X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FFeatureSettings.java;h=ec7001d9b458981fdbd727e229581d69e15073cb;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=b6c3640b3e00c2150a51f1d97e86daffee3d1c51;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/binding/FeatureSettings.java b/src/jalview/binding/FeatureSettings.java
old mode 100755
new mode 100644
index b6c3640..ec7001d
--- a/src/jalview/binding/FeatureSettings.java
+++ b/src/jalview/binding/FeatureSettings.java
@@ -1,26 +1,32 @@
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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/>.
+ *******************************************************************************/
 /*
- * 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
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
  */
+
 package jalview.binding;
 
-// ---------------------------------/
-// - Imported classes and packages -/
-// ---------------------------------/
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -30,275 +36,257 @@ 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 -/
-  // --------------------------/
 
-  /**
-   * Field _settingList.
-   */
-  private java.util.Vector _settingList;
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
 
-  // ----------------/
-  // - Constructors -/
-  // ----------------/
+    /**
+     * Field _settingList.
+     */
+    private java.util.Vector _settingList;
 
-  public FeatureSettings()
-  {
-    super();
-    this._settingList = new java.util.Vector();
-  }
 
-  // -----------/
-  // - Methods -/
-  // -----------/
+      //----------------/
+     //- Constructors -/
+    //----------------/
 
-  /**
-   * 
-   * 
-   * @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);
-  }
+    public FeatureSettings() {
+        super();
+        this._settingList = new java.util.Vector();
+    }
 
-  /**
-   * 
-   * 
-   * @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);
-  }
 
-  /**
-   * Method enumerateSetting.
-   * 
-   * @return an Enumeration over all jalview.binding.Setting elements
-   */
-  public java.util.Enumeration enumerateSetting()
-  {
-    return this._settingList.elements();
-  }
+      //-----------/
+     //- Methods -/
+    //-----------/
 
-  /**
-   * 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 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);
     }
 
-    return (jalview.binding.Setting) _settingList.get(index);
-  }
+    /**
+     * 
+     * 
+     * @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);
+    }
 
-  /**
-   * 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 enumerateSetting.
+     * 
+     * @return an Enumeration over all jalview.binding.Setting
+     * elements
+     */
+    public java.util.Enumeration enumerateSetting(
+    ) {
+        return this._settingList.elements();
+    }
 
-  /**
-   * Method getSettingCount.
-   * 
-   * @return the size of this collection
-   */
-  public int getSettingCount()
-  {
-    return this._settingList.size();
-  }
+    /**
+     * 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 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;
+    /**
+     * 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);
     }
-    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);
-  }
+    /**
+     * Method getSettingCount.
+     * 
+     * @return the size of this collection
+     */
+    public int getSettingCount(
+    ) {
+        return this._settingList.size();
+    }
 
-  /**
-   * 
-   * 
-   * @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 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;
+    }
 
-  /**
-   */
-  public void removeAllSetting()
-  {
-    this._settingList.clear();
-  }
+    /**
+     * 
+     * 
+     * @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 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 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 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;
-  }
+    /**
+     */
+    public void removeAllSetting(
+    ) {
+        this._settingList.clear();
+    }
 
-  /**
-   * 
-   * 
-   * @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 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;
     }
 
-    this._settingList.set(index, vSetting);
-  }
+    /**
+     * 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;
+    }
 
-  /**
-   * 
-   * 
-   * @param vSettingArray
-   */
-  public void setSetting(final jalview.binding.Setting[] vSettingArray)
-  {
-    // -- copy array
-    _settingList.clear();
+    /**
+     * 
+     * 
+     * @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);
+    }
 
-    for (int i = 0; i < vSettingArray.length; i++)
-    {
-      this._settingList.add(vSettingArray[i]);
+    /**
+     * 
+     * 
+     * @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]);
+        }
     }
-  }
 
-  /**
-   * 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);
+    }
 
 }