X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FAlcodonFrame.java;h=218e07e3d78f27a04f12a82fdc5920df7ccff2fb;hb=7308f8601e2037183869fd33509871e8c7a2b5e7;hp=683e421a56396d51003609bb27525689ab94fe84;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/schemabinding/version2/AlcodonFrame.java b/src/jalview/schemabinding/version2/AlcodonFrame.java index 683e421..218e07e 100644 --- a/src/jalview/schemabinding/version2/AlcodonFrame.java +++ b/src/jalview/schemabinding/version2/AlcodonFrame.java @@ -1,443 +1,466 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 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 AlcodonFrame. - * - * @version $Revision$ $Date$ - */ -public class AlcodonFrame implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _alcodonList. - */ - private java.util.Vector _alcodonList; - - /** - * Field _alcodMapList. - */ - private java.util.Vector _alcodMapList; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlcodonFrame() { - super(); - this._alcodonList = new java.util.Vector(); - this._alcodMapList = new java.util.Vector(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * - * - * @param vAlcodMap - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addAlcodMap( - final jalview.schemabinding.version2.AlcodMap vAlcodMap) - throws java.lang.IndexOutOfBoundsException { - this._alcodMapList.addElement(vAlcodMap); - } - - /** - * - * - * @param index - * @param vAlcodMap - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addAlcodMap( - final int index, - final jalview.schemabinding.version2.AlcodMap vAlcodMap) - throws java.lang.IndexOutOfBoundsException { - this._alcodMapList.add(index, vAlcodMap); - } - - /** - * - * - * @param vAlcodon - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addAlcodon( - final jalview.schemabinding.version2.Alcodon vAlcodon) - throws java.lang.IndexOutOfBoundsException { - this._alcodonList.addElement(vAlcodon); - } - - /** - * - * - * @param index - * @param vAlcodon - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void addAlcodon( - final int index, - final jalview.schemabinding.version2.Alcodon vAlcodon) - throws java.lang.IndexOutOfBoundsException { - this._alcodonList.add(index, vAlcodon); - } - - /** - * Method enumerateAlcodMap. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.AlcodMap elements - */ - public java.util.Enumeration enumerateAlcodMap( - ) { - return this._alcodMapList.elements(); - } - - /** - * Method enumerateAlcodon. - * - * @return an Enumeration over all - * jalview.schemabinding.version2.Alcodon elements - */ - public java.util.Enumeration enumerateAlcodon( - ) { - return this._alcodonList.elements(); - } - - /** - * Method getAlcodMap. - * - * @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.AlcodMap at the given index - */ - public jalview.schemabinding.version2.AlcodMap getAlcodMap( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._alcodMapList.size()) { - throw new IndexOutOfBoundsException("getAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.AlcodMap) _alcodMapList.get(index); - } - - /** - * Method getAlcodMap.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.AlcodMap[] getAlcodMap( - ) { - jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0]; - return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList.toArray(array); - } - - /** - * Method getAlcodMapCount. - * - * @return the size of this collection - */ - public int getAlcodMapCount( - ) { - return this._alcodMapList.size(); - } - - /** - * Method getAlcodon. - * - * @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.Alcodon at the given index - */ - public jalview.schemabinding.version2.Alcodon getAlcodon( - final int index) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._alcodonList.size()) { - throw new IndexOutOfBoundsException("getAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]"); - } - - return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index); - } - - /** - * Method getAlcodon.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.Alcodon[] getAlcodon( - ) { - jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0]; - return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList.toArray(array); - } - - /** - * Method getAlcodonCount. - * - * @return the size of this collection - */ - public int getAlcodonCount( - ) { - return this._alcodonList.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); - } - - /** - * Method removeAlcodMap. - * - * @param vAlcodMap - * @return true if the object was removed from the collection. - */ - public boolean removeAlcodMap( - final jalview.schemabinding.version2.AlcodMap vAlcodMap) { - boolean removed = _alcodMapList.remove(vAlcodMap); - return removed; - } - - /** - * Method removeAlcodMapAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt( - final int index) { - java.lang.Object obj = this._alcodMapList.remove(index); - return (jalview.schemabinding.version2.AlcodMap) obj; - } - - /** - * Method removeAlcodon. - * - * @param vAlcodon - * @return true if the object was removed from the collection. - */ - public boolean removeAlcodon( - final jalview.schemabinding.version2.Alcodon vAlcodon) { - boolean removed = _alcodonList.remove(vAlcodon); - return removed; - } - - /** - * Method removeAlcodonAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.schemabinding.version2.Alcodon removeAlcodonAt( - final int index) { - java.lang.Object obj = this._alcodonList.remove(index); - return (jalview.schemabinding.version2.Alcodon) obj; - } - - /** - */ - public void removeAllAlcodMap( - ) { - this._alcodMapList.clear(); - } - - /** - */ - public void removeAllAlcodon( - ) { - this._alcodonList.clear(); - } - - /** - * - * - * @param index - * @param vAlcodMap - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setAlcodMap( - final int index, - final jalview.schemabinding.version2.AlcodMap vAlcodMap) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._alcodMapList.size()) { - throw new IndexOutOfBoundsException("setAlcodMap: Index value '" + index + "' not in range [0.." + (this._alcodMapList.size() - 1) + "]"); - } - - this._alcodMapList.set(index, vAlcodMap); - } - - /** - * - * - * @param vAlcodMapArray - */ - public void setAlcodMap( - final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray) { - //-- copy array - _alcodMapList.clear(); - - for (int i = 0; i < vAlcodMapArray.length; i++) { - this._alcodMapList.add(vAlcodMapArray[i]); - } - } - - /** - * - * - * @param index - * @param vAlcodon - * @throws java.lang.IndexOutOfBoundsException if the index - * given is outside the bounds of the collection - */ - public void setAlcodon( - final int index, - final jalview.schemabinding.version2.Alcodon vAlcodon) - throws java.lang.IndexOutOfBoundsException { - // check bounds for index - if (index < 0 || index >= this._alcodonList.size()) { - throw new IndexOutOfBoundsException("setAlcodon: Index value '" + index + "' not in range [0.." + (this._alcodonList.size() - 1) + "]"); - } - - this._alcodonList.set(index, vAlcodon); - } - - /** - * - * - * @param vAlcodonArray - */ - public void setAlcodon( - final jalview.schemabinding.version2.Alcodon[] vAlcodonArray) { - //-- copy array - _alcodonList.clear(); - - for (int i = 0; i < vAlcodonArray.length; i++) { - this._alcodonList.add(vAlcodonArray[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.AlcodonFrame - */ - public static jalview.schemabinding.version2.AlcodonFrame unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodonFrame.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 AlcodonFrame. + * + * @version $Revision$ $Date$ + */ +public class AlcodonFrame implements java.io.Serializable +{ + + // --------------------------/ + // - Class/Member Variables -/ + // --------------------------/ + + /** + * Field _alcodonList. + */ + private java.util.Vector _alcodonList; + + /** + * Field _alcodMapList. + */ + private java.util.Vector _alcodMapList; + + // ----------------/ + // - Constructors -/ + // ----------------/ + + public AlcodonFrame() + { + super(); + this._alcodonList = new java.util.Vector(); + this._alcodMapList = new java.util.Vector(); + } + + // -----------/ + // - Methods -/ + // -----------/ + + /** + * + * + * @param vAlcodMap + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addAlcodMap( + final jalview.schemabinding.version2.AlcodMap vAlcodMap) + throws java.lang.IndexOutOfBoundsException + { + this._alcodMapList.addElement(vAlcodMap); + } + + /** + * + * + * @param index + * @param vAlcodMap + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addAlcodMap(final int index, + final jalview.schemabinding.version2.AlcodMap vAlcodMap) + throws java.lang.IndexOutOfBoundsException + { + this._alcodMapList.add(index, vAlcodMap); + } + + /** + * + * + * @param vAlcodon + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addAlcodon( + final jalview.schemabinding.version2.Alcodon vAlcodon) + throws java.lang.IndexOutOfBoundsException + { + this._alcodonList.addElement(vAlcodon); + } + + /** + * + * + * @param index + * @param vAlcodon + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void addAlcodon(final int index, + final jalview.schemabinding.version2.Alcodon vAlcodon) + throws java.lang.IndexOutOfBoundsException + { + this._alcodonList.add(index, vAlcodon); + } + + /** + * Method enumerateAlcodMap. + * + * @return an Enumeration over all jalview.schemabinding.version2.AlcodMap + * elements + */ + public java.util.Enumeration enumerateAlcodMap() + { + return this._alcodMapList.elements(); + } + + /** + * Method enumerateAlcodon. + * + * @return an Enumeration over all jalview.schemabinding.version2.Alcodon + * elements + */ + public java.util.Enumeration enumerateAlcodon() + { + return this._alcodonList.elements(); + } + + /** + * Method getAlcodMap. + * + * @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.AlcodMap at the + * given index + */ + public jalview.schemabinding.version2.AlcodMap getAlcodMap(final int index) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._alcodMapList.size()) + { + throw new IndexOutOfBoundsException("getAlcodMap: Index value '" + + index + "' not in range [0.." + + (this._alcodMapList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.AlcodMap) _alcodMapList + .get(index); + } + + /** + * Method getAlcodMap.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.AlcodMap[] getAlcodMap() + { + jalview.schemabinding.version2.AlcodMap[] array = new jalview.schemabinding.version2.AlcodMap[0]; + return (jalview.schemabinding.version2.AlcodMap[]) this._alcodMapList + .toArray(array); + } + + /** + * Method getAlcodMapCount. + * + * @return the size of this collection + */ + public int getAlcodMapCount() + { + return this._alcodMapList.size(); + } + + /** + * Method getAlcodon. + * + * @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.Alcodon at the + * given index + */ + public jalview.schemabinding.version2.Alcodon getAlcodon(final int index) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._alcodonList.size()) + { + throw new IndexOutOfBoundsException("getAlcodon: Index value '" + + index + "' not in range [0.." + + (this._alcodonList.size() - 1) + "]"); + } + + return (jalview.schemabinding.version2.Alcodon) _alcodonList.get(index); + } + + /** + * Method getAlcodon.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.Alcodon[] getAlcodon() + { + jalview.schemabinding.version2.Alcodon[] array = new jalview.schemabinding.version2.Alcodon[0]; + return (jalview.schemabinding.version2.Alcodon[]) this._alcodonList + .toArray(array); + } + + /** + * Method getAlcodonCount. + * + * @return the size of this collection + */ + public int getAlcodonCount() + { + return this._alcodonList.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); + } + + /** + * Method removeAlcodMap. + * + * @param vAlcodMap + * @return true if the object was removed from the collection. + */ + public boolean removeAlcodMap( + final jalview.schemabinding.version2.AlcodMap vAlcodMap) + { + boolean removed = _alcodMapList.remove(vAlcodMap); + return removed; + } + + /** + * Method removeAlcodMapAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.AlcodMap removeAlcodMapAt( + final int index) + { + java.lang.Object obj = this._alcodMapList.remove(index); + return (jalview.schemabinding.version2.AlcodMap) obj; + } + + /** + * Method removeAlcodon. + * + * @param vAlcodon + * @return true if the object was removed from the collection. + */ + public boolean removeAlcodon( + final jalview.schemabinding.version2.Alcodon vAlcodon) + { + boolean removed = _alcodonList.remove(vAlcodon); + return removed; + } + + /** + * Method removeAlcodonAt. + * + * @param index + * @return the element removed from the collection + */ + public jalview.schemabinding.version2.Alcodon removeAlcodonAt( + final int index) + { + java.lang.Object obj = this._alcodonList.remove(index); + return (jalview.schemabinding.version2.Alcodon) obj; + } + + /** + */ + public void removeAllAlcodMap() + { + this._alcodMapList.clear(); + } + + /** + */ + public void removeAllAlcodon() + { + this._alcodonList.clear(); + } + + /** + * + * + * @param index + * @param vAlcodMap + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setAlcodMap(final int index, + final jalview.schemabinding.version2.AlcodMap vAlcodMap) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._alcodMapList.size()) + { + throw new IndexOutOfBoundsException("setAlcodMap: Index value '" + + index + "' not in range [0.." + + (this._alcodMapList.size() - 1) + "]"); + } + + this._alcodMapList.set(index, vAlcodMap); + } + + /** + * + * + * @param vAlcodMapArray + */ + public void setAlcodMap( + final jalview.schemabinding.version2.AlcodMap[] vAlcodMapArray) + { + // -- copy array + _alcodMapList.clear(); + + for (int i = 0; i < vAlcodMapArray.length; i++) + { + this._alcodMapList.add(vAlcodMapArray[i]); + } + } + + /** + * + * + * @param index + * @param vAlcodon + * @throws java.lang.IndexOutOfBoundsException + * if the index given is outside the bounds of the collection + */ + public void setAlcodon(final int index, + final jalview.schemabinding.version2.Alcodon vAlcodon) + throws java.lang.IndexOutOfBoundsException + { + // check bounds for index + if (index < 0 || index >= this._alcodonList.size()) + { + throw new IndexOutOfBoundsException("setAlcodon: Index value '" + + index + "' not in range [0.." + + (this._alcodonList.size() - 1) + "]"); + } + + this._alcodonList.set(index, vAlcodon); + } + + /** + * + * + * @param vAlcodonArray + */ + public void setAlcodon( + final jalview.schemabinding.version2.Alcodon[] vAlcodonArray) + { + // -- copy array + _alcodonList.clear(); + + for (int i = 0; i < vAlcodonArray.length; i++) + { + this._alcodonList.add(vAlcodonArray[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.AlcodonFrame + */ + public static jalview.schemabinding.version2.AlcodonFrame unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException + { + return (jalview.schemabinding.version2.AlcodonFrame) Unmarshaller + .unmarshal(jalview.schemabinding.version2.AlcodonFrame.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); + } + +}