X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FAnnotation.java;h=fefdd12a4a2f007592fb3f845a72788242ec9e59;hb=206907e81392f14925eec7759d16d6cf07460f49;hp=4af694f695fc44b3427b3f1f5ebe9d1585ca394f;hpb=99c58ee0ae2a848f982552e53feaf6d5cb9925e5;p=jalview.git diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java index 4af694f..fefdd12 100755 --- a/src/jalview/binding/Annotation.java +++ b/src/jalview/binding/Annotation.java @@ -1,29 +1,10 @@ /* - * 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; //---------------------------------/ @@ -44,7 +25,7 @@ import org.xml.sax.ContentHandler; /** * Class Annotation. - * + * * @version $Revision$ $Date$ */ public class Annotation implements java.io.Serializable { @@ -96,22 +77,22 @@ public class Annotation implements java.io.Serializable { /** * 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 */ @@ -119,34 +100,34 @@ public class Annotation implements java.io.Serializable { 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() + } //-- void deleteGraph() /** * Method enumerateAnnotationElement - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateAnnotationElement() { return _annotationElementList.elements(); - } //-- java.util.Enumeration enumerateAnnotationElement() + } //-- java.util.Enumeration enumerateAnnotationElement() /** * Method getAnnotationElement - * - * - * + * + * + * * @param index * @return AnnotationElement */ @@ -157,15 +138,15 @@ public class Annotation implements java.io.Serializable { 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() @@ -176,70 +157,70 @@ public class Annotation implements java.io.Serializable { 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() { 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() { 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() { return this._graph; - } //-- boolean getGraph() + } //-- boolean getGraph() /** * Returns the value of field 'label'. - * + * * @return String * @return the value of field 'label'. */ public java.lang.String getLabel() { return this._label; - } //-- java.lang.String getLabel() + } //-- java.lang.String getLabel() /** * Method hasGraph - * - * - * + * + * + * * @return boolean */ public boolean hasGraph() { return this._has_graph; - } //-- boolean hasGraph() + } //-- boolean hasGraph() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() @@ -251,50 +232,50 @@ public class Annotation implements java.io.Serializable { 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 { - + 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 { - + Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + } //-- void marshal(org.xml.sax.ContentHandler) /** * Method removeAllAnnotationElement - * + * */ public void removeAllAnnotationElement() { _annotationElementList.removeAllElements(); - } //-- void removeAllAnnotationElement() + } //-- void removeAllAnnotationElement() /** * Method removeAnnotationElement - * - * - * + * + * + * * @param index * @return AnnotationElement */ @@ -303,13 +284,13 @@ public class Annotation implements java.io.Serializable { 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 */ @@ -321,13 +302,13 @@ public class Annotation implements java.io.Serializable { 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) @@ -337,44 +318,44 @@ public class Annotation implements java.io.Serializable { 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) { 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) { this._graph = graph; this._has_graph = true; - } //-- void setGraph(boolean) + } //-- void setGraph(boolean) /** * Sets the value of field 'label'. - * + * * @param label the value of field '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 */ @@ -382,17 +363,17 @@ public class Annotation implements java.io.Serializable { 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) + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ 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() }