-/*\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 Pdbids.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Pdbids extends jalview.schemabinding.version2.Pdbentry\r
- implements java.io.Serializable\r
-{\r
-\r
- // --------------------------/\r
- // - Class/Member Variables -/\r
- // --------------------------/\r
-\r
- /**\r
- * Field _structureStateList.\r
- */\r
- private java.util.Vector _structureStateList;\r
-\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
-\r
- public Pdbids()\r
- {\r
- super();\r
- this._structureStateList = new java.util.Vector();\r
- }\r
-\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
-\r
- /**\r
- * \r
- * \r
- * @param vStructureState\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addStructureState(\r
- final jalview.schemabinding.version2.StructureState vStructureState)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._structureStateList.addElement(vStructureState);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vStructureState\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void addStructureState(\r
- final int index,\r
- final jalview.schemabinding.version2.StructureState vStructureState)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- this._structureStateList.add(index, vStructureState);\r
- }\r
-\r
- /**\r
- * Method enumerateStructureState.\r
- * \r
- * @return an Enumeration over all\r
- * jalview.schemabinding.version2.StructureState elements\r
- */\r
- public java.util.Enumeration enumerateStructureState()\r
- {\r
- return this._structureStateList.elements();\r
- }\r
-\r
- /**\r
- * Method getStructureState.\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.StructureState at\r
- * the given index\r
- */\r
- public jalview.schemabinding.version2.StructureState getStructureState(\r
- final int index) throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._structureStateList.size())\r
- {\r
- throw new IndexOutOfBoundsException(\r
- "getStructureState: Index value '" + index\r
- + "' not in range [0.."\r
- + (this._structureStateList.size() - 1) + "]");\r
- }\r
-\r
- return (jalview.schemabinding.version2.StructureState) _structureStateList\r
- .get(index);\r
- }\r
-\r
- /**\r
- * Method getStructureState.Returns the contents of the collection in an\r
- * 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.StructureState[] getStructureState()\r
- {\r
- jalview.schemabinding.version2.StructureState[] array = new jalview.schemabinding.version2.StructureState[0];\r
- return (jalview.schemabinding.version2.StructureState[]) this._structureStateList\r
- .toArray(array);\r
- }\r
-\r
- /**\r
- * Method getStructureStateCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getStructureStateCount()\r
- {\r
- return this._structureStateList.size();\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 removeAllStructureState()\r
- {\r
- this._structureStateList.clear();\r
- }\r
-\r
- /**\r
- * Method removeStructureState.\r
- * \r
- * @param vStructureState\r
- * @return true if the object was removed from the collection.\r
- */\r
- public boolean removeStructureState(\r
- final jalview.schemabinding.version2.StructureState vStructureState)\r
- {\r
- boolean removed = _structureStateList.remove(vStructureState);\r
- return removed;\r
- }\r
-\r
- /**\r
- * Method removeStructureStateAt.\r
- * \r
- * @param index\r
- * @return the element removed from the collection\r
- */\r
- public jalview.schemabinding.version2.StructureState removeStructureStateAt(\r
- final int index)\r
- {\r
- java.lang.Object obj = this._structureStateList.remove(index);\r
- return (jalview.schemabinding.version2.StructureState) obj;\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param index\r
- * @param vStructureState\r
- * @throws java.lang.IndexOutOfBoundsException\r
- * if the index given is outside the bounds of the collection\r
- */\r
- public void setStructureState(\r
- final int index,\r
- final jalview.schemabinding.version2.StructureState vStructureState)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- // check bounds for index\r
- if (index < 0 || index >= this._structureStateList.size())\r
- {\r
- throw new IndexOutOfBoundsException(\r
- "setStructureState: Index value '" + index\r
- + "' not in range [0.."\r
- + (this._structureStateList.size() - 1) + "]");\r
- }\r
-\r
- this._structureStateList.set(index, vStructureState);\r
- }\r
-\r
- /**\r
- * \r
- * \r
- * @param vStructureStateArray\r
- */\r
- public void setStructureState(\r
- final jalview.schemabinding.version2.StructureState[] vStructureStateArray)\r
- {\r
- // -- copy array\r
- _structureStateList.clear();\r
-\r
- for (int i = 0; i < vStructureStateArray.length; i++)\r
- {\r
- this._structureStateList.add(vStructureStateArray[i]);\r
- }\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.Pdbids.class, 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 ($$Version-Rel$$)
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.schemabinding.version2;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.util.MessageManager;
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Pdbids.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Pdbids extends jalview.schemabinding.version2.Pdbentry
+ implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * Field _structureStateList.
+ */
+ private java.util.Vector _structureStateList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Pdbids()
+ {
+ super();
+ this._structureStateList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+ /**
+ * Method enumerateStructureState.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.StructureState elements
+ */
+ public java.util.Enumeration enumerateStructureState()
+ {
+ return this._structureStateList.elements();
+ }
+
+ /**
+ * 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "getStructureState",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._structureStateList.size() - 1)).toString()
+ }));
+ }
+
+ return (jalview.schemabinding.version2.StructureState) _structureStateList
+ .get(index);
+ }
+
+ /**
+ * 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 getStructureStateCount.
+ *
+ * @return the size of this collection
+ */
+ public int getStructureStateCount()
+ {
+ return this._structureStateList.size();
+ }
+
+ /**
+ * 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 removeAllStructureState()
+ {
+ this._structureStateList.clear();
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ *
+ *
+ * @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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+ "setStructureState",
+ Integer.valueOf(index).toString(),
+ Integer.valueOf((this._structureStateList.size() - 1)).toString()
+ }));
+ }
+
+ this._structureStateList.set(index, vStructureState);
+ }
+
+ /**
+ *
+ *
+ * @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]);
+ }
+ }
+
+ /**
+ * 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);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff