X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FAlignment.java;h=0116b44393eba47157843ede0032ccc5e7b532e8;hb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;hp=5b107b5e5d95657935f48a9fdb519715172dfb7e;hpb=9adf6bc4eac154c1f96a2be5867ce24d7c6470f1;p=jalview.git

diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java
index 5b107b5..0116b44 100644
--- a/src/jalview/binding/Alignment.java
+++ b/src/jalview/binding/Alignment.java
@@ -7,8 +7,8 @@
 
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,151 +19,162 @@ 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;
-        }
-        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);
+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);
+  }
 
 }