X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FAnnotation.java;h=fefdd12a4a2f007592fb3f845a72788242ec9e59;hb=ffe9b478a182cab3c8217b5c2bf002c7c1b6d7ec;hp=14b09c464e177d01a62aaae549881d9f9fd7182d;hpb=f016dfe567351051121cb0a7717ffa8f10f7625b;p=jalview.git

diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java
index 14b09c4..fefdd12 100755
--- a/src/jalview/binding/Annotation.java
+++ b/src/jalview/binding/Annotation.java
@@ -1,5 +1,5 @@
 /*
- * This class was automatically generated with
+ * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
  * Schema.
  * $Id$
@@ -7,385 +7,373 @@
 
 package jalview.binding;
 
+  //---------------------------------/
+ //- Imported classes and packages -/
 //---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import java.util.*;
 
-import org.exolab.castor.xml.*;
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
+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 Annotation.
- *
+ * 
  * @version $Revision$ $Date$
  */
-public class Annotation
-    implements java.io.Serializable
-{
-
-  //--------------------------/
-  //- Class/Member Variables -/
-  //--------------------------/
-
-  /**
-   * Field _graph
-   */
-  private boolean _graph;
-
-  /**
-   * keeps track of state for field: _graph
-   */
-  private boolean _has_graph;
-
-  /**
-   * Field _annotationElementList
-   */
-  private java.util.Vector _annotationElementList;
-
-  /**
-   * Field _label
-   */
-  private java.lang.String _label;
-
-  /**
-   * Field _description
-   */
-  private java.lang.String _description;
-
-  //----------------/
-  //- Constructors -/
-  //----------------/
-
-  public Annotation()
-  {
-    super();
-    _annotationElementList = new Vector();
-  } //-- jalview.binding.Annotation()
-
-  //-----------/
-  //- Methods -/
-  //-----------/
-
-  /**
-   * Method addAnnotationElement
-   *
-   *
-   *
-   * @param vAnnotationElement
-   */
-  public void addAnnotationElement(jalview.binding.AnnotationElement
-                                   vAnnotationElement)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _annotationElementList.addElement(vAnnotationElement);
-  } //-- void addAnnotationElement(jalview.binding.AnnotationElement)
-
-  /**
-   * Method addAnnotationElement
-   *
-   *
-   *
-   * @param index
-   * @param vAnnotationElement
-   */
-  public void addAnnotationElement(int index,
-                                   jalview.binding.AnnotationElement
-                                   vAnnotationElement)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    _annotationElementList.insertElementAt(vAnnotationElement, index);
-  } //-- void addAnnotationElement(int, jalview.binding.AnnotationElement)
-
-  /**
-   * Method deleteGraph
-   *
-   */
-  public void deleteGraph()
-  {
-    this._has_graph = false;
-  } //-- void deleteGraph()
-
-  /**
-   * Method enumerateAnnotationElement
-   *
-   *
-   *
-   * @return Enumeration
-   */
-  public java.util.Enumeration enumerateAnnotationElement()
-  {
-    return _annotationElementList.elements();
-  } //-- java.util.Enumeration enumerateAnnotationElement()
-
-  /**
-   * Method getAnnotationElement
-   *
-   *
-   *
-   * @param index
-   * @return AnnotationElement
-   */
-  public jalview.binding.AnnotationElement getAnnotationElement(int index)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _annotationElementList.size()))
+public class Annotation implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _graph
+     */
+    private boolean _graph;
+
+    /**
+     * keeps track of state for field: _graph
+     */
+    private boolean _has_graph;
+
+    /**
+     * Field _annotationElementList
+     */
+    private java.util.Vector _annotationElementList;
+
+    /**
+     * Field _label
+     */
+    private java.lang.String _label;
+
+    /**
+     * Field _description
+     */
+    private java.lang.String _description;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Annotation() {
+        super();
+        _annotationElementList = new Vector();
+    } //-- jalview.binding.Annotation()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method addAnnotationElement
+     * 
+     * 
+     * 
+     * @param vAnnotationElement
+     */
+    public void addAnnotationElement(jalview.binding.AnnotationElement vAnnotationElement)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _annotationElementList.addElement(vAnnotationElement);
+    } //-- void addAnnotationElement(jalview.binding.AnnotationElement) 
+
+    /**
+     * Method addAnnotationElement
+     * 
+     * 
+     * 
+     * @param index
+     * @param vAnnotationElement
+     */
+    public void addAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _annotationElementList.insertElementAt(vAnnotationElement, index);
+    } //-- void addAnnotationElement(int, jalview.binding.AnnotationElement) 
+
+    /**
+     * Method deleteGraph
+     * 
+     */
+    public void deleteGraph()
+    {
+        this._has_graph= false;
+    } //-- void deleteGraph() 
+
+    /**
+     * Method enumerateAnnotationElement
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateAnnotationElement()
+    {
+        return _annotationElementList.elements();
+    } //-- java.util.Enumeration enumerateAnnotationElement() 
+
+    /**
+     * Method getAnnotationElement
+     * 
+     * 
+     * 
+     * @param index
+     * @return AnnotationElement
+     */
+    public jalview.binding.AnnotationElement getAnnotationElement(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _annotationElementList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        
+        return (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index);
+    } //-- jalview.binding.AnnotationElement getAnnotationElement(int) 
+
+    /**
+     * Method getAnnotationElement
+     * 
+     * 
+     * 
+     * @return AnnotationElement
+     */
+    public jalview.binding.AnnotationElement[] getAnnotationElement()
+    {
+        int size = _annotationElementList.size();
+        jalview.binding.AnnotationElement[] mArray = new jalview.binding.AnnotationElement[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index);
+        }
+        return mArray;
+    } //-- jalview.binding.AnnotationElement[] getAnnotationElement() 
+
+    /**
+     * Method getAnnotationElementCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getAnnotationElementCount()
+    {
+        return _annotationElementList.size();
+    } //-- int getAnnotationElementCount() 
+
+    /**
+     * Returns the value of field 'description'.
+     * 
+     * @return String
+     * @return the value of field 'description'.
+     */
+    public java.lang.String getDescription()
+    {
+        return this._description;
+    } //-- java.lang.String getDescription() 
+
+    /**
+     * Returns the value of field 'graph'.
+     * 
+     * @return boolean
+     * @return the value of field 'graph'.
+     */
+    public boolean getGraph()
+    {
+        return this._graph;
+    } //-- boolean getGraph() 
+
+    /**
+     * Returns the value of field 'label'.
+     * 
+     * @return String
+     * @return the value of field 'label'.
+     */
+    public java.lang.String getLabel()
+    {
+        return this._label;
+    } //-- java.lang.String getLabel() 
+
+    /**
+     * Method hasGraph
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasGraph()
+    {
+        return this._has_graph;
+    } //-- boolean hasGraph() 
+
+    /**
+     * 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) 
+
+    /**
+     * Method removeAllAnnotationElement
+     * 
+     */
+    public void removeAllAnnotationElement()
+    {
+        _annotationElementList.removeAllElements();
+    } //-- void removeAllAnnotationElement() 
+
+    /**
+     * Method removeAnnotationElement
+     * 
+     * 
+     * 
+     * @param index
+     * @return AnnotationElement
+     */
+    public jalview.binding.AnnotationElement removeAnnotationElement(int index)
+    {
+        java.lang.Object obj = _annotationElementList.elementAt(index);
+        _annotationElementList.removeElementAt(index);
+        return (jalview.binding.AnnotationElement) obj;
+    } //-- jalview.binding.AnnotationElement removeAnnotationElement(int) 
+
+    /**
+     * Method setAnnotationElement
+     * 
+     * 
+     * 
+     * @param index
+     * @param vAnnotationElement
+     */
+    public void setAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _annotationElementList.size())) {
+            throw new IndexOutOfBoundsException();
+        }
+        _annotationElementList.setElementAt(vAnnotationElement, index);
+    } //-- void setAnnotationElement(int, jalview.binding.AnnotationElement) 
+
+    /**
+     * Method setAnnotationElement
+     * 
+     * 
+     * 
+     * @param annotationElementArray
+     */
+    public void setAnnotationElement(jalview.binding.AnnotationElement[] annotationElementArray)
     {
-      throw new IndexOutOfBoundsException();
-    }
-
-    return (jalview.binding.AnnotationElement) _annotationElementList.elementAt(
-        index);
-  } //-- jalview.binding.AnnotationElement getAnnotationElement(int)
-
-  /**
-   * Method getAnnotationElement
-   *
-   *
-   *
-   * @return AnnotationElement
-   */
-  public jalview.binding.AnnotationElement[] getAnnotationElement()
-  {
-    int size = _annotationElementList.size();
-    jalview.binding.AnnotationElement[] mArray = new jalview.binding.
-        AnnotationElement[size];
-    for (int index = 0; index < size; index++)
+        //-- copy array
+        _annotationElementList.removeAllElements();
+        for (int i = 0; i < annotationElementArray.length; i++) {
+            _annotationElementList.addElement(annotationElementArray[i]);
+        }
+    } //-- void setAnnotationElement(jalview.binding.AnnotationElement) 
+
+    /**
+     * Sets the value of field 'description'.
+     * 
+     * @param description the value of field 'description'.
+     */
+    public void setDescription(java.lang.String description)
     {
-      mArray[index] = (jalview.binding.AnnotationElement)
-          _annotationElementList.elementAt(index);
-    }
-    return mArray;
-  } //-- jalview.binding.AnnotationElement[] getAnnotationElement()
-
-  /**
-   * Method getAnnotationElementCount
-   *
-   *
-   *
-   * @return int
-   */
-  public int getAnnotationElementCount()
-  {
-    return _annotationElementList.size();
-  } //-- int getAnnotationElementCount()
-
-  /**
-   * Returns the value of field 'description'.
-   *
-   * @return String
-   * @return the value of field 'description'.
-   */
-  public java.lang.String getDescription()
-  {
-    return this._description;
-  } //-- java.lang.String getDescription()
-
-  /**
-   * Returns the value of field 'graph'.
-   *
-   * @return boolean
-   * @return the value of field 'graph'.
-   */
-  public boolean getGraph()
-  {
-    return this._graph;
-  } //-- boolean getGraph()
-
-  /**
-   * Returns the value of field 'label'.
-   *
-   * @return String
-   * @return the value of field 'label'.
-   */
-  public java.lang.String getLabel()
-  {
-    return this._label;
-  } //-- java.lang.String getLabel()
-
-  /**
-   * Method hasGraph
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean hasGraph()
-  {
-    return this._has_graph;
-  } //-- boolean hasGraph()
-
-  /**
-   * Method isValid
-   *
-   *
-   *
-   * @return boolean
-   */
-  public boolean isValid()
-  {
-    try
+        this._description = description;
+    } //-- void setDescription(java.lang.String) 
+
+    /**
+     * Sets the value of field 'graph'.
+     * 
+     * @param graph the value of field 'graph'.
+     */
+    public void setGraph(boolean graph)
     {
-      validate();
-    }
-    catch (org.exolab.castor.xml.ValidationException vex)
+        this._graph = graph;
+        this._has_graph = true;
+    } //-- void setGraph(boolean) 
+
+    /**
+     * Sets the value of field 'label'.
+     * 
+     * @param label the value of field 'label'.
+     */
+    public void setLabel(java.lang.String label)
     {
-      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)
-
-  /**
-   * Method removeAllAnnotationElement
-   *
-   */
-  public void removeAllAnnotationElement()
-  {
-    _annotationElementList.removeAllElements();
-  } //-- void removeAllAnnotationElement()
-
-  /**
-   * Method removeAnnotationElement
-   *
-   *
-   *
-   * @param index
-   * @return AnnotationElement
-   */
-  public jalview.binding.AnnotationElement removeAnnotationElement(int index)
-  {
-    java.lang.Object obj = _annotationElementList.elementAt(index);
-    _annotationElementList.removeElementAt(index);
-    return (jalview.binding.AnnotationElement) obj;
-  } //-- jalview.binding.AnnotationElement removeAnnotationElement(int)
-
-  /**
-   * Method setAnnotationElement
-   *
-   *
-   *
-   * @param index
-   * @param vAnnotationElement
-   */
-  public void setAnnotationElement(int index,
-                                   jalview.binding.AnnotationElement
-                                   vAnnotationElement)
-      throws java.lang.IndexOutOfBoundsException
-  {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _annotationElementList.size()))
+        this._label = label;
+    } //-- void setLabel(java.lang.String) 
+
+    /**
+     * 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
     {
-      throw new IndexOutOfBoundsException();
-    }
-    _annotationElementList.setElementAt(vAnnotationElement, index);
-  } //-- void setAnnotationElement(int, jalview.binding.AnnotationElement)
-
-  /**
-   * Method setAnnotationElement
-   *
-   *
-   *
-   * @param annotationElementArray
-   */
-  public void setAnnotationElement(jalview.binding.AnnotationElement[]
-                                   annotationElementArray)
-  {
-    //-- copy array
-    _annotationElementList.removeAllElements();
-    for (int i = 0; i < annotationElementArray.length; i++)
+        return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class, reader);
+    } //-- java.lang.Object unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
     {
-      _annotationElementList.addElement(annotationElementArray[i]);
-    }
-  } //-- void setAnnotationElement(jalview.binding.AnnotationElement)
-
-  /**
-   * Sets the value of field 'description'.
-   *
-   * @param description the value of field 'description'.
-   */
-  public void setDescription(java.lang.String description)
-  {
-    this._description = description;
-  } //-- void setDescription(java.lang.String)
-
-  /**
-   * Sets the value of field 'graph'.
-   *
-   * @param graph the value of field 'graph'.
-   */
-  public void setGraph(boolean graph)
-  {
-    this._graph = graph;
-    this._has_graph = true;
-  } //-- void setGraph(boolean)
-
-  /**
-   * Sets the value of field 'label'.
-   *
-   * @param label the value of field 'label'.
-   */
-  public void setLabel(java.lang.String label)
-  {
-    this._label = label;
-  } //-- void setLabel(java.lang.String)
-
-  /**
-   * 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.Annotation) Unmarshaller.unmarshal(jalview.binding.
-        Annotation.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()
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
 
 }