X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FAnnotation.java;h=95447d399ab22ad716dc35a8c209383628413332;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=b482598058f4c7ae45d446dace26d2add7267ae7;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java old mode 100755 new mode 100644 index b482598..95447d3 --- a/src/jalview/binding/Annotation.java +++ b/src/jalview/binding/Annotation.java @@ -1,24 +1,31 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5) - * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle - * +/******************************************************************************* + * 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 -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ import org.exolab.castor.xml.Marshaller; @@ -29,441 +36,414 @@ import org.exolab.castor.xml.Unmarshaller; * * @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) + "]"); +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); } - 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; + /** + * Method getAnnotationElementCount. + * + * @return the size of this collection + */ + public int getAnnotationElementCount( + ) { + return this._annotationElementList.size(); } - 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) + "]"); + + /** + * 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; } - 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]); + /** + * 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); } - } - - /** - * 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); - } }