X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FPdbentry.java;h=c34fd732f16deed1660ab3974f296694c7463fa6;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=93c274832c61d6872199813f383de448bdde9230;hpb=48df59aa393e03aa7269b2df662ac1b8d58cbb25;p=jalview.git
diff --git a/src/jalview/schemabinding/version2/Pdbentry.java b/src/jalview/schemabinding/version2/Pdbentry.java
old mode 100755
new mode 100644
index 93c2748..c34fd73
--- a/src/jalview/schemabinding/version2/Pdbentry.java
+++ b/src/jalview/schemabinding/version2/Pdbentry.java
@@ -1,352 +1,369 @@
-/*
- * This class was automatically generated with
- * Castor 0.9.6, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.schemabinding.version2;
-
- //---------------------------------/
- //- 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 _file
- */
- private java.lang.String _file;
-
- /**
- * Field _items
- */
- private java.util.Vector _items;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- public Pdbentry() {
- super();
- _items = new Vector();
- } //-- jalview.schemabinding.version2.Pdbentry()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addPdbentryItem
- *
- *
- *
- * @param vPdbentryItem
- */
- public void addPdbentryItem(jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
- throws java.lang.IndexOutOfBoundsException
- {
- _items.addElement(vPdbentryItem);
- } //-- void addPdbentryItem(jalview.schemabinding.version2.PdbentryItem)
-
- /**
- * Method addPdbentryItem
- *
- *
- *
- * @param index
- * @param vPdbentryItem
- */
- public void addPdbentryItem(int index, jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
- throws java.lang.IndexOutOfBoundsException
- {
- _items.insertElementAt(vPdbentryItem, index);
- } //-- void addPdbentryItem(int, jalview.schemabinding.version2.PdbentryItem)
-
- /**
- * Method enumeratePdbentryItem
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumeratePdbentryItem()
- {
- return _items.elements();
- } //-- java.util.Enumeration enumeratePdbentryItem()
-
- /**
- * Returns the value of field 'file'.
- *
- * @return String
- * @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'.
- */
- public java.lang.String getId()
- {
- return this._id;
- } //-- java.lang.String getId()
-
- /**
- * Method getPdbentryItem
- *
- *
- *
- * @param index
- * @return PdbentryItem
- */
- public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _items.size())) {
- throw new IndexOutOfBoundsException();
- }
-
- return (jalview.schemabinding.version2.PdbentryItem) _items.elementAt(index);
- } //-- jalview.schemabinding.version2.PdbentryItem getPdbentryItem(int)
-
- /**
- * Method getPdbentryItem
- *
- *
- *
- * @return PdbentryItem
- */
- 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()
-
- /**
- * 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.schemabinding.version2.PdbentryItem removePdbentryItem(int index)
- {
- java.lang.Object obj = _items.elementAt(index);
- _items.removeElementAt(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'.
- */
- public void setFile(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'.
- */
- 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.schemabinding.version2.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.schemabinding.version2.PdbentryItem)
-
- /**
- * Method setPdbentryItem
- *
- *
- *
- * @param pdbentryItemArray
- */
- public void setPdbentryItem(jalview.schemabinding.version2.PdbentryItem[] pdbentryItemArray)
- {
- //-- copy array
- _items.removeAllElements();
- for (int i = 0; i < pdbentryItemArray.length; i++) {
- _items.addElement(pdbentryItemArray[i]);
- }
- } //-- void setPdbentryItem(jalview.schemabinding.version2.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.schemabinding.version2.Pdbentry) Unmarshaller.unmarshal(jalview.schemabinding.version2.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 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 .
+ *******************************************************************************/
+/*
+ * This class was automatically generated with
+ * Castor 1.1, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * 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 _file.
+ */
+ private java.lang.String _file;
+
+ /**
+ * Field _items.
+ */
+ private java.util.Vector _items;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Pdbentry() {
+ super();
+ this._items = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vPdbentryItem
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addPdbentryItem(
+ final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+ throws java.lang.IndexOutOfBoundsException {
+ this._items.addElement(vPdbentryItem);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vPdbentryItem
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addPdbentryItem(
+ final int index,
+ final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)
+ throws java.lang.IndexOutOfBoundsException {
+ this._items.add(index, vPdbentryItem);
+ }
+
+ /**
+ * Method enumeratePdbentryItem.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.PdbentryItem elements
+ */
+ public java.util.Enumeration enumeratePdbentryItem(
+ ) {
+ return this._items.elements();
+ }
+
+ /**
+ * Returns the value of field 'file'.
+ *
+ * @return the value of field 'File'.
+ */
+ public java.lang.String getFile(
+ ) {
+ return this._file;
+ }
+
+ /**
+ * Returns the value of field 'id'.
+ *
+ * @return the value of field 'Id'.
+ */
+ public java.lang.String getId(
+ ) {
+ return this._id;
+ }
+
+ /**
+ * Method getPdbentryItem.
+ *
+ * @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.PdbentryItem at the given inde
+ */
+ public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._items.size()) {
+ throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.PdbentryItem) _items.get(index);
+ }
+
+ /**
+ * Method getPdbentryItem.Returns the contents of the
+ * collection in an Array. 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.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 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.schemabinding.version2.PdbentryItem vPdbentryItem) {
+ boolean removed = _items.remove(vPdbentryItem);
+ return removed;
+ }
+
+ /**
+ * Method removePdbentryItemAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt(
+ final int index) {
+ java.lang.Object obj = this._items.remove(index);
+ return (jalview.schemabinding.version2.PdbentryItem) obj;
+ }
+
+ /**
+ * Sets the value of field 'file'.
+ *
+ * @param file the value of field 'file'.
+ */
+ public void setFile(
+ final java.lang.String file) {
+ this._file = file;
+ }
+
+ /**
+ * 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.schemabinding.version2.PdbentryItem vPdbentryItem)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._items.size()) {
+ throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" + index + "' not in range [0.." + (this._items.size() - 1) + "]");
+ }
+
+ this._items.set(index, vPdbentryItem);
+ }
+
+ /**
+ *
+ *
+ * @param vPdbentryItemArray
+ */
+ public void setPdbentryItem(
+ final jalview.schemabinding.version2.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.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.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);
+ }
+
+}