X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FPdbentry.java;h=3aa6ad69afb5645dc73543ff033984607babe80e;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=cac4cf611063a322fcdbceaae29bdfc0eb6f7942;hpb=a95b88b05400d7e841f9523d4c4228c678307654;p=jalview.git

diff --git a/src/jalview/binding/Pdbentry.java b/src/jalview/binding/Pdbentry.java
old mode 100755
new mode 100644
index cac4cf6..3aa6ad6
--- a/src/jalview/binding/Pdbentry.java
+++ b/src/jalview/binding/Pdbentry.java
@@ -1,14 +1,25 @@
 /*
- * 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 2.8.0b1)
+ * 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.binding;
 
-  //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,308 +30,326 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Pdbentry implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _id.
-     */
-    private java.lang.String _id;
-
-    /**
-     * Field _type.
-     */
-    private java.lang.String _type;
-
-    /**
-     * Field _items.
-     */
-    private java.util.Vector _items;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public Pdbentry() {
-        super();
-        this._items = new java.util.Vector();
-    }
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * 
-     * 
-     * @param vPdbentryItem
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPdbentryItem(
-            final jalview.binding.PdbentryItem vPdbentryItem)
-    throws java.lang.IndexOutOfBoundsException {
-        this._items.addElement(vPdbentryItem);
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPdbentryItem
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void addPdbentryItem(
-            final int index,
-            final jalview.binding.PdbentryItem vPdbentryItem)
-    throws java.lang.IndexOutOfBoundsException {
-        this._items.add(index, vPdbentryItem);
-    }
-
-    /**
-     * Method enumeratePdbentryItem.
-     * 
-     * @return an Enumeration over all jalview.binding.PdbentryItem
-     * elements
-     */
-    public java.util.Enumeration enumeratePdbentryItem(
-    ) {
-        return this._items.elements();
-    }
-
-    /**
-     * Returns the value of field 'id'.
-     * 
-     * @return the value of field 'Id'.
-     */
-    public java.lang.String getId(
-    ) {
-        return this._id;
-    }
-
-    /**
-     * Method getPdbentryItem.
-     * 
-     * @param index
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     * @return the value of the jalview.binding.PdbentryItem at the
-     * given index
-     */
-    public jalview.binding.PdbentryItem getPdbentryItem(
-            final int index)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._items.size()) {
-            throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
-        }
-        
-        return (jalview.binding.PdbentryItem) _items.get(index);
-    }
-
-    /**
-     * Method getPdbentryItem.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.PdbentryItem[] getPdbentryItem(
-    ) {
-        jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0];
-        return (jalview.binding.PdbentryItem[]) this._items.toArray(array);
+public class Pdbentry implements java.io.Serializable
+{
+
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _id.
+   */
+  private java.lang.String _id;
+
+  /**
+   * Field _type.
+   */
+  private java.lang.String _type;
+
+  /**
+   * Field _items.
+   */
+  private java.util.Vector _items;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
+
+  public Pdbentry()
+  {
+    super();
+    this._items = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vPdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addPdbentryItem(
+          final jalview.binding.PdbentryItem vPdbentryItem)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._items.addElement(vPdbentryItem);
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void addPdbentryItem(final int index,
+          final jalview.binding.PdbentryItem vPdbentryItem)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._items.add(index, vPdbentryItem);
+  }
+
+  /**
+   * Method enumeratePdbentryItem.
+   * 
+   * @return an Enumeration over all jalview.binding.PdbentryItem elements
+   */
+  public java.util.Enumeration enumeratePdbentryItem()
+  {
+    return this._items.elements();
+  }
+
+  /**
+   * Returns the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
+   */
+  public java.lang.String getId()
+  {
+    return this._id;
+  }
+
+  /**
+   * Method getPdbentryItem.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.binding.PdbentryItem at the given index
+   */
+  public jalview.binding.PdbentryItem getPdbentryItem(final int index)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._items.size())
+    {
+      throw new IndexOutOfBoundsException("getPdbentryItem: Index value '"
+              + index + "' not in range [0.." + (this._items.size() - 1)
+              + "]");
     }
 
-    /**
-     * Method getPdbentryItemCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getPdbentryItemCount(
-    ) {
-        return this._items.size();
-    }
-
-    /**
-     * Returns the value of field 'type'.
-     * 
-     * @return the value of field 'Type'.
-     */
-    public java.lang.String getType(
-    ) {
-        return this._type;
-    }
-
-    /**
-     * 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);
-    }
-
-    /**
-     */
-    public void removeAllPdbentryItem(
-    ) {
-        this._items.clear();
-    }
-
-    /**
-     * Method removePdbentryItem.
-     * 
-     * @param vPdbentryItem
-     * @return true if the object was removed from the collection.
-     */
-    public boolean removePdbentryItem(
-            final jalview.binding.PdbentryItem vPdbentryItem) {
-        boolean removed = _items.remove(vPdbentryItem);
-        return removed;
-    }
-
-    /**
-     * Method removePdbentryItemAt.
-     * 
-     * @param index
-     * @return the element removed from the collection
-     */
-    public jalview.binding.PdbentryItem removePdbentryItemAt(
-            final int index) {
-        java.lang.Object obj = this._items.remove(index);
-        return (jalview.binding.PdbentryItem) obj;
-    }
-
-    /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(
-            final java.lang.String id) {
-        this._id = id;
-    }
-
-    /**
-     * 
-     * 
-     * @param index
-     * @param vPdbentryItem
-     * @throws java.lang.IndexOutOfBoundsException if the index
-     * given is outside the bounds of the collection
-     */
-    public void setPdbentryItem(
-            final int index,
-            final jalview.binding.PdbentryItem vPdbentryItem)
-    throws java.lang.IndexOutOfBoundsException {
-        // check bounds for index
-        if (index < 0 || index >= this._items.size()) {
-            throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
-        }
-        
-        this._items.set(index, vPdbentryItem);
+    return (jalview.binding.PdbentryItem) _items.get(index);
+  }
+
+  /**
+   * Method getPdbentryItem.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.PdbentryItem[] getPdbentryItem()
+  {
+    jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0];
+    return (jalview.binding.PdbentryItem[]) this._items.toArray(array);
+  }
+
+  /**
+   * Method getPdbentryItemCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getPdbentryItemCount()
+  {
+    return this._items.size();
+  }
+
+  /**
+   * Returns the value of field 'type'.
+   * 
+   * @return the value of field 'Type'.
+   */
+  public java.lang.String getType()
+  {
+    return this._type;
+  }
+
+  /**
+   * 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;
     }
-
-    /**
-     * 
-     * 
-     * @param vPdbentryItemArray
-     */
-    public void setPdbentryItem(
-            final jalview.binding.PdbentryItem[] vPdbentryItemArray) {
-        //-- copy array
-        _items.clear();
-        
-        for (int i = 0; i < vPdbentryItemArray.length; i++) {
-                this._items.add(vPdbentryItemArray[i]);
-        }
-    }
-
-    /**
-     * Sets the value of field 'type'.
-     * 
-     * @param type the value of field 'type'.
+    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);
+  }
+
+  /**
      */
-    public void setType(
-            final java.lang.String type) {
-        this._type = type;
+  public void removeAllPdbentryItem()
+  {
+    this._items.clear();
+  }
+
+  /**
+   * Method removePdbentryItem.
+   * 
+   * @param vPdbentryItem
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removePdbentryItem(
+          final jalview.binding.PdbentryItem vPdbentryItem)
+  {
+    boolean removed = _items.remove(vPdbentryItem);
+    return removed;
+  }
+
+  /**
+   * Method removePdbentryItemAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.binding.PdbentryItem removePdbentryItemAt(final int index)
+  {
+    java.lang.Object obj = this._items.remove(index);
+    return (jalview.binding.PdbentryItem) obj;
+  }
+
+  /**
+   * Sets the value of field 'id'.
+   * 
+   * @param id
+   *          the value of field 'id'.
+   */
+  public void setId(final java.lang.String id)
+  {
+    this._id = id;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vPdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   */
+  public void setPdbentryItem(final int index,
+          final jalview.binding.PdbentryItem vPdbentryItem)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._items.size())
+    {
+      throw new IndexOutOfBoundsException("setPdbentryItem: Index value '"
+              + index + "' not in range [0.." + (this._items.size() - 1)
+              + "]");
     }
 
-    /**
-     * 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.Pdbentry
-     */
-    public static jalview.binding.Pdbentry unmarshal(
-            final java.io.Reader reader)
-    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
-        return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(jalview.binding.Pdbentry.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);
+    this._items.set(index, vPdbentryItem);
+  }
+
+  /**
+   * 
+   * 
+   * @param vPdbentryItemArray
+   */
+  public void setPdbentryItem(
+          final jalview.binding.PdbentryItem[] vPdbentryItemArray)
+  {
+    // -- copy array
+    _items.clear();
+
+    for (int i = 0; i < vPdbentryItemArray.length; i++)
+    {
+      this._items.add(vPdbentryItemArray[i]);
     }
+  }
+
+  /**
+   * 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.Pdbentry
+   */
+  public static jalview.binding.Pdbentry unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
+  {
+    return (jalview.binding.Pdbentry) Unmarshaller.unmarshal(
+            jalview.binding.Pdbentry.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);
+  }
 
 }