X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FAlignment.java;h=0116b44393eba47157843ede0032ccc5e7b532e8;hb=a5f48be3f383f9d2a0de386c95647c593f7db1e3;hp=9a38f10c1d7c794c3d3d412fca7cb8277693543d;hpb=c68ce4c63bd79f23b87aac3eb0afa7f6b42a3098;p=jalview.git

diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java
old mode 100755
new mode 100644
index 9a38f10..0116b44
--- a/src/jalview/binding/Alignment.java
+++ b/src/jalview/binding/Alignment.java
@@ -1,173 +1,180 @@
-/*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
- * Schema.
- * $Id$
- */
-
-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 Alignment.
- * 
- * @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();
-    } //-- jalview.binding.Alignment()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Returns the value of field 'annotation'.
-     * 
-     * @return Annotation
-     * @return the value of field 'annotation'.
-     */
-    public jalview.binding.Annotation getAnnotation()
-    {
-        return this._annotation;
-    } //-- jalview.binding.Annotation getAnnotation() 
-
-    /**
-     * Returns the value of field 'sequenceSet'.
-     * 
-     * @return SequenceSet
-     * @return the value of field 'sequenceSet'.
-     */
-    public jalview.binding.SequenceSet getSequenceSet()
-    {
-        return this._sequenceSet;
-    } //-- jalview.binding.SequenceSet getSequenceSet() 
-
-    /**
-     * 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 'annotation'.
-     * 
-     * @param annotation the value of field 'annotation'.
-     */
-    public void setAnnotation(jalview.binding.Annotation annotation)
-    {
-        this._annotation = annotation;
-    } //-- void setAnnotation(jalview.binding.Annotation) 
-
-    /**
-     * Sets the value of field 'sequenceSet'.
-     * 
-     * @param sequenceSet the value of field 'sequenceSet'.
-     */
-    public void setSequenceSet(jalview.binding.SequenceSet sequenceSet)
-    {
-        this._sequenceSet = sequenceSet;
-    } //-- void setSequenceSet(jalview.binding.SequenceSet) 
-
-    /**
-     * 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.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.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() 
-
-}
+/*
+ * 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 -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Alignment.
+ * 
+ * @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);
+  }
+
+}