X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FPdbids.java;h=d0556c047ddde939356412171775a5277d0012a7;hb=506d60f0e188723ddc91c26824b41ac7034df3fe;hp=04685b9fe3536bdb7728a248f74d114a2fac4a98;hpb=60f2d6c034560415fd0139c8bc7df0c19cae1186;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/Pdbids.java b/src/jalview/schemabinding/version2/Pdbids.java
index 04685b9..d0556c0 100755
--- a/src/jalview/schemabinding/version2/Pdbids.java
+++ b/src/jalview/schemabinding/version2/Pdbids.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.schemabinding.version2;
 
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
+// ---------------------------------/
+// - Imported classes and packages -/
+// ---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -19,262 +30,289 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class Pdbids extends jalview.schemabinding.version2.Pdbentry 
-implements java.io.Serializable
+public class Pdbids extends jalview.schemabinding.version2.Pdbentry
+        implements java.io.Serializable
 {
 
+  // --------------------------/
+  // - Class/Member Variables -/
+  // --------------------------/
 
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
+  /**
+   * Field _structureStateList.
+   */
+  private java.util.Vector _structureStateList;
 
-    /**
-     * Field _structureStateList.
-     */
-    private java.util.Vector _structureStateList;
+  // ----------------/
+  // - Constructors -/
+  // ----------------/
 
+  public Pdbids()
+  {
+    super();
+    this._structureStateList = new java.util.Vector();
+  }
 
-      //----------------/
-     //- Constructors -/
-    //----------------/
+  // -----------/
+  // - Methods -/
+  // -----------/
 
-    public Pdbids() {
-        super();
-        this._structureStateList = new java.util.Vector();
-    }
+  /**
+   * 
+   * 
+   * @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);
+  }
 
+  /**
+   * 
+   * 
+   * @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);
+  }
 
-      //-----------/
-     //- Methods -/
-    //-----------/
+  /**
+   * Method enumerateStructureState.
+   * 
+   * @return an Enumeration over all
+   *         jalview.schemabinding.version2.StructureState elements
+   */
+  public java.util.Enumeration enumerateStructureState()
+  {
+    return this._structureStateList.elements();
+  }
 
-    /**
-     * 
-     * 
-     * @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);
+  /**
+   * 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) + "]");
     }
 
-    /**
-     * 
-     * 
-     * @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);
-    }
+    return (jalview.schemabinding.version2.StructureState) _structureStateList
+            .get(index);
+  }
 
-    /**
-     * Method enumerateStructureState.
-     * 
-     * @return an Enumeration over all
-     * jalview.schemabinding.version2.StructureState elements
-     */
-    public java.util.Enumeration enumerateStructureState(
-    ) {
-        return this._structureStateList.elements();
-    }
+  /**
+   * 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 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 getStructureStateCount.
+   * 
+   * @return the size of this collection
+   */
+  public int getStructureStateCount()
+  {
+    return this._structureStateList.size();
+  }
 
-    /**
-     * 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 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 getStructureStateCount.
-     * 
-     * @return the size of this collection
-     */
-    public int getStructureStateCount(
-    ) {
-        return this._structureStateList.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 removeAllStructureState()
+  {
+    this._structureStateList.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 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;
+  }
 
-    /**
-     */
-    public void removeAllStructureState(
-    ) {
-        this._structureStateList.clear();
-    }
+  /**
+   * 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;
+  }
 
-    /**
-     * 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;
+  /**
+   * 
+   * 
+   * @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) + "]");
     }
 
-    /**
-     * 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;
-    }
+    this._structureStateList.set(index, vStructureState);
+  }
 
-    /**
-     * 
-     * 
-     * @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();
 
-    /**
-     * 
-     * 
-     * @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]);
-        }
+    for (int i = 0; i < vStructureStateArray.length; i++)
+    {
+      this._structureStateList.add(vStructureStateArray[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.schemabinding.version2.Pdbentry
-     */
-    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.Pdbids.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.schemabinding.version2.Pdbentry
+   */
+  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.Pdbids.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);
+  }
 
 }