X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FFeatureSettings.java;h=b6c3640b3e00c2150a51f1d97e86daffee3d1c51;hp=f3d06be3707d568f0205113a335cac98d48e593b;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hpb=60f2d6c034560415fd0139c8bc7df0c19cae1186

diff --git a/src/jalview/binding/FeatureSettings.java b/src/jalview/binding/FeatureSettings.java
index f3d06be..b6c3640 100755
--- a/src/jalview/binding/FeatureSettings.java
+++ b/src/jalview/binding/FeatureSettings.java
@@ -1,15 +1,26 @@
 /*
- * 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 2.4)
+ * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 
+ * This program 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 2
+ * of the License, or (at your option) any later version.
+ * 
+ * This program 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 this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
  */
-
 package jalview.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,257 +30,275 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class FeatureSettings implements java.io.Serializable {
+public class FeatureSettings implements java.io.Serializable
+{
 
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
+  /**
+   * Field _settingList.
+   */
+  private java.util.Vector _settingList;
 
-    /**
-     * Field _settingList.
-     */
-    private java.util.Vector _settingList;
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
+  public FeatureSettings()
+  {
+    super();
+    this._settingList = new java.util.Vector();
+  }
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    public FeatureSettings() {
-        super();
-        this._settingList = new java.util.Vector();
-    }
+  /**
+   * 
+   * 
+   * @param vSetting
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSetting(final jalview.binding.Setting vSetting)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._settingList.addElement(vSetting);
+  }
 
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSetting
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addSetting(final int index,
+          final jalview.binding.Setting vSetting)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._settingList.add(index, vSetting);
+  }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Method enumerateSetting.
+   * 
+   * @return an Enumeration over all jalview.binding.Setting elements
+   */
+  public java.util.Enumeration enumerateSetting()
+  {
+    return this._settingList.elements();
+  }
 
-    /**
-     * 
-     * 
-     * @param vSetting
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSetting(
-            final jalview.binding.Setting vSetting)
-    throws java.lang.IndexOutOfBoundsException {
-        this._settingList.addElement(vSetting);
+  /**
+   * Method getSetting.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.Setting at the given index
+   */
+  public jalview.binding.Setting getSetting(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._settingList.size())
+    {
+      throw new IndexOutOfBoundsException("getSetting: Index value '"
+              + index + "' not in range [0.."
+              + (this._settingList.size() - 1) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSetting
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addSetting(
-            final int index,
-            final jalview.binding.Setting vSetting)
-    throws java.lang.IndexOutOfBoundsException {
-        this._settingList.add(index, vSetting);
-    }
+    return (jalview.binding.Setting) _settingList.get(index);
+  }
 
-    /**
-     * Method enumerateSetting.
-     * 
-     * @return an Enumeration over all jalview.binding.Setting
-     * elements
-     */
-    public java.util.Enumeration enumerateSetting(
-    ) {
-        return this._settingList.elements();
-    }
+  /**
+   * Method getSetting.Returns the contents of the collection in an Array.
+   * <p>
+   * Note: Just in case the collection contents are changing in another thread,
+   * we pass a 0-length Array of the correct type into the API call. This way we
+   * <i>know</i> that the Array returned is of exactly the correct length.
+   * 
+   * @return this collection as an Array
+   */
+  public jalview.binding.Setting[] getSetting()
+  {
+    jalview.binding.Setting[] array = new jalview.binding.Setting[0];
+    return (jalview.binding.Setting[]) this._settingList.toArray(array);
+  }
 
-    /**
-     * Method getSetting.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.Setting at the
-     * given index
-     */
-    public jalview.binding.Setting getSetting(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._settingList.size()) {
-            throw new IndexOutOfBoundsException("getSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.Setting) _settingList.get(index);
-    }
+  /**
+   * Method getSettingCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getSettingCount()
+  {
+    return this._settingList.size();
+  }
 
-    /**
-     * Method getSetting.Returns the contents of the collection in
-     * an Array.  <p>Note:  Just in case the collection contents
-     * are changing in another thread, we pass a 0-length Array of
-     * the correct type into the API call.  This way we <i>know</i>
-     * that the Array returned is of exactly the correct length.
-     * 
-     * @return this collection as an Array
-     */
-    public jalview.binding.Setting[] getSetting(
-    ) {
-        jalview.binding.Setting[] array = new jalview.binding.Setting[0];
-        return (jalview.binding.Setting[]) this._settingList.toArray(array);
+  /**
+   * 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;
+  }
 
-    /**
-     * Method getSettingCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getSettingCount(
-    ) {
-        return this._settingList.size();
-    }
+  /**
+   * 
+   * 
+   * @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);
+  }
 
-    /**
-     * 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 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);
+  }
 
-    /**
-     * 
-     * 
-     * @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);
-    }
+  /**
+   */
+  public void removeAllSetting()
+  {
+    this._settingList.clear();
+  }
 
-    /**
-     * 
-     * 
-     * @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);
-    }
+  /**
+   * Method removeSetting.
+   * 
+   * @param vSetting
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeSetting(final jalview.binding.Setting vSetting)
+  {
+    boolean removed = _settingList.remove(vSetting);
+    return removed;
+  }
 
-    /**
-     */
-    public void removeAllSetting(
-    ) {
-        this._settingList.clear();
-    }
+  /**
+   * Method removeSettingAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.Setting removeSettingAt(final int index)
+  {
+    java.lang.Object obj = this._settingList.remove(index);
+    return (jalview.binding.Setting) obj;
+  }
 
-    /**
-     * Method removeSetting.
-     * 
-     * @param vSetting
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removeSetting(
-            final jalview.binding.Setting vSetting) {
-        boolean removed = _settingList.remove(vSetting);
-        return removed;
+  /**
+   * 
+   * 
+   * @param index
+   * @param vSetting
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setSetting(final int index,
+          final jalview.binding.Setting vSetting)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._settingList.size())
+    {
+      throw new IndexOutOfBoundsException("setSetting: Index value '"
+              + index + "' not in range [0.."
+              + (this._settingList.size() - 1) + "]");
     }
 
-    /**
-     * Method removeSettingAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.Setting removeSettingAt(
-            final int index) {
-        java.lang.Object obj = this._settingList.remove(index);
-        return (jalview.binding.Setting) obj;
-    }
+    this._settingList.set(index, vSetting);
+  }
 
-    /**
-     * 
-     * 
-     * @param index
-     * @param vSetting
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setSetting(
-            final int index,
-            final jalview.binding.Setting vSetting)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._settingList.size()) {
-            throw new IndexOutOfBoundsException("setSetting: Index value '" + index + "' not in range [0.." + (this._settingList.size() - 1) + "]");
-        }
-        
-        this._settingList.set(index, vSetting);
-    }
+  /**
+   * 
+   * 
+   * @param vSettingArray
+   */
+  public void setSetting(final jalview.binding.Setting[] vSettingArray)
+  {
+    // -- copy array
+    _settingList.clear();
 
-    /**
-     * 
-     * 
-     * @param vSettingArray
-     */
-    public void setSetting(
-            final jalview.binding.Setting[] vSettingArray) {
-        //-- copy array
-        _settingList.clear();
-        
-        for (int i = 0; i < vSettingArray.length; i++) {
-                this._settingList.add(vSettingArray[i]);
-        }
+    for (int i = 0; i < vSettingArray.length; i++)
+    {
+      this._settingList.add(vSettingArray[i]);
     }
+  }
 
-    /**
-     * 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.FeatureSettings
-     */
-    public static jalview.binding.FeatureSettings unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(jalview.binding.FeatureSettings.class, reader);
-    }
+  /**
+   * 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.FeatureSettings
+   */
+  public static jalview.binding.FeatureSettings unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.FeatureSettings) Unmarshaller.unmarshal(
+            jalview.binding.FeatureSettings.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);
-    }
+  /**
+   * 
+   * 
+   * @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);
+  }
 
 }