X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FAnnotation.java;h=9ee76e353699790dff442494c234126ffa988dbb;hb=cd07a161a10680208029f76aa46710c1032aae46;hp=54811be5832ee7abc85084b30b6bd72c99ac6966;hpb=65df62f4b048a1615d32ea2c3576082ad2b63af8;p=jalview.git diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java index 54811be..9ee76e3 100755 --- a/src/jalview/schemabinding/version2/Annotation.java +++ b/src/jalview/schemabinding/version2/Annotation.java @@ -1,6 +1,6 @@ /* * This class was automatically generated with - * Castor 0.9.6, using an XML + * Castor 1.1, using an XML * Schema. * $Id$ */ @@ -11,17 +11,8 @@ package jalview.schemabinding.version2; //- 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. @@ -36,7 +27,7 @@ public class Annotation implements java.io.Serializable { //--------------------------/ /** - * Field _graph + * Field _graph. */ private boolean _graph; @@ -46,7 +37,7 @@ public class Annotation implements java.io.Serializable { private boolean _has_graph; /** - * Field _graphType + * Field _graphType. */ private int _graphType; @@ -56,20 +47,85 @@ public class Annotation implements java.io.Serializable { private boolean _has_graphType; /** - * Field _annotationElementList + * Field _sequenceRef. + */ + private java.lang.String _sequenceRef; + + /** + * Field _graphColour. + */ + private int _graphColour; + + /** + * keeps track of state for field: _graphColour + */ + private boolean _has_graphColour; + + /** + * Field _graphGroup. + */ + private int _graphGroup; + + /** + * keeps track of state for field: _graphGroup + */ + private boolean _has_graphGroup; + + /** + * Field _id. + */ + private java.lang.String _id; + + /** + * Field _scoreOnly. + */ + private boolean _scoreOnly = false; + + /** + * keeps track of state for field: _scoreOnly + */ + private boolean _has_scoreOnly; + + /** + * Field _score. + */ + private double _score; + + /** + * keeps track of state for field: _score + */ + private boolean _has_score; + + /** + * Field _visible. + */ + private boolean _visible; + + /** + * keeps track of state for field: _visible + */ + private boolean _has_visible; + + /** + * Field _annotationElementList. */ private java.util.Vector _annotationElementList; /** - * Field _label + * Field _label. */ private java.lang.String _label; /** - * Field _description + * Field _description. */ private java.lang.String _description; + /** + * Field _thresholdLine. + */ + private jalview.schemabinding.version2.ThresholdLine _thresholdLine; + //----------------/ //- Constructors -/ @@ -77,8 +133,8 @@ public class Annotation implements java.io.Serializable { public Annotation() { super(); - _annotationElementList = new Vector(); - } //-- jalview.schemabinding.version2.Annotation() + this._annotationElementList = new java.util.Vector(); + } //-----------/ @@ -86,347 +142,628 @@ public class Annotation implements java.io.Serializable { //-----------/ /** - * Method addAnnotationElement - * * * * @param vAnnotationElement + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection */ - public void addAnnotationElement(jalview.schemabinding.version2.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - _annotationElementList.addElement(vAnnotationElement); - } //-- void addAnnotationElement(jalview.schemabinding.version2.AnnotationElement) + public void addAnnotationElement( + final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException { + this._annotationElementList.addElement(vAnnotationElement); + } /** - * Method addAnnotationElement - * * * * @param index * @param vAnnotationElement + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection */ - public void addAnnotationElement(int index, jalview.schemabinding.version2.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - _annotationElementList.insertElementAt(vAnnotationElement, index); - } //-- void addAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement) + public void addAnnotationElement( + final int index, + final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException { + this._annotationElementList.add(index, vAnnotationElement); + } /** - * Method deleteGraph - * */ - public void deleteGraph() - { + public void deleteGraph( + ) { this._has_graph= false; - } //-- void deleteGraph() + } + + /** + */ + public void deleteGraphColour( + ) { + this._has_graphColour= false; + } + + /** + */ + public void deleteGraphGroup( + ) { + this._has_graphGroup= false; + } /** - * Method deleteGraphType - * */ - public void deleteGraphType() - { + public void deleteGraphType( + ) { this._has_graphType= false; - } //-- void deleteGraphType() + } /** - * Method enumerateAnnotationElement - * - * - * - * @return Enumeration */ - public java.util.Enumeration enumerateAnnotationElement() - { - return _annotationElementList.elements(); - } //-- java.util.Enumeration enumerateAnnotationElement() + public void deleteScore( + ) { + this._has_score= false; + } /** - * Method getAnnotationElement - * + */ + public void deleteScoreOnly( + ) { + this._has_scoreOnly= false; + } + + /** + */ + public void deleteVisible( + ) { + this._has_visible= false; + } + + /** + * Method enumerateAnnotationElement. * + * @return an Enumeration over all + * jalview.schemabinding.version2.AnnotationElement elements + */ + public java.util.Enumeration enumerateAnnotationElement( + ) { + return this._annotationElementList.elements(); + } + + /** + * Method getAnnotationElement. * * @param index - * @return AnnotationElement - */ - public jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _annotationElementList.size())) { - throw new IndexOutOfBoundsException(); + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + * @return the value of the + * jalview.schemabinding.version2.AnnotationElement at the + * given index + */ + public jalview.schemabinding.version2.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.schemabinding.version2.AnnotationElement) _annotationElementList.elementAt(index); - } //-- jalview.schemabinding.version2.AnnotationElement getAnnotationElement(int) + return (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.get(index); + } /** - * Method getAnnotationElement - * - * + * 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 AnnotationElement + * @return this collection as an Array */ - public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement() - { - int size = _annotationElementList.size(); - jalview.schemabinding.version2.AnnotationElement[] mArray = new jalview.schemabinding.version2.AnnotationElement[size]; - for (int index = 0; index < size; index++) { - mArray[index] = (jalview.schemabinding.version2.AnnotationElement) _annotationElementList.elementAt(index); - } - return mArray; - } //-- jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement() + public jalview.schemabinding.version2.AnnotationElement[] getAnnotationElement( + ) { + jalview.schemabinding.version2.AnnotationElement[] array = new jalview.schemabinding.version2.AnnotationElement[0]; + return (jalview.schemabinding.version2.AnnotationElement[]) this._annotationElementList.toArray(array); + } /** - * Method getAnnotationElementCount - * + * Method getAnnotationElementCount. * - * - * @return int + * @return the size of this collection */ - public int getAnnotationElementCount() - { - return _annotationElementList.size(); - } //-- int getAnnotationElementCount() + public int getAnnotationElementCount( + ) { + return this._annotationElementList.size(); + } /** * Returns the value of field 'description'. * - * @return String - * @return the value of field 'description'. + * @return the value of field 'Description'. */ - public java.lang.String getDescription() - { + 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'. + * @return the value of field 'Graph'. */ - public boolean getGraph() - { + public boolean getGraph( + ) { return this._graph; - } //-- boolean getGraph() + } + + /** + * Returns the value of field 'graphColour'. + * + * @return the value of field 'GraphColour'. + */ + public int getGraphColour( + ) { + return this._graphColour; + } + + /** + * Returns the value of field 'graphGroup'. + * + * @return the value of field 'GraphGroup'. + */ + public int getGraphGroup( + ) { + return this._graphGroup; + } /** * Returns the value of field 'graphType'. * - * @return int - * @return the value of field 'graphType'. + * @return the value of field 'GraphType'. */ - public int getGraphType() - { + public int getGraphType( + ) { return this._graphType; - } //-- int getGraphType() + } + + /** + * Returns the value of field 'id'. + * + * @return the value of field 'Id'. + */ + public java.lang.String getId( + ) { + return this._id; + } /** * Returns the value of field 'label'. * - * @return String - * @return the value of field 'label'. + * @return the value of field 'Label'. */ - public java.lang.String getLabel() - { + public java.lang.String getLabel( + ) { return this._label; - } //-- java.lang.String getLabel() + } /** - * Method hasGraph + * Returns the value of field 'score'. * + * @return the value of field 'Score'. + */ + public double getScore( + ) { + return this._score; + } + + /** + * Returns the value of field 'scoreOnly'. * + * @return the value of field 'ScoreOnly'. + */ + public boolean getScoreOnly( + ) { + return this._scoreOnly; + } + + /** + * Returns the value of field 'sequenceRef'. * - * @return boolean + * @return the value of field 'SequenceRef'. */ - public boolean hasGraph() - { + public java.lang.String getSequenceRef( + ) { + return this._sequenceRef; + } + + /** + * Returns the value of field 'thresholdLine'. + * + * @return the value of field 'ThresholdLine'. + */ + public jalview.schemabinding.version2.ThresholdLine getThresholdLine( + ) { + return this._thresholdLine; + } + + /** + * Returns the value of field 'visible'. + * + * @return the value of field 'Visible'. + */ + public boolean getVisible( + ) { + return this._visible; + } + + /** + * Method hasGraph. + * + * @return true if at least one Graph has been added + */ + public boolean hasGraph( + ) { return this._has_graph; - } //-- boolean hasGraph() + } /** - * Method hasGraphType + * Method hasGraphColour. * + * @return true if at least one GraphColour has been added + */ + public boolean hasGraphColour( + ) { + return this._has_graphColour; + } + + /** + * Method hasGraphGroup. * + * @return true if at least one GraphGroup has been added + */ + public boolean hasGraphGroup( + ) { + return this._has_graphGroup; + } + + /** + * Method hasGraphType. * - * @return boolean + * @return true if at least one GraphType has been added */ - public boolean hasGraphType() - { + public boolean hasGraphType( + ) { return this._has_graphType; - } //-- boolean hasGraphType() + } + + /** + * Method hasScore. + * + * @return true if at least one Score has been added + */ + public boolean hasScore( + ) { + return this._has_score; + } + + /** + * Method hasScoreOnly. + * + * @return true if at least one ScoreOnly has been added + */ + public boolean hasScoreOnly( + ) { + return this._has_scoreOnly; + } /** - * Method isValid + * Method hasVisible. * + * @return true if at least one Visible has been added + */ + public boolean hasVisible( + ) { + return this._has_visible; + } + + /** + * Returns the value of field 'graph'. * + * @return the value of field 'Graph'. + */ + public boolean isGraph( + ) { + return this._graph; + } + + /** + * Returns the value of field 'scoreOnly'. + * + * @return the value of field 'ScoreOnly'. + */ + public boolean isScoreOnly( + ) { + return this._scoreOnly; + } + + /** + * Method isValid. * - * @return boolean + * @return true if this object is valid according to the schema */ - 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() + } /** - * Method marshal + * Returns the value of field 'visible'. * + * @return the value of field 'Visible'. + */ + public boolean isVisible( + ) { + return this._visible; + } + + /** * * * @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 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); - } //-- 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 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); - } //-- void marshal(org.xml.sax.ContentHandler) + } /** - * Method removeAllAnnotationElement - * */ - public void removeAllAnnotationElement() - { - _annotationElementList.removeAllElements(); - } //-- void removeAllAnnotationElement() + public void removeAllAnnotationElement( + ) { + this._annotationElementList.clear(); + } /** - * Method removeAnnotationElement - * + * Method removeAnnotationElement. * + * @param vAnnotationElement + * @return true if the object was removed from the collection. + */ + public boolean removeAnnotationElement( + final jalview.schemabinding.version2.AnnotationElement vAnnotationElement) { + boolean removed = _annotationElementList.remove(vAnnotationElement); + return removed; + } + + /** + * Method removeAnnotationElementAt. * * @param index - * @return AnnotationElement + * @return the element removed from the collection */ - public jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int index) - { - java.lang.Object obj = _annotationElementList.elementAt(index); - _annotationElementList.removeElementAt(index); + public jalview.schemabinding.version2.AnnotationElement removeAnnotationElementAt( + final int index) { + java.lang.Object obj = this._annotationElementList.remove(index); return (jalview.schemabinding.version2.AnnotationElement) obj; - } //-- jalview.schemabinding.version2.AnnotationElement removeAnnotationElement(int) + } /** - * Method setAnnotationElement - * * * * @param index * @param vAnnotationElement - */ - public void setAnnotationElement(int index, jalview.schemabinding.version2.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ((index < 0) || (index > _annotationElementList.size())) { - throw new IndexOutOfBoundsException(); + * @throws java.lang.IndexOutOfBoundsException if the index + * given is outside the bounds of the collection + */ + public void setAnnotationElement( + final int index, + final jalview.schemabinding.version2.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) + "]"); } - _annotationElementList.setElementAt(vAnnotationElement, index); - } //-- void setAnnotationElement(int, jalview.schemabinding.version2.AnnotationElement) + + this._annotationElementList.set(index, vAnnotationElement); + } /** - * Method setAnnotationElement * * - * - * @param annotationElementArray + * @param vAnnotationElementArray */ - public void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement[] annotationElementArray) - { + public void setAnnotationElement( + final jalview.schemabinding.version2.AnnotationElement[] vAnnotationElementArray) { //-- copy array - _annotationElementList.removeAllElements(); - for (int i = 0; i < annotationElementArray.length; i++) { - _annotationElementList.addElement(annotationElementArray[i]); + _annotationElementList.clear(); + + for (int i = 0; i < vAnnotationElementArray.length; i++) { + this._annotationElementList.add(vAnnotationElementArray[i]); } - } //-- void setAnnotationElement(jalview.schemabinding.version2.AnnotationElement) + } /** * Sets the value of field 'description'. * * @param description the value of field 'description'. */ - public void setDescription(java.lang.String description) - { + public void setDescription( + final 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) - { + public void setGraph( + final boolean graph) { this._graph = graph; this._has_graph = true; - } //-- void setGraph(boolean) + } + + /** + * Sets the value of field 'graphColour'. + * + * @param graphColour the value of field 'graphColour'. + */ + public void setGraphColour( + final int graphColour) { + this._graphColour = graphColour; + this._has_graphColour = true; + } + + /** + * Sets the value of field 'graphGroup'. + * + * @param graphGroup the value of field 'graphGroup'. + */ + public void setGraphGroup( + final int graphGroup) { + this._graphGroup = graphGroup; + this._has_graphGroup = true; + } /** * Sets the value of field 'graphType'. * * @param graphType the value of field 'graphType'. */ - public void setGraphType(int graphType) - { + public void setGraphType( + final int graphType) { this._graphType = graphType; this._has_graphType = true; - } //-- void setGraphType(int) + } + + /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId( + final java.lang.String id) { + this._id = id; + } /** * Sets the value of field 'label'. * * @param label the value of field 'label'. */ - public void setLabel(java.lang.String label) - { + public void setLabel( + final java.lang.String label) { this._label = label; - } //-- void setLabel(java.lang.String) + } /** - * Method unmarshal + * Sets the value of field 'score'. * + * @param score the value of field 'score'. + */ + public void setScore( + final double score) { + this._score = score; + this._has_score = true; + } + + /** + * Sets the value of field 'scoreOnly'. * + * @param scoreOnly the value of field 'scoreOnly'. + */ + public void setScoreOnly( + final boolean scoreOnly) { + this._scoreOnly = scoreOnly; + this._has_scoreOnly = true; + } + + /** + * Sets the value of field 'sequenceRef'. * - * @param reader - * @return Object + * @param sequenceRef the value of field 'sequenceRef'. */ - public static java.lang.Object unmarshal(java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException - { + public void setSequenceRef( + final java.lang.String sequenceRef) { + this._sequenceRef = sequenceRef; + } + + /** + * Sets the value of field 'thresholdLine'. + * + * @param thresholdLine the value of field 'thresholdLine'. + */ + public void setThresholdLine( + final jalview.schemabinding.version2.ThresholdLine thresholdLine) { + this._thresholdLine = thresholdLine; + } + + /** + * Sets the value of field 'visible'. + * + * @param visible the value of field 'visible'. + */ + public void setVisible( + final boolean visible) { + this._visible = visible; + this._has_visible = true; + } + + /** + * 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.schemabinding.version2.Annotation + */ + public static jalview.schemabinding.version2.Annotation unmarshal( + final java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { return (jalview.schemabinding.version2.Annotation) Unmarshaller.unmarshal(jalview.schemabinding.version2.Annotation.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + } /** - * Method validate * + * + * @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 - { + 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() + } }