-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package jalview.schemabinding.version2;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import java.util.Enumeration;\r
-import java.util.Vector;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class Sequence.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Sequence extends jalview.schemabinding.version2.SequenceType \r
-implements java.io.Serializable\r
-{\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * Field _DBRefList\r
- */\r
- private java.util.Vector _DBRefList;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public Sequence() {\r
- super();\r
- _DBRefList = new Vector();\r
- } //-- jalview.schemabinding.version2.Sequence()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method addDBRef\r
- * \r
- * \r
- * \r
- * @param vDBRef\r
- */\r
- public void addDBRef(jalview.schemabinding.version2.DBRef vDBRef)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _DBRefList.addElement(vDBRef);\r
- } //-- void addDBRef(jalview.schemabinding.version2.DBRef) \r
-\r
- /**\r
- * Method addDBRef\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vDBRef\r
- */\r
- public void addDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- _DBRefList.insertElementAt(vDBRef, index);\r
- } //-- void addDBRef(int, jalview.schemabinding.version2.DBRef) \r
-\r
- /**\r
- * Method enumerateDBRef\r
- * \r
- * \r
- * \r
- * @return Enumeration\r
- */\r
- public java.util.Enumeration enumerateDBRef()\r
- {\r
- return _DBRefList.elements();\r
- } //-- java.util.Enumeration enumerateDBRef() \r
-\r
- /**\r
- * Method getDBRef\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return DBRef\r
- */\r
- public jalview.schemabinding.version2.DBRef getDBRef(int index)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _DBRefList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- \r
- return (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);\r
- } //-- jalview.schemabinding.version2.DBRef getDBRef(int) \r
-\r
- /**\r
- * Method getDBRef\r
- * \r
- * \r
- * \r
- * @return DBRef\r
- */\r
- public jalview.schemabinding.version2.DBRef[] getDBRef()\r
- {\r
- int size = _DBRefList.size();\r
- jalview.schemabinding.version2.DBRef[] mArray = new jalview.schemabinding.version2.DBRef[size];\r
- for (int index = 0; index < size; index++) {\r
- mArray[index] = (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);\r
- }\r
- return mArray;\r
- } //-- jalview.schemabinding.version2.DBRef[] getDBRef() \r
-\r
- /**\r
- * Method getDBRefCount\r
- * \r
- * \r
- * \r
- * @return int\r
- */\r
- public int getDBRefCount()\r
- {\r
- return _DBRefList.size();\r
- } //-- int getDBRefCount() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Method removeAllDBRef\r
- * \r
- */\r
- public void removeAllDBRef()\r
- {\r
- _DBRefList.removeAllElements();\r
- } //-- void removeAllDBRef() \r
-\r
- /**\r
- * Method removeDBRef\r
- * \r
- * \r
- * \r
- * @param index\r
- * @return DBRef\r
- */\r
- public jalview.schemabinding.version2.DBRef removeDBRef(int index)\r
- {\r
- java.lang.Object obj = _DBRefList.elementAt(index);\r
- _DBRefList.removeElementAt(index);\r
- return (jalview.schemabinding.version2.DBRef) obj;\r
- } //-- jalview.schemabinding.version2.DBRef removeDBRef(int) \r
-\r
- /**\r
- * Method setDBRef\r
- * \r
- * \r
- * \r
- * @param index\r
- * @param vDBRef\r
- */\r
- public void setDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)\r
- throws java.lang.IndexOutOfBoundsException\r
- {\r
- //-- check bounds for index\r
- if ((index < 0) || (index > _DBRefList.size())) {\r
- throw new IndexOutOfBoundsException();\r
- }\r
- _DBRefList.setElementAt(vDBRef, index);\r
- } //-- void setDBRef(int, jalview.schemabinding.version2.DBRef) \r
-\r
- /**\r
- * Method setDBRef\r
- * \r
- * \r
- * \r
- * @param DBRefArray\r
- */\r
- public void setDBRef(jalview.schemabinding.version2.DBRef[] DBRefArray)\r
- {\r
- //-- copy array\r
- _DBRefList.removeAllElements();\r
- for (int i = 0; i < DBRefArray.length; i++) {\r
- _DBRefList.addElement(DBRefArray[i]);\r
- }\r
- } //-- void setDBRef(jalview.schemabinding.version2.DBRef) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.schemabinding.version2.Sequence) Unmarshaller.unmarshal(jalview.schemabinding.version2.Sequence.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- 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
- } //-- void validate() \r
-\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 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 org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Sequence.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Sequence extends jalview.schemabinding.version2.SequenceType
+ implements java.io.Serializable
+{
+
+ // --------------------------/
+ // - Class/Member Variables -/
+ // --------------------------/
+
+ /**
+ * dataset sequence id for this sequence. Will be created as union of
+ * sequences.
+ *
+ */
+ private java.lang.String _dsseqid;
+
+ /**
+ * Field _DBRefList.
+ */
+ private java.util.Vector _DBRefList;
+
+ // ----------------/
+ // - Constructors -/
+ // ----------------/
+
+ public Sequence()
+ {
+ super();
+ this._DBRefList = new java.util.Vector();
+ }
+
+ // -----------/
+ // - Methods -/
+ // -----------/
+
+ /**
+ *
+ *
+ * @param vDBRef
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addDBRef(final jalview.schemabinding.version2.DBRef vDBRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._DBRefList.addElement(vDBRef);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vDBRef
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void addDBRef(final int index,
+ final jalview.schemabinding.version2.DBRef vDBRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ this._DBRefList.add(index, vDBRef);
+ }
+
+ /**
+ * Method enumerateDBRef.
+ *
+ * @return an Enumeration over all jalview.schemabinding.version2.DBRef
+ * elements
+ */
+ public java.util.Enumeration enumerateDBRef()
+ {
+ return this._DBRefList.elements();
+ }
+
+ /**
+ * Method getDBRef.
+ *
+ * @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.DBRef at the given
+ * index
+ */
+ public jalview.schemabinding.version2.DBRef getDBRef(final int index)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._DBRefList.size())
+ {
+ throw new IndexOutOfBoundsException("getDBRef: Index value '" + index
+ + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.DBRef) _DBRefList.get(index);
+ }
+
+ /**
+ * Method getDBRef.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.DBRef[] getDBRef()
+ {
+ jalview.schemabinding.version2.DBRef[] array = new jalview.schemabinding.version2.DBRef[0];
+ return (jalview.schemabinding.version2.DBRef[]) this._DBRefList
+ .toArray(array);
+ }
+
+ /**
+ * Method getDBRefCount.
+ *
+ * @return the size of this collection
+ */
+ public int getDBRefCount()
+ {
+ return this._DBRefList.size();
+ }
+
+ /**
+ * Returns the value of field 'dsseqid'. The field 'dsseqid' has the following
+ * description: dataset sequence id for this sequence. Will be created as
+ * union of sequences.
+ *
+ *
+ * @return the value of field 'Dsseqid'.
+ */
+ public java.lang.String getDsseqid()
+ {
+ return this._dsseqid;
+ }
+
+ /**
+ * 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 removeAllDBRef()
+ {
+ this._DBRefList.clear();
+ }
+
+ /**
+ * Method removeDBRef.
+ *
+ * @param vDBRef
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeDBRef(
+ final jalview.schemabinding.version2.DBRef vDBRef)
+ {
+ boolean removed = _DBRefList.remove(vDBRef);
+ return removed;
+ }
+
+ /**
+ * Method removeDBRefAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.DBRef removeDBRefAt(final int index)
+ {
+ java.lang.Object obj = this._DBRefList.remove(index);
+ return (jalview.schemabinding.version2.DBRef) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vDBRef
+ * @throws java.lang.IndexOutOfBoundsException
+ * if the index given is outside the bounds of the collection
+ */
+ public void setDBRef(final int index,
+ final jalview.schemabinding.version2.DBRef vDBRef)
+ throws java.lang.IndexOutOfBoundsException
+ {
+ // check bounds for index
+ if (index < 0 || index >= this._DBRefList.size())
+ {
+ throw new IndexOutOfBoundsException("setDBRef: Index value '" + index
+ + "' not in range [0.." + (this._DBRefList.size() - 1) + "]");
+ }
+
+ this._DBRefList.set(index, vDBRef);
+ }
+
+ /**
+ *
+ *
+ * @param vDBRefArray
+ */
+ public void setDBRef(
+ final jalview.schemabinding.version2.DBRef[] vDBRefArray)
+ {
+ // -- copy array
+ _DBRefList.clear();
+
+ for (int i = 0; i < vDBRefArray.length; i++)
+ {
+ this._DBRefList.add(vDBRefArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'dsseqid'. The field 'dsseqid' has the following
+ * description: dataset sequence id for this sequence. Will be created as
+ * union of sequences.
+ *
+ *
+ * @param dsseqid
+ * the value of field 'dsseqid'.
+ */
+ public void setDsseqid(final java.lang.String dsseqid)
+ {
+ this._dsseqid = dsseqid;
+ }
+
+ /**
+ * 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.SequenceType
+ */
+ public static jalview.schemabinding.version2.SequenceType unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException,
+ org.exolab.castor.xml.ValidationException
+ {
+ return (jalview.schemabinding.version2.SequenceType) Unmarshaller
+ .unmarshal(jalview.schemabinding.version2.Sequence.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