X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FPdbids.java;h=5214c31a50a1a38ce48f769da920f1c3d66d58d3;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=347ff351cbac44b17c44be03080a8ea8056f3815;hpb=48df59aa393e03aa7269b2df662ac1b8d58cbb25;p=jalview.git
diff --git a/src/jalview/schemabinding/version2/Pdbids.java b/src/jalview/schemabinding/version2/Pdbids.java
old mode 100755
new mode 100644
index 347ff35..5214c31
--- a/src/jalview/schemabinding/version2/Pdbids.java
+++ b/src/jalview/schemabinding/version2/Pdbids.java
@@ -1,276 +1,320 @@
-/*
- * 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 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();
- _structureStateList = new Vector();
- } //-- jalview.schemabinding.version2.Pdbids()
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method addStructureState
- *
- *
- *
- * @param vStructureState
- */
- public void addStructureState(jalview.schemabinding.version2.StructureState vStructureState)
- throws java.lang.IndexOutOfBoundsException
- {
- _structureStateList.addElement(vStructureState);
- } //-- void addStructureState(jalview.schemabinding.version2.StructureState)
-
- /**
- * Method addStructureState
- *
- *
- *
- * @param index
- * @param vStructureState
- */
- public void addStructureState(int index, jalview.schemabinding.version2.StructureState vStructureState)
- throws java.lang.IndexOutOfBoundsException
- {
- _structureStateList.insertElementAt(vStructureState, index);
- } //-- void addStructureState(int, jalview.schemabinding.version2.StructureState)
-
- /**
- * Method enumerateStructureState
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateStructureState()
- {
- return _structureStateList.elements();
- } //-- java.util.Enumeration enumerateStructureState()
-
- /**
- * Method getStructureState
- *
- *
- *
- * @param index
- * @return StructureState
- */
- public jalview.schemabinding.version2.StructureState getStructureState(int index)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _structureStateList.size())) {
- throw new IndexOutOfBoundsException();
- }
-
- return (jalview.schemabinding.version2.StructureState) _structureStateList.elementAt(index);
- } //-- jalview.schemabinding.version2.StructureState getStructureState(int)
-
- /**
- * Method getStructureState
- *
- *
- *
- * @return StructureState
- */
- public jalview.schemabinding.version2.StructureState[] getStructureState()
- {
- int size = _structureStateList.size();
- jalview.schemabinding.version2.StructureState[] mArray = new jalview.schemabinding.version2.StructureState[size];
- for (int index = 0; index < size; index++) {
- mArray[index] = (jalview.schemabinding.version2.StructureState) _structureStateList.elementAt(index);
- }
- return mArray;
- } //-- jalview.schemabinding.version2.StructureState[] getStructureState()
-
- /**
- * Method getStructureStateCount
- *
- *
- *
- * @return int
- */
- public int getStructureStateCount()
- {
- return _structureStateList.size();
- } //-- int getStructureStateCount()
-
- /**
- * 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 removeAllStructureState
- *
- */
- public void removeAllStructureState()
- {
- _structureStateList.removeAllElements();
- } //-- void removeAllStructureState()
-
- /**
- * Method removeStructureState
- *
- *
- *
- * @param index
- * @return StructureState
- */
- public jalview.schemabinding.version2.StructureState removeStructureState(int index)
- {
- java.lang.Object obj = _structureStateList.elementAt(index);
- _structureStateList.removeElementAt(index);
- return (jalview.schemabinding.version2.StructureState) obj;
- } //-- jalview.schemabinding.version2.StructureState removeStructureState(int)
-
- /**
- * Method setStructureState
- *
- *
- *
- * @param index
- * @param vStructureState
- */
- public void setStructureState(int index, jalview.schemabinding.version2.StructureState vStructureState)
- throws java.lang.IndexOutOfBoundsException
- {
- //-- check bounds for index
- if ((index < 0) || (index > _structureStateList.size())) {
- throw new IndexOutOfBoundsException();
- }
- _structureStateList.setElementAt(vStructureState, index);
- } //-- void setStructureState(int, jalview.schemabinding.version2.StructureState)
-
- /**
- * Method setStructureState
- *
- *
- *
- * @param structureStateArray
- */
- public void setStructureState(jalview.schemabinding.version2.StructureState[] structureStateArray)
- {
- //-- copy array
- _structureStateList.removeAllElements();
- for (int i = 0; i < structureStateArray.length; i++) {
- _structureStateList.addElement(structureStateArray[i]);
- }
- } //-- void setStructureState(jalview.schemabinding.version2.StructureState)
-
- /**
- * 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.Pdbids) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbids.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 ($$Version-Rel$$)
+ * 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
+ * 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.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); + } + +}