------------------------/
-  // - Class/Member Variables -/
-  // --------------------------/
-
-  /**
-   * Field _annotation.
-   */
-  private jalview.binding.Annotation _annotation;
-
-  /**
-   * Field _sequenceSet.
-   */
-  private jalview.binding.SequenceSet _sequenceSet;
-
-  // ----------------/
-  // - Constructors -/
-  // ----------------/
-
-  public Alignment()
-  {
-    super();
-  }
-
-  // -----------/
-  // - Methods -/
-  // -----------/
-
-  /**
-   * Returns the value of field 'annotation'.
-   * 
-   * @return the value of field 'Annotation'.
-   */
-  public jalview.binding.Annotation getAnnotation()
-  {
-    return this._annotation;
-  }
-
-  /**
-   * Returns the value of field 'sequenceSet'.
-   * 
-   * @return the value of field 'SequenceSet'.
-   */
-  public jalview.binding.SequenceSet getSequenceSet()
-  {
-    return this._sequenceSet;
-  }
-
-  /**
-   * 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;
+public class Alignment implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _annotation.
+     */
+    private jalview.binding.Annotation _annotation;
+
+    /**
+     * Field _sequenceSet.
+     */
+    private jalview.binding.SequenceSet _sequenceSet;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Alignment() {
+        super();
+    }
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Returns the value of field 'annotation'.
+     * 
+     * @return the value of field 'Annotation'.
+     */
+    public jalview.binding.Annotation getAnnotation(
+    ) {
+        return this._annotation;
+    }
+
+    /**
+     * Returns the value of field 'sequenceSet'.
+     * 
+     * @return the value of field 'SequenceSet'.
+     */
+    public jalview.binding.SequenceSet getSequenceSet(
+    ) {
+        return this._sequenceSet;
+    }
+
+    /**
+     * 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 'annotation'.
+     * 
+     * @param annotation the value of field 'annotation'.
+     */
+    public void setAnnotation(
+            final jalview.binding.Annotation annotation) {
+        this._annotation = annotation;
+    }
+
+    /**
+     * Sets the value of field 'sequenceSet'.
+     * 
+     * @param sequenceSet the value of field 'sequenceSet'.
+     */
+    public void setSequenceSet(
+            final jalview.binding.SequenceSet sequenceSet) {
+        this._sequenceSet = sequenceSet;
+    }
+
+    /**
+     * 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.Alignment
+     */
+    public static jalview.binding.Alignment unmarshal(
+            final java.io.Reader reader)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+        return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.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);
     }
-    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 'annotation'.
-   * 
-   * @param annotation
-   *          the value of field 'annotation'.
-   */
-  public void setAnnotation(final jalview.binding.Annotation annotation)
-  {
-    this._annotation = annotation;
-  }
-
-  /**
-   * Sets the value of field 'sequenceSet'.
-   * 
-   * @param sequenceSet
-   *          the value of field 'sequenceSet'.
-   */
-  public void setSequenceSet(final jalview.binding.SequenceSet sequenceSet)
-  {
-    this._sequenceSet = sequenceSet;
-  }
-
-  /**
-   * 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.Alignment
-   */
-  public static jalview.binding.Alignment unmarshal(
-          final java.io.Reader reader)
-          throws org.exolab.castor.xml.MarshalException,
-          org.exolab.castor.xml.ValidationException
-  {
-    return (jalview.binding.Alignment) Unmarshaller.unmarshal(
-            jalview.binding.Alignment.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);
-  }
 
 }