X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FAnnotation.java;h=66f183d3126e8b72cf658ac2f14c4757153cd5ee;hb=4a62141371fa3ab28aa2e21bab95399e97382142;hp=6879c963ece5a73b28004c0dc2f4c71f53718db1;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java index 6879c96..66f183d 100755 --- a/src/jalview/binding/Annotation.java +++ b/src/jalview/binding/Annotation.java @@ -1,56 +1,38 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ -/* -* Jalview - A Sequence Alignment Editor and Viewer -* Copyright (C) 2005 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.binding; - -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; +package jalview.binding; + //---------------------------------/ + //- 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 java.util.Enumeration; import java.util.Vector; - +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 Annotation. - * + * * @version $Revision$ $Date$ */ public class Annotation implements java.io.Serializable { - //--------------------------/ - //- Class/Member Variables -/ + + + //--------------------------/ + //- Class/Member Variables -/ //--------------------------/ /** @@ -64,6 +46,16 @@ public class Annotation implements java.io.Serializable { private boolean _has_graph; /** + * Field _graphType + */ + private int _graphType; + + /** + * keeps track of state for field: _graphType + */ + private boolean _has_graphType; + + /** * Field _annotationElementList */ private java.util.Vector _annotationElementList; @@ -78,317 +70,363 @@ public class Annotation implements java.io.Serializable { */ private java.lang.String _description; + + //----------------/ + //- Constructors -/ //----------------/ - //- Constructors -/ - //----------------/ + public Annotation() { super(); _annotationElementList = new Vector(); - } - //-- jalview.binding.Annotation() - //-----------/ + } //-- jalview.binding.Annotation() - public void addAnnotationElement( - jalview.binding.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException { + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method addAnnotationElement + * + * + * + * @param vAnnotationElement + */ + public void addAnnotationElement(jalview.binding.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException + { _annotationElementList.addElement(vAnnotationElement); - } - //-- void addAnnotationElement(jalview.binding.AnnotationElement) + } //-- void addAnnotationElement(jalview.binding.AnnotationElement) /** * Method addAnnotationElement - * - * - * + * + * + * * @param index * @param vAnnotationElement */ - public void addAnnotationElement(int index, - jalview.binding.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException { + public void addAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException + { _annotationElementList.insertElementAt(vAnnotationElement, index); - } - //-- void addAnnotationElement(int, jalview.binding.AnnotationElement) + } //-- void addAnnotationElement(int, jalview.binding.AnnotationElement) /** * Method deleteGraph - * + * */ - public void deleteGraph() { - this._has_graph = false; - } - //-- void deleteGraph() + public void deleteGraph() + { + this._has_graph= false; + } //-- void deleteGraph() + + /** + * Method deleteGraphType + * + */ + public void deleteGraphType() + { + this._has_graphType= false; + } //-- void deleteGraphType() /** * Method enumerateAnnotationElement - * - * - * + * + * + * * @return Enumeration */ - public java.util.Enumeration enumerateAnnotationElement() { + public java.util.Enumeration enumerateAnnotationElement() + { return _annotationElementList.elements(); - } - //-- java.util.Enumeration enumerateAnnotationElement() + } //-- java.util.Enumeration enumerateAnnotationElement() /** * Method getAnnotationElement - * - * - * + * + * + * * @param index * @return AnnotationElement */ public jalview.binding.AnnotationElement getAnnotationElement(int index) - throws java.lang.IndexOutOfBoundsException { + throws java.lang.IndexOutOfBoundsException + { //-- check bounds for index if ((index < 0) || (index > _annotationElementList.size())) { throw new IndexOutOfBoundsException(); } - + return (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index); - } - //-- jalview.binding.AnnotationElement getAnnotationElement(int) + } //-- jalview.binding.AnnotationElement getAnnotationElement(int) /** * Method getAnnotationElement - * - * - * + * + * + * * @return AnnotationElement */ - public jalview.binding.AnnotationElement[] getAnnotationElement() { + public jalview.binding.AnnotationElement[] getAnnotationElement() + { int size = _annotationElementList.size(); jalview.binding.AnnotationElement[] mArray = new jalview.binding.AnnotationElement[size]; - for (int index = 0; index < size; index++) { mArray[index] = (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index); } - return mArray; - } - //-- jalview.binding.AnnotationElement[] getAnnotationElement() + } //-- jalview.binding.AnnotationElement[] getAnnotationElement() /** * Method getAnnotationElementCount - * - * - * + * + * + * * @return int */ - public int getAnnotationElementCount() { + public int getAnnotationElementCount() + { return _annotationElementList.size(); - } - //-- int getAnnotationElementCount() + } //-- int getAnnotationElementCount() /** * Returns the value of field 'description'. - * + * * @return String * @return the value of field 'description'. */ - public java.lang.String getDescription() { + public java.lang.String getDescription() + { return this._description; - } - //-- java.lang.String getDescription() + } //-- java.lang.String getDescription() /** * Returns the value of field 'graph'. - * + * * @return boolean * @return the value of field 'graph'. */ - public boolean getGraph() { + public boolean getGraph() + { return this._graph; - } - //-- boolean getGraph() + } //-- boolean getGraph() + + /** + * Returns the value of field 'graphType'. + * + * @return int + * @return the value of field 'graphType'. + */ + public int getGraphType() + { + return this._graphType; + } //-- int getGraphType() /** * Returns the value of field 'label'. - * + * * @return String * @return the value of field 'label'. */ - public java.lang.String getLabel() { + public java.lang.String getLabel() + { return this._label; - } - //-- java.lang.String getLabel() + } //-- java.lang.String getLabel() /** * Method hasGraph - * - * - * + * + * + * * @return boolean */ - public boolean hasGraph() { + public boolean hasGraph() + { return this._has_graph; - } - //-- boolean hasGraph() + } //-- boolean hasGraph() + + /** + * Method hasGraphType + * + * + * + * @return boolean + */ + public boolean hasGraphType() + { + return this._has_graphType; + } //-- boolean hasGraphType() /** * Method isValid - * - * - * + * + * + * * @return boolean */ - public boolean isValid() { + public boolean isValid() + { try { validate(); - } catch (org.exolab.castor.xml.ValidationException vex) { + } + catch (org.exolab.castor.xml.ValidationException vex) { return false; } - return true; - } - //-- boolean isValid() + } //-- boolean isValid() /** * Method marshal - * - * - * + * + * + * * @param out */ public void marshal(java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException { + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + Marshaller.marshal(this, out); - } - //-- void marshal(java.io.Writer) + } //-- 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 { + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + Marshaller.marshal(this, handler); - } - //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Method removeAllAnnotationElement - * + * */ - public void removeAllAnnotationElement() { + public void removeAllAnnotationElement() + { _annotationElementList.removeAllElements(); - } - //-- void removeAllAnnotationElement() + } //-- void removeAllAnnotationElement() /** * Method removeAnnotationElement - * - * - * + * + * + * * @param index * @return AnnotationElement */ - public jalview.binding.AnnotationElement removeAnnotationElement(int index) { + public jalview.binding.AnnotationElement removeAnnotationElement(int index) + { java.lang.Object obj = _annotationElementList.elementAt(index); _annotationElementList.removeElementAt(index); - return (jalview.binding.AnnotationElement) obj; - } - //-- jalview.binding.AnnotationElement removeAnnotationElement(int) + } //-- jalview.binding.AnnotationElement removeAnnotationElement(int) /** * Method setAnnotationElement - * - * - * + * + * + * * @param index * @param vAnnotationElement */ - public void setAnnotationElement(int index, - jalview.binding.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException { + public void setAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException + { //-- check bounds for index if ((index < 0) || (index > _annotationElementList.size())) { throw new IndexOutOfBoundsException(); } - _annotationElementList.setElementAt(vAnnotationElement, index); - } - //-- void setAnnotationElement(int, jalview.binding.AnnotationElement) + } //-- void setAnnotationElement(int, jalview.binding.AnnotationElement) /** * Method setAnnotationElement - * - * - * + * + * + * * @param annotationElementArray */ - public void setAnnotationElement( - jalview.binding.AnnotationElement[] annotationElementArray) { + public void setAnnotationElement(jalview.binding.AnnotationElement[] annotationElementArray) + { //-- copy array _annotationElementList.removeAllElements(); - for (int i = 0; i < annotationElementArray.length; i++) { _annotationElementList.addElement(annotationElementArray[i]); } - } - //-- void setAnnotationElement(jalview.binding.AnnotationElement) + } //-- void setAnnotationElement(jalview.binding.AnnotationElement) /** * Sets the value of field 'description'. - * + * * @param description the value of field 'description'. */ - public void setDescription(java.lang.String description) { + public void setDescription(java.lang.String description) + { this._description = description; - } - //-- void setDescription(java.lang.String) + } //-- void setDescription(java.lang.String) /** * Sets the value of field 'graph'. - * + * * @param graph the value of field 'graph'. */ - public void setGraph(boolean graph) { + public void setGraph(boolean graph) + { this._graph = graph; this._has_graph = true; - } - //-- void setGraph(boolean) + } //-- void setGraph(boolean) + + /** + * Sets the value of field 'graphType'. + * + * @param graphType the value of field 'graphType'. + */ + public void setGraphType(int graphType) + { + this._graphType = graphType; + this._has_graphType = true; + } //-- void setGraphType(int) /** * Sets the value of field 'label'. - * + * * @param label the value of field 'label'. */ - public void setLabel(java.lang.String label) { + public void setLabel(java.lang.String label) + { this._label = label; - } - //-- void setLabel(java.lang.String) + } //-- void setLabel(java.lang.String) /** * Method unmarshal - * - * - * + * + * + * * @param reader * @return Object */ public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException { - return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class, - reader); - } - //-- java.lang.Object unmarshal(java.io.Reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class, reader); + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ - public void validate() throws org.exolab.castor.xml.ValidationException { + public void validate() + throws org.exolab.castor.xml.ValidationException + { org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); validator.validate(this); - } - //-- void validate() + } //-- void validate() + }