X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fbinding%2FPdbentry.java;h=b2bade565b50e00987fb46f4fb8d2712a08c1b49;hb=a6c05e6488b5acb43d0ad3aeced88c2dcbe83a4c;hp=7e0ae3061e8af5ee3468a19912586b1b3066d8a2;hpb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;p=jalview.git
diff --git a/src/jalview/binding/Pdbentry.java b/src/jalview/binding/Pdbentry.java
old mode 100755
new mode 100644
index 7e0ae30..b2bade5
--- a/src/jalview/binding/Pdbentry.java
+++ b/src/jalview/binding/Pdbentry.java
@@ -1,326 +1,363 @@
-/*
- * This class was automatically generated with
- * Castor 0.9.6, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.binding;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.io.IOException;
-import java.io.Reader;
-import java.io.Serializable;
-import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
-import org.exolab.castor.xml.MarshalException;
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-import org.exolab.castor.xml.ValidationException;
-import org.xml.sax.ContentHandler;
-
-/**
- * Class Pdbentry.
- *
- * @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();
- _items = new Vector();
- } //-- jalview.binding.Pdbentry()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addPdbentryItem
- *
- *
- *
- * @param vPdbentryItem
- */
- public void addPdbentryItem(jalview.binding.PdbentryItem vPdbentryItem)
- throws java.lang.IndexOutOfBoundsException
- {
- _items.addElement(vPdbentryItem);
- } //-- void addPdbentryItem(jalview.binding.PdbentryItem)
-
- /**
- * Method addPdbentryItem
- *
- *
- *
- * @param index
- * @param vPdbentryItem
- */
- public void addPdbentryItem(int index, jalview.binding.PdbentryItem vPdbentryItem)
- throws java.lang.IndexOutOfBoundsException
- {
- _items.insertElementAt(vPdbentryItem, index);
- } //-- void addPdbentryItem(int, jalview.binding.PdbentryItem)
-
- /**
- * Method enumeratePdbentryItem
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumeratePdbentryItem()
- {
- return _items.elements();
- } //-- java.util.Enumeration enumeratePdbentryItem()
-
- /**
- * Returns the value of field 'id'.
- *
- * @return String
- * @return the value of field 'id'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
- * Method getPdbentryItem
- *
- *
- *
- * @param index
- * @return PdbentryItem
- */
- public jalview.binding.PdbentryItem getPdbentryItem(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _items.size())) {
- throw new IndexOutOfBoundsException();
- }
-
- return (jalview.binding.PdbentryItem) _items.elementAt(index);
- } //-- jalview.binding.PdbentryItem getPdbentryItem(int)
-
- /**
- * Method getPdbentryItem
- *
- *
- *
- * @return PdbentryItem
- */
- public jalview.binding.PdbentryItem[] getPdbentryItem()
- {
- int size = _items.size();
- jalview.binding.PdbentryItem[] mArray = new jalview.binding.PdbentryItem[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (jalview.binding.PdbentryItem) _items.elementAt(index);
- }
- return mArray;
- } //-- jalview.binding.PdbentryItem[] getPdbentryItem()
-
- /**
- * Method getPdbentryItemCount
- *
- *
- *
- * @return int
- */
- public int getPdbentryItemCount()
- {
- return _items.size();
- } //-- int getPdbentryItemCount()
-
- /**
- * Returns the value of field 'type'.
- *
- * @return String
- * @return the value of field 'type'.
- */
- public java.lang.String getType()
- {
- return this._type;
- } //-- java.lang.String getType()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid()
- {
- try {
- validate();
- }
- catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
- return true;
- } //-- boolean isValid()
-
- /**
- * Method marshal
- *
- *
- *
- * @param out
- */
- public void marshal(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
- */
- public void marshal(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()
-
- /**
- * Method removePdbentryItem
- *
- *
- *
- * @param index
- * @return PdbentryItem
- */
- public jalview.binding.PdbentryItem removePdbentryItem(int index)
- {
- java.lang.Object obj = _items.elementAt(index);
- _items.removeElementAt(index);
- return (jalview.binding.PdbentryItem) obj;
- } //-- jalview.binding.PdbentryItem removePdbentryItem(int)
-
- /**
- * Sets the value of field 'id'.
- *
- * @param id the value of field 'id'.
- */
- public void setId(java.lang.String id)
- {
- this._id = id;
- } //-- void setId(java.lang.String)
-
- /**
- * Method setPdbentryItem
- *
- *
- *
- * @param index
- * @param vPdbentryItem
- */
- public void setPdbentryItem(int index, jalview.binding.PdbentryItem vPdbentryItem)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _items.size())) {
- throw new IndexOutOfBoundsException();
- }
- _items.setElementAt(vPdbentryItem, index);
- } //-- void setPdbentryItem(int, jalview.binding.PdbentryItem)
-
- /**
- * Method setPdbentryItem
- *
- *
- *
- * @param pdbentryItemArray
- */
- public void setPdbentryItem(jalview.binding.PdbentryItem[] pdbentryItemArray)
- {
- //-- copy array
- _items.removeAllElements();
- for (int i = 0; i < pdbentryItemArray.length; i++) {
- _items.addElement(pdbentryItemArray[i]);
- }
- } //-- void setPdbentryItem(jalview.binding.PdbentryItem)
-
- /**
- * Sets the value of field 'type'.
- *
- * @param type the value of field 'type'.
- */
- public void setType(java.lang.String type)
- {
- this._type = type;
- } //-- void setType(java.lang.String)
-
- /**
- * Method unmarshal
- *
- *
- *
- * @param reader
- * @return Object
- */
- public static java.lang.Object unmarshal(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);
- } //-- java.lang.Object unmarshal(java.io.Reader)
-
- /**
- * Method validate
- *
- */
- public void validate()
- throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- } //-- void validate()
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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
+ * 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 + * know 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; + } + 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{ + "setPdbentryItem", + Integer.valueOf(index).toString(), + Integer.valueOf((this._items.size() - 1)).toString() + })); + } + + 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); + } + +}