-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)\r
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- * \r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- * \r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- * \r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.schemabinding.version2;\r
-\r
-// ---------------------------------/\r
-// - Imported classes and packages -/\r
-// ---------------------------------/\r
-\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-\r
-/**\r
- * Class Pdbentry.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Pdbentry implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _id.\r
- */\r
- private java.lang.String _id;\r
-\r
- /**\r
- * Field _type.\r
- */\r
- private java.lang.String _type;\r
-\r
- /**\r
- * Field _file.\r
- */\r
- private java.lang.String _file;\r
-\r
- /**\r
- * Field _items.\r
- */\r
- private java.util.Vector _items;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public Pdbentry()\r
- {\r
- super();\r
- this._items = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vPdbentryItem\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addPdbentryItem(\r
- final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._items.addElement(vPdbentryItem);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vPdbentryItem\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addPdbentryItem(final int index,\r
- final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._items.add(index, vPdbentryItem);\r
- }\r
-\r
- /**\r
- * Method enumeratePdbentryItem.\r
- * \r
- * @return an Enumeration over all jalview.schemabinding.version2.PdbentryItem\r
- * elements\r
- */\r
- public java.util.Enumeration enumeratePdbentryItem()\r
- {\r
- return this._items.elements();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'file'.\r
- * \r
- * @return the value of field 'File'.\r
- */\r
- public java.lang.String getFile()\r
- {\r
- return this._file;\r
- }\r
-\r
- /**\r
- * Returns the value of field 'id'.\r
- * \r
- * @return the value of field 'Id'.\r
- */\r
- public java.lang.String getId()\r
- {\r
- return this._id;\r
- }\r
-\r
- /**\r
- * Method getPdbentryItem.\r
- * \r
- * @param index\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- * @return the value of the jalview.schemabinding.version2.PdbentryItem at the\r
- * given inde\r
- */\r
- public jalview.schemabinding.version2.PdbentryItem getPdbentryItem(\r
- final int index) throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._items.size())\r
- {\r
- throw new IndexOutOfBoundsException("getPdbentryItem: Index value '"\r
- + index + "' not in range [0.." + (this._items.size() - 1)\r
- + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.PdbentryItem) _items.get(index);\r
- }\r
-\r
- /**\r
- * Method getPdbentryItem.Returns the contents of the collection in an Array.\r
- * <p>\r
- * Note: Just in case the collection contents are changing in another thread,\r
- * we pass a 0-length Array of the correct type into the API call. This way we\r
- * <i>know</i> that the Array returned is of exactly the correct length.\r
- * \r
- * @return this collection as an Array\r
- */\r
- public jalview.schemabinding.version2.PdbentryItem[] getPdbentryItem()\r
- {\r
- jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0];\r
- return (jalview.schemabinding.version2.PdbentryItem[]) this._items\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getPdbentryItemCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getPdbentryItemCount()\r
- {\r
- return this._items.size();\r
- }\r
-\r
- /**\r
- * Returns the value of field 'type'.\r
- * \r
- * @return the value of field 'Type'.\r
- */\r
- public java.lang.String getType()\r
- {\r
- return this._type;\r
- }\r
-\r
- /**\r
- * Method isValid.\r
- * \r
- * @return true if this object is valid according to the schema\r
- */\r
- public boolean isValid()\r
- {\r
- try\r
- {\r
- validate();\r
- } catch (org.exolab.castor.xml.ValidationException vex)\r
- {\r
- return false;\r
- }\r
- return true;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param out\r
- * @throws org.exolab.castor.xml.MarshalException\r
- * if object is null or if any SAXException is thrown during\r
- * marshaling\r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the\r
- * schema\r
- */\r
- public void marshal(final java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
- Marshaller.marshal(this, out);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param handler\r
- * @throws java.io.IOException\r
- * if an IOException occurs during marshaling\r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the\r
- * schema\r
- * @throws org.exolab.castor.xml.MarshalException\r
- * if object is null or if any SAXException is thrown during\r
- * marshaling\r
- */\r
- public void marshal(final org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException,\r
- org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
- Marshaller.marshal(this, handler);\r
- }\r
-\r
- /**\r
- */\r
- public void removeAllPdbentryItem()\r
- {\r
- this._items.clear();\r
- }\r
-\r
- /**\r
- * Method removePdbentryItem.\r
- * \r
- * @param vPdbentryItem\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removePdbentryItem(\r
- final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
- {\r
- boolean removed = _items.remove(vPdbentryItem);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removePdbentryItemAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._items.remove(index);\r
- return (jalview.schemabinding.version2.PdbentryItem) obj;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'file'.\r
- * \r
- * @param file\r
- * the value of field 'file'.\r
- */\r
- public void setFile(final java.lang.String file)\r
- {\r
- this._file = file;\r
- }\r
-\r
- /**\r
- * Sets the value of field 'id'.\r
- * \r
- * @param id\r
- * the value of field 'id'.\r
- */\r
- public void setId(final java.lang.String id)\r
- {\r
- this._id = id;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vPdbentryItem\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setPdbentryItem(final int index,\r
- final jalview.schemabinding.version2.PdbentryItem vPdbentryItem)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._items.size())\r
- {\r
- throw new IndexOutOfBoundsException("setPdbentryItem: Index value '"\r
- + index + "' not in range [0.." + (this._items.size() - 1)\r
- + "]");\r
- }\r
-\r
- this._items.set(index, vPdbentryItem);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vPdbentryItemArray\r
- */\r
- public void setPdbentryItem(\r
- final jalview.schemabinding.version2.PdbentryItem[] vPdbentryItemArray)\r
- {\r
- // -- copy array\r
- _items.clear();\r
-\r
- for (int i = 0; i < vPdbentryItemArray.length; i++)\r
- {\r
- this._items.add(vPdbentryItemArray[i]);\r
- }\r
- }\r
-\r
- /**\r
- * Sets the value of field 'type'.\r
- * \r
- * @param type\r
- * the value of field 'type'.\r
- */\r
- public void setType(final java.lang.String type)\r
- {\r
- this._type = type;\r
- }\r
-\r
- /**\r
- * Method unmarshal.\r
- * \r
- * @param reader\r
- * @throws org.exolab.castor.xml.MarshalException\r
- * if object is null or if any SAXException is thrown during\r
- * marshaling\r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the\r
- * schema\r
- * @return the unmarshaled jalview.schemabinding.version2.Pdbentry\r
- */\r
- public static jalview.schemabinding.version2.Pdbentry unmarshal(\r
- final java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException,\r
- org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.schemabinding.version2.Pdbentry) Unmarshaller\r
- .unmarshal(jalview.schemabinding.version2.Pdbentry.class,\r
- reader);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @throws org.exolab.castor.xml.ValidationException\r
- * if this object is an invalid instance according to the\r
- * schema\r
- */\r
- public void validate() throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- }\r
-\r
-}\r
+/*******************************************************************************
+ * 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.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. <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.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);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff