X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FAlignment.java;h=db2a59e3a2947effea741160067b0c64dbc4e8df;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=86aca8a54ee1e5b48c3431361b0a808ecdbda40b;hpb=65540422b57569f5bb9766742eccacc75f1368f0;p=jalview.git diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java old mode 100755 new mode 100644 index 86aca8a..db2a59e --- a/src/jalview/binding/Alignment.java +++ b/src/jalview/binding/Alignment.java @@ -1,25 +1,25 @@ /* - * 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 2.8.2) + * Copyright (C) 2014 The Jalview Authors * - * 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. + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.binding; - //---------------------------------/ - //- Imported classes and packages -/ +//---------------------------------/ +//- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -30,151 +30,162 @@ import org.exolab.castor.xml.Unmarshaller; * * @version $Revision$ $Date$ */ -public class Alignment implements java.io.Serializable { - - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _annotation. - */ - private jalview.binding.Annotation _annotation; - - /** - * Field _sequenceSet. - */ - private jalview.binding.SequenceSet _sequenceSet; - - - //----------------/ - //- Constructors -/ - //----------------/ - - public Alignment() { - super(); - } - - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'annotation'. - * - * @return the value of field 'Annotation'. - */ - public jalview.binding.Annotation getAnnotation( - ) { - return this._annotation; - } - - /** - * Returns the value of field 'sequenceSet'. - * - * @return the value of field 'SequenceSet'. - */ - public jalview.binding.SequenceSet getSequenceSet( - ) { - return this._sequenceSet; - } - - /** - * 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 'annotation'. - * - * @param annotation the value of field 'annotation'. - */ - public void setAnnotation( - final jalview.binding.Annotation annotation) { - this._annotation = annotation; - } - - /** - * Sets the value of field 'sequenceSet'. - * - * @param sequenceSet the value of field 'sequenceSet'. - */ - public void setSequenceSet( - final jalview.binding.SequenceSet sequenceSet) { - this._sequenceSet = sequenceSet; - } - - /** - * 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.binding.Alignment - */ - public static jalview.binding.Alignment unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.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 Alignment implements java.io.Serializable +{ + + // --------------------------/ + // - Class/Member Variables -/ + // --------------------------/ + + /** + * Field _annotation. + */ + private jalview.binding.Annotation _annotation; + + /** + * Field _sequenceSet. + */ + private jalview.binding.SequenceSet _sequenceSet; + + // ----------------/ + // - Constructors -/ + // ----------------/ + + public Alignment() + { + super(); + } + + // -----------/ + // - Methods -/ + // -----------/ + + /** + * Returns the value of field 'annotation'. + * + * @return the value of field 'Annotation'. + */ + public jalview.binding.Annotation getAnnotation() + { + return this._annotation; + } + + /** + * Returns the value of field 'sequenceSet'. + * + * @return the value of field 'SequenceSet'. + */ + public jalview.binding.SequenceSet getSequenceSet() + { + return this._sequenceSet; + } + + /** + * 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 'annotation'. + * + * @param annotation + * the value of field 'annotation'. + */ + public void setAnnotation(final jalview.binding.Annotation annotation) + { + this._annotation = annotation; + } + + /** + * Sets the value of field 'sequenceSet'. + * + * @param sequenceSet + * the value of field 'sequenceSet'. + */ + public void setSequenceSet(final jalview.binding.SequenceSet sequenceSet) + { + this._sequenceSet = sequenceSet; + } + + /** + * 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.binding.Alignment + */ + public static jalview.binding.Alignment unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, + org.exolab.castor.xml.ValidationException + { + return (jalview.binding.Alignment) Unmarshaller.unmarshal( + jalview.binding.Alignment.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); + } }