X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FAnnotation.java;h=86f1a63f364c78a4adaf7d4864e19a78f566882f;hb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;hp=ec3e248a02f7343453ab9c4b5ba6c79fc2667ef1;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java old mode 100755 new mode 100644 index ec3e248..86f1a63 --- a/src/jalview/binding/Annotation.java +++ b/src/jalview/binding/Annotation.java @@ -1,26 +1,15 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 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 + * This class was automatically generated with + * Castor 1.1, using an XML + * Schema. + * $Id$ */ + package jalview.binding; -// ---------------------------------/ -// - Imported classes and packages -/ -// ---------------------------------/ +//---------------------------------/ +//- Imported classes and packages -/ +//---------------------------------/ import org.exolab.castor.xml.Marshaller; import org.exolab.castor.xml.Unmarshaller; @@ -91,7 +80,7 @@ public class Annotation implements java.io.Serializable * * @param vAnnotationElement * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * if the index given is outside the bounds of the collection */ public void addAnnotationElement( final jalview.binding.AnnotationElement vAnnotationElement) @@ -106,7 +95,7 @@ public class Annotation implements java.io.Serializable * @param index * @param vAnnotationElement * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * if the index given is outside the bounds of the collection */ public void addAnnotationElement(final int index, final jalview.binding.AnnotationElement vAnnotationElement) @@ -116,14 +105,14 @@ public class Annotation implements java.io.Serializable } /** - */ + */ public void deleteGraph() { this._has_graph = false; } /** - */ + */ public void deleteGraphType() { this._has_graphType = false; @@ -144,7 +133,7 @@ public class Annotation implements java.io.Serializable * * @param index * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * if the index given is outside the bounds of the collection * @return the value of the jalview.binding.AnnotationElement at the given * index */ @@ -283,11 +272,10 @@ public class Annotation implements java.io.Serializable * * @param out * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling + * 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 + * 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, @@ -301,13 +289,12 @@ public class Annotation implements java.io.Serializable * * @param handler * @throws java.io.IOException - * if an IOException occurs during marshaling + * if an IOException occurs during marshaling * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the - * schema + * 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 + * 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, @@ -318,7 +305,7 @@ public class Annotation implements java.io.Serializable } /** - */ + */ public void removeAllAnnotationElement() { this._annotationElementList.clear(); @@ -356,7 +343,7 @@ public class Annotation implements java.io.Serializable * @param index * @param vAnnotationElement * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection + * if the index given is outside the bounds of the collection */ public void setAnnotationElement(final int index, final jalview.binding.AnnotationElement vAnnotationElement) @@ -395,7 +382,7 @@ public class Annotation implements java.io.Serializable * Sets the value of field 'description'. * * @param description - * the value of field 'description'. + * the value of field 'description'. */ public void setDescription(final java.lang.String description) { @@ -406,7 +393,7 @@ public class Annotation implements java.io.Serializable * Sets the value of field 'graph'. * * @param graph - * the value of field 'graph'. + * the value of field 'graph'. */ public void setGraph(final boolean graph) { @@ -418,7 +405,7 @@ public class Annotation implements java.io.Serializable * Sets the value of field 'graphType'. * * @param graphType - * the value of field 'graphType'. + * the value of field 'graphType'. */ public void setGraphType(final int graphType) { @@ -430,7 +417,7 @@ public class Annotation implements java.io.Serializable * Sets the value of field 'label'. * * @param label - * the value of field 'label'. + * the value of field 'label'. */ public void setLabel(final java.lang.String label) { @@ -442,11 +429,10 @@ public class Annotation implements java.io.Serializable * * @param reader * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling + * 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 + * if this object is an invalid instance according to the schema * @return the unmarshaled jalview.binding.Annotation */ public static jalview.binding.Annotation unmarshal( @@ -462,8 +448,7 @@ public class Annotation implements java.io.Serializable * * * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the - * schema + * if this object is an invalid instance according to the schema */ public void validate() throws org.exolab.castor.xml.ValidationException {