X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FStructureState.java;h=25e7fdf6f9aa96358c88f43f8177a92d64252007;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=968a559ddee179d069eb5bc681aa9866802aae10;hpb=09ee1649c4427f534331aa2017a890529f0932f5;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java
index 968a559..25e7fdf 100644
--- a/src/jalview/schemabinding/version2/StructureState.java
+++ b/src/jalview/schemabinding/version2/StructureState.java
@@ -1,14 +1,27 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
  */
-
 package jalview.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,380 +32,655 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class StructureState implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * internal content storage
-     */
-    private java.lang.String _content = "";
-
-    /**
-     * Field _visible.
-     */
-    private boolean _visible;
-
-    /**
-     * keeps track of state for field: _visible
-     */
-    private boolean _has_visible;
-
-    /**
-     * Field _xpos.
-     */
-    private int _xpos;
-
-    /**
-     * keeps track of state for field: _xpos
-     */
-    private boolean _has_xpos;
-
-    /**
-     * Field _ypos.
-     */
-    private int _ypos;
-
-    /**
-     * keeps track of state for field: _ypos
-     */
-    private boolean _has_ypos;
-
-    /**
-     * Field _width.
-     */
-    private int _width;
-
-    /**
-     * keeps track of state for field: _width
-     */
-    private boolean _has_width;
-
-    /**
-     * Field _height.
-     */
-    private int _height;
-
-    /**
-     * keeps track of state for field: _height
-     */
-    private boolean _has_height;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public StructureState() {
-        super();
-        setContent("");
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     */
-    public void deleteHeight(
-    ) {
-        this._has_height= false;
-    }
-
-    /**
-     */
-    public void deleteVisible(
-    ) {
-        this._has_visible= false;
-    }
-
-    /**
-     */
-    public void deleteWidth(
-    ) {
-        this._has_width= false;
-    }
-
-    /**
-     */
-    public void deleteXpos(
-    ) {
-        this._has_xpos= false;
-    }
-
-    /**
-     */
-    public void deleteYpos(
-    ) {
-        this._has_ypos= false;
-    }
-
-    /**
-     * Returns the value of field 'content'. The field 'content'
-     * has the following description: internal content storage
-     * 
-     * @return the value of field 'Content'.
-     */
-    public java.lang.String getContent(
-    ) {
-        return this._content;
-    }
-
-    /**
-     * Returns the value of field 'height'.
-     * 
-     * @return the value of field 'Height'.
-     */
-    public int getHeight(
-    ) {
-        return this._height;
-    }
-
-    /**
-     * Returns the value of field 'visible'.
-     * 
-     * @return the value of field 'Visible'.
-     */
-    public boolean getVisible(
-    ) {
-        return this._visible;
-    }
-
-    /**
-     * Returns the value of field 'width'.
-     * 
-     * @return the value of field 'Width'.
-     */
-    public int getWidth(
-    ) {
-        return this._width;
-    }
-
-    /**
-     * Returns the value of field 'xpos'.
-     * 
-     * @return the value of field 'Xpos'.
-     */
-    public int getXpos(
-    ) {
-        return this._xpos;
-    }
-
-    /**
-     * Returns the value of field 'ypos'.
-     * 
-     * @return the value of field 'Ypos'.
-     */
-    public int getYpos(
-    ) {
-        return this._ypos;
-    }
-
-    /**
-     * Method hasHeight.
-     * 
-     * @return true if at least one Height has been added
-     */
-    public boolean hasHeight(
-    ) {
-        return this._has_height;
-    }
-
-    /**
-     * Method hasVisible.
-     * 
-     * @return true if at least one Visible has been added
-     */
-    public boolean hasVisible(
-    ) {
-        return this._has_visible;
-    }
-
-    /**
-     * Method hasWidth.
-     * 
-     * @return true if at least one Width has been added
-     */
-    public boolean hasWidth(
-    ) {
-        return this._has_width;
-    }
-
-    /**
-     * Method hasXpos.
-     * 
-     * @return true if at least one Xpos has been added
-     */
-    public boolean hasXpos(
-    ) {
-        return this._has_xpos;
-    }
-
-    /**
-     * Method hasYpos.
-     * 
-     * @return true if at least one Ypos has been added
-     */
-    public boolean hasYpos(
-    ) {
-        return this._has_ypos;
-    }
-
-    /**
-     * 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;
-    }
-
-    /**
-     * Returns the value of field 'visible'.
-     * 
-     * @return the value of field 'Visible'.
-     */
-    public boolean isVisible(
-    ) {
-        return this._visible;
-    }
-
-    /**
-     * 
-     * 
-     * @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 'content'. The field 'content' has
-     * the following description: internal content storage
-     * 
-     * @param content the value of field 'content'.
-     */
-    public void setContent(
-            final java.lang.String content) {
-        this._content = content;
-    }
-
-    /**
-     * Sets the value of field 'height'.
-     * 
-     * @param height the value of field 'height'.
-     */
-    public void setHeight(
-            final int height) {
-        this._height = height;
-        this._has_height = true;
-    }
-
-    /**
-     * Sets the value of field 'visible'.
-     * 
-     * @param visible the value of field 'visible'.
-     */
-    public void setVisible(
-            final boolean visible) {
-        this._visible = visible;
-        this._has_visible = true;
-    }
-
-    /**
-     * Sets the value of field 'width'.
-     * 
-     * @param width the value of field 'width'.
-     */
-    public void setWidth(
-            final int width) {
-        this._width = width;
-        this._has_width = true;
-    }
-
-    /**
-     * Sets the value of field 'xpos'.
-     * 
-     * @param xpos the value of field 'xpos'.
-     */
-    public void setXpos(
-            final int xpos) {
-        this._xpos = xpos;
-        this._has_xpos = true;
-    }
-
-    /**
-     * Sets the value of field 'ypos'.
-     * 
-     * @param ypos the value of field 'ypos'.
-     */
-    public void setYpos(
-            final int ypos) {
-        this._ypos = ypos;
-        this._has_ypos = true;
-    }
-
-    /**
-     * 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.schemabinding.version2.StructureState
-     */
-    public static jalview.schemabinding.version2.StructureState unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.schemabinding.version2.StructureState) Unmarshaller.unmarshal(jalview.schemabinding.version2.StructureState.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 StructureState implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * internal content storage
+   */
+  private java.lang.String _content = "";
+
+  /**
+   * Field _visible.
+   */
+  private boolean _visible;
+
+  /**
+   * keeps track of state for field: _visible
+   */
+  private boolean _has_visible;
+
+  /**
+   * additional identifier which properly disambiguates the structure view from
+   * any other view with the same attributes. This is not an ID, because it is
+   * possible to have many references to the same physical structure view from
+   * different sequences in an alignment. A structureState element citing the
+   * same viewId will appear for each instance.
+   * 
+   */
+  private java.lang.String _viewId;
+
+  /**
+   * Flag set if the alignment panel containing this JSeq should be included in
+   * those used to perform a structure superposition (since Jalview 2.7).
+   * 
+   */
+  private boolean _alignwithAlignPanel = true;
+
+  /**
+   * keeps track of state for field: _alignwithAlignPanel
+   */
+  private boolean _has_alignwithAlignPanel;
+
+  /**
+   * Flag set if the alignment panel containing this JSeq should be included in
+   * those used to colour its associated sequences in this structureState(since
+   * Jalview 2.7).
+   * 
+   */
+  private boolean _colourwithAlignPanel = false;
+
+  /**
+   * keeps track of state for field: _colourwithAlignPanel
+   */
+  private boolean _has_colourwithAlignPanel;
+
+  /**
+   * Flag set if the structure display is coloured by the Jmol state, rather
+   * than by one or more linked alignment views.
+   * 
+   */
+  private boolean _colourByJmol = true;
+
+  /**
+   * keeps track of state for field: _colourByJmol
+   */
+  private boolean _has_colourByJmol;
+
+  /**
+   * Field _width.
+   */
+  private int _width;
+
+  /**
+   * keeps track of state for field: _width
+   */
+  private boolean _has_width;
+
+  /**
+   * Field _height.
+   */
+  private int _height;
+
+  /**
+   * keeps track of state for field: _height
+   */
+  private boolean _has_height;
+
+  /**
+   * Field _xpos.
+   */
+  private int _xpos;
+
+  /**
+   * keeps track of state for field: _xpos
+   */
+  private boolean _has_xpos;
+
+  /**
+   * Field _ypos.
+   */
+  private int _ypos;
+
+  /**
+   * keeps track of state for field: _ypos
+   */
+  private boolean _has_ypos;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public StructureState()
+  {
+    super();
+    setContent("");
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+     */
+  public void deleteAlignwithAlignPanel()
+  {
+    this._has_alignwithAlignPanel = false;
+  }
+
+  /**
+     */
+  public void deleteColourByJmol()
+  {
+    this._has_colourByJmol = false;
+  }
+
+  /**
+     */
+  public void deleteColourwithAlignPanel()
+  {
+    this._has_colourwithAlignPanel = false;
+  }
+
+  /**
+     */
+  public void deleteHeight()
+  {
+    this._has_height = false;
+  }
+
+  /**
+     */
+  public void deleteVisible()
+  {
+    this._has_visible = false;
+  }
+
+  /**
+     */
+  public void deleteWidth()
+  {
+    this._has_width = false;
+  }
+
+  /**
+     */
+  public void deleteXpos()
+  {
+    this._has_xpos = false;
+  }
+
+  /**
+     */
+  public void deleteYpos()
+  {
+    this._has_ypos = false;
+  }
+
+  /**
+   * Returns the value of field 'alignwithAlignPanel'. The field
+   * 'alignwithAlignPanel' has the following description: Flag set if the
+   * alignment panel containing this JSeq should be included in those used to
+   * perform a structure superposition (since Jalview 2.7).
+   * 
+   * 
+   * @return the value of field 'AlignwithAlignPanel'.
+   */
+  public boolean getAlignwithAlignPanel()
+  {
+    return this._alignwithAlignPanel;
+  }
+
+  /**
+   * Returns the value of field 'colourByJmol'. The field 'colourByJmol' has the
+   * following description: Flag set if the structure display is coloured by the
+   * Jmol state, rather than by one or more linked alignment views.
+   * 
+   * 
+   * @return the value of field 'ColourByJmol'.
+   */
+  public boolean getColourByJmol()
+  {
+    return this._colourByJmol;
+  }
+
+  /**
+   * Returns the value of field 'colourwithAlignPanel'. The field
+   * 'colourwithAlignPanel' has the following description: Flag set if the
+   * alignment panel containing this JSeq should be included in those used to
+   * colour its associated sequences in this structureState(since Jalview 2.7).
+   * 
+   * 
+   * @return the value of field 'ColourwithAlignPanel'.
+   */
+  public boolean getColourwithAlignPanel()
+  {
+    return this._colourwithAlignPanel;
+  }
+
+  /**
+   * Returns the value of field 'content'. The field 'content' has the following
+   * description: internal content storage
+   * 
+   * @return the value of field 'Content'.
+   */
+  public java.lang.String getContent()
+  {
+    return this._content;
+  }
+
+  /**
+   * Returns the value of field 'height'.
+   * 
+   * @return the value of field 'Height'.
+   */
+  public int getHeight()
+  {
+    return this._height;
+  }
+
+  /**
+   * Returns the value of field 'viewId'. The field 'viewId' has the following
+   * description: additional identifier which properly disambiguates the
+   * structure view from any other view with the same attributes. This is not an
+   * ID, because it is possible to have many references to the same physical
+   * structure view from different sequences in an alignment. A structureState
+   * element citing the same viewId will appear for each instance.
+   * 
+   * 
+   * @return the value of field 'ViewId'.
+   */
+  public java.lang.String getViewId()
+  {
+    return this._viewId;
+  }
+
+  /**
+   * Returns the value of field 'visible'.
+   * 
+   * @return the value of field 'Visible'.
+   */
+  public boolean getVisible()
+  {
+    return this._visible;
+  }
+
+  /**
+   * Returns the value of field 'width'.
+   * 
+   * @return the value of field 'Width'.
+   */
+  public int getWidth()
+  {
+    return this._width;
+  }
+
+  /**
+   * Returns the value of field 'xpos'.
+   * 
+   * @return the value of field 'Xpos'.
+   */
+  public int getXpos()
+  {
+    return this._xpos;
+  }
+
+  /**
+   * Returns the value of field 'ypos'.
+   * 
+   * @return the value of field 'Ypos'.
+   */
+  public int getYpos()
+  {
+    return this._ypos;
+  }
+
+  /**
+   * Method hasAlignwithAlignPanel.
+   * 
+   * @return true if at least one AlignwithAlignPanel has been added
+   */
+  public boolean hasAlignwithAlignPanel()
+  {
+    return this._has_alignwithAlignPanel;
+  }
+
+  /**
+   * Method hasColourByJmol.
+   * 
+   * @return true if at least one ColourByJmol has been added
+   */
+  public boolean hasColourByJmol()
+  {
+    return this._has_colourByJmol;
+  }
+
+  /**
+   * Method hasColourwithAlignPanel.
+   * 
+   * @return true if at least one ColourwithAlignPanel has been added
+   */
+  public boolean hasColourwithAlignPanel()
+  {
+    return this._has_colourwithAlignPanel;
+  }
+
+  /**
+   * Method hasHeight.
+   * 
+   * @return true if at least one Height has been added
+   */
+  public boolean hasHeight()
+  {
+    return this._has_height;
+  }
+
+  /**
+   * Method hasVisible.
+   * 
+   * @return true if at least one Visible has been added
+   */
+  public boolean hasVisible()
+  {
+    return this._has_visible;
+  }
+
+  /**
+   * Method hasWidth.
+   * 
+   * @return true if at least one Width has been added
+   */
+  public boolean hasWidth()
+  {
+    return this._has_width;
+  }
+
+  /**
+   * Method hasXpos.
+   * 
+   * @return true if at least one Xpos has been added
+   */
+  public boolean hasXpos()
+  {
+    return this._has_xpos;
+  }
+
+  /**
+   * Method hasYpos.
+   * 
+   * @return true if at least one Ypos has been added
+   */
+  public boolean hasYpos()
+  {
+    return this._has_ypos;
+  }
+
+  /**
+   * Returns the value of field 'alignwithAlignPanel'. The field
+   * 'alignwithAlignPanel' has the following description: Flag set if the
+   * alignment panel containing this JSeq should be included in those used to
+   * perform a structure superposition (since Jalview 2.7).
+   * 
+   * 
+   * @return the value of field 'AlignwithAlignPanel'.
+   */
+  public boolean isAlignwithAlignPanel()
+  {
+    return this._alignwithAlignPanel;
+  }
+
+  /**
+   * Returns the value of field 'colourByJmol'. The field 'colourByJmol' has the
+   * following description: Flag set if the structure display is coloured by the
+   * Jmol state, rather than by one or more linked alignment views.
+   * 
+   * 
+   * @return the value of field 'ColourByJmol'.
+   */
+  public boolean isColourByJmol()
+  {
+    return this._colourByJmol;
+  }
+
+  /**
+   * Returns the value of field 'colourwithAlignPanel'. The field
+   * 'colourwithAlignPanel' has the following description: Flag set if the
+   * alignment panel containing this JSeq should be included in those used to
+   * colour its associated sequences in this structureState(since Jalview 2.7).
+   * 
+   * 
+   * @return the value of field 'ColourwithAlignPanel'.
+   */
+  public boolean isColourwithAlignPanel()
+  {
+    return this._colourwithAlignPanel;
+  }
+
+  /**
+   * 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;
+  }
+
+  /**
+   * Returns the value of field 'visible'.
+   * 
+   * @return the value of field 'Visible'.
+   */
+  public boolean isVisible()
+  {
+    return this._visible;
+  }
+
+  /**
+   * 
+   * 
+   * @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 'alignwithAlignPanel'. The field
+   * 'alignwithAlignPanel' has the following description: Flag set if the
+   * alignment panel containing this JSeq should be included in those used to
+   * perform a structure superposition (since Jalview 2.7).
+   * 
+   * 
+   * @param alignwithAlignPanel
+   *          the value of field 'alignwithAlignPanel'.
+   */
+  public void setAlignwithAlignPanel(final boolean alignwithAlignPanel)
+  {
+    this._alignwithAlignPanel = alignwithAlignPanel;
+    this._has_alignwithAlignPanel = true;
+  }
+
+  /**
+   * Sets the value of field 'colourByJmol'. The field 'colourByJmol' has the
+   * following description: Flag set if the structure display is coloured by the
+   * Jmol state, rather than by one or more linked alignment views.
+   * 
+   * 
+   * @param colourByJmol
+   *          the value of field 'colourByJmol'.
+   */
+  public void setColourByJmol(final boolean colourByJmol)
+  {
+    this._colourByJmol = colourByJmol;
+    this._has_colourByJmol = true;
+  }
+
+  /**
+   * Sets the value of field 'colourwithAlignPanel'. The field
+   * 'colourwithAlignPanel' has the following description: Flag set if the
+   * alignment panel containing this JSeq should be included in those used to
+   * colour its associated sequences in this structureState(since Jalview 2.7).
+   * 
+   * 
+   * @param colourwithAlignPanel
+   *          the value of field 'colourwithAlignPanel'.
+   */
+  public void setColourwithAlignPanel(final boolean colourwithAlignPanel)
+  {
+    this._colourwithAlignPanel = colourwithAlignPanel;
+    this._has_colourwithAlignPanel = true;
+  }
+
+  /**
+   * Sets the value of field 'content'. The field 'content' has the following
+   * description: internal content storage
+   * 
+   * @param content
+   *          the value of field 'content'.
+   */
+  public void setContent(final java.lang.String content)
+  {
+    this._content = content;
+  }
+
+  /**
+   * Sets the value of field 'height'.
+   * 
+   * @param height
+   *          the value of field 'height'.
+   */
+  public void setHeight(final int height)
+  {
+    this._height = height;
+    this._has_height = true;
+  }
+
+  /**
+   * Sets the value of field 'viewId'. The field 'viewId' has the following
+   * description: additional identifier which properly disambiguates the
+   * structure view from any other view with the same attributes. This is not an
+   * ID, because it is possible to have many references to the same physical
+   * structure view from different sequences in an alignment. A structureState
+   * element citing the same viewId will appear for each instance.
+   * 
+   * 
+   * @param viewId
+   *          the value of field 'viewId'.
+   */
+  public void setViewId(final java.lang.String viewId)
+  {
+    this._viewId = viewId;
+  }
+
+  /**
+   * Sets the value of field 'visible'.
+   * 
+   * @param visible
+   *          the value of field 'visible'.
+   */
+  public void setVisible(final boolean visible)
+  {
+    this._visible = visible;
+    this._has_visible = true;
+  }
+
+  /**
+   * Sets the value of field 'width'.
+   * 
+   * @param width
+   *          the value of field 'width'.
+   */
+  public void setWidth(final int width)
+  {
+    this._width = width;
+    this._has_width = true;
+  }
+
+  /**
+   * Sets the value of field 'xpos'.
+   * 
+   * @param xpos
+   *          the value of field 'xpos'.
+   */
+  public void setXpos(final int xpos)
+  {
+    this._xpos = xpos;
+    this._has_xpos = true;
+  }
+
+  /**
+   * Sets the value of field 'ypos'.
+   * 
+   * @param ypos
+   *          the value of field 'ypos'.
+   */
+  public void setYpos(final int ypos)
+  {
+    this._ypos = ypos;
+    this._has_ypos = true;
+  }
+
+  /**
+   * 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.schemabinding.version2.StructureState
+   */
+  public static jalview.schemabinding.version2.StructureState unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.schemabinding.version2.StructureState) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.StructureState.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);
+  }
 
 }