X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FPdbentry.java;h=6721c5b1455212ddec0ef1ea47cc8d75d42ae68e;hb=6b71746c98f7c1118b474b0b920db3bd7b2a15c0;hp=f4fa4fe44e63614cb1ee67040860505e18fe8011;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/Pdbentry.java b/src/jalview/schemabinding/version2/Pdbentry.java
index f4fa4fe..6721c5b 100755
--- a/src/jalview/schemabinding/version2/Pdbentry.java
+++ b/src/jalview/schemabinding/version2/Pdbentry.java
@@ -1,364 +1,385 @@
 /*
- * This class was automatically generated with
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * 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.schemabinding.version2;
 
 //---------------------------------/
 //- Imported classes and packages -/
 //---------------------------------/
 
-import java.util.*;
-
-import org.exolab.castor.xml.*;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
 
 /**
  * Class Pdbentry.
- *
+ * 
  * @version $Revision$ $Date$
  */
-public class Pdbentry
-    implements java.io.Serializable
+public class Pdbentry implements java.io.Serializable
 {
 
-  //--------------------------/
-  //- Class/Member Variables -/
-  //--------------------------/
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
   /**
-   * Field _id
+   * Field _id.
    */
   private java.lang.String _id;
 
   /**
-   * Field _type
+   * Field _type.
    */
   private java.lang.String _type;
 
   /**
-   * Field _file
+   * Field _file.
    */
   private java.lang.String _file;
 
   /**
-   * Field _items
+   * Field _items.
    */
   private java.util.Vector _items;
 
-  //----------------/
-  //- Constructors -/
-  //----------------/
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
   public Pdbentry()
   {
     super();
-    _items = new Vector();
-  } //-- jalview.schemabinding.version2.Pdbentry()
+    this._items = new java.util.Vector();
+  }
 
-  //-----------/
-  //- Methods -/
-  //-----------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
   /**
-   * Method addPdbentryItem
-   *
-   *
-   *
+   * 
+   * 
    * @param vPdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
    */
-  public void addPdbentryItem(jalview.schemabinding.version2.PdbentryItem
-                              vPdbentryItem)
-      throws java.lang.IndexOutOfBoundsException
+  public void addPdbentryItem(
+          final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _items.addElement(vPdbentryItem);
-  } //-- void addPdbentryItem(jalview.schemabinding.version2.PdbentryItem)
+    this._items.addElement(vPdbentryItem);
+  }
 
   /**
-   * Method addPdbentryItem
-   *
-   *
-   *
+   * 
+   * 
    * @param index
    * @param vPdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
    */
-  public void addPdbentryItem(int index,
-                              jalview.schemabinding.version2.PdbentryItem
-                              vPdbentryItem)
-      throws java.lang.IndexOutOfBoundsException
+  public void addPdbentryItem(final int index,
+          final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+          throws java.lang.IndexOutOfBoundsException
   {
-    _items.insertElementAt(vPdbentryItem, index);
-  } //-- void addPdbentryItem(int, jalview.schemabinding.version2.PdbentryItem)
+    this._items.add(index, vPdbentryItem);
+  }
 
   /**
-   * Method enumeratePdbentryItem
-   *
-   *
-   *
-   * @return Enumeration
+   * Method enumeratePdbentryItem.
+   * 
+   * @return an Enumeration over all jalview.schemabinding.version2.PdbentryItem
+   *         elements
    */
   public java.util.Enumeration enumeratePdbentryItem()
   {
-    return _items.elements();
-  } //-- java.util.Enumeration enumeratePdbentryItem()
+    return this._items.elements();
+  }
 
   /**
    * Returns the value of field 'file'.
-   *
-   * @return String
-   * @return the value of field 'file'.
+   * 
+   * @return the value of field 'File'.
    */
   public java.lang.String getFile()
   {
     return this._file;
-  } //-- java.lang.String getFile()
+  }
 
   /**
    * Returns the value of field 'id'.
-   *
-   * @return String
-   * @return the value of field 'id'.
+   * 
+   * @return the value of field 'Id'.
    */
   public java.lang.String getId()
   {
     return this._id;
-  } //-- java.lang.String getId()
+  }
 
   /**
-   * Method getPdbentryItem
-   *
-   *
-   *
+   * Method getPdbentryItem.
+   * 
    * @param index
-   * @return PdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.PdbentryItem at the
+   *         given inde
    */
-  public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(int index)
-      throws java.lang.IndexOutOfBoundsException
+  public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(
+          final int index) throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _items.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._items.size())
     {
-      throw new IndexOutOfBoundsException();
+      throw new IndexOutOfBoundsException("getPdbentryItem: Index value '"
+              + index + "' not in range [0.." + (this._items.size() - 1)
+              + "]");
     }
 
-    return (jalview.schemabinding.version2.PdbentryItem) _items.elementAt(index);
-  } //-- jalview.schemabinding.version2.PdbentryItem getPdbentryItem(int)
+    return (jalview.schemabinding.version2.PdbentryItem) _items.get(index);
+  }
 
   /**
-   * Method getPdbentryItem
-   *
-   *
-   *
-   * @return PdbentryItem
+   * 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.schemabinding.version2.PdbentryItem[] getPdbentryItem()
   {
-    int size = _items.size();
-    jalview.schemabinding.version2.PdbentryItem[] mArray = new jalview.
-        schemabinding.version2.PdbentryItem[size];
-    for (int index = 0; index < size; index++)
-    {
-      mArray[index] = (jalview.schemabinding.version2.PdbentryItem) _items.
-          elementAt(index);
-    }
-    return mArray;
-  } //-- jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem()
+    jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0];
+    return (jalview.schemabinding.version2.PdbentryItem[]) this._items
+            .toArray(array);
+  }
 
   /**
-   * Method getPdbentryItemCount
-   *
-   *
-   *
-   * @return int
+   * Method getPdbentryItemCount.
+   * 
+   * @return the size of this collection
    */
   public int getPdbentryItemCount()
   {
-    return _items.size();
-  } //-- int getPdbentryItemCount()
+    return this._items.size();
+  }
 
   /**
    * Returns the value of field 'type'.
-   *
-   * @return String
-   * @return the value of field 'type'.
+   * 
+   * @return the value of field 'Type'.
    */
   public java.lang.String getType()
   {
     return this._type;
-  } //-- java.lang.String getType()
+  }
 
   /**
-   * Method isValid
-   *
-   *
-   *
-   * @return boolean
+   * 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)
+    } catch (org.exolab.castor.xml.ValidationException vex)
     {
       return false;
     }
     return true;
-  } //-- boolean isValid()
+  }
 
   /**
-   * Method marshal
-   *
-   *
-   *
+   * 
+   * 
    * @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(java.io.Writer out)
-      throws org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
+  public void marshal(final 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
+   * @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(org.xml.sax.ContentHandler handler)
-      throws java.io.IOException, org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
+  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);
-  } //-- void marshal(org.xml.sax.ContentHandler)
+  }
 
   /**
-   * Method removeAllPdbentryItem
-   *
-   */
+     */
   public void removeAllPdbentryItem()
   {
-    _items.removeAllElements();
-  } //-- void removeAllPdbentryItem()
+    this._items.clear();
+  }
 
   /**
-   * Method removePdbentryItem
-   *
-   *
-   *
+   * Method removePdbentryItem.
+   * 
+   * @param vPdbentryItem
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removePdbentryItem(
+          final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+  {
+    boolean removed = _items.remove(vPdbentryItem);
+    return removed;
+  }
+
+  /**
+   * Method removePdbentryItemAt.
+   * 
    * @param index
-   * @return PdbentryItem
+   * @return the element removed from the collection
    */
-  public jalview.schemabinding.version2.PdbentryItem removePdbentryItem(int
-      index)
+  public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt(
+          final int index)
   {
-    java.lang.Object obj = _items.elementAt(index);
-    _items.removeElementAt(index);
+    java.lang.Object obj = this._items.remove(index);
     return (jalview.schemabinding.version2.PdbentryItem) obj;
-  } //-- jalview.schemabinding.version2.PdbentryItem removePdbentryItem(int)
+  }
 
   /**
    * Sets the value of field 'file'.
-   *
-   * @param file the value of field 'file'.
+   * 
+   * @param file
+   *          the value of field 'file'.
    */
-  public void setFile(java.lang.String file)
+  public void setFile(final java.lang.String file)
   {
     this._file = file;
-  } //-- void setFile(java.lang.String)
+  }
 
   /**
    * Sets the value of field 'id'.
-   *
-   * @param id the value of field 'id'.
+   * 
+   * @param id
+   *          the value of field 'id'.
    */
-  public void setId(java.lang.String id)
+  public void setId(final java.lang.String id)
   {
     this._id = id;
-  } //-- void setId(java.lang.String)
+  }
 
   /**
-   * Method setPdbentryItem
-   *
-   *
-   *
+   * 
+   * 
    * @param index
    * @param vPdbentryItem
+   * @throws java.lang.IndexOutOfBoundsException
+   *           if the index given is outside the bounds of the collection
    */
-  public void setPdbentryItem(int index,
-                              jalview.schemabinding.version2.PdbentryItem
-                              vPdbentryItem)
-      throws java.lang.IndexOutOfBoundsException
+  public void setPdbentryItem(final int index,
+          final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+          throws java.lang.IndexOutOfBoundsException
   {
-    //-- check bounds for index
-    if ( (index < 0) || (index > _items.size()))
+    // check bounds for index
+    if (index < 0 || index >= this._items.size())
     {
-      throw new IndexOutOfBoundsException();
+      throw new IndexOutOfBoundsException("setPdbentryItem: Index value '"
+              + index + "' not in range [0.." + (this._items.size() - 1)
+              + "]");
     }
-    _items.setElementAt(vPdbentryItem, index);
-  } //-- void setPdbentryItem(int, jalview.schemabinding.version2.PdbentryItem)
+
+    this._items.set(index, vPdbentryItem);
+  }
 
   /**
-   * Method setPdbentryItem
-   *
-   *
-   *
-   * @param pdbentryItemArray
+   * 
+   * 
+   * @param vPdbentryItemArray
    */
-  public void setPdbentryItem(jalview.schemabinding.version2.PdbentryItem[]
-                              pdbentryItemArray)
+  public void setPdbentryItem(
+          final jalview.schemabinding.version2.PdbentryItem[] vPdbentryItemArray)
   {
-    //-- copy array
-    _items.removeAllElements();
-    for (int i = 0; i < pdbentryItemArray.length; i++)
+    // -- copy array
+    _items.clear();
+
+    for (int i = 0; i < vPdbentryItemArray.length; i++)
     {
-      _items.addElement(pdbentryItemArray[i]);
+      this._items.add(vPdbentryItemArray[i]);
     }
-  } //-- void setPdbentryItem(jalview.schemabinding.version2.PdbentryItem)
+  }
 
   /**
    * Sets the value of field 'type'.
-   *
-   * @param type the value of field 'type'.
+   * 
+   * @param type
+   *          the value of field 'type'.
    */
-  public void setType(java.lang.String type)
+  public void setType(final java.lang.String type)
   {
     this._type = type;
-  } //-- void setType(java.lang.String)
+  }
 
   /**
-   * Method unmarshal
-   *
-   *
-   *
+   * Method unmarshal.
+   * 
    * @param reader
-   * @return Object
+   * @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.schemabinding.version2.Pdbentry
    */
-  public static java.lang.Object unmarshal(java.io.Reader reader)
-      throws org.exolab.castor.xml.MarshalException,
-      org.exolab.castor.xml.ValidationException
+  public static jalview.schemabinding.version2.Pdbentry unmarshal(
+          final java.io.Reader reader)
+          throws org.exolab.castor.xml.MarshalException,
+          org.exolab.castor.xml.ValidationException
   {
-    return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(
-        jalview.schemabinding.version2.Pdbentry.class, reader);
-  } //-- java.lang.Object unmarshal(java.io.Reader)
+    return (jalview.schemabinding.version2.Pdbentry) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Pdbentry.class,
+                    reader);
+  }
 
   /**
-   * Method validate
-   *
+   * 
+   * 
+   * @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
+  public void validate() throws org.exolab.castor.xml.ValidationException
   {
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.
-        Validator();
+    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
     validator.validate(this);
-  } //-- void validate()
+  }
 
 }