X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FFeature.java;h=ec2584f306816f48808c736ee9444a316f9e95c0;hb=93642d621a7f86318a7777b0a70f6113dcd299dc;hp=95d5192af981c1c620ab6dfd039795282bd8862d;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/binding/Feature.java b/src/jalview/binding/Feature.java
index 95d5192..ec2584f 100755
--- a/src/jalview/binding/Feature.java
+++ b/src/jalview/binding/Feature.java
@@ -1,305 +1,314 @@
-/*
- * 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 Feature.
- * 
- * @version $Revision$ $Date$
- */
-public class Feature implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _begin
-     */
-    private int _begin;
-
-    /**
-     * keeps track of state for field: _begin
-     */
-    private boolean _has_begin;
-
-    /**
-     * Field _end
-     */
-    private int _end;
-
-    /**
-     * keeps track of state for field: _end
-     */
-    private boolean _has_end;
-
-    /**
-     * Field _type
-     */
-    private java.lang.String _type;
-
-    /**
-     * Field _description
-     */
-    private java.lang.String _description;
-
-    /**
-     * Field _status
-     */
-    private java.lang.String _status;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Feature() {
-        super();
-    } //-- jalview.binding.Feature()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method deleteBegin
-     * 
-     */
-    public void deleteBegin()
-    {
-        this._has_begin= false;
-    } //-- void deleteBegin() 
-
-    /**
-     * Method deleteEnd
-     * 
-     */
-    public void deleteEnd()
-    {
-        this._has_end= false;
-    } //-- void deleteEnd() 
-
-    /**
-     * Returns the value of field 'begin'.
-     * 
-     * @return int
-     * @return the value of field 'begin'.
-     */
-    public int getBegin()
-    {
-        return this._begin;
-    } //-- int getBegin() 
-
-    /**
-     * 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 'end'.
-     * 
-     * @return int
-     * @return the value of field 'end'.
-     */
-    public int getEnd()
-    {
-        return this._end;
-    } //-- int getEnd() 
-
-    /**
-     * Returns the value of field 'status'.
-     * 
-     * @return String
-     * @return the value of field 'status'.
-     */
-    public java.lang.String getStatus()
-    {
-        return this._status;
-    } //-- java.lang.String getStatus() 
-
-    /**
-     * Returns the value of field 'type'.
-     * 
-     * @return String
-     * @return the value of field 'type'.
-     */
-    public java.lang.String getType()
-    {
-        return this._type;
-    } //-- java.lang.String getType() 
-
-    /**
-     * Method hasBegin
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasBegin()
-    {
-        return this._has_begin;
-    } //-- boolean hasBegin() 
-
-    /**
-     * Method hasEnd
-     * 
-     * 
-     * 
-     * @return boolean
-     */
-    public boolean hasEnd()
-    {
-        return this._has_end;
-    } //-- boolean hasEnd() 
-
-    /**
-     * 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 'begin'.
-     * 
-     * @param begin the value of field 'begin'.
-     */
-    public void setBegin(int begin)
-    {
-        this._begin = begin;
-        this._has_begin = true;
-    } //-- void setBegin(int) 
-
-    /**
-     * 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 'end'.
-     * 
-     * @param end the value of field 'end'.
-     */
-    public void setEnd(int end)
-    {
-        this._end = end;
-        this._has_end = true;
-    } //-- void setEnd(int) 
-
-    /**
-     * Sets the value of field 'status'.
-     * 
-     * @param status the value of field 'status'.
-     */
-    public void setStatus(java.lang.String status)
-    {
-        this._status = status;
-    } //-- void setStatus(java.lang.String) 
-
-    /**
-     * Sets the value of field 'type'.
-     * 
-     * @param type the value of field 'type'.
-     */
-    public void setType(java.lang.String type)
-    {
-        this._type = type;
-    } //-- void setType(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.Feature) Unmarshaller.unmarshal(jalview.binding.Feature.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() 
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * 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/>.
+ */
+package jalview.binding;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Feature.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Feature implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _begin.
+   */
+  private int _begin;
+
+  /**
+   * keeps track of state for field: _begin
+   */
+  private boolean _has_begin;
+
+  /**
+   * Field _end.
+   */
+  private int _end;
+
+  /**
+   * keeps track of state for field: _end
+   */
+  private boolean _has_end;
+
+  /**
+   * Field _type.
+   */
+  private java.lang.String _type;
+
+  /**
+   * Field _description.
+   */
+  private java.lang.String _description;
+
+  /**
+   * Field _status.
+   */
+  private java.lang.String _status;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Feature()
+  {
+    super();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+     */
+  public void deleteBegin()
+  {
+    this._has_begin = false;
+  }
+
+  /**
+     */
+  public void deleteEnd()
+  {
+    this._has_end = false;
+  }
+
+  /**
+   * Returns the value of field 'begin'.
+   * 
+   * @return the value of field 'Begin'.
+   */
+  public int getBegin()
+  {
+    return this._begin;
+  }
+
+  /**
+   * Returns the value of field 'description'.
+   * 
+   * @return the value of field 'Description'.
+   */
+  public java.lang.String getDescription()
+  {
+    return this._description;
+  }
+
+  /**
+   * Returns the value of field 'end'.
+   * 
+   * @return the value of field 'End'.
+   */
+  public int getEnd()
+  {
+    return this._end;
+  }
+
+  /**
+   * Returns the value of field 'status'.
+   * 
+   * @return the value of field 'Status'.
+   */
+  public java.lang.String getStatus()
+  {
+    return this._status;
+  }
+
+  /**
+   * Returns the value of field 'type'.
+   * 
+   * @return the value of field 'Type'.
+   */
+  public java.lang.String getType()
+  {
+    return this._type;
+  }
+
+  /**
+   * Method hasBegin.
+   * 
+   * @return true if at least one Begin has been added
+   */
+  public boolean hasBegin()
+  {
+    return this._has_begin;
+  }
+
+  /**
+   * Method hasEnd.
+   * 
+   * @return true if at least one End has been added
+   */
+  public boolean hasEnd()
+  {
+    return this._has_end;
+  }
+
+  /**
+   * 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 'begin'.
+   * 
+   * @param begin
+   *          the value of field 'begin'.
+   */
+  public void setBegin(final int begin)
+  {
+    this._begin = begin;
+    this._has_begin = true;
+  }
+
+  /**
+   * Sets the value of field 'description'.
+   * 
+   * @param description
+   *          the value of field 'description'.
+   */
+  public void setDescription(final java.lang.String description)
+  {
+    this._description = description;
+  }
+
+  /**
+   * Sets the value of field 'end'.
+   * 
+   * @param end
+   *          the value of field 'end'.
+   */
+  public void setEnd(final int end)
+  {
+    this._end = end;
+    this._has_end = true;
+  }
+
+  /**
+   * Sets the value of field 'status'.
+   * 
+   * @param status
+   *          the value of field 'status'.
+   */
+  public void setStatus(final java.lang.String status)
+  {
+    this._status = status;
+  }
+
+  /**
+   * Sets the value of field 'type'.
+   * 
+   * @param type
+   *          the value of field 'type'.
+   */
+  public void setType(final java.lang.String type)
+  {
+    this._type = type;
+  }
+
+  /**
+   * 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.Feature
+   */
+  public static jalview.binding.Feature unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Feature) Unmarshaller.unmarshal(
+            jalview.binding.Feature.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);
+  }
+
+}