X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FPdbids.java;h=d0556c047ddde939356412171775a5277d0012a7;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=8625b88a5d1bcdbc7c496343c5c5ddeacca0c7d9;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/Pdbids.java b/src/jalview/schemabinding/version2/Pdbids.java
index 8625b88..d0556c0 100755
--- a/src/jalview/schemabinding/version2/Pdbids.java
+++ b/src/jalview/schemabinding/version2/Pdbids.java
@@ -1,116 +1,318 @@
 /*
- * 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 2.4)
+ * 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.schemabinding.version2;
 
-//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
-import org.exolab.castor.xml.*;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
 
 /**
  * Class Pdbids.
- *
+ * 
  * @version $Revision$ $Date$
  */
-public class Pdbids
-    extends Pdbentry implements java.io.Serializable
+public class Pdbids extends jalview.schemabinding.version2.Pdbentry
+        implements java.io.Serializable
 {
 
-  //----------------/
-  //- Constructors -/
-  //----------------/
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
+
+  /**
+   * Field _structureStateList.
+   */
+  private java.util.Vector _structureStateList;
+
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
   public Pdbids()
   {
     super();
-  } //-- jalview.schemabinding.version2.Pdbids()
+    this._structureStateList = new java.util.Vector();
+  }
+
+  // -----------/
+  // - Methods -/
+  // -----------/
+
+  /**
+   * 
+   * 
+   * @param vStructureState
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addStructureState(
+          final jalview.schemabinding.version2.StructureState vStructureState)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._structureStateList.addElement(vStructureState);
+  }
 
-  //-----------/
-  //- Methods -/
-  //-----------/
+  /**
+   * 
+   * 
+   * @param index
+   * @param vStructureState
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void addStructureState(
+          final int index,
+          final jalview.schemabinding.version2.StructureState vStructureState)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    this._structureStateList.add(index, vStructureState);
+  }
 
   /**
-   * Method isValid
-   *
-   *
-   *
-   * @return boolean
+   * Method enumerateStructureState.
+   * 
+   * @return an Enumeration over all
+   *         jalview.schemabinding.version2.StructureState elements
+   */
+  public java.util.Enumeration enumerateStructureState()
+  {
+    return this._structureStateList.elements();
+  }
+
+  /**
+   * Method getStructureState.
+   * 
+   * @param index
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   * @return the value of the jalview.schemabinding.version2.StructureState at
+   *         the given index
+   */
+  public jalview.schemabinding.version2.StructureState getStructureState(
+          final int index) throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._structureStateList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "getStructureState: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._structureStateList.size() - 1) + "]");
+    }
+
+    return (jalview.schemabinding.version2.StructureState) _structureStateList
+            .get(index);
+  }
+
+  /**
+   * Method getStructureState.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.StructureState[] getStructureState()
+  {
+    jalview.schemabinding.version2.StructureState[] array = new jalview.schemabinding.version2.StructureState[0];
+    return (jalview.schemabinding.version2.StructureState[]) this._structureStateList
+            .toArray(array);
+  }
+
+  /**
+   * Method getStructureStateCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getStructureStateCount()
+  {
+    return this._structureStateList.size();
+  }
+
+  /**
+   * 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)
+  }
+
+  /**
+   */
+  public void removeAllStructureState()
+  {
+    this._structureStateList.clear();
+  }
+
+  /**
+   * Method removeStructureState.
+   * 
+   * @param vStructureState
+   * @return true if the object was removed from the collection.
+   */
+  public boolean removeStructureState(
+          final jalview.schemabinding.version2.StructureState vStructureState)
+  {
+    boolean removed = _structureStateList.remove(vStructureState);
+    return removed;
+  }
+
+  /**
+   * Method removeStructureStateAt.
+   * 
+   * @param index
+   * @return the element removed from the collection
+   */
+  public jalview.schemabinding.version2.StructureState removeStructureStateAt(
+          final int index)
+  {
+    java.lang.Object obj = this._structureStateList.remove(index);
+    return (jalview.schemabinding.version2.StructureState) obj;
+  }
+
+  /**
+   * 
+   * 
+   * @param index
+   * @param vStructureState
+   * @throws java.lang.IndexOutOfBoundsException
+   *                 if the index given is outside the bounds of the collection
+   */
+  public void setStructureState(
+          final int index,
+          final jalview.schemabinding.version2.StructureState vStructureState)
+          throws java.lang.IndexOutOfBoundsException
+  {
+    // check bounds for index
+    if (index < 0 || index >= this._structureStateList.size())
+    {
+      throw new IndexOutOfBoundsException(
+              "setStructureState: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._structureStateList.size() - 1) + "]");
+    }
+
+    this._structureStateList.set(index, vStructureState);
+  }
+
+  /**
+   * 
+   * 
+   * @param vStructureStateArray
+   */
+  public void setStructureState(
+          final jalview.schemabinding.version2.StructureState[] vStructureStateArray)
+  {
+    // -- copy array
+    _structureStateList.clear();
+
+    for (int i = 0; i < vStructureStateArray.length; i++)
+    {
+      this._structureStateList.add(vStructureStateArray[i]);
+    }
+  }
 
   /**
-   * 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.Pdbids) Unmarshaller.unmarshal(
-        jalview.schemabinding.version2.Pdbids.class, reader);
-  } //-- java.lang.Object unmarshal(java.io.Reader)
+    return (jalview.schemabinding.version2.Pdbentry) Unmarshaller
+            .unmarshal(jalview.schemabinding.version2.Pdbids.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()
+  }
 
 }