X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FAnnotation.java;h=95447d399ab22ad716dc35a8c209383628413332;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=6879c963ece5a73b28004c0dc2f4c71f53718db1;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git
diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java
old mode 100755
new mode 100644
index 6879c96..95447d3
--- a/src/jalview/binding/Annotation.java
+++ b/src/jalview/binding/Annotation.java
@@ -1,394 +1,449 @@
-/*
- * 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;
-
-//---------------------------------/
-//- 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;
-
-
-/**
- * Class Annotation.
- *
- * @version $Revision$ $Date$
- */
-public class Annotation implements java.io.Serializable {
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * Field _graph
- */
- private boolean _graph;
-
- /**
- * keeps track of state for field: _graph
- */
- private boolean _has_graph;
-
- /**
- * Field _annotationElementList
- */
- private java.util.Vector _annotationElementList;
-
- /**
- * Field _label
- */
- private java.lang.String _label;
-
- /**
- * Field _description
- */
- private java.lang.String _description;
-
- //----------------/
- //- Constructors -/
- //----------------/
- public Annotation() {
- super();
- _annotationElementList = new Vector();
- }
- //-- jalview.binding.Annotation()
- //-----------/
-
- public void addAnnotationElement(
- jalview.binding.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException {
- _annotationElementList.addElement(vAnnotationElement);
- }
- //-- void addAnnotationElement(jalview.binding.AnnotationElement)
-
- /**
- * Method addAnnotationElement
- *
- *
- *
- * @param index
- * @param vAnnotationElement
- */
- public void addAnnotationElement(int index,
- jalview.binding.AnnotationElement vAnnotationElement)
- throws java.lang.IndexOutOfBoundsException {
- _annotationElementList.insertElementAt(vAnnotationElement, index);
- }
- //-- void addAnnotationElement(int, jalview.binding.AnnotationElement)
-
- /**
- * Method deleteGraph
- *
- */
- public void deleteGraph() {
- this._has_graph = false;
- }
- //-- void deleteGraph()
-
- /**
- * Method enumerateAnnotationElement
- *
- *
- *
- * @return Enumeration
- */
- public java.util.Enumeration enumerateAnnotationElement() {
- return _annotationElementList.elements();
- }
- //-- java.util.Enumeration enumerateAnnotationElement()
-
- /**
- * Method getAnnotationElement
- *
- *
- *
- * @param index
- * @return AnnotationElement
- */
- public jalview.binding.AnnotationElement getAnnotationElement(int index)
- 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)
-
- /**
- * Method getAnnotationElement
- *
- *
- *
- * @return AnnotationElement
- */
- 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()
-
- /**
- * Method getAnnotationElementCount
- *
- *
- *
- * @return int
- */
- public int getAnnotationElementCount() {
- return _annotationElementList.size();
- }
- //-- 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()
-
- /**
- * Returns the value of field 'graph'.
- *
- * @return boolean
- * @return the value of field 'graph'.
- */
- public boolean getGraph() {
- return this._graph;
- }
- //-- 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()
-
- /**
- * Method hasGraph
- *
- *
- *
- * @return boolean
- */
- public boolean hasGraph() {
- return this._has_graph;
- }
- //-- boolean hasGraph()
-
- /**
- * Method isValid
- *
- *
- *
- * @return boolean
- */
- public boolean isValid() {
- try {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex) {
- return false;
- }
-
- return true;
- }
- //-- 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)
-
- /**
- * 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)
-
- /**
- * Method removeAllAnnotationElement
- *
- */
- public void removeAllAnnotationElement() {
- _annotationElementList.removeAllElements();
- }
- //-- void removeAllAnnotationElement()
-
- /**
- * Method removeAnnotationElement
- *
- *
- *
- * @param index
- * @return AnnotationElement
- */
- 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)
-
- /**
- * Method setAnnotationElement
- *
- *
- *
- * @param index
- * @param vAnnotationElement
- */
- 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)
-
- /**
- * Method setAnnotationElement
- *
- *
- *
- * @param 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)
-
- /**
- * 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)
-
- /**
- * 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)
-
- /**
- * 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)
-
- /**
- * 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)
-
- /**
- * 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()
-}
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * 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 Jalview. If not, see .
+ *******************************************************************************/
+/*
+ * This class was automatically generated with
+ * Castor 1.1, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.binding;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Class Annotation.
+ *
+ * @version $Revision$ $Date$
+ */
+public class Annotation implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _graph.
+ */
+ private boolean _graph;
+
+ /**
+ * keeps track of state for field: _graph
+ */
+ 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;
+
+ /**
+ * Field _label.
+ */
+ private java.lang.String _label;
+
+ /**
+ * Field _description.
+ */
+ private java.lang.String _description;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public Annotation() {
+ super();
+ this._annotationElementList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAnnotationElement(
+ final jalview.binding.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException {
+ this._annotationElementList.addElement(vAnnotationElement);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addAnnotationElement(
+ final int index,
+ final jalview.binding.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException {
+ this._annotationElementList.add(index, vAnnotationElement);
+ }
+
+ /**
+ */
+ public void deleteGraph(
+ ) {
+ this._has_graph= false;
+ }
+
+ /**
+ */
+ public void deleteGraphType(
+ ) {
+ this._has_graphType= false;
+ }
+
+ /**
+ * Method enumerateAnnotationElement.
+ *
+ * @return an Enumeration over all
+ * jalview.binding.AnnotationElement elements
+ */
+ public java.util.Enumeration enumerateAnnotationElement(
+ ) {
+ return this._annotationElementList.elements();
+ }
+
+ /**
+ * Method getAnnotationElement.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the jalview.binding.AnnotationElement
+ * at the given index
+ */
+ public jalview.binding.AnnotationElement getAnnotationElement(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationElementList.size()) {
+ throw new IndexOutOfBoundsException("getAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
+ }
+
+ return (jalview.binding.AnnotationElement) _annotationElementList.get(index);
+ }
+
+ /**
+ * Method getAnnotationElement.Returns the contents of the
+ * collection in an Array. Note: Just in case the
+ * collection contents are changing in another thread, we pass
+ * a 0-length Array of the correct type into the API call.
+ * This way we know that the Array returned is of
+ * exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.binding.AnnotationElement[] getAnnotationElement(
+ ) {
+ jalview.binding.AnnotationElement[] array = new jalview.binding.AnnotationElement[0];
+ return (jalview.binding.AnnotationElement[]) this._annotationElementList.toArray(array);
+ }
+
+ /**
+ * Method getAnnotationElementCount.
+ *
+ * @return the size of this collection
+ */
+ public int getAnnotationElementCount(
+ ) {
+ return this._annotationElementList.size();
+ }
+
+ /**
+ * Returns the value of field 'description'.
+ *
+ * @return the value of field 'Description'.
+ */
+ public java.lang.String getDescription(
+ ) {
+ return this._description;
+ }
+
+ /**
+ * Returns the value of field 'graph'.
+ *
+ * @return the value of field 'Graph'.
+ */
+ public boolean getGraph(
+ ) {
+ return this._graph;
+ }
+
+ /**
+ * Returns the value of field 'graphType'.
+ *
+ * @return the value of field 'GraphType'.
+ */
+ public int getGraphType(
+ ) {
+ return this._graphType;
+ }
+
+ /**
+ * Returns the value of field 'label'.
+ *
+ * @return the value of field 'Label'.
+ */
+ public java.lang.String getLabel(
+ ) {
+ return this._label;
+ }
+
+ /**
+ * Method hasGraph.
+ *
+ * @return true if at least one Graph has been added
+ */
+ public boolean hasGraph(
+ ) {
+ return this._has_graph;
+ }
+
+ /**
+ * Method hasGraphType.
+ *
+ * @return true if at least one GraphType has been added
+ */
+ public boolean hasGraphType(
+ ) {
+ return this._has_graphType;
+ }
+
+ /**
+ * Returns the value of field 'graph'.
+ *
+ * @return the value of field 'Graph'.
+ */
+ public boolean isGraph(
+ ) {
+ return this._graph;
+ }
+
+ /**
+ * 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);
+ }
+
+ /**
+ */
+ public void removeAllAnnotationElement(
+ ) {
+ this._annotationElementList.clear();
+ }
+
+ /**
+ * Method removeAnnotationElement.
+ *
+ * @param vAnnotationElement
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeAnnotationElement(
+ final jalview.binding.AnnotationElement vAnnotationElement) {
+ boolean removed = _annotationElementList.remove(vAnnotationElement);
+ return removed;
+ }
+
+ /**
+ * Method removeAnnotationElementAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.binding.AnnotationElement removeAnnotationElementAt(
+ final int index) {
+ java.lang.Object obj = this._annotationElementList.remove(index);
+ return (jalview.binding.AnnotationElement) obj;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vAnnotationElement
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setAnnotationElement(
+ final int index,
+ final jalview.binding.AnnotationElement vAnnotationElement)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._annotationElementList.size()) {
+ throw new IndexOutOfBoundsException("setAnnotationElement: Index value '" + index + "' not in range [0.." + (this._annotationElementList.size() - 1) + "]");
+ }
+
+ this._annotationElementList.set(index, vAnnotationElement);
+ }
+
+ /**
+ *
+ *
+ * @param vAnnotationElementArray
+ */
+ public void setAnnotationElement(
+ final jalview.binding.AnnotationElement[] vAnnotationElementArray) {
+ //-- copy array
+ _annotationElementList.clear();
+
+ for (int i = 0; i < vAnnotationElementArray.length; i++) {
+ this._annotationElementList.add(vAnnotationElementArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'description'.
+ *
+ * @param description the value of field 'description'.
+ */
+ public void setDescription(
+ final java.lang.String description) {
+ this._description = description;
+ }
+
+ /**
+ * Sets the value of field 'graph'.
+ *
+ * @param graph the value of field 'graph'.
+ */
+ public void setGraph(
+ final boolean graph) {
+ this._graph = graph;
+ this._has_graph = true;
+ }
+
+ /**
+ * Sets the value of field 'graphType'.
+ *
+ * @param graphType the value of field 'graphType'.
+ */
+ public void setGraphType(
+ final int graphType) {
+ this._graphType = graphType;
+ this._has_graphType = true;
+ }
+
+ /**
+ * Sets the value of field 'label'.
+ *
+ * @param label the value of field 'label'.
+ */
+ public void setLabel(
+ final java.lang.String label) {
+ this._label = label;
+ }
+
+ /**
+ * 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.Annotation
+ */
+ public static jalview.binding.Annotation unmarshal(
+ final 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);
+ }
+
+ /**
+ *
+ *
+ * @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);
+ }
+
+}