/*\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
+ * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)\r
+ * Copyright (C) 2009 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
*/\r
package jalview.schemabinding.version2;\r
\r
-// ---------------------------------/\r
-// - Imported classes and packages -/\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
* @version $Revision$ $Date$\r
*/\r
-public class Pdbids extends jalview.schemabinding.version2.Pdbentry\r
- implements java.io.Serializable\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
+ //- Class/Member Variables -/\r
+ //--------------------------/\r
\r
- // ----------------/\r
- // - Constructors -/\r
- // ----------------/\r
+ /**\r
+ * Field _structureStateList.\r
+ */\r
+ private java.util.Vector _structureStateList;\r
\r
- public Pdbids()\r
- {\r
- super();\r
- this._structureStateList = new java.util.Vector();\r
- }\r
\r
- // -----------/\r
- // - Methods -/\r
- // -----------/\r
+ //----------------/\r
+ //- Constructors -/\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
+ public Pdbids() {\r
+ super();\r
+ this._structureStateList = new java.util.Vector();\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
+ //- Methods -/\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
+ * \r
+ * @param vStructureState\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * 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
+ this._structureStateList.addElement(vStructureState);\r
}\r
\r
- return (jalview.schemabinding.version2.StructureState) _structureStateList\r
- .get(index);\r
- }\r
+ /**\r
+ * \r
+ * \r
+ * @param index\r
+ * @param vStructureState\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * 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
+ this._structureStateList.add(index, vStructureState);\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
+ * 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 getStructureStateCount.\r
- * \r
- * @return the size of this collection\r
- */\r
- public int getStructureStateCount()\r
- {\r
- return this._structureStateList.size();\r
- }\r
+ /**\r
+ * Method getStructureState.\r
+ * \r
+ * @param index\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * given is outside the bounds of the collection\r
+ * @return the value of the\r
+ * jalview.schemabinding.version2.StructureState at the given\r
+ * index\r
+ */\r
+ public jalview.schemabinding.version2.StructureState getStructureState(\r
+ final int index)\r
+ throws java.lang.IndexOutOfBoundsException {\r
+ // check bounds for index\r
+ if (index < 0 || index >= this._structureStateList.size()) {\r
+ throw new IndexOutOfBoundsException("getStructureState: Index value '" + index + "' not in range [0.." + (this._structureStateList.size() - 1) + "]");\r
+ }\r
+ \r
+ return (jalview.schemabinding.version2.StructureState) _structureStateList.get(index);\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
+ * Method getStructureState.Returns the contents of the\r
+ * collection in an Array. <p>Note: Just in case the\r
+ * collection contents are changing in another thread, we pass\r
+ * a 0-length Array of the correct type into the API call. \r
+ * This way we <i>know</i> that the Array returned is of\r
+ * 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.toArray(array);\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
+ * 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
- * \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
+ * Method isValid.\r
+ * \r
+ * @return true if this object is valid according to the schema\r
+ */\r
+ public boolean isValid(\r
+ ) {\r
+ try {\r
+ validate();\r
+ } catch (org.exolab.castor.xml.ValidationException vex) {\r
+ return false;\r
+ }\r
+ return true;\r
+ }\r
\r
- /**\r
- */\r
- public void removeAllStructureState()\r
- {\r
- this._structureStateList.clear();\r
- }\r
+ /**\r
+ * \r
+ * \r
+ * @param out\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void marshal(\r
+ final java.io.Writer out)\r
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, out);\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
+ * \r
+ * @param handler\r
+ * @throws java.io.IOException if an IOException occurs during\r
+ * marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ */\r
+ public void marshal(\r
+ final org.xml.sax.ContentHandler handler)\r
+ throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {\r
+ Marshaller.marshal(this, handler);\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
+ public void removeAllStructureState(\r
+ ) {\r
+ this._structureStateList.clear();\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
+ * 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
+ boolean removed = _structureStateList.remove(vStructureState);\r
+ return removed;\r
}\r
\r
- this._structureStateList.set(index, vStructureState);\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
+ java.lang.Object obj = this._structureStateList.remove(index);\r
+ return (jalview.schemabinding.version2.StructureState) obj;\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
+ * \r
+ * \r
+ * @param index\r
+ * @param vStructureState\r
+ * @throws java.lang.IndexOutOfBoundsException if the index\r
+ * 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
+ // check bounds for index\r
+ if (index < 0 || index >= this._structureStateList.size()) {\r
+ throw new IndexOutOfBoundsException("setStructureState: Index value '" + index + "' not in range [0.." + (this._structureStateList.size() - 1) + "]");\r
+ }\r
+ \r
+ this._structureStateList.set(index, vStructureState);\r
+ }\r
\r
- for (int i = 0; i < vStructureStateArray.length; i++)\r
- {\r
- this._structureStateList.add(vStructureStateArray[i]);\r
+ /**\r
+ * \r
+ * \r
+ * @param vStructureStateArray\r
+ */\r
+ public void setStructureState(\r
+ final jalview.schemabinding.version2.StructureState[] vStructureStateArray) {\r
+ //-- copy array\r
+ _structureStateList.clear();\r
+ \r
+ for (int i = 0; i < vStructureStateArray.length; i++) {\r
+ this._structureStateList.add(vStructureStateArray[i]);\r
+ }\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
+ * Method unmarshal.\r
+ * \r
+ * @param reader\r
+ * @throws org.exolab.castor.xml.MarshalException if object is\r
+ * null or if any SAXException is thrown during marshaling\r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ * @return the unmarshaled\r
+ * 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, org.exolab.castor.xml.ValidationException {\r
+ return (jalview.schemabinding.version2.Pdbentry) Unmarshaller.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
+ * \r
+ * @throws org.exolab.castor.xml.ValidationException if this\r
+ * object is an invalid instance according to the schema\r
+ */\r
+ public void validate(\r
+ )\r
+ throws org.exolab.castor.xml.ValidationException {\r
+ org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+ validator.validate(this);\r
+ }\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff