X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FPdbentryItem.java;h=ea36590c394f1694844331294a919557e7bff7f3;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=d797520bd5dfdee23b5feec5d1c2cba42732c261;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git

diff --git a/src/jalview/binding/PdbentryItem.java b/src/jalview/binding/PdbentryItem.java
old mode 100755
new mode 100644
index d797520..ea36590
--- a/src/jalview/binding/PdbentryItem.java
+++ b/src/jalview/binding/PdbentryItem.java
@@ -1,197 +1,209 @@
-/*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.binding;
-
-  //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.Serializable;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-
-/**
- * Class PdbentryItem.
- * 
- * @version $Revision$ $Date$
- */
-public class PdbentryItem implements java.io.Serializable {
-
-
-      //--------------------------/
-     //- Class/Member Variables -/
-    //--------------------------/
-
-    /**
-     * Field _propertyList
-     */
-    private java.util.Vector _propertyList;
-
-
-      //----------------/
-     //- Constructors -/
-    //----------------/
-
-    public PdbentryItem() {
-        super();
-        _propertyList = new Vector();
-    } //-- jalview.binding.PdbentryItem()
-
-
-      //-----------/
-     //- Methods -/
-    //-----------/
-
-    /**
-     * Method addProperty
-     * 
-     * 
-     * 
-     * @param vProperty
-     */
-    public void addProperty(jalview.binding.Property vProperty)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _propertyList.addElement(vProperty);
-    } //-- void addProperty(jalview.binding.Property) 
-
-    /**
-     * Method addProperty
-     * 
-     * 
-     * 
-     * @param index
-     * @param vProperty
-     */
-    public void addProperty(int index, jalview.binding.Property vProperty)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _propertyList.insertElementAt(vProperty, index);
-    } //-- void addProperty(int, jalview.binding.Property) 
-
-    /**
-     * Method enumerateProperty
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateProperty()
-    {
-        return _propertyList.elements();
-    } //-- java.util.Enumeration enumerateProperty() 
-
-    /**
-     * Method getProperty
-     * 
-     * 
-     * 
-     * @param index
-     * @return Property
-     */
-    public jalview.binding.Property getProperty(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _propertyList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        
-        return (jalview.binding.Property) _propertyList.elementAt(index);
-    } //-- jalview.binding.Property getProperty(int) 
-
-    /**
-     * Method getProperty
-     * 
-     * 
-     * 
-     * @return Property
-     */
-    public jalview.binding.Property[] getProperty()
-    {
-        int size = _propertyList.size();
-        jalview.binding.Property[] mArray = new jalview.binding.Property[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (jalview.binding.Property) _propertyList.elementAt(index);
-        }
-        return mArray;
-    } //-- jalview.binding.Property[] getProperty() 
-
-    /**
-     * Method getPropertyCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getPropertyCount()
-    {
-        return _propertyList.size();
-    } //-- int getPropertyCount() 
-
-    /**
-     * Method removeAllProperty
-     * 
-     */
-    public void removeAllProperty()
-    {
-        _propertyList.removeAllElements();
-    } //-- void removeAllProperty() 
-
-    /**
-     * Method removeProperty
-     * 
-     * 
-     * 
-     * @param index
-     * @return Property
-     */
-    public jalview.binding.Property removeProperty(int index)
-    {
-        java.lang.Object obj = _propertyList.elementAt(index);
-        _propertyList.removeElementAt(index);
-        return (jalview.binding.Property) obj;
-    } //-- jalview.binding.Property removeProperty(int) 
-
-    /**
-     * Method setProperty
-     * 
-     * 
-     * 
-     * @param index
-     * @param vProperty
-     */
-    public void setProperty(int index, jalview.binding.Property vProperty)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _propertyList.size())) {
-            throw new IndexOutOfBoundsException();
-        }
-        _propertyList.setElementAt(vProperty, index);
-    } //-- void setProperty(int, jalview.binding.Property) 
-
-    /**
-     * Method setProperty
-     * 
-     * 
-     * 
-     * @param propertyArray
-     */
-    public void setProperty(jalview.binding.Property[] propertyArray)
-    {
-        //-- copy array
-        _propertyList.removeAllElements();
-        for (int i = 0; i < propertyArray.length; i++) {
-            _propertyList.addElement(propertyArray[i]);
-        }
-    } //-- void setProperty(jalview.binding.Property) 
-
-}
+/*******************************************************************************
+ * 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/>.
+ *******************************************************************************/
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+/**
+ * Class PdbentryItem.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class PdbentryItem implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _propertyList.
+     */
+    private java.util.Vector _propertyList;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public PdbentryItem() {
+        super();
+        this._propertyList = new java.util.Vector();
+    }
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * 
+     * 
+     * @param vProperty
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addProperty(
+            final jalview.binding.Property vProperty)
+    throws java.lang.IndexOutOfBoundsException {
+        this._propertyList.addElement(vProperty);
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vProperty
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void addProperty(
+            final int index,
+            final jalview.binding.Property vProperty)
+    throws java.lang.IndexOutOfBoundsException {
+        this._propertyList.add(index, vProperty);
+    }
+
+    /**
+     * Method enumerateProperty.
+     * 
+     * @return an Enumeration over all jalview.binding.Property
+     * elements
+     */
+    public java.util.Enumeration enumerateProperty(
+    ) {
+        return this._propertyList.elements();
+    }
+
+    /**
+     * Method getProperty.
+     * 
+     * @param index
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     * @return the value of the jalview.binding.Property at the
+     * given index
+     */
+    public jalview.binding.Property getProperty(
+            final int index)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._propertyList.size()) {
+            throw new IndexOutOfBoundsException("getProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
+        }
+        
+        return (jalview.binding.Property) _propertyList.get(index);
+    }
+
+    /**
+     * Method getProperty.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.Property[] getProperty(
+    ) {
+        jalview.binding.Property[] array = new jalview.binding.Property[0];
+        return (jalview.binding.Property[]) this._propertyList.toArray(array);
+    }
+
+    /**
+     * Method getPropertyCount.
+     * 
+     * @return the size of this collection
+     */
+    public int getPropertyCount(
+    ) {
+        return this._propertyList.size();
+    }
+
+    /**
+     */
+    public void removeAllProperty(
+    ) {
+        this._propertyList.clear();
+    }
+
+    /**
+     * Method removeProperty.
+     * 
+     * @param vProperty
+     * @return true if the object was removed from the collection.
+     */
+    public boolean removeProperty(
+            final jalview.binding.Property vProperty) {
+        boolean removed = _propertyList.remove(vProperty);
+        return removed;
+    }
+
+    /**
+     * Method removePropertyAt.
+     * 
+     * @param index
+     * @return the element removed from the collection
+     */
+    public jalview.binding.Property removePropertyAt(
+            final int index) {
+        java.lang.Object obj = this._propertyList.remove(index);
+        return (jalview.binding.Property) obj;
+    }
+
+    /**
+     * 
+     * 
+     * @param index
+     * @param vProperty
+     * @throws java.lang.IndexOutOfBoundsException if the index
+     * given is outside the bounds of the collection
+     */
+    public void setProperty(
+            final int index,
+            final jalview.binding.Property vProperty)
+    throws java.lang.IndexOutOfBoundsException {
+        // check bounds for index
+        if (index < 0 || index >= this._propertyList.size()) {
+            throw new IndexOutOfBoundsException("setProperty: Index value '" + index + "' not in range [0.." + (this._propertyList.size() - 1) + "]");
+        }
+        
+        this._propertyList.set(index, vProperty);
+    }
+
+    /**
+     * 
+     * 
+     * @param vPropertyArray
+     */
+    public void setProperty(
+            final jalview.binding.Property[] vPropertyArray) {
+        //-- copy array
+        _propertyList.clear();
+        
+        for (int i = 0; i < vPropertyArray.length; i++) {
+                this._propertyList.add(vPropertyArray[i]);
+        }
+    }
+
+}