X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FPdbids.java;h=18c41148ac22a9c1bfc266cfa4275835ab3ce95c;hb=93642d621a7f86318a7777b0a70f6113dcd299dc;hp=53b2e91d49d4390f2fb6a270e40d2535362a3bcc;hpb=65df62f4b048a1615d32ea2c3576082ad2b63af8;p=jalview.git diff --git a/src/jalview/schemabinding/version2/Pdbids.java b/src/jalview/schemabinding/version2/Pdbids.java index 53b2e91..18c4114 100755 --- a/src/jalview/schemabinding/version2/Pdbids.java +++ b/src/jalview/schemabinding/version2/Pdbids.java @@ -1,118 +1,313 @@ /* - * This class was automatically generated with - * Castor 0.9.6, using an XML - * Schema. - * $Id$ + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5.1) + * Copyright (C) 2010 J Procter, AM Waterhouse, 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 . */ - package jalview.schemabinding.version2; - //---------------------------------/ - //- Imported classes and packages -/ +//---------------------------------/ +//- Imported classes and packages -/ //---------------------------------/ -import java.io.IOException; -import java.io.Reader; -import java.io.Serializable; -import java.io.Writer; -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 Pdbentry -implements java.io.Serializable +public class Pdbids extends jalview.schemabinding.version2.Pdbentry + implements java.io.Serializable { + // --------------------------/ + // - Class/Member Variables -/ + // --------------------------/ - //----------------/ - //- Constructors -/ - //----------------/ + /** + * Field _structureStateList. + */ + private java.util.Vector _structureStateList; - public Pdbids() { - super(); - } //-- jalview.schemabinding.version2.Pdbids() + // ----------------/ + // - Constructors -/ + // ----------------/ + public Pdbids() + { + super(); + this._structureStateList = new java.util.Vector(); + } - //-----------/ - //- Methods -/ - //-----------/ + // -----------/ + // - Methods -/ + // -----------/ - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() + /** + * + * + * @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()) { - 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 + throw new IndexOutOfBoundsException( + "getStructureState: Index value '" + index + + "' not in range [0.." + + (this._structureStateList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.StructureState) _structureStateList + .get(index); + } + + /** + * Method getStructureState.Returns the contents of the collection in an + * Array. + *

+ * 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 { - - 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 + validate(); + } catch (org.exolab.castor.xml.ValidationException vex) { - - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) - - /** - * Method unmarshal - * - * - * - * @param reader - * @return Object + 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 static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + 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()) { - return (jalview.schemabinding.version2.Pdbids) Unmarshaller.unmarshal(jalview.schemabinding.version2.Pdbids.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + throw new IndexOutOfBoundsException( + "setStructureState: Index value '" + index + + "' not in range [0.." + + (this._structureStateList.size() - 1) + "]"); + } - /** - * Method validate - * - */ - public void validate() - throws org.exolab.castor.xml.ValidationException + 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++) { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } //-- void validate() + 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); + } }