X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FPdbentry.java;h=65de364f45f5498f8839c4dcf3615d2319714fd9;hb=7308f8601e2037183869fd33509871e8c7a2b5e7;hp=1d4fff06224db0a7f494dd4b062a94ffd114032f;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/schemabinding/version2/Pdbentry.java b/src/jalview/schemabinding/version2/Pdbentry.java old mode 100755 new mode 100644 index 1d4fff0..65de364 --- a/src/jalview/schemabinding/version2/Pdbentry.java +++ b/src/jalview/schemabinding/version2/Pdbentry.java @@ -1,390 +1,375 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program 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 2 - * of the License, or (at your option) any later version. - * - * This program 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.schemabinding.version2; - -// ---------------------------------/ -// - Imported classes and packages -/ -// ---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Pdbentry. - * - * @version $Revision$ $Date$ - */ -public class Pdbentry implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _type. - */ - private java.lang.String _type; - - /** - * Field _file. - */ - private java.lang.String _file; - - /** - * Field _items. - */ - private java.util.Vector _items; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Pdbentry() - { - super(); - this._items = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vPdbentryItem - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addPdbentryItem( - final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - this._items.addElement(vPdbentryItem); - } - - /** - * - * - * @param index - * @param vPdbentryItem - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addPdbentryItem(final int index, - final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - this._items.add(index, vPdbentryItem); - } - - /** - * Method enumeratePdbentryItem. - * - * @return an Enumeration over all jalview.schemabinding.version2.PdbentryItem - * elements - */ - public java.util.Enumeration enumeratePdbentryItem() - { - return this._items.elements(); - } - - /** - * Returns the value of field 'file'. - * - * @return the value of field 'File'. - */ - public java.lang.String getFile() - { - return this._file; - } - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * Method getPdbentryItem. - * - * @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.PdbentryItem at the - * given inde - */ - public jalview.schemabinding.version2.PdbentryItem getPdbentryItem( - final int index) throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._items.size()) - { - throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" - + index + "' not in range [0.." + (this._items.size() - 1) - + "]"); - } - - return (jalview.schemabinding.version2.PdbentryItem) _items.get(index); - } - - /** - * Method getPdbentryItem.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.PdbentryItem[] getPdbentryItem() - { - jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0]; - return (jalview.schemabinding.version2.PdbentryItem[]) this._items - .toArray(array); - } - - /** - * Method getPdbentryItemCount. - * - * @return the size of this collection - */ - public int getPdbentryItemCount() - { - return this._items.size(); - } - - /** - * Returns the value of field 'type'. - * - * @return the value of field 'Type'. - */ - public java.lang.String getType() - { - return this._type; - } - - /** - * 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 removeAllPdbentryItem() - { - this._items.clear(); - } - - /** - * Method removePdbentryItem. - * - * @param vPdbentryItem - * @return true if the object was removed from the collection. - */ - public boolean removePdbentryItem( - final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) - { - boolean removed = _items.remove(vPdbentryItem); - return removed; - } - - /** - * Method removePdbentryItemAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt( - final int index) - { - java.lang.Object obj = this._items.remove(index); - return (jalview.schemabinding.version2.PdbentryItem) obj; - } - - /** - * Sets the value of field 'file'. - * - * @param file - * the value of field 'file'. - */ - public void setFile(final java.lang.String file) - { - this._file = file; - } - - /** - * Sets the value of field 'id'. - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * - * - * @param index - * @param vPdbentryItem - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setPdbentryItem(final int index, - final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._items.size()) - { - throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" - + index + "' not in range [0.." + (this._items.size() - 1) - + "]"); - } - - this._items.set(index, vPdbentryItem); - } - - /** - * - * - * @param vPdbentryItemArray - */ - public void setPdbentryItem( - final jalview.schemabinding.version2.PdbentryItem[] vPdbentryItemArray) - { - // -- copy array - _items.clear(); - - for (int i = 0; i < vPdbentryItemArray.length; i++) - { - this._items.add(vPdbentryItemArray[i]); - } - } - - /** - * Sets the value of field 'type'. - * - * @param type - * the value of field 'type'. - */ - public void setType(final java.lang.String type) - { - this._type = type; - } - - /** - * 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.Pdbentry.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); - } - -} +/* + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ + */ + +package jalview.schemabinding.version2; + +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ + +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; + +/** + * Class Pdbentry. + * + * @version $Revision$ $Date$ + */ +public class Pdbentry implements java.io.Serializable +{ + + // --------------------------/ + // - Class/Member Variables -/ + // --------------------------/ + + /** + * Field _id. + */ + private java.lang.String _id; + + /** + * Field _type. + */ + private java.lang.String _type; + + /** + * Field _file. + */ + private java.lang.String _file; + + /** + * Field _items. + */ + private java.util.Vector _items; + + // ----------------/ + // - Constructors -/ + // ----------------/ + + public Pdbentry() + { + super(); + this._items = new java.util.Vector(); + } + + // -----------/ + // - Methods -/ + // -----------/ + + /** + * + * + * @param vPdbentryItem + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addPdbentryItem( + final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) + throws java.lang.IndexOutOfBoundsException + { + this._items.addElement(vPdbentryItem); + } + + /** + * + * + * @param index + * @param vPdbentryItem + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addPdbentryItem(final int index, + final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) + throws java.lang.IndexOutOfBoundsException + { + this._items.add(index, vPdbentryItem); + } + + /** + * Method enumeratePdbentryItem. + * + * @return an Enumeration over all jalview.schemabinding.version2.PdbentryItem + * elements + */ + public java.util.Enumeration enumeratePdbentryItem() + { + return this._items.elements(); + } + + /** + * Returns the value of field 'file'. + * + * @return the value of field 'File'. + */ + public java.lang.String getFile() + { + return this._file; + } + + /** + * Returns the value of field 'id'. + * + * @return the value of field 'Id'. + */ + public java.lang.String getId() + { + return this._id; + } + + /** + * Method getPdbentryItem. + * + * @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.PdbentryItem at the + * given inde + */ + public jalview.schemabinding.version2.PdbentryItem getPdbentryItem( + final int index) throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._items.size()) + { + throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" + + index + "' not in range [0.." + (this._items.size() - 1) + + "]"); + } + + return (jalview.schemabinding.version2.PdbentryItem) _items.get(index); + } + + /** + * Method getPdbentryItem.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.PdbentryItem[] getPdbentryItem() + { + jalview.schemabinding.version2.PdbentryItem[] array = new jalview.schemabinding.version2.PdbentryItem[0]; + return (jalview.schemabinding.version2.PdbentryItem[]) this._items + .toArray(array); + } + + /** + * Method getPdbentryItemCount. + * + * @return the size of this collection + */ + public int getPdbentryItemCount() + { + return this._items.size(); + } + + /** + * Returns the value of field 'type'. + * + * @return the value of field 'Type'. + */ + public java.lang.String getType() + { + return this._type; + } + + /** + * 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 removeAllPdbentryItem() + { + this._items.clear(); + } + + /** + * Method removePdbentryItem. + * + * @param vPdbentryItem + * @return true if the object was removed from the collection. + */ + public boolean removePdbentryItem( + final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) + { + boolean removed = _items.remove(vPdbentryItem); + return removed; + } + + /** + * Method removePdbentryItemAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.PdbentryItem removePdbentryItemAt( + final int index) + { + java.lang.Object obj = this._items.remove(index); + return (jalview.schemabinding.version2.PdbentryItem) obj; + } + + /** + * Sets the value of field 'file'. + * + * @param file + * the value of field 'file'. + */ + public void setFile(final java.lang.String file) + { + this._file = file; + } + + /** + * Sets the value of field 'id'. + * + * @param id + * the value of field 'id'. + */ + public void setId(final java.lang.String id) + { + this._id = id; + } + + /** + * + * + * @param index + * @param vPdbentryItem + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setPdbentryItem(final int index, + final jalview.schemabinding.version2.PdbentryItem vPdbentryItem) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._items.size()) + { + throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" + + index + "' not in range [0.." + (this._items.size() - 1) + + "]"); + } + + this._items.set(index, vPdbentryItem); + } + + /** + * + * + * @param vPdbentryItemArray + */ + public void setPdbentryItem( + final jalview.schemabinding.version2.PdbentryItem[] vPdbentryItemArray) + { + // -- copy array + _items.clear(); + + for (int i = 0; i < vPdbentryItemArray.length; i++) + { + this._items.add(vPdbentryItemArray[i]); + } + } + + /** + * Sets the value of field 'type'. + * + * @param type + * the value of field 'type'. + */ + public void setType(final java.lang.String type) + { + this._type = type; + } + + /** + * 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.Pdbentry.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); + } + +}