castor-1.1 compatible classes from ant task

diff --git a/src/jalview/binding/JalviewUserColoursItem.java b/src/jalview/binding/JalviewUserColoursItem.java
deleted file mode 100755 (executable)
index 9c88831..0000000
--- a/src/jalview/binding/JalviewUserColoursItem.java
+++ /dev/null
@@ -1,68 +0,0 @@
-/*\r
- * This class was automatically generated with\r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-package jalview.binding;\r
-\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-import java.io.Serializable;\r
-\r
-\r
-/**\r
- * Class JalviewUserColoursItem.\r
- *\r
- * @version $Revision$ $Date$\r
- */\r
-public class JalviewUserColoursItem implements java.io.Serializable\r
-{\r
-    //--------------------------/\r
-    //- Class/Member Variables -/\r
-    //--------------------------/\r
-\r
-    /**\r
-     * Field _colour\r
-     */\r
-    private jalview.binding.Colour _colour;\r
-\r
-    //----------------/\r
-    //- Constructors -/\r
-    //----------------/\r
-    public JalviewUserColoursItem()\r
-    {\r
-        super();\r
-    }\r
-\r
-    //-- jalview.binding.JalviewUserColoursItem()\r
-    //-----------/\r
-\r
-    /**\r
-     * DOCUMENT ME!\r
-     *\r
-     * @return DOCUMENT ME!\r
-     */\r
-    public jalview.binding.Colour getColour()\r
-    {\r
-        return this._colour;\r
-    }\r
-\r
-    //-- jalview.binding.Colour getColour() \r
-\r
-    /**\r
-     * Sets the value of field 'colour'.\r
-     *\r
-     * @param colour the value of field 'colour'.\r
-     */\r
-    public void setColour(jalview.binding.Colour colour)\r
-    {\r
-        this._colour = colour;\r
-    }\r
-\r
-    //-- void setColour(jalview.binding.Colour) \r
-}\r

diff --git a/src/jalview/binding/Residue.java b/src/jalview/binding/Residue.java
deleted file mode 100755 (executable)
index 2588f38..0000000
--- a/src/jalview/binding/Residue.java
+++ /dev/null
@@ -1,199 +0,0 @@
-/*\r
- * This class was automatically generated with\r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package jalview.binding;\r
-\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.xml.*;\r
-\r
-/**\r
- * Class Residue.\r
- *\r
- * @version $Revision$ $Date$\r
- */\r
-public class Residue\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _name\r
-   */\r
-  private java.lang.String _name;\r
-\r
-  /**\r
-   * Field _RGB\r
-   */\r
-  private int _RGB;\r
-\r
-  /**\r
-   * keeps track of state for field: _RGB\r
-   */\r
-  private boolean _has_RGB;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public Residue()\r
-  {\r
-    super();\r
-  } //-- jalview.binding.Residue()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method deleteRGB\r
-   *\r
-   */\r
-  public void deleteRGB()\r
-  {\r
-    this._has_RGB = false;\r
-  } //-- void deleteRGB()\r
-\r
-  /**\r
-   * Returns the value of field 'name'.\r
-   *\r
-   * @return String\r
-   * @return the value of field 'name'.\r
-   */\r
-  public java.lang.String getName()\r
-  {\r
-    return this._name;\r
-  } //-- java.lang.String getName()\r
-\r
-  /**\r
-   * Returns the value of field 'RGB'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'RGB'.\r
-   */\r
-  public int getRGB()\r
-  {\r
-    return this._RGB;\r
-  } //-- int getRGB()\r
-\r
-  /**\r
-   * Method hasRGB\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasRGB()\r
-  {\r
-    return this._has_RGB;\r
-  } //-- boolean hasRGB()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
-    {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
-    {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Sets the value of field 'name'.\r
-   *\r
-   * @param name the value of field 'name'.\r
-   */\r
-  public void setName(java.lang.String name)\r
-  {\r
-    this._name = name;\r
-  } //-- void setName(java.lang.String)\r
-\r
-  /**\r
-   * Sets the value of field 'RGB'.\r
-   *\r
-   * @param RGB the value of field 'RGB'.\r
-   */\r
-  public void setRGB(int RGB)\r
-  {\r
-    this._RGB = RGB;\r
-    this._has_RGB = true;\r
-  } //-- void setRGB(int)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.binding.Residue) Unmarshaller.unmarshal(jalview.binding.\r
-        Residue.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
-\r
-}\r

diff --git a/src/jalview/binding/UserColour.java b/src/jalview/binding/UserColour.java
deleted file mode 100755 (executable)
index 1d27451..0000000
--- a/src/jalview/binding/UserColour.java
+++ /dev/null
@@ -1,200 +0,0 @@
-/*\r
- * This class was automatically generated with\r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package jalview.binding;\r
-\r
-//---------------------------------/\r
-//- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.xml.*;\r
-\r
-/**\r
- * Class UserColour.\r
- *\r
- * @version $Revision$ $Date$\r
- */\r
-public class UserColour\r
-    implements java.io.Serializable\r
-{\r
-\r
-  //--------------------------/\r
-  //- Class/Member Variables -/\r
-  //--------------------------/\r
-\r
-  /**\r
-   * Field _id\r
-   */\r
-  private int _id;\r
-\r
-  /**\r
-   * keeps track of state for field: _id\r
-   */\r
-  private boolean _has_id;\r
-\r
-  /**\r
-   * Field _userColourScheme\r
-   */\r
-  private jalview.binding.UserColourScheme _userColourScheme;\r
-\r
-  //----------------/\r
-  //- Constructors -/\r
-  //----------------/\r
-\r
-  public UserColour()\r
-  {\r
-    super();\r
-  } //-- jalview.binding.UserColour()\r
-\r
-  //-----------/\r
-  //- Methods -/\r
-  //-----------/\r
-\r
-  /**\r
-   * Method deleteId\r
-   *\r
-   */\r
-  public void deleteId()\r
-  {\r
-    this._has_id = false;\r
-  } //-- void deleteId()\r
-\r
-  /**\r
-   * Returns the value of field 'id'.\r
-   *\r
-   * @return int\r
-   * @return the value of field 'id'.\r
-   */\r
-  public int getId()\r
-  {\r
-    return this._id;\r
-  } //-- int getId()\r
-\r
-  /**\r
-   * Returns the value of field 'userColourScheme'.\r
-   *\r
-   * @return UserColourScheme\r
-   * @return the value of field 'userColourScheme'.\r
-   */\r
-  public jalview.binding.UserColourScheme getUserColourScheme()\r
-  {\r
-    return this._userColourScheme;\r
-  } //-- jalview.binding.UserColourScheme getUserColourScheme()\r
-\r
-  /**\r
-   * Method hasId\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean hasId()\r
-  {\r
-    return this._has_id;\r
-  } //-- boolean hasId()\r
-\r
-  /**\r
-   * Method isValid\r
-   *\r
-   *\r
-   *\r
-   * @return boolean\r
-   */\r
-  public boolean isValid()\r
-  {\r
-    try\r
-    {\r
-      validate();\r
-    }\r
-    catch (org.exolab.castor.xml.ValidationException vex)\r
-    {\r
-      return false;\r
-    }\r
-    return true;\r
-  } //-- boolean isValid()\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param out\r
-   */\r
-  public void marshal(java.io.Writer out)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, out);\r
-  } //-- void marshal(java.io.Writer)\r
-\r
-  /**\r
-   * Method marshal\r
-   *\r
-   *\r
-   *\r
-   * @param handler\r
-   */\r
-  public void marshal(org.xml.sax.ContentHandler handler)\r
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-\r
-    Marshaller.marshal(this, handler);\r
-  } //-- void marshal(org.xml.sax.ContentHandler)\r
-\r
-  /**\r
-   * Sets the value of field 'id'.\r
-   *\r
-   * @param id the value of field 'id'.\r
-   */\r
-  public void setId(int id)\r
-  {\r
-    this._id = id;\r
-    this._has_id = true;\r
-  } //-- void setId(int)\r
-\r
-  /**\r
-   * Sets the value of field 'userColourScheme'.\r
-   *\r
-   * @param userColourScheme the value of field 'userColourScheme'\r
-   */\r
-  public void setUserColourScheme(jalview.binding.UserColourScheme\r
-                                  userColourScheme)\r
-  {\r
-    this._userColourScheme = userColourScheme;\r
-  } //-- void setUserColourScheme(jalview.binding.UserColourScheme)\r
-\r
-  /**\r
-   * Method unmarshal\r
-   *\r
-   *\r
-   *\r
-   * @param reader\r
-   * @return Object\r
-   */\r
-  public static java.lang.Object unmarshal(java.io.Reader reader)\r
-      throws org.exolab.castor.xml.MarshalException,\r
-      org.exolab.castor.xml.ValidationException\r
-  {\r
-    return (jalview.binding.UserColour) Unmarshaller.unmarshal(jalview.binding.\r
-        UserColour.class, reader);\r
-  } //-- java.lang.Object unmarshal(java.io.Reader)\r
-\r
-  /**\r
-   * Method validate\r
-   *\r
-   */\r
-  public void validate()\r
-      throws org.exolab.castor.xml.ValidationException\r
-  {\r
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.\r
-        Validator();\r
-    validator.validate(this);\r
-  } //-- void validate()\r
-\r
-}\r