X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FAlcodMap.java;h=3b1aa1b6de6dac4d1e8cac1a5bb89648ab4f7047;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=47b52b9c38314e872cd3aa253352302edf383eae;hpb=65540422b57569f5bb9766742eccacc75f1368f0;p=jalview.git diff --git a/src/jalview/schemabinding/version2/AlcodMap.java b/src/jalview/schemabinding/version2/AlcodMap.java index 47b52b9..3b1aa1b 100644 --- a/src/jalview/schemabinding/version2/AlcodMap.java +++ b/src/jalview/schemabinding/version2/AlcodMap.java @@ -1,25 +1,24 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, 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 file is part of Jalview. * - * 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. + * 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. * - * 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 + * 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 org.exolab.castor.xml.Marshaller; @@ -30,166 +29,174 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class AlcodMap implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * internal jalview id for the dnasq for this mapping. - * - */ - private java.lang.String _dnasq; - - /** - * a Mapping entry and an associated protein sequence - * - */ - private jalview.schemabinding.version2.Mapping _mapping; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public AlcodMap() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'dnasq'. The field 'dnasq' has - * the following description: internal jalview id for the dnasq - * for this mapping. - * - * - * @return the value of field 'Dnasq'. - */ - public java.lang.String getDnasq( - ) { - return this._dnasq; - } - - /** - * Returns the value of field 'mapping'. The field 'mapping' - * has the following description: a Mapping entry and an - * associated protein sequence - * - * - * @return the value of field 'Mapping'. - */ - public jalview.schemabinding.version2.Mapping getMapping( - ) { - return this._mapping; - } - - /** - * 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); - } - - /** - * Sets the value of field 'dnasq'. The field 'dnasq' has the - * following description: internal jalview id for the dnasq for - * this mapping. - * - * - * @param dnasq the value of field 'dnasq'. - */ - public void setDnasq( - final java.lang.String dnasq) { - this._dnasq = dnasq; - } - - /** - * Sets the value of field 'mapping'. The field 'mapping' has - * the following description: a Mapping entry and an associated - * protein sequence - * - * - * @param mapping the value of field 'mapping'. - */ - public void setMapping( - final jalview.schemabinding.version2.Mapping mapping) { - this._mapping = mapping; - } - - /** - * 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.AlcodMap - */ - public static jalview.schemabinding.version2.AlcodMap unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.schemabinding.version2.AlcodMap) Unmarshaller.unmarshal(jalview.schemabinding.version2.AlcodMap.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); +public class AlcodMap implements java.io.Serializable +{ + + // --------------------------/ + // - Class/Member Variables -/ + // --------------------------/ + + /** + * internal jalview id for the dnasq for this mapping. + * + */ + private java.lang.String _dnasq; + + /** + * a Mapping entry and an associated protein sequence + * + */ + private jalview.schemabinding.version2.Mapping _mapping; + + // ----------------/ + // - Constructors -/ + // ----------------/ + + public AlcodMap() + { + super(); + } + + // -----------/ + // - Methods -/ + // -----------/ + + /** + * Returns the value of field 'dnasq'. The field 'dnasq' has the following + * description: internal jalview id for the dnasq for this mapping. + * + * + * @return the value of field 'Dnasq'. + */ + public java.lang.String getDnasq() + { + return this._dnasq; + } + + /** + * Returns the value of field 'mapping'. The field 'mapping' has the following + * description: a Mapping entry and an associated protein sequence + * + * + * @return the value of field 'Mapping'. + */ + public jalview.schemabinding.version2.Mapping getMapping() + { + return this._mapping; + } + + /** + * 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); + } + + /** + * Sets the value of field 'dnasq'. The field 'dnasq' has the following + * description: internal jalview id for the dnasq for this mapping. + * + * + * @param dnasq + * the value of field 'dnasq'. + */ + public void setDnasq(final java.lang.String dnasq) + { + this._dnasq = dnasq; + } + + /** + * Sets the value of field 'mapping'. The field 'mapping' has the following + * description: a Mapping entry and an associated protein sequence + * + * + * @param mapping + * the value of field 'mapping'. + */ + public void setMapping( + final jalview.schemabinding.version2.Mapping mapping) + { + this._mapping = mapping; + } + + /** + * 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.AlcodMap + */ + public static jalview.schemabinding.version2.AlcodMap unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException + { + return (jalview.schemabinding.version2.AlcodMap) Unmarshaller + .unmarshal(jalview.schemabinding.version2.AlcodMap.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); + } }