From ffe9b478a182cab3c8217b5c2bf002c7c1b6d7ec Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Wed, 17 Aug 2005 09:12:03 +0000 Subject: [PATCH] Rebuilt with new schema --- src/jalview/binding/Alignment.java | 145 +- src/jalview/binding/Annotation.java | 724 ++++--- src/jalview/binding/AnnotationElement.java | 213 +- src/jalview/binding/Colour.java | 145 +- src/jalview/binding/JGroup.java | 512 ++--- src/jalview/binding/JSeq.java | 237 +-- src/jalview/binding/JalviewModel.java | 173 +- src/jalview/binding/JalviewModelSequence.java | 1744 ++++++++------- src/jalview/binding/JalviewUserColours.java | 258 ++- src/jalview/binding/Sequence.java | 178 +- src/jalview/binding/SequenceSet.java | 393 ++-- src/jalview/binding/SequenceType.java | 359 ++-- src/jalview/binding/Tree.java | 563 ++--- src/jalview/binding/UserColourScheme.java | 178 +- src/jalview/binding/UserColours.java | 308 +-- src/jalview/binding/VAMSAS.java | 1133 +++++----- src/jalview/binding/VamsasModel.java | 113 +- src/jalview/binding/Viewport.java | 2805 +++++++++++++------------ 18 files changed, 4841 insertions(+), 5340 deletions(-) diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java index 78fff89..9a38f10 100755 --- a/src/jalview/binding/Alignment.java +++ b/src/jalview/binding/Alignment.java @@ -1,36 +1,36 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ -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; +package jalview.binding; + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ + import java.io.IOException; import java.io.Reader; import java.io.Serializable; import java.io.Writer; - +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 Alignment. - * + * * @version $Revision$ $Date$ */ -public class Alignment implements java.io.Serializable -{ - //--------------------------/ - //- Class/Member Variables -/ +public class Alignment implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ //--------------------------/ /** @@ -43,148 +43,131 @@ public class Alignment implements java.io.Serializable */ private jalview.binding.SequenceSet _sequenceSet; + + //----------------/ + //- Constructors -/ //----------------/ - //- Constructors -/ - //----------------/ - public Alignment() - { + + public Alignment() { super(); - } + } //-- jalview.binding.Alignment() - //-- jalview.binding.Alignment() + + //-----------/ + //- Methods -/ //-----------/ /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * Returns the value of field 'annotation'. + * + * @return Annotation + * @return the value of field 'annotation'. */ public jalview.binding.Annotation getAnnotation() { return this._annotation; - } - - //-- jalview.binding.Annotation getAnnotation() + } //-- jalview.binding.Annotation getAnnotation() /** * Returns the value of field 'sequenceSet'. - * + * * @return SequenceSet * @return the value of field 'sequenceSet'. */ public jalview.binding.SequenceSet getSequenceSet() { return this._sequenceSet; - } - - //-- jalview.binding.SequenceSet getSequenceSet() + } //-- jalview.binding.SequenceSet getSequenceSet() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() { - try - { + try { validate(); } - catch (org.exolab.castor.xml.ValidationException vex) - { + catch (org.exolab.castor.xml.ValidationException vex) { 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 + 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 + 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) /** * Sets the value of field 'annotation'. - * + * * @param annotation the value of field 'annotation'. */ public void setAnnotation(jalview.binding.Annotation annotation) { this._annotation = annotation; - } - - //-- void setAnnotation(jalview.binding.Annotation) + } //-- void setAnnotation(jalview.binding.Annotation) /** * Sets the value of field 'sequenceSet'. - * + * * @param sequenceSet the value of field 'sequenceSet'. */ public void setSequenceSet(jalview.binding.SequenceSet sequenceSet) { this._sequenceSet = sequenceSet; - } - - //-- void setSequenceSet(jalview.binding.SequenceSet) + } //-- void setSequenceSet(jalview.binding.SequenceSet) /** * 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 + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class, - reader); - } - - //-- java.lang.Object unmarshal(java.io.Reader) + return (jalview.binding.Alignment) Unmarshaller.unmarshal(jalview.binding.Alignment.class, reader); + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ - 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() - //-- void validate() } diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java index 14b09c4..fefdd12 100755 --- a/src/jalview/binding/Annotation.java +++ b/src/jalview/binding/Annotation.java @@ -1,5 +1,5 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ @@ -7,385 +7,373 @@ package jalview.binding; + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import java.util.*; -import org.exolab.castor.xml.*; +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. - * + * * @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() - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAnnotationElement - * - * - * - * @param vAnnotationElement - */ - 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())) +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() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method addAnnotationElement + * + * + * + * @param vAnnotationElement + */ + 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) { - 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++) + //-- 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) { - 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 + 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) { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) + 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) { - 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())) + 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 { - 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++) + 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 { - _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() + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } //-- void validate() } diff --git a/src/jalview/binding/AnnotationElement.java b/src/jalview/binding/AnnotationElement.java index 16c3dab..e4aec31 100755 --- a/src/jalview/binding/AnnotationElement.java +++ b/src/jalview/binding/AnnotationElement.java @@ -1,36 +1,36 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ -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; +package jalview.binding; + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ + import java.io.IOException; import java.io.Reader; import java.io.Serializable; import java.io.Writer; - +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 AnnotationElement. - * + * * @version $Revision$ $Date$ */ -public class AnnotationElement implements java.io.Serializable -{ - //--------------------------/ - //- Class/Member Variables -/ +public class AnnotationElement implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ //--------------------------/ /** @@ -68,276 +68,239 @@ public class AnnotationElement implements java.io.Serializable */ private boolean _has_value; + + //----------------/ + //- Constructors -/ //----------------/ - //- Constructors -/ - //----------------/ - public AnnotationElement() - { + + public AnnotationElement() { super(); - } + } //-- jalview.binding.AnnotationElement() + - //-- jalview.binding.AnnotationElement() + //-----------/ + //- Methods -/ //-----------/ /** - * DOCUMENT ME! + * Method deletePosition + * */ public void deletePosition() { - this._has_position = false; - } - - //-- void deletePosition() + this._has_position= false; + } //-- void deletePosition() /** * Method deleteValue - * + * */ public void deleteValue() { - this._has_value = false; - } - - //-- void deleteValue() + this._has_value= false; + } //-- void deleteValue() /** * 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 'displayCharacter'. - * + * * @return String * @return the value of field 'displayCharacter'. */ public java.lang.String getDisplayCharacter() { return this._displayCharacter; - } - - //-- java.lang.String getDisplayCharacter() + } //-- java.lang.String getDisplayCharacter() /** * Returns the value of field 'position'. - * + * * @return int * @return the value of field 'position'. */ public int getPosition() { return this._position; - } - - //-- int getPosition() + } //-- int getPosition() /** * Returns the value of field 'secondaryStructure'. - * + * * @return String * @return the value of field 'secondaryStructure'. */ public java.lang.String getSecondaryStructure() { return this._secondaryStructure; - } - - //-- java.lang.String getSecondaryStructure() + } //-- java.lang.String getSecondaryStructure() /** * Returns the value of field 'value'. - * + * * @return float * @return the value of field 'value'. */ public float getValue() { return this._value; - } - - //-- float getValue() + } //-- float getValue() /** * Method hasPosition - * - * - * + * + * + * * @return boolean */ public boolean hasPosition() { return this._has_position; - } - - //-- boolean hasPosition() + } //-- boolean hasPosition() /** * Method hasValue - * - * - * + * + * + * * @return boolean */ public boolean hasValue() { return this._has_value; - } - - //-- boolean hasValue() + } //-- boolean hasValue() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() { - try - { + try { validate(); } - catch (org.exolab.castor.xml.ValidationException vex) - { + catch (org.exolab.castor.xml.ValidationException vex) { 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 + 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 + 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) /** * 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 'displayCharacter'. - * + * * @param displayCharacter the value of field 'displayCharacter' */ public void setDisplayCharacter(java.lang.String displayCharacter) { this._displayCharacter = displayCharacter; - } - - //-- void setDisplayCharacter(java.lang.String) + } //-- void setDisplayCharacter(java.lang.String) /** * Sets the value of field 'position'. - * + * * @param position the value of field 'position'. */ public void setPosition(int position) { this._position = position; this._has_position = true; - } - - //-- void setPosition(int) + } //-- void setPosition(int) /** * Sets the value of field 'secondaryStructure'. - * + * * @param secondaryStructure the value of field * 'secondaryStructure'. */ public void setSecondaryStructure(java.lang.String secondaryStructure) { this._secondaryStructure = secondaryStructure; - } - - //-- void setSecondaryStructure(java.lang.String) + } //-- void setSecondaryStructure(java.lang.String) /** * Sets the value of field 'value'. - * + * * @param value the value of field 'value'. */ public void setValue(float value) { this._value = value; this._has_value = true; - } - - //-- void setValue(float) + } //-- void setValue(float) /** * 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 + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, - reader); - } - - //-- java.lang.Object unmarshal(java.io.Reader) + return (jalview.binding.AnnotationElement) Unmarshaller.unmarshal(jalview.binding.AnnotationElement.class, reader); + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ - 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() - //-- void validate() } diff --git a/src/jalview/binding/Colour.java b/src/jalview/binding/Colour.java index 4e57c3f..a51102b 100755 --- a/src/jalview/binding/Colour.java +++ b/src/jalview/binding/Colour.java @@ -1,36 +1,36 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ -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; +package jalview.binding; + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ + import java.io.IOException; import java.io.Reader; import java.io.Serializable; import java.io.Writer; - +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 Colour. - * + * * @version $Revision$ $Date$ */ -public class Colour implements java.io.Serializable -{ - //--------------------------/ - //- Class/Member Variables -/ +public class Colour implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ //--------------------------/ /** @@ -43,148 +43,131 @@ public class Colour implements java.io.Serializable */ private java.lang.String _RGB; + + //----------------/ + //- Constructors -/ //----------------/ - //- Constructors -/ - //----------------/ - public Colour() - { + + public Colour() { super(); - } + } //-- jalview.binding.Colour() + - //-- jalview.binding.Colour() + //-----------/ + //- Methods -/ //-----------/ /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * Returns the value of field 'name'. + * + * @return String + * @return the value of field 'name'. */ public java.lang.String getName() { return this._name; - } - - //-- java.lang.String getName() + } //-- java.lang.String getName() /** * Returns the value of field 'RGB'. - * + * * @return String * @return the value of field 'RGB'. */ public java.lang.String getRGB() { return this._RGB; - } - - //-- java.lang.String getRGB() + } //-- java.lang.String getRGB() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() { - try - { + try { validate(); } - catch (org.exolab.castor.xml.ValidationException vex) - { + catch (org.exolab.castor.xml.ValidationException vex) { 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 + 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 + 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) /** * Sets the value of field 'name'. - * + * * @param name the value of field 'name'. */ public void setName(java.lang.String name) { this._name = name; - } - - //-- void setName(java.lang.String) + } //-- void setName(java.lang.String) /** * Sets the value of field 'RGB'. - * + * * @param RGB the value of field 'RGB'. */ public void setRGB(java.lang.String RGB) { this._RGB = RGB; - } - - //-- void setRGB(java.lang.String) + } //-- void setRGB(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 + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class, - reader); - } - - //-- java.lang.Object unmarshal(java.io.Reader) + return (jalview.binding.Colour) Unmarshaller.unmarshal(jalview.binding.Colour.class, reader); + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ - 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() - //-- void validate() } diff --git a/src/jalview/binding/JGroup.java b/src/jalview/binding/JGroup.java index 5b6d74e..6473149 100755 --- a/src/jalview/binding/JGroup.java +++ b/src/jalview/binding/JGroup.java @@ -1,39 +1,38 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ -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; +package jalview.binding; + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -//- 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 JGroup. - * + * * @version $Revision$ $Date$ */ -public class JGroup implements java.io.Serializable -{ - //--------------------------/ - //- Class/Member Variables -/ +public class JGroup implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ //--------------------------/ /** @@ -131,37 +130,39 @@ public class JGroup implements java.io.Serializable */ private java.util.Vector _seqList; + + //----------------/ + //- Constructors -/ //----------------/ - //- Constructors -/ - //----------------/ - public JGroup() - { + + public JGroup() { super(); _seqList = new Vector(); - } + } //-- jalview.binding.JGroup() + - //-- jalview.binding.JGroup() + //-----------/ + //- Methods -/ //-----------/ /** - * DOCUMENT ME! - * - * @param vSeq DOCUMENT ME! - * - * @throws java.lang.IndexOutOfBoundsException DOCUMENT ME! + * Method addSeq + * + * + * + * @param vSeq */ - public void addSeq(int vSeq) throws java.lang.IndexOutOfBoundsException + public void addSeq(int vSeq) + throws java.lang.IndexOutOfBoundsException { _seqList.addElement(new java.lang.Integer(vSeq)); - } - - //-- void addSeq(int) + } //-- void addSeq(int) /** * Method addSeq - * - * - * + * + * + * * @param index * @param vSeq */ @@ -169,482 +170,406 @@ public class JGroup implements java.io.Serializable throws java.lang.IndexOutOfBoundsException { _seqList.insertElementAt(new java.lang.Integer(vSeq), index); - } - - //-- void addSeq(int, int) + } //-- void addSeq(int, int) /** * Method deleteColourText - * + * */ public void deleteColourText() { - this._has_colourText = false; - } - - //-- void deleteColourText() + this._has_colourText= false; + } //-- void deleteColourText() /** * Method deleteConsThreshold - * + * */ public void deleteConsThreshold() { - this._has_consThreshold = false; - } - - //-- void deleteConsThreshold() + this._has_consThreshold= false; + } //-- void deleteConsThreshold() /** * Method deleteDisplayBoxes - * + * */ public void deleteDisplayBoxes() { - this._has_displayBoxes = false; - } - - //-- void deleteDisplayBoxes() + this._has_displayBoxes= false; + } //-- void deleteDisplayBoxes() /** * Method deleteDisplayText - * + * */ public void deleteDisplayText() { - this._has_displayText = false; - } - - //-- void deleteDisplayText() + this._has_displayText= false; + } //-- void deleteDisplayText() /** * Method deleteEnd - * + * */ public void deleteEnd() { - this._has_end = false; - } - - //-- void deleteEnd() + this._has_end= false; + } //-- void deleteEnd() /** * Method deleteOutlineColour - * + * */ public void deleteOutlineColour() { - this._has_outlineColour = false; - } - - //-- void deleteOutlineColour() + this._has_outlineColour= false; + } //-- void deleteOutlineColour() /** * Method deletePidThreshold - * + * */ public void deletePidThreshold() { - this._has_pidThreshold = false; - } - - //-- void deletePidThreshold() + this._has_pidThreshold= false; + } //-- void deletePidThreshold() /** * Method deleteStart - * + * */ public void deleteStart() { - this._has_start = false; - } - - //-- void deleteStart() + this._has_start= false; + } //-- void deleteStart() /** * Method enumerateSeq - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateSeq() { return _seqList.elements(); - } - - //-- java.util.Enumeration enumerateSeq() + } //-- java.util.Enumeration enumerateSeq() /** * Returns the value of field 'colour'. - * + * * @return String * @return the value of field 'colour'. */ public java.lang.String getColour() { return this._colour; - } - - //-- java.lang.String getColour() + } //-- java.lang.String getColour() /** * Returns the value of field 'colourText'. - * + * * @return boolean * @return the value of field 'colourText'. */ public boolean getColourText() { return this._colourText; - } - - //-- boolean getColourText() + } //-- boolean getColourText() /** * Returns the value of field 'consThreshold'. - * + * * @return int * @return the value of field 'consThreshold'. */ public int getConsThreshold() { return this._consThreshold; - } - - //-- int getConsThreshold() + } //-- int getConsThreshold() /** * Returns the value of field 'displayBoxes'. - * + * * @return boolean * @return the value of field 'displayBoxes'. */ public boolean getDisplayBoxes() { return this._displayBoxes; - } - - //-- boolean getDisplayBoxes() + } //-- boolean getDisplayBoxes() /** * Returns the value of field 'displayText'. - * + * * @return boolean * @return the value of field 'displayText'. */ public boolean getDisplayText() { return this._displayText; - } - - //-- boolean getDisplayText() + } //-- boolean getDisplayText() /** * Returns the value of field 'end'. - * + * * @return int * @return the value of field 'end'. */ public int getEnd() { return this._end; - } - - //-- int getEnd() + } //-- int getEnd() /** * Returns the value of field 'name'. - * + * * @return String * @return the value of field 'name'. */ public java.lang.String getName() { return this._name; - } - - //-- java.lang.String getName() + } //-- java.lang.String getName() /** * Returns the value of field 'outlineColour'. - * + * * @return int * @return the value of field 'outlineColour'. */ public int getOutlineColour() { return this._outlineColour; - } - - //-- int getOutlineColour() + } //-- int getOutlineColour() /** * Returns the value of field 'pidThreshold'. - * + * * @return int * @return the value of field 'pidThreshold'. */ public int getPidThreshold() { return this._pidThreshold; - } - - //-- int getPidThreshold() + } //-- int getPidThreshold() /** * Method getSeq - * - * - * + * + * + * * @param index * @return int */ - public int getSeq(int index) throws java.lang.IndexOutOfBoundsException + public int getSeq(int index) + throws java.lang.IndexOutOfBoundsException { //-- check bounds for index - if ((index < 0) || (index > _seqList.size())) - { + if ((index < 0) || (index > _seqList.size())) { throw new IndexOutOfBoundsException(); } - - return ((java.lang.Integer) _seqList.elementAt(index)).intValue(); - } - - //-- int getSeq(int) + + return ((java.lang.Integer)_seqList.elementAt(index)).intValue(); + } //-- int getSeq(int) /** * Method getSeq - * - * - * + * + * + * * @return int */ public int[] getSeq() { int size = _seqList.size(); int[] mArray = new int[size]; - - for (int index = 0; index < size; index++) - { - mArray[index] = ((java.lang.Integer) _seqList.elementAt(index)).intValue(); + for (int index = 0; index < size; index++) { + mArray[index] = ((java.lang.Integer)_seqList.elementAt(index)).intValue(); } - return mArray; - } - - //-- int[] getSeq() + } //-- int[] getSeq() /** * Method getSeqCount - * - * - * + * + * + * * @return int */ public int getSeqCount() { return _seqList.size(); - } - - //-- int getSeqCount() + } //-- int getSeqCount() /** * Returns the value of field 'start'. - * + * * @return int * @return the value of field 'start'. */ public int getStart() { return this._start; - } - - //-- int getStart() + } //-- int getStart() /** * Method hasColourText - * - * - * + * + * + * * @return boolean */ public boolean hasColourText() { return this._has_colourText; - } - - //-- boolean hasColourText() + } //-- boolean hasColourText() /** * Method hasConsThreshold - * - * - * + * + * + * * @return boolean */ public boolean hasConsThreshold() { return this._has_consThreshold; - } - - //-- boolean hasConsThreshold() + } //-- boolean hasConsThreshold() /** * Method hasDisplayBoxes - * - * - * + * + * + * * @return boolean */ public boolean hasDisplayBoxes() { return this._has_displayBoxes; - } - - //-- boolean hasDisplayBoxes() + } //-- boolean hasDisplayBoxes() /** * Method hasDisplayText - * - * - * + * + * + * * @return boolean */ public boolean hasDisplayText() { return this._has_displayText; - } - - //-- boolean hasDisplayText() + } //-- boolean hasDisplayText() /** * Method hasEnd - * - * - * + * + * + * * @return boolean */ public boolean hasEnd() { return this._has_end; - } - - //-- boolean hasEnd() + } //-- boolean hasEnd() /** * Method hasOutlineColour - * - * - * + * + * + * * @return boolean */ public boolean hasOutlineColour() { return this._has_outlineColour; - } - - //-- boolean hasOutlineColour() + } //-- boolean hasOutlineColour() /** * Method hasPidThreshold - * - * - * + * + * + * * @return boolean */ public boolean hasPidThreshold() { return this._has_pidThreshold; - } - - //-- boolean hasPidThreshold() + } //-- boolean hasPidThreshold() /** * Method hasStart - * - * - * + * + * + * * @return boolean */ public boolean hasStart() { return this._has_start; - } - - //-- boolean hasStart() + } //-- boolean hasStart() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() { - try - { + try { validate(); } - catch (org.exolab.castor.xml.ValidationException vex) - { + catch (org.exolab.castor.xml.ValidationException vex) { 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 + 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 + 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 removeAllSeq - * + * */ public void removeAllSeq() { _seqList.removeAllElements(); - } - - //-- void removeAllSeq() + } //-- void removeAllSeq() /** * Method removeSeq - * - * - * + * + * + * * @param index * @return int */ @@ -652,132 +577,111 @@ public class JGroup implements java.io.Serializable { java.lang.Object obj = _seqList.elementAt(index); _seqList.removeElementAt(index); - - return ((java.lang.Integer) obj).intValue(); - } - - //-- int removeSeq(int) + return ((java.lang.Integer)obj).intValue(); + } //-- int removeSeq(int) /** * Sets the value of field 'colour'. - * + * * @param colour the value of field 'colour'. */ public void setColour(java.lang.String colour) { this._colour = colour; - } - - //-- void setColour(java.lang.String) + } //-- void setColour(java.lang.String) /** * Sets the value of field 'colourText'. - * + * * @param colourText the value of field 'colourText'. */ public void setColourText(boolean colourText) { this._colourText = colourText; this._has_colourText = true; - } - - //-- void setColourText(boolean) + } //-- void setColourText(boolean) /** * Sets the value of field 'consThreshold'. - * + * * @param consThreshold the value of field 'consThreshold'. */ public void setConsThreshold(int consThreshold) { this._consThreshold = consThreshold; this._has_consThreshold = true; - } - - //-- void setConsThreshold(int) + } //-- void setConsThreshold(int) /** * Sets the value of field 'displayBoxes'. - * + * * @param displayBoxes the value of field 'displayBoxes'. */ public void setDisplayBoxes(boolean displayBoxes) { this._displayBoxes = displayBoxes; this._has_displayBoxes = true; - } - - //-- void setDisplayBoxes(boolean) + } //-- void setDisplayBoxes(boolean) /** * Sets the value of field 'displayText'. - * + * * @param displayText the value of field 'displayText'. */ public void setDisplayText(boolean displayText) { this._displayText = displayText; this._has_displayText = true; - } - - //-- void setDisplayText(boolean) + } //-- void setDisplayText(boolean) /** * Sets the value of field 'end'. - * + * * @param end the value of field 'end'. */ public void setEnd(int end) { this._end = end; this._has_end = true; - } - - //-- void setEnd(int) + } //-- void setEnd(int) /** * Sets the value of field 'name'. - * + * * @param name the value of field 'name'. */ public void setName(java.lang.String name) { this._name = name; - } - - //-- void setName(java.lang.String) + } //-- void setName(java.lang.String) /** * Sets the value of field 'outlineColour'. - * + * * @param outlineColour the value of field 'outlineColour'. */ public void setOutlineColour(int outlineColour) { this._outlineColour = outlineColour; this._has_outlineColour = true; - } - - //-- void setOutlineColour(int) + } //-- void setOutlineColour(int) /** * Sets the value of field 'pidThreshold'. - * + * * @param pidThreshold the value of field 'pidThreshold'. */ public void setPidThreshold(int pidThreshold) { this._pidThreshold = pidThreshold; this._has_pidThreshold = true; - } - - //-- void setPidThreshold(int) + } //-- void setPidThreshold(int) /** * Method setSeq - * - * - * + * + * + * * @param index * @param vSeq */ @@ -785,76 +689,62 @@ public class JGroup implements java.io.Serializable throws java.lang.IndexOutOfBoundsException { //-- check bounds for index - if ((index < 0) || (index > _seqList.size())) - { + if ((index < 0) || (index > _seqList.size())) { throw new IndexOutOfBoundsException(); } - _seqList.setElementAt(new java.lang.Integer(vSeq), index); - } - - //-- void setSeq(int, int) + } //-- void setSeq(int, int) /** * Method setSeq - * - * - * + * + * + * * @param seqArray */ public void setSeq(int[] seqArray) { //-- copy array _seqList.removeAllElements(); - - for (int i = 0; i < seqArray.length; i++) - { + for (int i = 0; i < seqArray.length; i++) { _seqList.addElement(new java.lang.Integer(seqArray[i])); } - } - - //-- void setSeq(int) + } //-- void setSeq(int) /** * Sets the value of field 'start'. - * + * * @param start the value of field 'start'. */ public void setStart(int start) { this._start = start; this._has_start = true; - } - - //-- void setStart(int) + } //-- void setStart(int) /** * 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 + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, - reader); - } - - //-- java.lang.Object unmarshal(java.io.Reader) + return (jalview.binding.JGroup) Unmarshaller.unmarshal(jalview.binding.JGroup.class, reader); + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ - 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() - //-- void validate() } diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java index 9b8ddcb..751409f 100755 --- a/src/jalview/binding/JSeq.java +++ b/src/jalview/binding/JSeq.java @@ -1,36 +1,36 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ -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; +package jalview.binding; + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ + import java.io.IOException; import java.io.Reader; import java.io.Serializable; import java.io.Writer; - +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 JSeq. - * + * * @version $Revision$ $Date$ */ -public class JSeq implements java.io.Serializable -{ - //--------------------------/ - //- Class/Member Variables -/ +public class JSeq implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ //--------------------------/ /** @@ -73,302 +73,261 @@ public class JSeq implements java.io.Serializable */ private boolean _has_id; + + //----------------/ + //- Constructors -/ //----------------/ - //- Constructors -/ - //----------------/ - public JSeq() - { + + public JSeq() { super(); - } + } //-- jalview.binding.JSeq() - //-- jalview.binding.JSeq() + + //-----------/ + //- Methods -/ //-----------/ /** - * DOCUMENT ME! + * Method deleteColour + * */ public void deleteColour() { - this._has_colour = false; - } - - //-- void deleteColour() + this._has_colour= false; + } //-- void deleteColour() /** * Method deleteEnd - * + * */ public void deleteEnd() { - this._has_end = false; - } - - //-- void deleteEnd() + this._has_end= false; + } //-- void deleteEnd() /** * Method deleteId - * + * */ public void deleteId() { - this._has_id = false; - } - - //-- void deleteId() + this._has_id= false; + } //-- void deleteId() /** * Method deleteStart - * + * */ public void deleteStart() { - this._has_start = false; - } - - //-- void deleteStart() + this._has_start= false; + } //-- void deleteStart() /** * Returns the value of field 'colour'. - * + * * @return int * @return the value of field 'colour'. */ public int getColour() { return this._colour; - } - - //-- int getColour() + } //-- int getColour() /** * Returns the value of field 'end'. - * + * * @return int * @return the value of field 'end'. */ public int getEnd() { return this._end; - } - - //-- int getEnd() + } //-- int getEnd() /** * Returns the value of field 'id'. - * + * * @return int * @return the value of field 'id'. */ public int getId() { return this._id; - } - - //-- int getId() + } //-- int getId() /** * Returns the value of field 'start'. - * + * * @return int * @return the value of field 'start'. */ public int getStart() { return this._start; - } - - //-- int getStart() + } //-- int getStart() /** * Method hasColour - * - * - * + * + * + * * @return boolean */ public boolean hasColour() { return this._has_colour; - } - - //-- boolean hasColour() + } //-- boolean hasColour() /** * Method hasEnd - * - * - * + * + * + * * @return boolean */ public boolean hasEnd() { return this._has_end; - } - - //-- boolean hasEnd() + } //-- boolean hasEnd() /** * Method hasId - * - * - * + * + * + * * @return boolean */ public boolean hasId() { return this._has_id; - } - - //-- boolean hasId() + } //-- boolean hasId() /** * Method hasStart - * - * - * + * + * + * * @return boolean */ public boolean hasStart() { return this._has_start; - } - - //-- boolean hasStart() + } //-- boolean hasStart() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() { - try - { + try { validate(); } - catch (org.exolab.castor.xml.ValidationException vex) - { + catch (org.exolab.castor.xml.ValidationException vex) { 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 + 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 + 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) /** * Sets the value of field 'colour'. - * + * * @param colour the value of field 'colour'. */ public void setColour(int colour) { this._colour = colour; this._has_colour = true; - } - - //-- void setColour(int) + } //-- void setColour(int) /** * Sets the value of field 'end'. - * + * * @param end the value of field 'end'. */ public void setEnd(int end) { this._end = end; this._has_end = true; - } - - //-- void setEnd(int) + } //-- void setEnd(int) /** * Sets the value of field 'id'. - * + * * @param id the value of field 'id'. */ public void setId(int id) { this._id = id; this._has_id = true; - } - - //-- void setId(int) + } //-- void setId(int) /** * Sets the value of field 'start'. - * + * * @param start the value of field 'start'. */ public void setStart(int start) { this._start = start; this._has_start = true; - } - - //-- void setStart(int) + } //-- void setStart(int) /** * 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 + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, - reader); - } - - //-- java.lang.Object unmarshal(java.io.Reader) + return (jalview.binding.JSeq) Unmarshaller.unmarshal(jalview.binding.JSeq.class, reader); + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ - 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() - //-- void validate() } diff --git a/src/jalview/binding/JalviewModel.java b/src/jalview/binding/JalviewModel.java index bfdbddc..8edd012 100755 --- a/src/jalview/binding/JalviewModel.java +++ b/src/jalview/binding/JalviewModel.java @@ -1,38 +1,37 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ -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; +package jalview.binding; + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ + import java.io.IOException; import java.io.Reader; import java.io.Serializable; import java.io.Writer; - import java.util.Date; - +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 JalviewModel. - * + * * @version $Revision$ $Date$ */ -public class JalviewModel implements java.io.Serializable -{ - //--------------------------/ - //- Class/Member Variables -/ +public class JalviewModel implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ //--------------------------/ /** @@ -55,200 +54,174 @@ public class JalviewModel implements java.io.Serializable */ private jalview.binding.JalviewModelSequence _jalviewModelSequence; + + //----------------/ + //- Constructors -/ //----------------/ - //- Constructors -/ - //----------------/ - public JalviewModel() - { + + public JalviewModel() { super(); - } + } //-- jalview.binding.JalviewModel() - //-- jalview.binding.JalviewModel() + + //-----------/ + //- Methods -/ //-----------/ /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * Returns the value of field 'creationDate'. + * + * @return Date + * @return the value of field 'creationDate'. */ public java.util.Date getCreationDate() { return this._creationDate; - } - - //-- java.util.Date getCreationDate() + } //-- java.util.Date getCreationDate() /** * Returns the value of field 'jalviewModelSequence'. - * + * * @return JalviewModelSequence * @return the value of field 'jalviewModelSequence'. */ public jalview.binding.JalviewModelSequence getJalviewModelSequence() { return this._jalviewModelSequence; - } - - //-- jalview.binding.JalviewModelSequence getJalviewModelSequence() + } //-- jalview.binding.JalviewModelSequence getJalviewModelSequence() /** * Returns the value of field 'vamsasModel'. - * + * * @return VamsasModel * @return the value of field 'vamsasModel'. */ public jalview.binding.VamsasModel getVamsasModel() { return this._vamsasModel; - } - - //-- jalview.binding.VamsasModel getVamsasModel() + } //-- jalview.binding.VamsasModel getVamsasModel() /** * Returns the value of field 'version'. - * + * * @return String * @return the value of field 'version'. */ public java.lang.String getVersion() { return this._version; - } - - //-- java.lang.String getVersion() + } //-- java.lang.String getVersion() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() { - try - { + try { validate(); } - catch (org.exolab.castor.xml.ValidationException vex) - { + catch (org.exolab.castor.xml.ValidationException vex) { 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 + 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 + 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) /** * Sets the value of field 'creationDate'. - * + * * @param creationDate the value of field 'creationDate'. */ public void setCreationDate(java.util.Date creationDate) { this._creationDate = creationDate; - } - - //-- void setCreationDate(java.util.Date) + } //-- void setCreationDate(java.util.Date) /** * Sets the value of field 'jalviewModelSequence'. - * + * * @param jalviewModelSequence the value of field * 'jalviewModelSequence'. */ - public void setJalviewModelSequence( - jalview.binding.JalviewModelSequence jalviewModelSequence) + public void setJalviewModelSequence(jalview.binding.JalviewModelSequence jalviewModelSequence) { this._jalviewModelSequence = jalviewModelSequence; - } - - //-- void setJalviewModelSequence(jalview.binding.JalviewModelSequence) + } //-- void setJalviewModelSequence(jalview.binding.JalviewModelSequence) /** * Sets the value of field 'vamsasModel'. - * + * * @param vamsasModel the value of field 'vamsasModel'. */ public void setVamsasModel(jalview.binding.VamsasModel vamsasModel) { this._vamsasModel = vamsasModel; - } - - //-- void setVamsasModel(jalview.binding.VamsasModel) + } //-- void setVamsasModel(jalview.binding.VamsasModel) /** * Sets the value of field 'version'. - * + * * @param version the value of field 'version'. */ public void setVersion(java.lang.String version) { this._version = version; - } - - //-- void setVersion(java.lang.String) + } //-- void setVersion(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 + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class, - reader); - } - - //-- java.lang.Object unmarshal(java.io.Reader) + return (jalview.binding.JalviewModel) Unmarshaller.unmarshal(jalview.binding.JalviewModel.class, reader); + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ - 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() - //-- void validate() } diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java index 2c2abff..4ac40d5 100755 --- a/src/jalview/binding/JalviewModelSequence.java +++ b/src/jalview/binding/JalviewModelSequence.java @@ -1,5 +1,5 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ @@ -7,894 +7,872 @@ package jalview.binding; + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import java.util.*; -import org.exolab.castor.xml.*; +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 JalviewModelSequence. - * + * * @version $Revision$ $Date$ */ -public class JalviewModelSequence - implements java.io.Serializable -{ - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _JSeqList - */ - private java.util.Vector _JSeqList; - - /** - * Field _JGroupList - */ - private java.util.Vector _JGroupList; - - /** - * Field _viewportList - */ - private java.util.Vector _viewportList; - - /** - * Field _userColoursList - */ - private java.util.Vector _userColoursList; - - /** - * Field _treeList - */ - private java.util.Vector _treeList; - - //----------------/ - //- Constructors -/ - //----------------/ - - public JalviewModelSequence() - { - super(); - _JSeqList = new Vector(); - _JGroupList = new Vector(); - _viewportList = new Vector(); - _userColoursList = new Vector(); - _treeList = new Vector(); - } //-- jalview.binding.JalviewModelSequence() - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addJGroup - * - * - * - * @param vJGroup - */ - public void addJGroup(jalview.binding.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException - { - _JGroupList.addElement(vJGroup); - } //-- void addJGroup(jalview.binding.JGroup) - - /** - * Method addJGroup - * - * - * - * @param index - * @param vJGroup - */ - public void addJGroup(int index, jalview.binding.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException - { - _JGroupList.insertElementAt(vJGroup, index); - } //-- void addJGroup(int, jalview.binding.JGroup) - - /** - * Method addJSeq - * - * - * - * @param vJSeq - */ - public void addJSeq(jalview.binding.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException - { - _JSeqList.addElement(vJSeq); - } //-- void addJSeq(jalview.binding.JSeq) - - /** - * Method addJSeq - * - * - * - * @param index - * @param vJSeq - */ - public void addJSeq(int index, jalview.binding.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException - { - _JSeqList.insertElementAt(vJSeq, index); - } //-- void addJSeq(int, jalview.binding.JSeq) - - /** - * Method addTree - * - * - * - * @param vTree - */ - public void addTree(jalview.binding.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.addElement(vTree); - } //-- void addTree(jalview.binding.Tree) - - /** - * Method addTree - * - * - * - * @param index - * @param vTree - */ - public void addTree(int index, jalview.binding.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.insertElementAt(vTree, index); - } //-- void addTree(int, jalview.binding.Tree) - - /** - * Method addUserColours - * - * - * - * @param vUserColours - */ - public void addUserColours(jalview.binding.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException - { - _userColoursList.addElement(vUserColours); - } //-- void addUserColours(jalview.binding.UserColours) - - /** - * Method addUserColours - * - * - * - * @param index - * @param vUserColours - */ - public void addUserColours(int index, - jalview.binding.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException - { - _userColoursList.insertElementAt(vUserColours, index); - } //-- void addUserColours(int, jalview.binding.UserColours) - - /** - * Method addViewport - * - * - * - * @param vViewport - */ - public void addViewport(jalview.binding.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - _viewportList.addElement(vViewport); - } //-- void addViewport(jalview.binding.Viewport) - - /** - * Method addViewport - * - * - * - * @param index - * @param vViewport - */ - public void addViewport(int index, jalview.binding.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - _viewportList.insertElementAt(vViewport, index); - } //-- void addViewport(int, jalview.binding.Viewport) - - /** - * Method enumerateJGroup - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateJGroup() - { - return _JGroupList.elements(); - } //-- java.util.Enumeration enumerateJGroup() - - /** - * Method enumerateJSeq - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateJSeq() - { - return _JSeqList.elements(); - } //-- java.util.Enumeration enumerateJSeq() - - /** - * Method enumerateTree - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateTree() - { - return _treeList.elements(); - } //-- java.util.Enumeration enumerateTree() - - /** - * Method enumerateUserColours - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateUserColours() - { - return _userColoursList.elements(); - } //-- java.util.Enumeration enumerateUserColours() - - /** - * Method enumerateViewport - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateViewport() - { - return _viewportList.elements(); - } //-- java.util.Enumeration enumerateViewport() - - /** - * Method getJGroup - * - * - * - * @param index - * @return JGroup - */ - public jalview.binding.JGroup getJGroup(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ( (index < 0) || (index > _JGroupList.size())) - { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.JGroup) _JGroupList.elementAt(index); - } //-- jalview.binding.JGroup getJGroup(int) - - /** - * Method getJGroup - * - * - * - * @return JGroup - */ - public jalview.binding.JGroup[] getJGroup() - { - int size = _JGroupList.size(); - jalview.binding.JGroup[] mArray = new jalview.binding.JGroup[size]; - for (int index = 0; index < size; index++) - { - mArray[index] = (jalview.binding.JGroup) _JGroupList.elementAt(index); - } - return mArray; - } //-- jalview.binding.JGroup[] getJGroup() - - /** - * Method getJGroupCount - * - * - * - * @return int - */ - public int getJGroupCount() - { - return _JGroupList.size(); - } //-- int getJGroupCount() - - /** - * Method getJSeq - * - * - * - * @param index - * @return JSeq - */ - public jalview.binding.JSeq getJSeq(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ( (index < 0) || (index > _JSeqList.size())) - { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.JSeq) _JSeqList.elementAt(index); - } //-- jalview.binding.JSeq getJSeq(int) - - /** - * Method getJSeq - * - * - * - * @return JSeq - */ - public jalview.binding.JSeq[] getJSeq() - { - int size = _JSeqList.size(); - jalview.binding.JSeq[] mArray = new jalview.binding.JSeq[size]; - for (int index = 0; index < size; index++) - { - mArray[index] = (jalview.binding.JSeq) _JSeqList.elementAt(index); - } - return mArray; - } //-- jalview.binding.JSeq[] getJSeq() - - /** - * Method getJSeqCount - * - * - * - * @return int - */ - public int getJSeqCount() - { - return _JSeqList.size(); - } //-- int getJSeqCount() - - /** - * Method getTree - * - * - * - * @param index - * @return Tree - */ - public jalview.binding.Tree getTree(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ( (index < 0) || (index > _treeList.size())) - { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.Tree) _treeList.elementAt(index); - } //-- jalview.binding.Tree getTree(int) - - /** - * Method getTree - * - * - * - * @return Tree - */ - public jalview.binding.Tree[] getTree() - { - int size = _treeList.size(); - jalview.binding.Tree[] mArray = new jalview.binding.Tree[size]; - for (int index = 0; index < size; index++) - { - mArray[index] = (jalview.binding.Tree) _treeList.elementAt(index); - } - return mArray; - } //-- jalview.binding.Tree[] getTree() - - /** - * Method getTreeCount - * - * - * - * @return int - */ - public int getTreeCount() - { - return _treeList.size(); - } //-- int getTreeCount() - - /** - * Method getUserColours - * - * - * - * @param index - * @return UserColours - */ - public jalview.binding.UserColours getUserColours(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ( (index < 0) || (index > _userColoursList.size())) - { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.UserColours) _userColoursList.elementAt(index); - } //-- jalview.binding.UserColours getUserColours(int) - - /** - * Method getUserColours - * - * - * - * @return UserColours - */ - public jalview.binding.UserColours[] getUserColours() - { - int size = _userColoursList.size(); - jalview.binding.UserColours[] mArray = new jalview.binding.UserColours[size]; - for (int index = 0; index < size; index++) - { - mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt( - index); - } - return mArray; - } //-- jalview.binding.UserColours[] getUserColours() - - /** - * Method getUserColoursCount - * - * - * - * @return int - */ - public int getUserColoursCount() - { - return _userColoursList.size(); - } //-- int getUserColoursCount() - - /** - * Method getViewport - * - * - * - * @param index - * @return Viewport - */ - public jalview.binding.Viewport getViewport(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ( (index < 0) || (index > _viewportList.size())) - { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.Viewport) _viewportList.elementAt(index); - } //-- jalview.binding.Viewport getViewport(int) - - /** - * Method getViewport - * - * - * - * @return Viewport - */ - public jalview.binding.Viewport[] getViewport() - { - int size = _viewportList.size(); - jalview.binding.Viewport[] mArray = new jalview.binding.Viewport[size]; - for (int index = 0; index < size; index++) - { - mArray[index] = (jalview.binding.Viewport) _viewportList.elementAt(index); - } - return mArray; - } //-- jalview.binding.Viewport[] getViewport() - - /** - * Method getViewportCount - * - * - * - * @return int - */ - public int getViewportCount() - { - return _viewportList.size(); - } //-- int getViewportCount() - - /** - * 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 removeAllJGroup - * - */ - public void removeAllJGroup() - { - _JGroupList.removeAllElements(); - } //-- void removeAllJGroup() - - /** - * Method removeAllJSeq - * - */ - public void removeAllJSeq() - { - _JSeqList.removeAllElements(); - } //-- void removeAllJSeq() - - /** - * Method removeAllTree - * - */ - public void removeAllTree() - { - _treeList.removeAllElements(); - } //-- void removeAllTree() - - /** - * Method removeAllUserColours - * - */ - public void removeAllUserColours() - { - _userColoursList.removeAllElements(); - } //-- void removeAllUserColours() - - /** - * Method removeAllViewport - * - */ - public void removeAllViewport() - { - _viewportList.removeAllElements(); - } //-- void removeAllViewport() - - /** - * Method removeJGroup - * - * - * - * @param index - * @return JGroup - */ - public jalview.binding.JGroup removeJGroup(int index) - { - java.lang.Object obj = _JGroupList.elementAt(index); - _JGroupList.removeElementAt(index); - return (jalview.binding.JGroup) obj; - } //-- jalview.binding.JGroup removeJGroup(int) - - /** - * Method removeJSeq - * - * - * - * @param index - * @return JSeq - */ - public jalview.binding.JSeq removeJSeq(int index) - { - java.lang.Object obj = _JSeqList.elementAt(index); - _JSeqList.removeElementAt(index); - return (jalview.binding.JSeq) obj; - } //-- jalview.binding.JSeq removeJSeq(int) - - /** - * Method removeTree - * - * - * - * @param index - * @return Tree - */ - public jalview.binding.Tree removeTree(int index) - { - java.lang.Object obj = _treeList.elementAt(index); - _treeList.removeElementAt(index); - return (jalview.binding.Tree) obj; - } //-- jalview.binding.Tree removeTree(int) - - /** - * Method removeUserColours - * - * - * - * @param index - * @return UserColours - */ - public jalview.binding.UserColours removeUserColours(int index) - { - java.lang.Object obj = _userColoursList.elementAt(index); - _userColoursList.removeElementAt(index); - return (jalview.binding.UserColours) obj; - } //-- jalview.binding.UserColours removeUserColours(int) - - /** - * Method removeViewport - * - * - * - * @param index - * @return Viewport - */ - public jalview.binding.Viewport removeViewport(int index) - { - java.lang.Object obj = _viewportList.elementAt(index); - _viewportList.removeElementAt(index); - return (jalview.binding.Viewport) obj; - } //-- jalview.binding.Viewport removeViewport(int) - - /** - * Method setJGroup - * - * - * - * @param index - * @param vJGroup - */ - public void setJGroup(int index, jalview.binding.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ( (index < 0) || (index > _JGroupList.size())) - { - throw new IndexOutOfBoundsException(); - } - _JGroupList.setElementAt(vJGroup, index); - } //-- void setJGroup(int, jalview.binding.JGroup) - - /** - * Method setJGroup - * - * - * - * @param JGroupArray - */ - public void setJGroup(jalview.binding.JGroup[] JGroupArray) - { - //-- copy array - _JGroupList.removeAllElements(); - for (int i = 0; i < JGroupArray.length; i++) - { - _JGroupList.addElement(JGroupArray[i]); - } - } //-- void setJGroup(jalview.binding.JGroup) - - /** - * Method setJSeq - * - * - * - * @param index - * @param vJSeq - */ - public void setJSeq(int index, jalview.binding.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ( (index < 0) || (index > _JSeqList.size())) - { - throw new IndexOutOfBoundsException(); - } - _JSeqList.setElementAt(vJSeq, index); - } //-- void setJSeq(int, jalview.binding.JSeq) - - /** - * Method setJSeq - * - * - * - * @param JSeqArray - */ - public void setJSeq(jalview.binding.JSeq[] JSeqArray) - { - //-- copy array - _JSeqList.removeAllElements(); - for (int i = 0; i < JSeqArray.length; i++) - { - _JSeqList.addElement(JSeqArray[i]); - } - } //-- void setJSeq(jalview.binding.JSeq) - - /** - * Method setTree - * - * - * - * @param index - * @param vTree - */ - public void setTree(int index, jalview.binding.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ( (index < 0) || (index > _treeList.size())) - { - throw new IndexOutOfBoundsException(); - } - _treeList.setElementAt(vTree, index); - } //-- void setTree(int, jalview.binding.Tree) - - /** - * Method setTree - * - * - * - * @param treeArray - */ - public void setTree(jalview.binding.Tree[] treeArray) - { - //-- copy array - _treeList.removeAllElements(); - for (int i = 0; i < treeArray.length; i++) - { - _treeList.addElement(treeArray[i]); - } - } //-- void setTree(jalview.binding.Tree) - - /** - * Method setUserColours - * - * - * - * @param index - * @param vUserColours - */ - public void setUserColours(int index, - jalview.binding.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ( (index < 0) || (index > _userColoursList.size())) - { - throw new IndexOutOfBoundsException(); - } - _userColoursList.setElementAt(vUserColours, index); - } //-- void setUserColours(int, jalview.binding.UserColours) - - /** - * Method setUserColours - * - * - * - * @param userColoursArray - */ - public void setUserColours(jalview.binding.UserColours[] userColoursArray) - { - //-- copy array - _userColoursList.removeAllElements(); - for (int i = 0; i < userColoursArray.length; i++) - { - _userColoursList.addElement(userColoursArray[i]); - } - } //-- void setUserColours(jalview.binding.UserColours) - - /** - * Method setViewport - * - * - * - * @param index - * @param vViewport - */ - public void setViewport(int index, jalview.binding.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ( (index < 0) || (index > _viewportList.size())) - { - throw new IndexOutOfBoundsException(); - } - _viewportList.setElementAt(vViewport, index); - } //-- void setViewport(int, jalview.binding.Viewport) - - /** - * Method setViewport - * - * - * - * @param viewportArray - */ - public void setViewport(jalview.binding.Viewport[] viewportArray) - { - //-- copy array - _viewportList.removeAllElements(); - for (int i = 0; i < viewportArray.length; i++) - { - _viewportList.addElement(viewportArray[i]); - } - } //-- void setViewport(jalview.binding.Viewport) - - /** - * 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.JalviewModelSequence) Unmarshaller.unmarshal( - jalview.binding.JalviewModelSequence.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() +public class JalviewModelSequence implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _JSeqList + */ + private java.util.Vector _JSeqList; + + /** + * Field _JGroupList + */ + private java.util.Vector _JGroupList; + + /** + * Field _viewportList + */ + private java.util.Vector _viewportList; + + /** + * Field _userColoursList + */ + private java.util.Vector _userColoursList; + + /** + * Field _treeList + */ + private java.util.Vector _treeList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JalviewModelSequence() { + super(); + _JSeqList = new Vector(); + _JGroupList = new Vector(); + _viewportList = new Vector(); + _userColoursList = new Vector(); + _treeList = new Vector(); + } //-- jalview.binding.JalviewModelSequence() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method addJGroup + * + * + * + * @param vJGroup + */ + public void addJGroup(jalview.binding.JGroup vJGroup) + throws java.lang.IndexOutOfBoundsException + { + _JGroupList.addElement(vJGroup); + } //-- void addJGroup(jalview.binding.JGroup) + + /** + * Method addJGroup + * + * + * + * @param index + * @param vJGroup + */ + public void addJGroup(int index, jalview.binding.JGroup vJGroup) + throws java.lang.IndexOutOfBoundsException + { + _JGroupList.insertElementAt(vJGroup, index); + } //-- void addJGroup(int, jalview.binding.JGroup) + + /** + * Method addJSeq + * + * + * + * @param vJSeq + */ + public void addJSeq(jalview.binding.JSeq vJSeq) + throws java.lang.IndexOutOfBoundsException + { + _JSeqList.addElement(vJSeq); + } //-- void addJSeq(jalview.binding.JSeq) + + /** + * Method addJSeq + * + * + * + * @param index + * @param vJSeq + */ + public void addJSeq(int index, jalview.binding.JSeq vJSeq) + throws java.lang.IndexOutOfBoundsException + { + _JSeqList.insertElementAt(vJSeq, index); + } //-- void addJSeq(int, jalview.binding.JSeq) + + /** + * Method addTree + * + * + * + * @param vTree + */ + public void addTree(jalview.binding.Tree vTree) + throws java.lang.IndexOutOfBoundsException + { + _treeList.addElement(vTree); + } //-- void addTree(jalview.binding.Tree) + + /** + * Method addTree + * + * + * + * @param index + * @param vTree + */ + public void addTree(int index, jalview.binding.Tree vTree) + throws java.lang.IndexOutOfBoundsException + { + _treeList.insertElementAt(vTree, index); + } //-- void addTree(int, jalview.binding.Tree) + + /** + * Method addUserColours + * + * + * + * @param vUserColours + */ + public void addUserColours(jalview.binding.UserColours vUserColours) + throws java.lang.IndexOutOfBoundsException + { + _userColoursList.addElement(vUserColours); + } //-- void addUserColours(jalview.binding.UserColours) + + /** + * Method addUserColours + * + * + * + * @param index + * @param vUserColours + */ + public void addUserColours(int index, jalview.binding.UserColours vUserColours) + throws java.lang.IndexOutOfBoundsException + { + _userColoursList.insertElementAt(vUserColours, index); + } //-- void addUserColours(int, jalview.binding.UserColours) + + /** + * Method addViewport + * + * + * + * @param vViewport + */ + public void addViewport(jalview.binding.Viewport vViewport) + throws java.lang.IndexOutOfBoundsException + { + _viewportList.addElement(vViewport); + } //-- void addViewport(jalview.binding.Viewport) + + /** + * Method addViewport + * + * + * + * @param index + * @param vViewport + */ + public void addViewport(int index, jalview.binding.Viewport vViewport) + throws java.lang.IndexOutOfBoundsException + { + _viewportList.insertElementAt(vViewport, index); + } //-- void addViewport(int, jalview.binding.Viewport) + + /** + * Method enumerateJGroup + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateJGroup() + { + return _JGroupList.elements(); + } //-- java.util.Enumeration enumerateJGroup() + + /** + * Method enumerateJSeq + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateJSeq() + { + return _JSeqList.elements(); + } //-- java.util.Enumeration enumerateJSeq() + + /** + * Method enumerateTree + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateTree() + { + return _treeList.elements(); + } //-- java.util.Enumeration enumerateTree() + + /** + * Method enumerateUserColours + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateUserColours() + { + return _userColoursList.elements(); + } //-- java.util.Enumeration enumerateUserColours() + + /** + * Method enumerateViewport + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateViewport() + { + return _viewportList.elements(); + } //-- java.util.Enumeration enumerateViewport() + + /** + * Method getJGroup + * + * + * + * @param index + * @return JGroup + */ + public jalview.binding.JGroup getJGroup(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _JGroupList.size())) { + throw new IndexOutOfBoundsException(); + } + + return (jalview.binding.JGroup) _JGroupList.elementAt(index); + } //-- jalview.binding.JGroup getJGroup(int) + + /** + * Method getJGroup + * + * + * + * @return JGroup + */ + public jalview.binding.JGroup[] getJGroup() + { + int size = _JGroupList.size(); + jalview.binding.JGroup[] mArray = new jalview.binding.JGroup[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (jalview.binding.JGroup) _JGroupList.elementAt(index); + } + return mArray; + } //-- jalview.binding.JGroup[] getJGroup() + + /** + * Method getJGroupCount + * + * + * + * @return int + */ + public int getJGroupCount() + { + return _JGroupList.size(); + } //-- int getJGroupCount() + + /** + * Method getJSeq + * + * + * + * @param index + * @return JSeq + */ + public jalview.binding.JSeq getJSeq(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _JSeqList.size())) { + throw new IndexOutOfBoundsException(); + } + + return (jalview.binding.JSeq) _JSeqList.elementAt(index); + } //-- jalview.binding.JSeq getJSeq(int) + + /** + * Method getJSeq + * + * + * + * @return JSeq + */ + public jalview.binding.JSeq[] getJSeq() + { + int size = _JSeqList.size(); + jalview.binding.JSeq[] mArray = new jalview.binding.JSeq[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (jalview.binding.JSeq) _JSeqList.elementAt(index); + } + return mArray; + } //-- jalview.binding.JSeq[] getJSeq() + + /** + * Method getJSeqCount + * + * + * + * @return int + */ + public int getJSeqCount() + { + return _JSeqList.size(); + } //-- int getJSeqCount() + + /** + * Method getTree + * + * + * + * @param index + * @return Tree + */ + public jalview.binding.Tree getTree(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _treeList.size())) { + throw new IndexOutOfBoundsException(); + } + + return (jalview.binding.Tree) _treeList.elementAt(index); + } //-- jalview.binding.Tree getTree(int) + + /** + * Method getTree + * + * + * + * @return Tree + */ + public jalview.binding.Tree[] getTree() + { + int size = _treeList.size(); + jalview.binding.Tree[] mArray = new jalview.binding.Tree[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (jalview.binding.Tree) _treeList.elementAt(index); + } + return mArray; + } //-- jalview.binding.Tree[] getTree() + + /** + * Method getTreeCount + * + * + * + * @return int + */ + public int getTreeCount() + { + return _treeList.size(); + } //-- int getTreeCount() + + /** + * Method getUserColours + * + * + * + * @param index + * @return UserColours + */ + public jalview.binding.UserColours getUserColours(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _userColoursList.size())) { + throw new IndexOutOfBoundsException(); + } + + return (jalview.binding.UserColours) _userColoursList.elementAt(index); + } //-- jalview.binding.UserColours getUserColours(int) + + /** + * Method getUserColours + * + * + * + * @return UserColours + */ + public jalview.binding.UserColours[] getUserColours() + { + int size = _userColoursList.size(); + jalview.binding.UserColours[] mArray = new jalview.binding.UserColours[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (jalview.binding.UserColours) _userColoursList.elementAt(index); + } + return mArray; + } //-- jalview.binding.UserColours[] getUserColours() + + /** + * Method getUserColoursCount + * + * + * + * @return int + */ + public int getUserColoursCount() + { + return _userColoursList.size(); + } //-- int getUserColoursCount() + + /** + * Method getViewport + * + * + * + * @param index + * @return Viewport + */ + public jalview.binding.Viewport getViewport(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _viewportList.size())) { + throw new IndexOutOfBoundsException(); + } + + return (jalview.binding.Viewport) _viewportList.elementAt(index); + } //-- jalview.binding.Viewport getViewport(int) + + /** + * Method getViewport + * + * + * + * @return Viewport + */ + public jalview.binding.Viewport[] getViewport() + { + int size = _viewportList.size(); + jalview.binding.Viewport[] mArray = new jalview.binding.Viewport[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (jalview.binding.Viewport) _viewportList.elementAt(index); + } + return mArray; + } //-- jalview.binding.Viewport[] getViewport() + + /** + * Method getViewportCount + * + * + * + * @return int + */ + public int getViewportCount() + { + return _viewportList.size(); + } //-- int getViewportCount() + + /** + * 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 removeAllJGroup + * + */ + public void removeAllJGroup() + { + _JGroupList.removeAllElements(); + } //-- void removeAllJGroup() + + /** + * Method removeAllJSeq + * + */ + public void removeAllJSeq() + { + _JSeqList.removeAllElements(); + } //-- void removeAllJSeq() + + /** + * Method removeAllTree + * + */ + public void removeAllTree() + { + _treeList.removeAllElements(); + } //-- void removeAllTree() + + /** + * Method removeAllUserColours + * + */ + public void removeAllUserColours() + { + _userColoursList.removeAllElements(); + } //-- void removeAllUserColours() + + /** + * Method removeAllViewport + * + */ + public void removeAllViewport() + { + _viewportList.removeAllElements(); + } //-- void removeAllViewport() + + /** + * Method removeJGroup + * + * + * + * @param index + * @return JGroup + */ + public jalview.binding.JGroup removeJGroup(int index) + { + java.lang.Object obj = _JGroupList.elementAt(index); + _JGroupList.removeElementAt(index); + return (jalview.binding.JGroup) obj; + } //-- jalview.binding.JGroup removeJGroup(int) + + /** + * Method removeJSeq + * + * + * + * @param index + * @return JSeq + */ + public jalview.binding.JSeq removeJSeq(int index) + { + java.lang.Object obj = _JSeqList.elementAt(index); + _JSeqList.removeElementAt(index); + return (jalview.binding.JSeq) obj; + } //-- jalview.binding.JSeq removeJSeq(int) + + /** + * Method removeTree + * + * + * + * @param index + * @return Tree + */ + public jalview.binding.Tree removeTree(int index) + { + java.lang.Object obj = _treeList.elementAt(index); + _treeList.removeElementAt(index); + return (jalview.binding.Tree) obj; + } //-- jalview.binding.Tree removeTree(int) + + /** + * Method removeUserColours + * + * + * + * @param index + * @return UserColours + */ + public jalview.binding.UserColours removeUserColours(int index) + { + java.lang.Object obj = _userColoursList.elementAt(index); + _userColoursList.removeElementAt(index); + return (jalview.binding.UserColours) obj; + } //-- jalview.binding.UserColours removeUserColours(int) + + /** + * Method removeViewport + * + * + * + * @param index + * @return Viewport + */ + public jalview.binding.Viewport removeViewport(int index) + { + java.lang.Object obj = _viewportList.elementAt(index); + _viewportList.removeElementAt(index); + return (jalview.binding.Viewport) obj; + } //-- jalview.binding.Viewport removeViewport(int) + + /** + * Method setJGroup + * + * + * + * @param index + * @param vJGroup + */ + public void setJGroup(int index, jalview.binding.JGroup vJGroup) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _JGroupList.size())) { + throw new IndexOutOfBoundsException(); + } + _JGroupList.setElementAt(vJGroup, index); + } //-- void setJGroup(int, jalview.binding.JGroup) + + /** + * Method setJGroup + * + * + * + * @param JGroupArray + */ + public void setJGroup(jalview.binding.JGroup[] JGroupArray) + { + //-- copy array + _JGroupList.removeAllElements(); + for (int i = 0; i < JGroupArray.length; i++) { + _JGroupList.addElement(JGroupArray[i]); + } + } //-- void setJGroup(jalview.binding.JGroup) + + /** + * Method setJSeq + * + * + * + * @param index + * @param vJSeq + */ + public void setJSeq(int index, jalview.binding.JSeq vJSeq) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _JSeqList.size())) { + throw new IndexOutOfBoundsException(); + } + _JSeqList.setElementAt(vJSeq, index); + } //-- void setJSeq(int, jalview.binding.JSeq) + + /** + * Method setJSeq + * + * + * + * @param JSeqArray + */ + public void setJSeq(jalview.binding.JSeq[] JSeqArray) + { + //-- copy array + _JSeqList.removeAllElements(); + for (int i = 0; i < JSeqArray.length; i++) { + _JSeqList.addElement(JSeqArray[i]); + } + } //-- void setJSeq(jalview.binding.JSeq) + + /** + * Method setTree + * + * + * + * @param index + * @param vTree + */ + public void setTree(int index, jalview.binding.Tree vTree) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _treeList.size())) { + throw new IndexOutOfBoundsException(); + } + _treeList.setElementAt(vTree, index); + } //-- void setTree(int, jalview.binding.Tree) + + /** + * Method setTree + * + * + * + * @param treeArray + */ + public void setTree(jalview.binding.Tree[] treeArray) + { + //-- copy array + _treeList.removeAllElements(); + for (int i = 0; i < treeArray.length; i++) { + _treeList.addElement(treeArray[i]); + } + } //-- void setTree(jalview.binding.Tree) + + /** + * Method setUserColours + * + * + * + * @param index + * @param vUserColours + */ + public void setUserColours(int index, jalview.binding.UserColours vUserColours) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _userColoursList.size())) { + throw new IndexOutOfBoundsException(); + } + _userColoursList.setElementAt(vUserColours, index); + } //-- void setUserColours(int, jalview.binding.UserColours) + + /** + * Method setUserColours + * + * + * + * @param userColoursArray + */ + public void setUserColours(jalview.binding.UserColours[] userColoursArray) + { + //-- copy array + _userColoursList.removeAllElements(); + for (int i = 0; i < userColoursArray.length; i++) { + _userColoursList.addElement(userColoursArray[i]); + } + } //-- void setUserColours(jalview.binding.UserColours) + + /** + * Method setViewport + * + * + * + * @param index + * @param vViewport + */ + public void setViewport(int index, jalview.binding.Viewport vViewport) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _viewportList.size())) { + throw new IndexOutOfBoundsException(); + } + _viewportList.setElementAt(vViewport, index); + } //-- void setViewport(int, jalview.binding.Viewport) + + /** + * Method setViewport + * + * + * + * @param viewportArray + */ + public void setViewport(jalview.binding.Viewport[] viewportArray) + { + //-- copy array + _viewportList.removeAllElements(); + for (int i = 0; i < viewportArray.length; i++) { + _viewportList.addElement(viewportArray[i]); + } + } //-- void setViewport(jalview.binding.Viewport) + + /** + * 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.JalviewModelSequence) Unmarshaller.unmarshal(jalview.binding.JalviewModelSequence.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() } diff --git a/src/jalview/binding/JalviewUserColours.java b/src/jalview/binding/JalviewUserColours.java index 8df0d44..eeb051b 100755 --- a/src/jalview/binding/JalviewUserColours.java +++ b/src/jalview/binding/JalviewUserColours.java @@ -1,78 +1,83 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ -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; +package jalview.binding; + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -//- 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 JalviewUserColours. - * + * * @version $Revision$ $Date$ */ -public class JalviewUserColours implements java.io.Serializable -{ - //--------------------------/ - //- Class/Member Variables -/ +public class JalviewUserColours implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ //--------------------------/ /** + * Field _schemeName + */ + private java.lang.String _schemeName; + + /** * Field _colourList */ private java.util.Vector _colourList; + + //----------------/ + //- Constructors -/ //----------------/ - //- Constructors -/ - //----------------/ - public JalviewUserColours() - { + + public JalviewUserColours() { super(); _colourList = new Vector(); - } + } //-- jalview.binding.JalviewUserColours() + - //-- jalview.binding.JalviewUserColours() + //-----------/ + //- Methods -/ //-----------/ /** - * DOCUMENT ME! - * - * @param vColour DOCUMENT ME! - * - * @throws java.lang.IndexOutOfBoundsException DOCUMENT ME! + * Method addColour + * + * + * + * @param vColour */ public void addColour(jalview.binding.Colour vColour) throws java.lang.IndexOutOfBoundsException { _colourList.addElement(vColour); - } - - //-- void addColour(jalview.binding.Colour) + } //-- void addColour(jalview.binding.Colour) /** * Method addColour - * - * - * + * + * + * * @param index * @param vColour */ @@ -80,29 +85,25 @@ public class JalviewUserColours implements java.io.Serializable throws java.lang.IndexOutOfBoundsException { _colourList.insertElementAt(vColour, index); - } - - //-- void addColour(int, jalview.binding.Colour) + } //-- void addColour(int, jalview.binding.Colour) /** * Method enumerateColour - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateColour() { return _colourList.elements(); - } - - //-- java.util.Enumeration enumerateColour() + } //-- java.util.Enumeration enumerateColour() /** * Method getColour - * - * - * + * + * + * * @param index * @return Colour */ @@ -110,123 +111,113 @@ public class JalviewUserColours implements java.io.Serializable throws java.lang.IndexOutOfBoundsException { //-- check bounds for index - if ((index < 0) || (index > _colourList.size())) - { + if ((index < 0) || (index > _colourList.size())) { throw new IndexOutOfBoundsException(); } - + return (jalview.binding.Colour) _colourList.elementAt(index); - } - - //-- jalview.binding.Colour getColour(int) + } //-- jalview.binding.Colour getColour(int) /** * Method getColour - * - * - * + * + * + * * @return Colour */ public jalview.binding.Colour[] getColour() { int size = _colourList.size(); jalview.binding.Colour[] mArray = new jalview.binding.Colour[size]; - - for (int index = 0; index < size; index++) - { + for (int index = 0; index < size; index++) { mArray[index] = (jalview.binding.Colour) _colourList.elementAt(index); } - return mArray; - } - - //-- jalview.binding.Colour[] getColour() + } //-- jalview.binding.Colour[] getColour() /** * Method getColourCount - * - * - * + * + * + * * @return int */ public int getColourCount() { return _colourList.size(); - } + } //-- int getColourCount() - //-- int getColourCount() + /** + * Returns the value of field 'schemeName'. + * + * @return String + * @return the value of field 'schemeName'. + */ + public java.lang.String getSchemeName() + { + return this._schemeName; + } //-- java.lang.String getSchemeName() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() { - try - { + try { validate(); } - catch (org.exolab.castor.xml.ValidationException vex) - { + catch (org.exolab.castor.xml.ValidationException vex) { 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 + 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 + 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 removeAllColour - * + * */ public void removeAllColour() { _colourList.removeAllElements(); - } - - //-- void removeAllColour() + } //-- void removeAllColour() /** * Method removeColour - * - * - * + * + * + * * @param index * @return Colour */ @@ -234,17 +225,14 @@ public class JalviewUserColours implements java.io.Serializable { java.lang.Object obj = _colourList.elementAt(index); _colourList.removeElementAt(index); - return (jalview.binding.Colour) obj; - } - - //-- jalview.binding.Colour removeColour(int) + } //-- jalview.binding.Colour removeColour(int) /** * Method setColour - * - * - * + * + * + * * @param index * @param vColour */ @@ -252,63 +240,61 @@ public class JalviewUserColours implements java.io.Serializable throws java.lang.IndexOutOfBoundsException { //-- check bounds for index - if ((index < 0) || (index > _colourList.size())) - { + if ((index < 0) || (index > _colourList.size())) { throw new IndexOutOfBoundsException(); } - _colourList.setElementAt(vColour, index); - } - - //-- void setColour(int, jalview.binding.Colour) + } //-- void setColour(int, jalview.binding.Colour) /** * Method setColour - * - * - * + * + * + * * @param colourArray */ public void setColour(jalview.binding.Colour[] colourArray) { //-- copy array _colourList.removeAllElements(); - - for (int i = 0; i < colourArray.length; i++) - { + for (int i = 0; i < colourArray.length; i++) { _colourList.addElement(colourArray[i]); } - } + } //-- void setColour(jalview.binding.Colour) - //-- void setColour(jalview.binding.Colour) + /** + * Sets the value of field 'schemeName'. + * + * @param schemeName the value of field 'schemeName'. + */ + public void setSchemeName(java.lang.String schemeName) + { + this._schemeName = schemeName; + } //-- void setSchemeName(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 + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class, - reader); - } - - //-- java.lang.Object unmarshal(java.io.Reader) + return (jalview.binding.JalviewUserColours) Unmarshaller.unmarshal(jalview.binding.JalviewUserColours.class, reader); + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ - 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() - //-- void validate() } diff --git a/src/jalview/binding/Sequence.java b/src/jalview/binding/Sequence.java index b583b4e..f3fd4e4 100755 --- a/src/jalview/binding/Sequence.java +++ b/src/jalview/binding/Sequence.java @@ -1,5 +1,5 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ @@ -7,110 +7,112 @@ package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -import org.exolab.castor.xml.*; +import java.io.IOException; +import java.io.Reader; +import java.io.Serializable; +import java.io.Writer; +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 Sequence. - * + * * @version $Revision$ $Date$ */ -public class Sequence - extends SequenceType implements java.io.Serializable +public class Sequence extends SequenceType +implements java.io.Serializable { - //----------------/ - //- Constructors -/ - //----------------/ - public Sequence() - { - super(); - } //-- jalview.binding.Sequence() + //----------------/ + //- Constructors -/ + //----------------/ - //-----------/ - //- Methods -/ - //-----------/ + public Sequence() { + super(); + } //-- jalview.binding.Sequence() - /** - * 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 - { + //-----------/ + //- Methods -/ + //-----------/ - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + /** + * 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 handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { + /** + * 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) - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + /** + * 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 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.Sequence) Unmarshaller.unmarshal(jalview.binding. - Sequence.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + /** + * 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.Sequence) Unmarshaller.unmarshal(jalview.binding.Sequence.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() + /** + * 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() } diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java index a0d116e..7ed3b52 100755 --- a/src/jalview/binding/SequenceSet.java +++ b/src/jalview/binding/SequenceSet.java @@ -1,39 +1,38 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ -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; +package jalview.binding; + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -//- 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 SequenceSet. - * + * * @version $Revision$ $Date$ */ -public class SequenceSet implements java.io.Serializable -{ - //--------------------------/ - //- Class/Member Variables -/ +public class SequenceSet implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ //--------------------------/ /** @@ -61,39 +60,40 @@ public class SequenceSet implements java.io.Serializable */ private java.util.Vector _annotationList; + + //----------------/ + //- Constructors -/ //----------------/ - //- Constructors -/ - //----------------/ - public SequenceSet() - { + + public SequenceSet() { super(); _sequenceList = new Vector(); _annotationList = new Vector(); - } + } //-- jalview.binding.SequenceSet() + - //-- jalview.binding.SequenceSet() + //-----------/ + //- Methods -/ //-----------/ /** - * DOCUMENT ME! - * - * @param vAnnotation DOCUMENT ME! - * - * @throws java.lang.IndexOutOfBoundsException DOCUMENT ME! + * Method addAnnotation + * + * + * + * @param vAnnotation */ public void addAnnotation(jalview.binding.Annotation vAnnotation) throws java.lang.IndexOutOfBoundsException { _annotationList.addElement(vAnnotation); - } - - //-- void addAnnotation(jalview.binding.Annotation) + } //-- void addAnnotation(jalview.binding.Annotation) /** * Method addAnnotation - * - * - * + * + * + * * @param index * @param vAnnotation */ @@ -101,30 +101,26 @@ public class SequenceSet implements java.io.Serializable throws java.lang.IndexOutOfBoundsException { _annotationList.insertElementAt(vAnnotation, index); - } - - //-- void addAnnotation(int, jalview.binding.Annotation) + } //-- void addAnnotation(int, jalview.binding.Annotation) /** * Method addSequence - * - * - * + * + * + * * @param vSequence */ public void addSequence(jalview.binding.Sequence vSequence) throws java.lang.IndexOutOfBoundsException { _sequenceList.addElement(vSequence); - } - - //-- void addSequence(jalview.binding.Sequence) + } //-- void addSequence(jalview.binding.Sequence) /** * Method addSequence - * - * - * + * + * + * * @param index * @param vSequence */ @@ -132,67 +128,57 @@ public class SequenceSet implements java.io.Serializable throws java.lang.IndexOutOfBoundsException { _sequenceList.insertElementAt(vSequence, index); - } - - //-- void addSequence(int, jalview.binding.Sequence) + } //-- void addSequence(int, jalview.binding.Sequence) /** * Method deleteAligned - * + * */ public void deleteAligned() { - this._has_aligned = false; - } - - //-- void deleteAligned() + this._has_aligned= false; + } //-- void deleteAligned() /** * Method enumerateAnnotation - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateAnnotation() { return _annotationList.elements(); - } - - //-- java.util.Enumeration enumerateAnnotation() + } //-- java.util.Enumeration enumerateAnnotation() /** * Method enumerateSequence - * - * - * + * + * + * * @return Enumeration */ public java.util.Enumeration enumerateSequence() { return _sequenceList.elements(); - } - - //-- java.util.Enumeration enumerateSequence() + } //-- java.util.Enumeration enumerateSequence() /** * Returns the value of field 'aligned'. - * + * * @return boolean * @return the value of field 'aligned'. */ public boolean getAligned() { return this._aligned; - } - - //-- boolean getAligned() + } //-- boolean getAligned() /** * Method getAnnotation - * - * - * + * + * + * * @param index * @return Annotation */ @@ -200,70 +186,58 @@ public class SequenceSet implements java.io.Serializable throws java.lang.IndexOutOfBoundsException { //-- check bounds for index - if ((index < 0) || (index > _annotationList.size())) - { + if ((index < 0) || (index > _annotationList.size())) { throw new IndexOutOfBoundsException(); } - + return (jalview.binding.Annotation) _annotationList.elementAt(index); - } - - //-- jalview.binding.Annotation getAnnotation(int) + } //-- jalview.binding.Annotation getAnnotation(int) /** * Method getAnnotation - * - * - * + * + * + * * @return Annotation */ public jalview.binding.Annotation[] getAnnotation() { int size = _annotationList.size(); jalview.binding.Annotation[] mArray = new jalview.binding.Annotation[size]; - - for (int index = 0; index < size; index++) - { + for (int index = 0; index < size; index++) { mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index); } - return mArray; - } - - //-- jalview.binding.Annotation[] getAnnotation() + } //-- jalview.binding.Annotation[] getAnnotation() /** * Method getAnnotationCount - * - * - * + * + * + * * @return int */ public int getAnnotationCount() { return _annotationList.size(); - } - - //-- int getAnnotationCount() + } //-- int getAnnotationCount() /** * Returns the value of field 'gapChar'. - * + * * @return String * @return the value of field 'gapChar'. */ public java.lang.String getGapChar() { return this._gapChar; - } - - //-- java.lang.String getGapChar() + } //-- java.lang.String getGapChar() /** * Method getSequence - * - * - * + * + * + * * @param index * @return Sequence */ @@ -271,148 +245,123 @@ public class SequenceSet implements java.io.Serializable throws java.lang.IndexOutOfBoundsException { //-- check bounds for index - if ((index < 0) || (index > _sequenceList.size())) - { + if ((index < 0) || (index > _sequenceList.size())) { throw new IndexOutOfBoundsException(); } - + return (jalview.binding.Sequence) _sequenceList.elementAt(index); - } - - //-- jalview.binding.Sequence getSequence(int) + } //-- jalview.binding.Sequence getSequence(int) /** * Method getSequence - * - * - * + * + * + * * @return Sequence */ public jalview.binding.Sequence[] getSequence() { int size = _sequenceList.size(); jalview.binding.Sequence[] mArray = new jalview.binding.Sequence[size]; - - for (int index = 0; index < size; index++) - { + for (int index = 0; index < size; index++) { mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index); } - return mArray; - } - - //-- jalview.binding.Sequence[] getSequence() + } //-- jalview.binding.Sequence[] getSequence() /** * Method getSequenceCount - * - * - * + * + * + * * @return int */ public int getSequenceCount() { return _sequenceList.size(); - } - - //-- int getSequenceCount() + } //-- int getSequenceCount() /** * Method hasAligned - * - * - * + * + * + * * @return boolean */ public boolean hasAligned() { return this._has_aligned; - } - - //-- boolean hasAligned() + } //-- boolean hasAligned() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() { - try - { + try { validate(); } - catch (org.exolab.castor.xml.ValidationException vex) - { + catch (org.exolab.castor.xml.ValidationException vex) { 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 + 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 + 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 removeAllAnnotation - * + * */ public void removeAllAnnotation() { _annotationList.removeAllElements(); - } - - //-- void removeAllAnnotation() + } //-- void removeAllAnnotation() /** * Method removeAllSequence - * + * */ public void removeAllSequence() { _sequenceList.removeAllElements(); - } - - //-- void removeAllSequence() + } //-- void removeAllSequence() /** * Method removeAnnotation - * - * - * + * + * + * * @param index * @return Annotation */ @@ -420,17 +369,14 @@ public class SequenceSet implements java.io.Serializable { java.lang.Object obj = _annotationList.elementAt(index); _annotationList.removeElementAt(index); - return (jalview.binding.Annotation) obj; - } - - //-- jalview.binding.Annotation removeAnnotation(int) + } //-- jalview.binding.Annotation removeAnnotation(int) /** * Method removeSequence - * - * - * + * + * + * * @param index * @return Sequence */ @@ -438,30 +384,25 @@ public class SequenceSet implements java.io.Serializable { java.lang.Object obj = _sequenceList.elementAt(index); _sequenceList.removeElementAt(index); - return (jalview.binding.Sequence) obj; - } - - //-- jalview.binding.Sequence removeSequence(int) + } //-- jalview.binding.Sequence removeSequence(int) /** * Sets the value of field 'aligned'. - * + * * @param aligned the value of field 'aligned'. */ public void setAligned(boolean aligned) { this._aligned = aligned; this._has_aligned = true; - } - - //-- void setAligned(boolean) + } //-- void setAligned(boolean) /** * Method setAnnotation - * - * - * + * + * + * * @param index * @param vAnnotation */ @@ -469,53 +410,43 @@ public class SequenceSet implements java.io.Serializable throws java.lang.IndexOutOfBoundsException { //-- check bounds for index - if ((index < 0) || (index > _annotationList.size())) - { + if ((index < 0) || (index > _annotationList.size())) { throw new IndexOutOfBoundsException(); } - _annotationList.setElementAt(vAnnotation, index); - } - - //-- void setAnnotation(int, jalview.binding.Annotation) + } //-- void setAnnotation(int, jalview.binding.Annotation) /** * Method setAnnotation - * - * - * + * + * + * * @param annotationArray */ public void setAnnotation(jalview.binding.Annotation[] annotationArray) { //-- copy array _annotationList.removeAllElements(); - - for (int i = 0; i < annotationArray.length; i++) - { + for (int i = 0; i < annotationArray.length; i++) { _annotationList.addElement(annotationArray[i]); } - } - - //-- void setAnnotation(jalview.binding.Annotation) + } //-- void setAnnotation(jalview.binding.Annotation) /** * Sets the value of field 'gapChar'. - * + * * @param gapChar the value of field 'gapChar'. */ public void setGapChar(java.lang.String gapChar) { this._gapChar = gapChar; - } - - //-- void setGapChar(java.lang.String) + } //-- void setGapChar(java.lang.String) /** * Method setSequence - * - * - * + * + * + * * @param index * @param vSequence */ @@ -523,63 +454,51 @@ public class SequenceSet implements java.io.Serializable throws java.lang.IndexOutOfBoundsException { //-- check bounds for index - if ((index < 0) || (index > _sequenceList.size())) - { + if ((index < 0) || (index > _sequenceList.size())) { throw new IndexOutOfBoundsException(); } - _sequenceList.setElementAt(vSequence, index); - } - - //-- void setSequence(int, jalview.binding.Sequence) + } //-- void setSequence(int, jalview.binding.Sequence) /** * Method setSequence - * - * - * + * + * + * * @param sequenceArray */ public void setSequence(jalview.binding.Sequence[] sequenceArray) { //-- copy array _sequenceList.removeAllElements(); - - for (int i = 0; i < sequenceArray.length; i++) - { + for (int i = 0; i < sequenceArray.length; i++) { _sequenceList.addElement(sequenceArray[i]); } - } - - //-- void setSequence(jalview.binding.Sequence) + } //-- void setSequence(jalview.binding.Sequence) /** * 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 + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class, - reader); - } - - //-- java.lang.Object unmarshal(java.io.Reader) + return (jalview.binding.SequenceSet) Unmarshaller.unmarshal(jalview.binding.SequenceSet.class, reader); + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ - 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() - //-- void validate() } diff --git a/src/jalview/binding/SequenceType.java b/src/jalview/binding/SequenceType.java index 780c8ba..3a935e4 100755 --- a/src/jalview/binding/SequenceType.java +++ b/src/jalview/binding/SequenceType.java @@ -1,5 +1,5 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ @@ -7,192 +7,193 @@ package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -import org.exolab.castor.xml.*; +import java.io.IOException; +import java.io.Reader; +import java.io.Serializable; +import java.io.Writer; +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 SequenceType. - * + * * @version $Revision$ $Date$ */ -public class SequenceType - implements java.io.Serializable -{ - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _id - */ - private java.lang.String _id; - - /** - * Field _sequence - */ - private java.lang.String _sequence; - - /** - * Field _name - */ - private java.lang.String _name; - - //----------------/ - //- Constructors -/ - //----------------/ - - public SequenceType() - { - super(); - } //-- jalview.binding.SequenceType() - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'id'. - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'name'. - * - * @return String - * @return the value of field 'name'. - */ - public java.lang.String getName() - { - return this._name; - } //-- java.lang.String getName() - - /** - * Returns the value of field 'sequence'. - * - * @return String - * @return the value of field 'sequence'. - */ - public java.lang.String getSequence() - { - return this._sequence; - } //-- java.lang.String getSequence() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try +public class SequenceType implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _id + */ + private java.lang.String _id; + + /** + * Field _sequence + */ + private java.lang.String _sequence; + + /** + * Field _name + */ + private java.lang.String _name; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceType() { + super(); + } //-- jalview.binding.SequenceType() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'id'. + * + * @return String + * @return the value of field 'id'. + */ + public java.lang.String getId() + { + return this._id; + } //-- java.lang.String getId() + + /** + * Returns the value of field 'name'. + * + * @return String + * @return the value of field 'name'. + */ + public java.lang.String getName() + { + return this._name; + } //-- java.lang.String getName() + + /** + * Returns the value of field 'sequence'. + * + * @return String + * @return the value of field 'sequence'. + */ + public java.lang.String getSequence() + { + return this._sequence; + } //-- java.lang.String getSequence() + + /** + * 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) + + /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId(java.lang.String id) + { + this._id = id; + } //-- void setId(java.lang.String) + + /** + * Sets the value of field 'name'. + * + * @param name the value of field 'name'. + */ + public void setName(java.lang.String name) + { + this._name = name; + } //-- void setName(java.lang.String) + + /** + * Sets the value of field 'sequence'. + * + * @param sequence the value of field 'sequence'. + */ + public void setSequence(java.lang.String sequence) + { + this._sequence = sequence; + } //-- void setSequence(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 { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) + return (jalview.binding.SequenceType) Unmarshaller.unmarshal(jalview.binding.SequenceType.class, reader); + } //-- java.lang.Object unmarshal(java.io.Reader) + + /** + * Method validate + * + */ + public void validate() + throws org.exolab.castor.xml.ValidationException { - 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) - - /** - * Sets the value of field 'id'. - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'name'. - * - * @param name the value of field 'name'. - */ - public void setName(java.lang.String name) - { - this._name = name; - } //-- void setName(java.lang.String) - - /** - * Sets the value of field 'sequence'. - * - * @param sequence the value of field 'sequence'. - */ - public void setSequence(java.lang.String sequence) - { - this._sequence = sequence; - } //-- void setSequence(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.SequenceType) Unmarshaller.unmarshal(jalview. - binding.SequenceType.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() + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } //-- void validate() } diff --git a/src/jalview/binding/Tree.java b/src/jalview/binding/Tree.java index 9fc63d2..56943c7 100755 --- a/src/jalview/binding/Tree.java +++ b/src/jalview/binding/Tree.java @@ -1,92 +1,77 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ -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; +package jalview.binding; + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ + import java.io.IOException; import java.io.Reader; import java.io.Serializable; import java.io.Writer; - +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 Tree. - * + * * @version $Revision$ $Date$ */ -public class Tree implements java.io.Serializable -{ - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ +public class Tree implements java.io.Serializable { - /** - * Field _title - */ - private java.lang.String _title; - /** - * Field _currentTree - */ - private boolean _currentTree; - - /** - * keeps track of state for field: _currentTree - */ - private boolean _has_currentTree; + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ /** - * Field _fitToWindow + * Field _width */ - private boolean _fitToWindow; + private int _width; /** - * keeps track of state for field: _fitToWindow + * keeps track of state for field: _width */ - private boolean _has_fitToWindow; + private boolean _has_width; /** - * Field _showDistances + * Field _height */ - private boolean _showDistances; + private int _height; /** - * keeps track of state for field: _showDistances + * keeps track of state for field: _height */ - private boolean _has_showDistances; + private boolean _has_height; /** - * Field _showBootstrap + * Field _xpos */ - private boolean _showBootstrap; + private int _xpos; /** - * keeps track of state for field: _showBootstrap + * keeps track of state for field: _xpos */ - private boolean _has_showBootstrap; + private boolean _has_xpos; /** - * Field _markUnlinked + * Field _ypos */ - private boolean _markUnlinked; + private int _ypos; /** - * keeps track of state for field: _markUnlinked + * keeps track of state for field: _ypos */ - private boolean _has_markUnlinked; + private boolean _has_ypos; /** * Field _fontSize @@ -109,753 +94,663 @@ public class Tree implements java.io.Serializable private boolean _has_threshold; /** - * Field _xpos + * Field _showBootstrap */ - private int _xpos; + private boolean _showBootstrap; /** - * keeps track of state for field: _xpos + * keeps track of state for field: _showBootstrap */ - private boolean _has_xpos; + private boolean _has_showBootstrap; /** - * Field _ypos + * Field _showDistances */ - private int _ypos; + private boolean _showDistances; /** - * keeps track of state for field: _ypos + * keeps track of state for field: _showDistances */ - private boolean _has_ypos; + private boolean _has_showDistances; /** - * Field _width + * Field _markUnlinked */ - private int _width; + private boolean _markUnlinked; /** - * keeps track of state for field: _width + * keeps track of state for field: _markUnlinked */ - private boolean _has_width; + private boolean _has_markUnlinked; /** - * Field _height + * Field _fitToWindow */ - private int _height; + private boolean _fitToWindow; /** - * keeps track of state for field: _height + * keeps track of state for field: _fitToWindow */ - private boolean _has_height; + private boolean _has_fitToWindow; + + /** + * Field _currentTree + */ + private boolean _currentTree; + + /** + * keeps track of state for field: _currentTree + */ + private boolean _has_currentTree; + + /** + * Field _title + */ + private java.lang.String _title; /** * Field _newick */ private java.lang.String _newick; + + //----------------/ + //- Constructors -/ //----------------/ - //- Constructors -/ - //----------------/ - public Tree() - { + + public Tree() { super(); - } + } //-- jalview.binding.Tree() - //-- jalview.binding.Tree() + + //-----------/ + //- Methods -/ //-----------/ /** - * DOCUMENT ME! + * Method deleteCurrentTree + * */ public void deleteCurrentTree() { - this._has_currentTree = false; - } - - //-- void deleteCurrentTree() + this._has_currentTree= false; + } //-- void deleteCurrentTree() /** * Method deleteFitToWindow - * + * */ public void deleteFitToWindow() { - this._has_fitToWindow = false; - } - - //-- void deleteFitToWindow() + this._has_fitToWindow= false; + } //-- void deleteFitToWindow() /** * Method deleteFontSize - * + * */ public void deleteFontSize() { - this._has_fontSize = false; - } - - //-- void deleteFontSize() + this._has_fontSize= false; + } //-- void deleteFontSize() /** * Method deleteHeight - * + * */ public void deleteHeight() { - this._has_height = false; - } - - //-- void deleteHeight() + this._has_height= false; + } //-- void deleteHeight() /** * Method deleteMarkUnlinked - * + * */ public void deleteMarkUnlinked() { - this._has_markUnlinked = false; - } - - //-- void deleteMarkUnlinked() + this._has_markUnlinked= false; + } //-- void deleteMarkUnlinked() /** * Method deleteShowBootstrap - * + * */ public void deleteShowBootstrap() { - this._has_showBootstrap = false; - } - - //-- void deleteShowBootstrap() + this._has_showBootstrap= false; + } //-- void deleteShowBootstrap() /** * Method deleteShowDistances - * + * */ public void deleteShowDistances() { - this._has_showDistances = false; - } - - //-- void deleteShowDistances() + this._has_showDistances= false; + } //-- void deleteShowDistances() /** * Method deleteThreshold - * + * */ public void deleteThreshold() { - this._has_threshold = false; - } - - //-- void deleteThreshold() + this._has_threshold= false; + } //-- void deleteThreshold() /** * Method deleteWidth - * + * */ public void deleteWidth() { - this._has_width = false; - } - - //-- void deleteWidth() + this._has_width= false; + } //-- void deleteWidth() /** * Method deleteXpos - * + * */ public void deleteXpos() { - this._has_xpos = false; - } - - //-- void deleteXpos() + this._has_xpos= false; + } //-- void deleteXpos() /** * Method deleteYpos - * + * */ public void deleteYpos() { - this._has_ypos = false; - } - - //-- void deleteYpos() + this._has_ypos= false; + } //-- void deleteYpos() /** * Returns the value of field 'currentTree'. - * + * * @return boolean * @return the value of field 'currentTree'. */ public boolean getCurrentTree() { return this._currentTree; - } - - //-- boolean getCurrentTree() + } //-- boolean getCurrentTree() /** * Returns the value of field 'fitToWindow'. - * + * * @return boolean * @return the value of field 'fitToWindow'. */ public boolean getFitToWindow() { return this._fitToWindow; - } - - //-- boolean getFitToWindow() + } //-- boolean getFitToWindow() /** * Returns the value of field 'fontSize'. - * + * * @return int * @return the value of field 'fontSize'. */ public int getFontSize() { return this._fontSize; - } - - //-- int getFontSize() + } //-- int getFontSize() /** * Returns the value of field 'height'. - * + * * @return int * @return the value of field 'height'. */ public int getHeight() { return this._height; - } - - //-- int getHeight() + } //-- int getHeight() /** * Returns the value of field 'markUnlinked'. - * + * * @return boolean * @return the value of field 'markUnlinked'. */ public boolean getMarkUnlinked() { return this._markUnlinked; - } - - //-- boolean getMarkUnlinked() + } //-- boolean getMarkUnlinked() /** * Returns the value of field 'newick'. - * + * * @return String * @return the value of field 'newick'. */ public java.lang.String getNewick() { return this._newick; - } - - //-- java.lang.String getNewick() + } //-- java.lang.String getNewick() /** * Returns the value of field 'showBootstrap'. - * + * * @return boolean * @return the value of field 'showBootstrap'. */ public boolean getShowBootstrap() { return this._showBootstrap; - } - - //-- boolean getShowBootstrap() + } //-- boolean getShowBootstrap() /** * Returns the value of field 'showDistances'. - * + * * @return boolean * @return the value of field 'showDistances'. */ public boolean getShowDistances() { return this._showDistances; - } - - //-- boolean getShowDistances() + } //-- boolean getShowDistances() /** * Returns the value of field 'threshold'. - * + * * @return float * @return the value of field 'threshold'. */ public float getThreshold() { return this._threshold; - } - - //-- float getThreshold() + } //-- float getThreshold() /** * Returns the value of field 'title'. - * + * * @return String * @return the value of field 'title'. */ public java.lang.String getTitle() { return this._title; - } - - //-- java.lang.String getTitle() + } //-- java.lang.String getTitle() /** * Returns the value of field 'width'. - * + * * @return int * @return the value of field 'width'. */ public int getWidth() { return this._width; - } - - //-- int getWidth() + } //-- int getWidth() /** * Returns the value of field 'xpos'. - * + * * @return int * @return the value of field 'xpos'. */ public int getXpos() { return this._xpos; - } - - //-- int getXpos() + } //-- int getXpos() /** * Returns the value of field 'ypos'. - * + * * @return int * @return the value of field 'ypos'. */ public int getYpos() { return this._ypos; - } - - //-- int getYpos() + } //-- int getYpos() /** * Method hasCurrentTree - * - * - * + * + * + * * @return boolean */ public boolean hasCurrentTree() { return this._has_currentTree; - } - - //-- boolean hasCurrentTree() + } //-- boolean hasCurrentTree() /** * Method hasFitToWindow - * - * - * + * + * + * * @return boolean */ public boolean hasFitToWindow() { return this._has_fitToWindow; - } - - //-- boolean hasFitToWindow() + } //-- boolean hasFitToWindow() /** * Method hasFontSize - * - * - * + * + * + * * @return boolean */ public boolean hasFontSize() { return this._has_fontSize; - } - - //-- boolean hasFontSize() + } //-- boolean hasFontSize() /** * Method hasHeight - * - * - * + * + * + * * @return boolean */ public boolean hasHeight() { return this._has_height; - } - - //-- boolean hasHeight() + } //-- boolean hasHeight() /** * Method hasMarkUnlinked - * - * - * + * + * + * * @return boolean */ public boolean hasMarkUnlinked() { return this._has_markUnlinked; - } - - //-- boolean hasMarkUnlinked() + } //-- boolean hasMarkUnlinked() /** * Method hasShowBootstrap - * - * - * + * + * + * * @return boolean */ public boolean hasShowBootstrap() { return this._has_showBootstrap; - } - - //-- boolean hasShowBootstrap() + } //-- boolean hasShowBootstrap() /** * Method hasShowDistances - * - * - * + * + * + * * @return boolean */ public boolean hasShowDistances() { return this._has_showDistances; - } - - //-- boolean hasShowDistances() + } //-- boolean hasShowDistances() /** * Method hasThreshold - * - * - * + * + * + * * @return boolean */ public boolean hasThreshold() { return this._has_threshold; - } - - //-- boolean hasThreshold() + } //-- boolean hasThreshold() /** * Method hasWidth - * - * - * + * + * + * * @return boolean */ public boolean hasWidth() { return this._has_width; - } - - //-- boolean hasWidth() + } //-- boolean hasWidth() /** * Method hasXpos - * - * - * + * + * + * * @return boolean */ public boolean hasXpos() { return this._has_xpos; - } - - //-- boolean hasXpos() + } //-- boolean hasXpos() /** * Method hasYpos - * - * - * + * + * + * * @return boolean */ public boolean hasYpos() { return this._has_ypos; - } - - //-- boolean hasYpos() + } //-- boolean hasYpos() /** * Method isValid - * - * - * + * + * + * * @return boolean */ public boolean isValid() { - try - { + try { validate(); } - catch (org.exolab.castor.xml.ValidationException vex) - { + catch (org.exolab.castor.xml.ValidationException vex) { 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 + 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 + 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) /** * Sets the value of field 'currentTree'. - * + * * @param currentTree the value of field 'currentTree'. */ public void setCurrentTree(boolean currentTree) { this._currentTree = currentTree; this._has_currentTree = true; - } - - //-- void setCurrentTree(boolean) + } //-- void setCurrentTree(boolean) /** * Sets the value of field 'fitToWindow'. - * + * * @param fitToWindow the value of field 'fitToWindow'. */ public void setFitToWindow(boolean fitToWindow) { this._fitToWindow = fitToWindow; this._has_fitToWindow = true; - } - - //-- void setFitToWindow(boolean) + } //-- void setFitToWindow(boolean) /** * Sets the value of field 'fontSize'. - * + * * @param fontSize the value of field 'fontSize'. */ public void setFontSize(int fontSize) { this._fontSize = fontSize; this._has_fontSize = true; - } - - //-- void setFontSize(int) + } //-- void setFontSize(int) /** * Sets the value of field 'height'. - * + * * @param height the value of field 'height'. */ public void setHeight(int height) { this._height = height; this._has_height = true; - } - - //-- void setHeight(int) + } //-- void setHeight(int) /** * Sets the value of field 'markUnlinked'. - * + * * @param markUnlinked the value of field 'markUnlinked'. */ public void setMarkUnlinked(boolean markUnlinked) { this._markUnlinked = markUnlinked; this._has_markUnlinked = true; - } - - //-- void setMarkUnlinked(boolean) + } //-- void setMarkUnlinked(boolean) /** * Sets the value of field 'newick'. - * + * * @param newick the value of field 'newick'. */ public void setNewick(java.lang.String newick) { this._newick = newick; - } - - //-- void setNewick(java.lang.String) + } //-- void setNewick(java.lang.String) /** * Sets the value of field 'showBootstrap'. - * + * * @param showBootstrap the value of field 'showBootstrap'. */ public void setShowBootstrap(boolean showBootstrap) { this._showBootstrap = showBootstrap; this._has_showBootstrap = true; - } - - //-- void setShowBootstrap(boolean) + } //-- void setShowBootstrap(boolean) /** * Sets the value of field 'showDistances'. - * + * * @param showDistances the value of field 'showDistances'. */ public void setShowDistances(boolean showDistances) { this._showDistances = showDistances; this._has_showDistances = true; - } - - //-- void setShowDistances(boolean) + } //-- void setShowDistances(boolean) /** * Sets the value of field 'threshold'. - * + * * @param threshold the value of field 'threshold'. */ public void setThreshold(float threshold) { this._threshold = threshold; this._has_threshold = true; - } - - //-- void setThreshold(float) + } //-- void setThreshold(float) /** * Sets the value of field 'title'. - * + * * @param title the value of field 'title'. */ public void setTitle(java.lang.String title) { this._title = title; - } - - //-- void setTitle(java.lang.String) + } //-- void setTitle(java.lang.String) /** * Sets the value of field 'width'. - * + * * @param width the value of field 'width'. */ public void setWidth(int width) { this._width = width; this._has_width = true; - } - - //-- void setWidth(int) + } //-- void setWidth(int) /** * Sets the value of field 'xpos'. - * + * * @param xpos the value of field 'xpos'. */ public void setXpos(int xpos) { this._xpos = xpos; this._has_xpos = true; - } - - //-- void setXpos(int) + } //-- void setXpos(int) /** * Sets the value of field 'ypos'. - * + * * @param ypos the value of field 'ypos'. */ public void setYpos(int ypos) { this._ypos = ypos; this._has_ypos = true; - } - - //-- void setYpos(int) + } //-- void setYpos(int) /** * 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 + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.binding.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.class, - reader); - } - - //-- java.lang.Object unmarshal(java.io.Reader) + return (jalview.binding.Tree) Unmarshaller.unmarshal(jalview.binding.Tree.class, reader); + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ - 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() - //-- void validate() } diff --git a/src/jalview/binding/UserColourScheme.java b/src/jalview/binding/UserColourScheme.java index 6d6c265..79ea637 100755 --- a/src/jalview/binding/UserColourScheme.java +++ b/src/jalview/binding/UserColourScheme.java @@ -1,5 +1,5 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ @@ -7,110 +7,112 @@ package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -import org.exolab.castor.xml.*; +import java.io.IOException; +import java.io.Reader; +import java.io.Serializable; +import java.io.Writer; +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 UserColourScheme. - * + * * @version $Revision$ $Date$ */ -public class UserColourScheme - extends JalviewUserColours implements java.io.Serializable +public class UserColourScheme extends JalviewUserColours +implements java.io.Serializable { - //----------------/ - //- Constructors -/ - //----------------/ - public UserColourScheme() - { - super(); - } //-- jalview.binding.UserColourScheme() + //----------------/ + //- Constructors -/ + //----------------/ - //-----------/ - //- Methods -/ - //-----------/ + public UserColourScheme() { + super(); + } //-- jalview.binding.UserColourScheme() - /** - * 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 - { + //-----------/ + //- Methods -/ + //-----------/ - Marshaller.marshal(this, out); - } //-- void marshal(java.io.Writer) + /** + * 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 handler - */ - public void marshal(org.xml.sax.ContentHandler handler) - throws java.io.IOException, org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { + /** + * 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) - Marshaller.marshal(this, handler); - } //-- void marshal(org.xml.sax.ContentHandler) + /** + * 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 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.UserColourScheme) Unmarshaller.unmarshal(jalview. - binding.UserColourScheme.class, reader); - } //-- java.lang.Object unmarshal(java.io.Reader) + /** + * 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.UserColourScheme) Unmarshaller.unmarshal(jalview.binding.UserColourScheme.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() + /** + * 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() } diff --git a/src/jalview/binding/UserColours.java b/src/jalview/binding/UserColours.java index f00e341..241aaab 100755 --- a/src/jalview/binding/UserColours.java +++ b/src/jalview/binding/UserColours.java @@ -1,5 +1,5 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ @@ -7,167 +7,167 @@ package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -import org.exolab.castor.xml.*; +import java.io.IOException; +import java.io.Reader; +import java.io.Serializable; +import java.io.Writer; +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 UserColours. - * + * * @version $Revision$ $Date$ */ -public class UserColours - implements java.io.Serializable -{ - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _id - */ - private java.lang.String _id; - - /** - * Field _userColourScheme - */ - private jalview.binding.UserColourScheme _userColourScheme; - - //----------------/ - //- Constructors -/ - //----------------/ - - public UserColours() - { - super(); - } //-- jalview.binding.UserColours() - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Returns the value of field 'id'. - * - * @return String - * @return the value of field 'id'. - */ - public java.lang.String getId() - { - return this._id; - } //-- java.lang.String getId() - - /** - * Returns the value of field 'userColourScheme'. - * - * @return UserColourScheme - * @return the value of field 'userColourScheme'. - */ - public jalview.binding.UserColourScheme getUserColourScheme() - { - return this._userColourScheme; - } //-- jalview.binding.UserColourScheme getUserColourScheme() - - /** - * Method isValid - * - * - * - * @return boolean - */ - public boolean isValid() - { - try +public class UserColours implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _id + */ + private java.lang.String _id; + + /** + * Field _userColourScheme + */ + private jalview.binding.UserColourScheme _userColourScheme; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public UserColours() { + super(); + } //-- jalview.binding.UserColours() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Returns the value of field 'id'. + * + * @return String + * @return the value of field 'id'. + */ + public java.lang.String getId() + { + return this._id; + } //-- java.lang.String getId() + + /** + * Returns the value of field 'userColourScheme'. + * + * @return UserColourScheme + * @return the value of field 'userColourScheme'. + */ + public jalview.binding.UserColourScheme getUserColourScheme() + { + return this._userColourScheme; + } //-- jalview.binding.UserColourScheme getUserColourScheme() + + /** + * 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) + + /** + * Sets the value of field 'id'. + * + * @param id the value of field 'id'. + */ + public void setId(java.lang.String id) + { + this._id = id; + } //-- void setId(java.lang.String) + + /** + * Sets the value of field 'userColourScheme'. + * + * @param userColourScheme the value of field 'userColourScheme' + */ + public void setUserColourScheme(jalview.binding.UserColourScheme userColourScheme) + { + this._userColourScheme = userColourScheme; + } //-- void setUserColourScheme(jalview.binding.UserColourScheme) + + /** + * 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 { - validate(); - } - catch (org.exolab.castor.xml.ValidationException vex) + return (jalview.binding.UserColours) Unmarshaller.unmarshal(jalview.binding.UserColours.class, reader); + } //-- java.lang.Object unmarshal(java.io.Reader) + + /** + * Method validate + * + */ + public void validate() + throws org.exolab.castor.xml.ValidationException { - 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) - - /** - * Sets the value of field 'id'. - * - * @param id the value of field 'id'. - */ - public void setId(java.lang.String id) - { - this._id = id; - } //-- void setId(java.lang.String) - - /** - * Sets the value of field 'userColourScheme'. - * - * @param userColourScheme the value of field 'userColourScheme' - */ - public void setUserColourScheme(jalview.binding.UserColourScheme - userColourScheme) - { - this._userColourScheme = userColourScheme; - } //-- void setUserColourScheme(jalview.binding.UserColourScheme) - - /** - * 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.UserColours) Unmarshaller.unmarshal(jalview.binding. - UserColours.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() + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } //-- void validate() } diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java index 037bd3d..b4237b8 100755 --- a/src/jalview/binding/VAMSAS.java +++ b/src/jalview/binding/VAMSAS.java @@ -1,5 +1,5 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ @@ -7,585 +7,570 @@ package jalview.binding; + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import java.util.*; -import org.exolab.castor.xml.*; +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 VAMSAS. - * + * * @version $Revision$ $Date$ */ -public class VAMSAS - implements java.io.Serializable -{ - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _alignmentList - */ - private java.util.Vector _alignmentList; - - /** - * Field _treeList - */ - private java.util.Vector _treeList; - - /** - * Field _sequenceSetList - */ - private java.util.Vector _sequenceSetList; - - //----------------/ - //- Constructors -/ - //----------------/ - - public VAMSAS() - { - super(); - _alignmentList = new Vector(); - _treeList = new Vector(); - _sequenceSetList = new Vector(); - } //-- jalview.binding.VAMSAS() - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method addAlignment - * - * - * - * @param vAlignment - */ - public void addAlignment(jalview.binding.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - _alignmentList.addElement(vAlignment); - } //-- void addAlignment(jalview.binding.Alignment) - - /** - * Method addAlignment - * - * - * - * @param index - * @param vAlignment - */ - public void addAlignment(int index, jalview.binding.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - _alignmentList.insertElementAt(vAlignment, index); - } //-- void addAlignment(int, jalview.binding.Alignment) - - /** - * Method addSequenceSet - * - * - * - * @param vSequenceSet - */ - public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - _sequenceSetList.addElement(vSequenceSet); - } //-- void addSequenceSet(jalview.binding.SequenceSet) - - /** - * Method addSequenceSet - * - * - * - * @param index - * @param vSequenceSet - */ - public void addSequenceSet(int index, - jalview.binding.SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - _sequenceSetList.insertElementAt(vSequenceSet, index); - } //-- void addSequenceSet(int, jalview.binding.SequenceSet) - - /** - * Method addTree - * - * - * - * @param vTree - */ - public void addTree(java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.addElement(vTree); - } //-- void addTree(java.lang.String) - - /** - * Method addTree - * - * - * - * @param index - * @param vTree - */ - public void addTree(int index, java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - _treeList.insertElementAt(vTree, index); - } //-- void addTree(int, java.lang.String) - - /** - * Method enumerateAlignment - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateAlignment() - { - return _alignmentList.elements(); - } //-- java.util.Enumeration enumerateAlignment() - - /** - * Method enumerateSequenceSet - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateSequenceSet() - { - return _sequenceSetList.elements(); - } //-- java.util.Enumeration enumerateSequenceSet() - - /** - * Method enumerateTree - * - * - * - * @return Enumeration - */ - public java.util.Enumeration enumerateTree() - { - return _treeList.elements(); - } //-- java.util.Enumeration enumerateTree() - - /** - * Method getAlignment - * - * - * - * @param index - * @return Alignment - */ - public jalview.binding.Alignment getAlignment(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ( (index < 0) || (index > _alignmentList.size())) - { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.Alignment) _alignmentList.elementAt(index); - } //-- jalview.binding.Alignment getAlignment(int) - - /** - * Method getAlignment - * - * - * - * @return Alignment - */ - public jalview.binding.Alignment[] getAlignment() - { - int size = _alignmentList.size(); - jalview.binding.Alignment[] mArray = new jalview.binding.Alignment[size]; - for (int index = 0; index < size; index++) - { - mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt( - index); - } - return mArray; - } //-- jalview.binding.Alignment[] getAlignment() - - /** - * Method getAlignmentCount - * - * - * - * @return int - */ - public int getAlignmentCount() - { - return _alignmentList.size(); - } //-- int getAlignmentCount() - - /** - * Method getSequenceSet - * - * - * - * @param index - * @return SequenceSet - */ - public jalview.binding.SequenceSet getSequenceSet(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ( (index < 0) || (index > _sequenceSetList.size())) - { - throw new IndexOutOfBoundsException(); - } - - return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index); - } //-- jalview.binding.SequenceSet getSequenceSet(int) - - /** - * Method getSequenceSet - * - * - * - * @return SequenceSet - */ - public jalview.binding.SequenceSet[] getSequenceSet() - { - int size = _sequenceSetList.size(); - jalview.binding.SequenceSet[] mArray = new jalview.binding.SequenceSet[size]; - for (int index = 0; index < size; index++) - { - mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt( - index); - } - return mArray; - } //-- jalview.binding.SequenceSet[] getSequenceSet() - - /** - * Method getSequenceSetCount - * - * - * - * @return int - */ - public int getSequenceSetCount() - { - return _sequenceSetList.size(); - } //-- int getSequenceSetCount() - - /** - * Method getTree - * - * - * - * @param index - * @return String - */ - public java.lang.String getTree(int index) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ( (index < 0) || (index > _treeList.size())) - { - throw new IndexOutOfBoundsException(); - } - - return (String) _treeList.elementAt(index); - } //-- java.lang.String getTree(int) - - /** - * Method getTree - * - * - * - * @return String - */ - public java.lang.String[] getTree() - { - int size = _treeList.size(); - java.lang.String[] mArray = new java.lang.String[size]; - for (int index = 0; index < size; index++) - { - mArray[index] = (String) _treeList.elementAt(index); - } - return mArray; - } //-- java.lang.String[] getTree() - - /** - * Method getTreeCount - * - * - * - * @return int - */ - public int getTreeCount() - { - return _treeList.size(); - } //-- int getTreeCount() - - /** - * 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 removeAlignment - * - * - * - * @param index - * @return Alignment - */ - public jalview.binding.Alignment removeAlignment(int index) - { - java.lang.Object obj = _alignmentList.elementAt(index); - _alignmentList.removeElementAt(index); - return (jalview.binding.Alignment) obj; - } //-- jalview.binding.Alignment removeAlignment(int) - - /** - * Method removeAllAlignment - * - */ - public void removeAllAlignment() - { - _alignmentList.removeAllElements(); - } //-- void removeAllAlignment() - - /** - * Method removeAllSequenceSet - * - */ - public void removeAllSequenceSet() - { - _sequenceSetList.removeAllElements(); - } //-- void removeAllSequenceSet() - - /** - * Method removeAllTree - * - */ - public void removeAllTree() - { - _treeList.removeAllElements(); - } //-- void removeAllTree() - - /** - * Method removeSequenceSet - * - * - * - * @param index - * @return SequenceSet - */ - public jalview.binding.SequenceSet removeSequenceSet(int index) - { - java.lang.Object obj = _sequenceSetList.elementAt(index); - _sequenceSetList.removeElementAt(index); - return (jalview.binding.SequenceSet) obj; - } //-- jalview.binding.SequenceSet removeSequenceSet(int) - - /** - * Method removeTree - * - * - * - * @param index - * @return String - */ - public java.lang.String removeTree(int index) - { - java.lang.Object obj = _treeList.elementAt(index); - _treeList.removeElementAt(index); - return (String) obj; - } //-- java.lang.String removeTree(int) - - /** - * Method setAlignment - * - * - * - * @param index - * @param vAlignment - */ - public void setAlignment(int index, jalview.binding.Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ( (index < 0) || (index > _alignmentList.size())) - { - throw new IndexOutOfBoundsException(); - } - _alignmentList.setElementAt(vAlignment, index); - } //-- void setAlignment(int, jalview.binding.Alignment) - - /** - * Method setAlignment - * - * - * - * @param alignmentArray - */ - public void setAlignment(jalview.binding.Alignment[] alignmentArray) - { - //-- copy array - _alignmentList.removeAllElements(); - for (int i = 0; i < alignmentArray.length; i++) - { - _alignmentList.addElement(alignmentArray[i]); - } - } //-- void setAlignment(jalview.binding.Alignment) - - /** - * Method setSequenceSet - * - * - * - * @param index - * @param vSequenceSet - */ - public void setSequenceSet(int index, - jalview.binding.SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ( (index < 0) || (index > _sequenceSetList.size())) - { - throw new IndexOutOfBoundsException(); - } - _sequenceSetList.setElementAt(vSequenceSet, index); - } //-- void setSequenceSet(int, jalview.binding.SequenceSet) - - /** - * Method setSequenceSet - * - * - * - * @param sequenceSetArray - */ - public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray) - { - //-- copy array - _sequenceSetList.removeAllElements(); - for (int i = 0; i < sequenceSetArray.length; i++) - { - _sequenceSetList.addElement(sequenceSetArray[i]); - } - } //-- void setSequenceSet(jalview.binding.SequenceSet) - - /** - * Method setTree - * - * - * - * @param index - * @param vTree - */ - public void setTree(int index, java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - //-- check bounds for index - if ( (index < 0) || (index > _treeList.size())) - { - throw new IndexOutOfBoundsException(); - } - _treeList.setElementAt(vTree, index); - } //-- void setTree(int, java.lang.String) - - /** - * Method setTree - * - * - * - * @param treeArray - */ - public void setTree(java.lang.String[] treeArray) - { - //-- copy array - _treeList.removeAllElements(); - for (int i = 0; i < treeArray.length; i++) - { - _treeList.addElement(treeArray[i]); - } - } //-- void setTree(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.VAMSAS) Unmarshaller.unmarshal(jalview.binding. - VAMSAS.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() +public class VAMSAS implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _alignmentList + */ + private java.util.Vector _alignmentList; + + /** + * Field _treeList + */ + private java.util.Vector _treeList; + + /** + * Field _sequenceSetList + */ + private java.util.Vector _sequenceSetList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public VAMSAS() { + super(); + _alignmentList = new Vector(); + _treeList = new Vector(); + _sequenceSetList = new Vector(); + } //-- jalview.binding.VAMSAS() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method addAlignment + * + * + * + * @param vAlignment + */ + public void addAlignment(jalview.binding.Alignment vAlignment) + throws java.lang.IndexOutOfBoundsException + { + _alignmentList.addElement(vAlignment); + } //-- void addAlignment(jalview.binding.Alignment) + + /** + * Method addAlignment + * + * + * + * @param index + * @param vAlignment + */ + public void addAlignment(int index, jalview.binding.Alignment vAlignment) + throws java.lang.IndexOutOfBoundsException + { + _alignmentList.insertElementAt(vAlignment, index); + } //-- void addAlignment(int, jalview.binding.Alignment) + + /** + * Method addSequenceSet + * + * + * + * @param vSequenceSet + */ + public void addSequenceSet(jalview.binding.SequenceSet vSequenceSet) + throws java.lang.IndexOutOfBoundsException + { + _sequenceSetList.addElement(vSequenceSet); + } //-- void addSequenceSet(jalview.binding.SequenceSet) + + /** + * Method addSequenceSet + * + * + * + * @param index + * @param vSequenceSet + */ + public void addSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet) + throws java.lang.IndexOutOfBoundsException + { + _sequenceSetList.insertElementAt(vSequenceSet, index); + } //-- void addSequenceSet(int, jalview.binding.SequenceSet) + + /** + * Method addTree + * + * + * + * @param vTree + */ + public void addTree(java.lang.String vTree) + throws java.lang.IndexOutOfBoundsException + { + _treeList.addElement(vTree); + } //-- void addTree(java.lang.String) + + /** + * Method addTree + * + * + * + * @param index + * @param vTree + */ + public void addTree(int index, java.lang.String vTree) + throws java.lang.IndexOutOfBoundsException + { + _treeList.insertElementAt(vTree, index); + } //-- void addTree(int, java.lang.String) + + /** + * Method enumerateAlignment + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateAlignment() + { + return _alignmentList.elements(); + } //-- java.util.Enumeration enumerateAlignment() + + /** + * Method enumerateSequenceSet + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateSequenceSet() + { + return _sequenceSetList.elements(); + } //-- java.util.Enumeration enumerateSequenceSet() + + /** + * Method enumerateTree + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateTree() + { + return _treeList.elements(); + } //-- java.util.Enumeration enumerateTree() + + /** + * Method getAlignment + * + * + * + * @param index + * @return Alignment + */ + public jalview.binding.Alignment getAlignment(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _alignmentList.size())) { + throw new IndexOutOfBoundsException(); + } + + return (jalview.binding.Alignment) _alignmentList.elementAt(index); + } //-- jalview.binding.Alignment getAlignment(int) + + /** + * Method getAlignment + * + * + * + * @return Alignment + */ + public jalview.binding.Alignment[] getAlignment() + { + int size = _alignmentList.size(); + jalview.binding.Alignment[] mArray = new jalview.binding.Alignment[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (jalview.binding.Alignment) _alignmentList.elementAt(index); + } + return mArray; + } //-- jalview.binding.Alignment[] getAlignment() + + /** + * Method getAlignmentCount + * + * + * + * @return int + */ + public int getAlignmentCount() + { + return _alignmentList.size(); + } //-- int getAlignmentCount() + + /** + * Method getSequenceSet + * + * + * + * @param index + * @return SequenceSet + */ + public jalview.binding.SequenceSet getSequenceSet(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _sequenceSetList.size())) { + throw new IndexOutOfBoundsException(); + } + + return (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index); + } //-- jalview.binding.SequenceSet getSequenceSet(int) + + /** + * Method getSequenceSet + * + * + * + * @return SequenceSet + */ + public jalview.binding.SequenceSet[] getSequenceSet() + { + int size = _sequenceSetList.size(); + jalview.binding.SequenceSet[] mArray = new jalview.binding.SequenceSet[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (jalview.binding.SequenceSet) _sequenceSetList.elementAt(index); + } + return mArray; + } //-- jalview.binding.SequenceSet[] getSequenceSet() + + /** + * Method getSequenceSetCount + * + * + * + * @return int + */ + public int getSequenceSetCount() + { + return _sequenceSetList.size(); + } //-- int getSequenceSetCount() + + /** + * Method getTree + * + * + * + * @param index + * @return String + */ + public java.lang.String getTree(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _treeList.size())) { + throw new IndexOutOfBoundsException(); + } + + return (String)_treeList.elementAt(index); + } //-- java.lang.String getTree(int) + + /** + * Method getTree + * + * + * + * @return String + */ + public java.lang.String[] getTree() + { + int size = _treeList.size(); + java.lang.String[] mArray = new java.lang.String[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (String)_treeList.elementAt(index); + } + return mArray; + } //-- java.lang.String[] getTree() + + /** + * Method getTreeCount + * + * + * + * @return int + */ + public int getTreeCount() + { + return _treeList.size(); + } //-- int getTreeCount() + + /** + * 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 removeAlignment + * + * + * + * @param index + * @return Alignment + */ + public jalview.binding.Alignment removeAlignment(int index) + { + java.lang.Object obj = _alignmentList.elementAt(index); + _alignmentList.removeElementAt(index); + return (jalview.binding.Alignment) obj; + } //-- jalview.binding.Alignment removeAlignment(int) + + /** + * Method removeAllAlignment + * + */ + public void removeAllAlignment() + { + _alignmentList.removeAllElements(); + } //-- void removeAllAlignment() + + /** + * Method removeAllSequenceSet + * + */ + public void removeAllSequenceSet() + { + _sequenceSetList.removeAllElements(); + } //-- void removeAllSequenceSet() + + /** + * Method removeAllTree + * + */ + public void removeAllTree() + { + _treeList.removeAllElements(); + } //-- void removeAllTree() + + /** + * Method removeSequenceSet + * + * + * + * @param index + * @return SequenceSet + */ + public jalview.binding.SequenceSet removeSequenceSet(int index) + { + java.lang.Object obj = _sequenceSetList.elementAt(index); + _sequenceSetList.removeElementAt(index); + return (jalview.binding.SequenceSet) obj; + } //-- jalview.binding.SequenceSet removeSequenceSet(int) + + /** + * Method removeTree + * + * + * + * @param index + * @return String + */ + public java.lang.String removeTree(int index) + { + java.lang.Object obj = _treeList.elementAt(index); + _treeList.removeElementAt(index); + return (String)obj; + } //-- java.lang.String removeTree(int) + + /** + * Method setAlignment + * + * + * + * @param index + * @param vAlignment + */ + public void setAlignment(int index, jalview.binding.Alignment vAlignment) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _alignmentList.size())) { + throw new IndexOutOfBoundsException(); + } + _alignmentList.setElementAt(vAlignment, index); + } //-- void setAlignment(int, jalview.binding.Alignment) + + /** + * Method setAlignment + * + * + * + * @param alignmentArray + */ + public void setAlignment(jalview.binding.Alignment[] alignmentArray) + { + //-- copy array + _alignmentList.removeAllElements(); + for (int i = 0; i < alignmentArray.length; i++) { + _alignmentList.addElement(alignmentArray[i]); + } + } //-- void setAlignment(jalview.binding.Alignment) + + /** + * Method setSequenceSet + * + * + * + * @param index + * @param vSequenceSet + */ + public void setSequenceSet(int index, jalview.binding.SequenceSet vSequenceSet) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _sequenceSetList.size())) { + throw new IndexOutOfBoundsException(); + } + _sequenceSetList.setElementAt(vSequenceSet, index); + } //-- void setSequenceSet(int, jalview.binding.SequenceSet) + + /** + * Method setSequenceSet + * + * + * + * @param sequenceSetArray + */ + public void setSequenceSet(jalview.binding.SequenceSet[] sequenceSetArray) + { + //-- copy array + _sequenceSetList.removeAllElements(); + for (int i = 0; i < sequenceSetArray.length; i++) { + _sequenceSetList.addElement(sequenceSetArray[i]); + } + } //-- void setSequenceSet(jalview.binding.SequenceSet) + + /** + * Method setTree + * + * + * + * @param index + * @param vTree + */ + public void setTree(int index, java.lang.String vTree) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _treeList.size())) { + throw new IndexOutOfBoundsException(); + } + _treeList.setElementAt(vTree, index); + } //-- void setTree(int, java.lang.String) + + /** + * Method setTree + * + * + * + * @param treeArray + */ + public void setTree(java.lang.String[] treeArray) + { + //-- copy array + _treeList.removeAllElements(); + for (int i = 0; i < treeArray.length; i++) { + _treeList.addElement(treeArray[i]); + } + } //-- void setTree(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.VAMSAS) Unmarshaller.unmarshal(jalview.binding.VAMSAS.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() } diff --git a/src/jalview/binding/VamsasModel.java b/src/jalview/binding/VamsasModel.java index 74aa86e..a4d4362 100755 --- a/src/jalview/binding/VamsasModel.java +++ b/src/jalview/binding/VamsasModel.java @@ -1,125 +1,118 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ */ -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; +package jalview.binding; + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ + import java.io.IOException; import java.io.Reader; import java.io.Serializable; import java.io.Writer; - +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 VamsasModel. - * + * * @version $Revision$ $Date$ */ -public class VamsasModel extends VAMSAS implements java.io.Serializable +public class VamsasModel extends VAMSAS +implements java.io.Serializable { + + + //----------------/ + //- Constructors -/ //----------------/ - //- Constructors -/ - //----------------/ - public VamsasModel() - { + + public VamsasModel() { super(); - } + } //-- jalview.binding.VamsasModel() - //-- jalview.binding.VamsasModel() + + //-----------/ + //- Methods -/ //-----------/ /** - * DOCUMENT ME! - * - * @return DOCUMENT ME! + * Method isValid + * + * + * + * @return boolean */ public boolean isValid() { - try - { + try { validate(); } - catch (org.exolab.castor.xml.ValidationException vex) - { + catch (org.exolab.castor.xml.ValidationException vex) { 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 + 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 + 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 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 + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException { - return (jalview.binding.VamsasModel) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class, - reader); - } - - //-- java.lang.Object unmarshal(java.io.Reader) + return (jalview.binding.VamsasModel) Unmarshaller.unmarshal(jalview.binding.VamsasModel.class, reader); + } //-- java.lang.Object unmarshal(java.io.Reader) /** * Method validate - * + * */ - 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() - //-- void validate() } diff --git a/src/jalview/binding/Viewport.java b/src/jalview/binding/Viewport.java index 07622b3..911061b 100755 --- a/src/jalview/binding/Viewport.java +++ b/src/jalview/binding/Viewport.java @@ -1,5 +1,5 @@ /* - * This class was automatically generated with + * This class was automatically generated with * Castor 0.9.6, using an XML * Schema. * $Id$ @@ -7,1413 +7,1414 @@ package jalview.binding; -//---------------------------------/ -//- Imported classes and packages -/ + //---------------------------------/ + //- Imported classes and packages -/ //---------------------------------/ -import org.exolab.castor.xml.*; +import java.io.IOException; +import java.io.Reader; +import java.io.Serializable; +import java.io.Writer; +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 Viewport. - * + * * @version $Revision$ $Date$ */ -public class Viewport - implements java.io.Serializable -{ - - //--------------------------/ - //- Class/Member Variables -/ - //--------------------------/ - - /** - * Field _conservationSelected - */ - private boolean _conservationSelected; - - /** - * keeps track of state for field: _conservationSelected - */ - private boolean _has_conservationSelected; - - /** - * Field _pidSelected - */ - private boolean _pidSelected; - - /** - * keeps track of state for field: _pidSelected - */ - private boolean _has_pidSelected; - - /** - * Field _bgColour - */ - private java.lang.String _bgColour; - - /** - * Field _consThreshold - */ - private int _consThreshold; - - /** - * keeps track of state for field: _consThreshold - */ - private boolean _has_consThreshold; - - /** - * Field _pidThreshold - */ - private int _pidThreshold; - - /** - * keeps track of state for field: _pidThreshold - */ - private boolean _has_pidThreshold; - - /** - * Field _title - */ - private java.lang.String _title; - - /** - * Field _showFullId - */ - private boolean _showFullId; - - /** - * keeps track of state for field: _showFullId - */ - private boolean _has_showFullId; - - /** - * Field _showText - */ - private boolean _showText; - - /** - * keeps track of state for field: _showText - */ - private boolean _has_showText; - - /** - * Field _showColourText - */ - private boolean _showColourText; - - /** - * keeps track of state for field: _showColourText - */ - private boolean _has_showColourText; - - /** - * Field _showBoxes - */ - private boolean _showBoxes; - - /** - * keeps track of state for field: _showBoxes - */ - private boolean _has_showBoxes; - - /** - * Field _wrapAlignment - */ - private boolean _wrapAlignment; - - /** - * keeps track of state for field: _wrapAlignment - */ - private boolean _has_wrapAlignment; - - /** - * Field _renderGaps - */ - private boolean _renderGaps; - - /** - * keeps track of state for field: _renderGaps - */ - private boolean _has_renderGaps; - - /** - * Field _showSequenceFeatures - */ - private boolean _showSequenceFeatures; - - /** - * keeps track of state for field: _showSequenceFeatures - */ - private boolean _has_showSequenceFeatures; - - /** - * Field _showAnnotation - */ - private boolean _showAnnotation; - - /** - * keeps track of state for field: _showAnnotation - */ - private boolean _has_showAnnotation; - - /** - * Field _showConservation - */ - private boolean _showConservation; - - /** - * keeps track of state for field: _showConservation - */ - private boolean _has_showConservation; - - /** - * Field _showQuality - */ - private boolean _showQuality; - - /** - * keeps track of state for field: _showQuality - */ - private boolean _has_showQuality; - - /** - * Field _showIdentity - */ - private boolean _showIdentity; - - /** - * keeps track of state for field: _showIdentity - */ - private boolean _has_showIdentity; - - /** - * Field _xpos - */ - private int _xpos; - - /** - * keeps track of state for field: _xpos - */ - private boolean _has_xpos; - - /** - * Field _ypos - */ - private int _ypos; - - /** - * keeps track of state for field: _ypos - */ - private boolean _has_ypos; - - /** - * Field _width - */ - private int _width; - - /** - * keeps track of state for field: _width - */ - private boolean _has_width; - - /** - * Field _height - */ - private int _height; - - /** - * keeps track of state for field: _height - */ - private boolean _has_height; - - /** - * Field _startRes - */ - private int _startRes; - - /** - * keeps track of state for field: _startRes - */ - private boolean _has_startRes; - - /** - * Field _startSeq - */ - private int _startSeq; - - /** - * keeps track of state for field: _startSeq - */ - private boolean _has_startSeq; - - /** - * Field _fontName - */ - private java.lang.String _fontName; - - /** - * Field _fontSize - */ - private int _fontSize; - - /** - * keeps track of state for field: _fontSize - */ - private boolean _has_fontSize; - - /** - * Field _fontStyle - */ - private int _fontStyle; - - /** - * keeps track of state for field: _fontStyle - */ - private boolean _has_fontStyle; - - //----------------/ - //- Constructors -/ - //----------------/ - - public Viewport() - { - super(); - } //-- jalview.binding.Viewport() - - //-----------/ - //- Methods -/ - //-----------/ - - /** - * Method deleteConsThreshold - * - */ - public void deleteConsThreshold() - { - this._has_consThreshold = false; - } //-- void deleteConsThreshold() - - /** - * Method deleteConservationSelected - * - */ - public void deleteConservationSelected() - { - this._has_conservationSelected = false; - } //-- void deleteConservationSelected() - - /** - * Method deleteFontSize - * - */ - public void deleteFontSize() - { - this._has_fontSize = false; - } //-- void deleteFontSize() - - /** - * Method deleteFontStyle - * - */ - public void deleteFontStyle() - { - this._has_fontStyle = false; - } //-- void deleteFontStyle() - - /** - * Method deleteHeight - * - */ - public void deleteHeight() - { - this._has_height = false; - } //-- void deleteHeight() - - /** - * Method deletePidSelected - * - */ - public void deletePidSelected() - { - this._has_pidSelected = false; - } //-- void deletePidSelected() - - /** - * Method deletePidThreshold - * - */ - public void deletePidThreshold() - { - this._has_pidThreshold = false; - } //-- void deletePidThreshold() - - /** - * Method deleteRenderGaps - * - */ - public void deleteRenderGaps() - { - this._has_renderGaps = false; - } //-- void deleteRenderGaps() - - /** - * Method deleteShowAnnotation - * - */ - public void deleteShowAnnotation() - { - this._has_showAnnotation = false; - } //-- void deleteShowAnnotation() - - /** - * Method deleteShowBoxes - * - */ - public void deleteShowBoxes() - { - this._has_showBoxes = false; - } //-- void deleteShowBoxes() - - /** - * Method deleteShowColourText - * - */ - public void deleteShowColourText() - { - this._has_showColourText = false; - } //-- void deleteShowColourText() - - /** - * Method deleteShowConservation - * - */ - public void deleteShowConservation() - { - this._has_showConservation = false; - } //-- void deleteShowConservation() - - /** - * Method deleteShowFullId - * - */ - public void deleteShowFullId() - { - this._has_showFullId = false; - } //-- void deleteShowFullId() - - /** - * Method deleteShowIdentity - * - */ - public void deleteShowIdentity() - { - this._has_showIdentity = false; - } //-- void deleteShowIdentity() - - /** - * Method deleteShowQuality - * - */ - public void deleteShowQuality() - { - this._has_showQuality = false; - } //-- void deleteShowQuality() - - /** - * Method deleteShowSequenceFeatures - * - */ - public void deleteShowSequenceFeatures() - { - this._has_showSequenceFeatures = false; - } //-- void deleteShowSequenceFeatures() - - /** - * Method deleteShowText - * - */ - public void deleteShowText() - { - this._has_showText = false; - } //-- void deleteShowText() - - /** - * Method deleteStartRes - * - */ - public void deleteStartRes() - { - this._has_startRes = false; - } //-- void deleteStartRes() - - /** - * Method deleteStartSeq - * - */ - public void deleteStartSeq() - { - this._has_startSeq = false; - } //-- void deleteStartSeq() - - /** - * Method deleteWidth - * - */ - public void deleteWidth() - { - this._has_width = false; - } //-- void deleteWidth() - - /** - * Method deleteWrapAlignment - * - */ - public void deleteWrapAlignment() - { - this._has_wrapAlignment = false; - } //-- void deleteWrapAlignment() - - /** - * Method deleteXpos - * - */ - public void deleteXpos() - { - this._has_xpos = false; - } //-- void deleteXpos() - - /** - * Method deleteYpos - * - */ - public void deleteYpos() - { - this._has_ypos = false; - } //-- void deleteYpos() - - /** - * Returns the value of field 'bgColour'. - * - * @return String - * @return the value of field 'bgColour'. - */ - public java.lang.String getBgColour() - { - return this._bgColour; - } //-- java.lang.String getBgColour() - - /** - * Returns the value of field 'consThreshold'. - * - * @return int - * @return the value of field 'consThreshold'. - */ - public int getConsThreshold() - { - return this._consThreshold; - } //-- int getConsThreshold() - - /** - * Returns the value of field 'conservationSelected'. - * - * @return boolean - * @return the value of field 'conservationSelected'. - */ - public boolean getConservationSelected() - { - return this._conservationSelected; - } //-- boolean getConservationSelected() - - /** - * Returns the value of field 'fontName'. - * - * @return String - * @return the value of field 'fontName'. - */ - public java.lang.String getFontName() - { - return this._fontName; - } //-- java.lang.String getFontName() - - /** - * Returns the value of field 'fontSize'. - * - * @return int - * @return the value of field 'fontSize'. - */ - public int getFontSize() - { - return this._fontSize; - } //-- int getFontSize() - - /** - * Returns the value of field 'fontStyle'. - * - * @return int - * @return the value of field 'fontStyle'. - */ - public int getFontStyle() - { - return this._fontStyle; - } //-- int getFontStyle() - - /** - * Returns the value of field 'height'. - * - * @return int - * @return the value of field 'height'. - */ - public int getHeight() - { - return this._height; - } //-- int getHeight() - - /** - * Returns the value of field 'pidSelected'. - * - * @return boolean - * @return the value of field 'pidSelected'. - */ - public boolean getPidSelected() - { - return this._pidSelected; - } //-- boolean getPidSelected() - - /** - * Returns the value of field 'pidThreshold'. - * - * @return int - * @return the value of field 'pidThreshold'. - */ - public int getPidThreshold() - { - return this._pidThreshold; - } //-- int getPidThreshold() - - /** - * Returns the value of field 'renderGaps'. - * - * @return boolean - * @return the value of field 'renderGaps'. - */ - public boolean getRenderGaps() - { - return this._renderGaps; - } //-- boolean getRenderGaps() - - /** - * Returns the value of field 'showAnnotation'. - * - * @return boolean - * @return the value of field 'showAnnotation'. - */ - public boolean getShowAnnotation() - { - return this._showAnnotation; - } //-- boolean getShowAnnotation() - - /** - * Returns the value of field 'showBoxes'. - * - * @return boolean - * @return the value of field 'showBoxes'. - */ - public boolean getShowBoxes() - { - return this._showBoxes; - } //-- boolean getShowBoxes() - - /** - * Returns the value of field 'showColourText'. - * - * @return boolean - * @return the value of field 'showColourText'. - */ - public boolean getShowColourText() - { - return this._showColourText; - } //-- boolean getShowColourText() - - /** - * Returns the value of field 'showConservation'. - * - * @return boolean - * @return the value of field 'showConservation'. - */ - public boolean getShowConservation() - { - return this._showConservation; - } //-- boolean getShowConservation() - - /** - * Returns the value of field 'showFullId'. - * - * @return boolean - * @return the value of field 'showFullId'. - */ - public boolean getShowFullId() - { - return this._showFullId; - } //-- boolean getShowFullId() - - /** - * Returns the value of field 'showIdentity'. - * - * @return boolean - * @return the value of field 'showIdentity'. - */ - public boolean getShowIdentity() - { - return this._showIdentity; - } //-- boolean getShowIdentity() - - /** - * Returns the value of field 'showQuality'. - * - * @return boolean - * @return the value of field 'showQuality'. - */ - public boolean getShowQuality() - { - return this._showQuality; - } //-- boolean getShowQuality() - - /** - * Returns the value of field 'showSequenceFeatures'. - * - * @return boolean - * @return the value of field 'showSequenceFeatures'. - */ - public boolean getShowSequenceFeatures() - { - return this._showSequenceFeatures; - } //-- boolean getShowSequenceFeatures() - - /** - * Returns the value of field 'showText'. - * - * @return boolean - * @return the value of field 'showText'. - */ - public boolean getShowText() - { - return this._showText; - } //-- boolean getShowText() - - /** - * Returns the value of field 'startRes'. - * - * @return int - * @return the value of field 'startRes'. - */ - public int getStartRes() - { - return this._startRes; - } //-- int getStartRes() - - /** - * Returns the value of field 'startSeq'. - * - * @return int - * @return the value of field 'startSeq'. - */ - public int getStartSeq() - { - return this._startSeq; - } //-- int getStartSeq() - - /** - * Returns the value of field 'title'. - * - * @return String - * @return the value of field 'title'. - */ - public java.lang.String getTitle() - { - return this._title; - } //-- java.lang.String getTitle() - - /** - * Returns the value of field 'width'. - * - * @return int - * @return the value of field 'width'. - */ - public int getWidth() - { - return this._width; - } //-- int getWidth() - - /** - * Returns the value of field 'wrapAlignment'. - * - * @return boolean - * @return the value of field 'wrapAlignment'. - */ - public boolean getWrapAlignment() - { - return this._wrapAlignment; - } //-- boolean getWrapAlignment() - - /** - * Returns the value of field 'xpos'. - * - * @return int - * @return the value of field 'xpos'. - */ - public int getXpos() - { - return this._xpos; - } //-- int getXpos() - - /** - * Returns the value of field 'ypos'. - * - * @return int - * @return the value of field 'ypos'. - */ - public int getYpos() - { - return this._ypos; - } //-- int getYpos() - - /** - * Method hasConsThreshold - * - * - * - * @return boolean - */ - public boolean hasConsThreshold() - { - return this._has_consThreshold; - } //-- boolean hasConsThreshold() - - /** - * Method hasConservationSelected - * - * - * - * @return boolean - */ - public boolean hasConservationSelected() - { - return this._has_conservationSelected; - } //-- boolean hasConservationSelected() - - /** - * Method hasFontSize - * - * - * - * @return boolean - */ - public boolean hasFontSize() - { - return this._has_fontSize; - } //-- boolean hasFontSize() - - /** - * Method hasFontStyle - * - * - * - * @return boolean - */ - public boolean hasFontStyle() - { - return this._has_fontStyle; - } //-- boolean hasFontStyle() - - /** - * Method hasHeight - * - * - * - * @return boolean - */ - public boolean hasHeight() - { - return this._has_height; - } //-- boolean hasHeight() - - /** - * Method hasPidSelected - * - * - * - * @return boolean - */ - public boolean hasPidSelected() - { - return this._has_pidSelected; - } //-- boolean hasPidSelected() - - /** - * Method hasPidThreshold - * - * - * - * @return boolean - */ - public boolean hasPidThreshold() - { - return this._has_pidThreshold; - } //-- boolean hasPidThreshold() - - /** - * Method hasRenderGaps - * - * - * - * @return boolean - */ - public boolean hasRenderGaps() - { - return this._has_renderGaps; - } //-- boolean hasRenderGaps() - - /** - * Method hasShowAnnotation - * - * - * - * @return boolean - */ - public boolean hasShowAnnotation() - { - return this._has_showAnnotation; - } //-- boolean hasShowAnnotation() - - /** - * Method hasShowBoxes - * - * - * - * @return boolean - */ - public boolean hasShowBoxes() - { - return this._has_showBoxes; - } //-- boolean hasShowBoxes() - - /** - * Method hasShowColourText - * - * - * - * @return boolean - */ - public boolean hasShowColourText() - { - return this._has_showColourText; - } //-- boolean hasShowColourText() - - /** - * Method hasShowConservation - * - * - * - * @return boolean - */ - public boolean hasShowConservation() - { - return this._has_showConservation; - } //-- boolean hasShowConservation() - - /** - * Method hasShowFullId - * - * - * - * @return boolean - */ - public boolean hasShowFullId() - { - return this._has_showFullId; - } //-- boolean hasShowFullId() - - /** - * Method hasShowIdentity - * - * - * - * @return boolean - */ - public boolean hasShowIdentity() - { - return this._has_showIdentity; - } //-- boolean hasShowIdentity() - - /** - * Method hasShowQuality - * - * - * - * @return boolean - */ - public boolean hasShowQuality() - { - return this._has_showQuality; - } //-- boolean hasShowQuality() - - /** - * Method hasShowSequenceFeatures - * - * - * - * @return boolean - */ - public boolean hasShowSequenceFeatures() - { - return this._has_showSequenceFeatures; - } //-- boolean hasShowSequenceFeatures() - - /** - * Method hasShowText - * - * - * - * @return boolean - */ - public boolean hasShowText() - { - return this._has_showText; - } //-- boolean hasShowText() - - /** - * Method hasStartRes - * - * - * - * @return boolean - */ - public boolean hasStartRes() - { - return this._has_startRes; - } //-- boolean hasStartRes() - - /** - * Method hasStartSeq - * - * - * - * @return boolean - */ - public boolean hasStartSeq() - { - return this._has_startSeq; - } //-- boolean hasStartSeq() - - /** - * Method hasWidth - * - * - * - * @return boolean - */ - public boolean hasWidth() - { - return this._has_width; - } //-- boolean hasWidth() - - /** - * Method hasWrapAlignment - * - * - * - * @return boolean - */ - public boolean hasWrapAlignment() - { - return this._has_wrapAlignment; - } //-- boolean hasWrapAlignment() - - /** - * Method hasXpos - * - * - * - * @return boolean - */ - public boolean hasXpos() - { - return this._has_xpos; - } //-- boolean hasXpos() - - /** - * Method hasYpos - * - * - * - * @return boolean - */ - public boolean hasYpos() - { - return this._has_ypos; - } //-- boolean hasYpos() - - /** - * 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) - - /** - * Sets the value of field 'bgColour'. - * - * @param bgColour the value of field 'bgColour'. - */ - public void setBgColour(java.lang.String bgColour) - { - this._bgColour = bgColour; - } //-- void setBgColour(java.lang.String) - - /** - * Sets the value of field 'consThreshold'. - * - * @param consThreshold the value of field 'consThreshold'. - */ - public void setConsThreshold(int consThreshold) - { - this._consThreshold = consThreshold; - this._has_consThreshold = true; - } //-- void setConsThreshold(int) - - /** - * Sets the value of field 'conservationSelected'. - * - * @param conservationSelected the value of field - * 'conservationSelected'. - */ - public void setConservationSelected(boolean conservationSelected) - { - this._conservationSelected = conservationSelected; - this._has_conservationSelected = true; - } //-- void setConservationSelected(boolean) - - /** - * Sets the value of field 'fontName'. - * - * @param fontName the value of field 'fontName'. - */ - public void setFontName(java.lang.String fontName) - { - this._fontName = fontName; - } //-- void setFontName(java.lang.String) - - /** - * Sets the value of field 'fontSize'. - * - * @param fontSize the value of field 'fontSize'. - */ - public void setFontSize(int fontSize) - { - this._fontSize = fontSize; - this._has_fontSize = true; - } //-- void setFontSize(int) - - /** - * Sets the value of field 'fontStyle'. - * - * @param fontStyle the value of field 'fontStyle'. - */ - public void setFontStyle(int fontStyle) - { - this._fontStyle = fontStyle; - this._has_fontStyle = true; - } //-- void setFontStyle(int) - - /** - * Sets the value of field 'height'. - * - * @param height the value of field 'height'. - */ - public void setHeight(int height) - { - this._height = height; - this._has_height = true; - } //-- void setHeight(int) - - /** - * Sets the value of field 'pidSelected'. - * - * @param pidSelected the value of field 'pidSelected'. - */ - public void setPidSelected(boolean pidSelected) - { - this._pidSelected = pidSelected; - this._has_pidSelected = true; - } //-- void setPidSelected(boolean) - - /** - * Sets the value of field 'pidThreshold'. - * - * @param pidThreshold the value of field 'pidThreshold'. - */ - public void setPidThreshold(int pidThreshold) - { - this._pidThreshold = pidThreshold; - this._has_pidThreshold = true; - } //-- void setPidThreshold(int) - - /** - * Sets the value of field 'renderGaps'. - * - * @param renderGaps the value of field 'renderGaps'. - */ - public void setRenderGaps(boolean renderGaps) - { - this._renderGaps = renderGaps; - this._has_renderGaps = true; - } //-- void setRenderGaps(boolean) - - /** - * Sets the value of field 'showAnnotation'. - * - * @param showAnnotation the value of field 'showAnnotation'. - */ - public void setShowAnnotation(boolean showAnnotation) - { - this._showAnnotation = showAnnotation; - this._has_showAnnotation = true; - } //-- void setShowAnnotation(boolean) - - /** - * Sets the value of field 'showBoxes'. - * - * @param showBoxes the value of field 'showBoxes'. - */ - public void setShowBoxes(boolean showBoxes) - { - this._showBoxes = showBoxes; - this._has_showBoxes = true; - } //-- void setShowBoxes(boolean) - - /** - * Sets the value of field 'showColourText'. - * - * @param showColourText the value of field 'showColourText'. - */ - public void setShowColourText(boolean showColourText) - { - this._showColourText = showColourText; - this._has_showColourText = true; - } //-- void setShowColourText(boolean) - - /** - * Sets the value of field 'showConservation'. - * - * @param showConservation the value of field 'showConservation' - */ - public void setShowConservation(boolean showConservation) - { - this._showConservation = showConservation; - this._has_showConservation = true; - } //-- void setShowConservation(boolean) - - /** - * Sets the value of field 'showFullId'. - * - * @param showFullId the value of field 'showFullId'. - */ - public void setShowFullId(boolean showFullId) - { - this._showFullId = showFullId; - this._has_showFullId = true; - } //-- void setShowFullId(boolean) - - /** - * Sets the value of field 'showIdentity'. - * - * @param showIdentity the value of field 'showIdentity'. - */ - public void setShowIdentity(boolean showIdentity) - { - this._showIdentity = showIdentity; - this._has_showIdentity = true; - } //-- void setShowIdentity(boolean) - - /** - * Sets the value of field 'showQuality'. - * - * @param showQuality the value of field 'showQuality'. - */ - public void setShowQuality(boolean showQuality) - { - this._showQuality = showQuality; - this._has_showQuality = true; - } //-- void setShowQuality(boolean) - - /** - * Sets the value of field 'showSequenceFeatures'. - * - * @param showSequenceFeatures the value of field - * 'showSequenceFeatures'. - */ - public void setShowSequenceFeatures(boolean showSequenceFeatures) - { - this._showSequenceFeatures = showSequenceFeatures; - this._has_showSequenceFeatures = true; - } //-- void setShowSequenceFeatures(boolean) - - /** - * Sets the value of field 'showText'. - * - * @param showText the value of field 'showText'. - */ - public void setShowText(boolean showText) - { - this._showText = showText; - this._has_showText = true; - } //-- void setShowText(boolean) - - /** - * Sets the value of field 'startRes'. - * - * @param startRes the value of field 'startRes'. - */ - public void setStartRes(int startRes) - { - this._startRes = startRes; - this._has_startRes = true; - } //-- void setStartRes(int) - - /** - * Sets the value of field 'startSeq'. - * - * @param startSeq the value of field 'startSeq'. - */ - public void setStartSeq(int startSeq) - { - this._startSeq = startSeq; - this._has_startSeq = true; - } //-- void setStartSeq(int) - - /** - * Sets the value of field 'title'. - * - * @param title the value of field 'title'. - */ - public void setTitle(java.lang.String title) - { - this._title = title; - } //-- void setTitle(java.lang.String) - - /** - * Sets the value of field 'width'. - * - * @param width the value of field 'width'. - */ - public void setWidth(int width) - { - this._width = width; - this._has_width = true; - } //-- void setWidth(int) - - /** - * Sets the value of field 'wrapAlignment'. - * - * @param wrapAlignment the value of field 'wrapAlignment'. - */ - public void setWrapAlignment(boolean wrapAlignment) - { - this._wrapAlignment = wrapAlignment; - this._has_wrapAlignment = true; - } //-- void setWrapAlignment(boolean) - - /** - * Sets the value of field 'xpos'. - * - * @param xpos the value of field 'xpos'. - */ - public void setXpos(int xpos) - { - this._xpos = xpos; - this._has_xpos = true; - } //-- void setXpos(int) - - /** - * Sets the value of field 'ypos'. - * - * @param ypos the value of field 'ypos'. - */ - public void setYpos(int ypos) - { - this._ypos = ypos; - this._has_ypos = true; - } //-- void setYpos(int) - - /** - * 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.Viewport) Unmarshaller.unmarshal(jalview.binding. - Viewport.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() +public class Viewport implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _conservationSelected + */ + private boolean _conservationSelected; + + /** + * keeps track of state for field: _conservationSelected + */ + private boolean _has_conservationSelected; + + /** + * Field _pidSelected + */ + private boolean _pidSelected; + + /** + * keeps track of state for field: _pidSelected + */ + private boolean _has_pidSelected; + + /** + * Field _bgColour + */ + private java.lang.String _bgColour; + + /** + * Field _consThreshold + */ + private int _consThreshold; + + /** + * keeps track of state for field: _consThreshold + */ + private boolean _has_consThreshold; + + /** + * Field _pidThreshold + */ + private int _pidThreshold; + + /** + * keeps track of state for field: _pidThreshold + */ + private boolean _has_pidThreshold; + + /** + * Field _title + */ + private java.lang.String _title; + + /** + * Field _showFullId + */ + private boolean _showFullId; + + /** + * keeps track of state for field: _showFullId + */ + private boolean _has_showFullId; + + /** + * Field _showText + */ + private boolean _showText; + + /** + * keeps track of state for field: _showText + */ + private boolean _has_showText; + + /** + * Field _showColourText + */ + private boolean _showColourText; + + /** + * keeps track of state for field: _showColourText + */ + private boolean _has_showColourText; + + /** + * Field _showBoxes + */ + private boolean _showBoxes; + + /** + * keeps track of state for field: _showBoxes + */ + private boolean _has_showBoxes; + + /** + * Field _wrapAlignment + */ + private boolean _wrapAlignment; + + /** + * keeps track of state for field: _wrapAlignment + */ + private boolean _has_wrapAlignment; + + /** + * Field _renderGaps + */ + private boolean _renderGaps; + + /** + * keeps track of state for field: _renderGaps + */ + private boolean _has_renderGaps; + + /** + * Field _showSequenceFeatures + */ + private boolean _showSequenceFeatures; + + /** + * keeps track of state for field: _showSequenceFeatures + */ + private boolean _has_showSequenceFeatures; + + /** + * Field _showAnnotation + */ + private boolean _showAnnotation; + + /** + * keeps track of state for field: _showAnnotation + */ + private boolean _has_showAnnotation; + + /** + * Field _showConservation + */ + private boolean _showConservation; + + /** + * keeps track of state for field: _showConservation + */ + private boolean _has_showConservation; + + /** + * Field _showQuality + */ + private boolean _showQuality; + + /** + * keeps track of state for field: _showQuality + */ + private boolean _has_showQuality; + + /** + * Field _showIdentity + */ + private boolean _showIdentity; + + /** + * keeps track of state for field: _showIdentity + */ + private boolean _has_showIdentity; + + /** + * Field _xpos + */ + private int _xpos; + + /** + * keeps track of state for field: _xpos + */ + private boolean _has_xpos; + + /** + * Field _ypos + */ + private int _ypos; + + /** + * keeps track of state for field: _ypos + */ + private boolean _has_ypos; + + /** + * Field _width + */ + private int _width; + + /** + * keeps track of state for field: _width + */ + private boolean _has_width; + + /** + * Field _height + */ + private int _height; + + /** + * keeps track of state for field: _height + */ + private boolean _has_height; + + /** + * Field _startRes + */ + private int _startRes; + + /** + * keeps track of state for field: _startRes + */ + private boolean _has_startRes; + + /** + * Field _startSeq + */ + private int _startSeq; + + /** + * keeps track of state for field: _startSeq + */ + private boolean _has_startSeq; + + /** + * Field _fontName + */ + private java.lang.String _fontName; + + /** + * Field _fontSize + */ + private int _fontSize; + + /** + * keeps track of state for field: _fontSize + */ + private boolean _has_fontSize; + + /** + * Field _fontStyle + */ + private int _fontStyle; + + /** + * keeps track of state for field: _fontStyle + */ + private boolean _has_fontStyle; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Viewport() { + super(); + } //-- jalview.binding.Viewport() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method deleteConsThreshold + * + */ + public void deleteConsThreshold() + { + this._has_consThreshold= false; + } //-- void deleteConsThreshold() + + /** + * Method deleteConservationSelected + * + */ + public void deleteConservationSelected() + { + this._has_conservationSelected= false; + } //-- void deleteConservationSelected() + + /** + * Method deleteFontSize + * + */ + public void deleteFontSize() + { + this._has_fontSize= false; + } //-- void deleteFontSize() + + /** + * Method deleteFontStyle + * + */ + public void deleteFontStyle() + { + this._has_fontStyle= false; + } //-- void deleteFontStyle() + + /** + * Method deleteHeight + * + */ + public void deleteHeight() + { + this._has_height= false; + } //-- void deleteHeight() + + /** + * Method deletePidSelected + * + */ + public void deletePidSelected() + { + this._has_pidSelected= false; + } //-- void deletePidSelected() + + /** + * Method deletePidThreshold + * + */ + public void deletePidThreshold() + { + this._has_pidThreshold= false; + } //-- void deletePidThreshold() + + /** + * Method deleteRenderGaps + * + */ + public void deleteRenderGaps() + { + this._has_renderGaps= false; + } //-- void deleteRenderGaps() + + /** + * Method deleteShowAnnotation + * + */ + public void deleteShowAnnotation() + { + this._has_showAnnotation= false; + } //-- void deleteShowAnnotation() + + /** + * Method deleteShowBoxes + * + */ + public void deleteShowBoxes() + { + this._has_showBoxes= false; + } //-- void deleteShowBoxes() + + /** + * Method deleteShowColourText + * + */ + public void deleteShowColourText() + { + this._has_showColourText= false; + } //-- void deleteShowColourText() + + /** + * Method deleteShowConservation + * + */ + public void deleteShowConservation() + { + this._has_showConservation= false; + } //-- void deleteShowConservation() + + /** + * Method deleteShowFullId + * + */ + public void deleteShowFullId() + { + this._has_showFullId= false; + } //-- void deleteShowFullId() + + /** + * Method deleteShowIdentity + * + */ + public void deleteShowIdentity() + { + this._has_showIdentity= false; + } //-- void deleteShowIdentity() + + /** + * Method deleteShowQuality + * + */ + public void deleteShowQuality() + { + this._has_showQuality= false; + } //-- void deleteShowQuality() + + /** + * Method deleteShowSequenceFeatures + * + */ + public void deleteShowSequenceFeatures() + { + this._has_showSequenceFeatures= false; + } //-- void deleteShowSequenceFeatures() + + /** + * Method deleteShowText + * + */ + public void deleteShowText() + { + this._has_showText= false; + } //-- void deleteShowText() + + /** + * Method deleteStartRes + * + */ + public void deleteStartRes() + { + this._has_startRes= false; + } //-- void deleteStartRes() + + /** + * Method deleteStartSeq + * + */ + public void deleteStartSeq() + { + this._has_startSeq= false; + } //-- void deleteStartSeq() + + /** + * Method deleteWidth + * + */ + public void deleteWidth() + { + this._has_width= false; + } //-- void deleteWidth() + + /** + * Method deleteWrapAlignment + * + */ + public void deleteWrapAlignment() + { + this._has_wrapAlignment= false; + } //-- void deleteWrapAlignment() + + /** + * Method deleteXpos + * + */ + public void deleteXpos() + { + this._has_xpos= false; + } //-- void deleteXpos() + + /** + * Method deleteYpos + * + */ + public void deleteYpos() + { + this._has_ypos= false; + } //-- void deleteYpos() + + /** + * Returns the value of field 'bgColour'. + * + * @return String + * @return the value of field 'bgColour'. + */ + public java.lang.String getBgColour() + { + return this._bgColour; + } //-- java.lang.String getBgColour() + + /** + * Returns the value of field 'consThreshold'. + * + * @return int + * @return the value of field 'consThreshold'. + */ + public int getConsThreshold() + { + return this._consThreshold; + } //-- int getConsThreshold() + + /** + * Returns the value of field 'conservationSelected'. + * + * @return boolean + * @return the value of field 'conservationSelected'. + */ + public boolean getConservationSelected() + { + return this._conservationSelected; + } //-- boolean getConservationSelected() + + /** + * Returns the value of field 'fontName'. + * + * @return String + * @return the value of field 'fontName'. + */ + public java.lang.String getFontName() + { + return this._fontName; + } //-- java.lang.String getFontName() + + /** + * Returns the value of field 'fontSize'. + * + * @return int + * @return the value of field 'fontSize'. + */ + public int getFontSize() + { + return this._fontSize; + } //-- int getFontSize() + + /** + * Returns the value of field 'fontStyle'. + * + * @return int + * @return the value of field 'fontStyle'. + */ + public int getFontStyle() + { + return this._fontStyle; + } //-- int getFontStyle() + + /** + * Returns the value of field 'height'. + * + * @return int + * @return the value of field 'height'. + */ + public int getHeight() + { + return this._height; + } //-- int getHeight() + + /** + * Returns the value of field 'pidSelected'. + * + * @return boolean + * @return the value of field 'pidSelected'. + */ + public boolean getPidSelected() + { + return this._pidSelected; + } //-- boolean getPidSelected() + + /** + * Returns the value of field 'pidThreshold'. + * + * @return int + * @return the value of field 'pidThreshold'. + */ + public int getPidThreshold() + { + return this._pidThreshold; + } //-- int getPidThreshold() + + /** + * Returns the value of field 'renderGaps'. + * + * @return boolean + * @return the value of field 'renderGaps'. + */ + public boolean getRenderGaps() + { + return this._renderGaps; + } //-- boolean getRenderGaps() + + /** + * Returns the value of field 'showAnnotation'. + * + * @return boolean + * @return the value of field 'showAnnotation'. + */ + public boolean getShowAnnotation() + { + return this._showAnnotation; + } //-- boolean getShowAnnotation() + + /** + * Returns the value of field 'showBoxes'. + * + * @return boolean + * @return the value of field 'showBoxes'. + */ + public boolean getShowBoxes() + { + return this._showBoxes; + } //-- boolean getShowBoxes() + + /** + * Returns the value of field 'showColourText'. + * + * @return boolean + * @return the value of field 'showColourText'. + */ + public boolean getShowColourText() + { + return this._showColourText; + } //-- boolean getShowColourText() + + /** + * Returns the value of field 'showConservation'. + * + * @return boolean + * @return the value of field 'showConservation'. + */ + public boolean getShowConservation() + { + return this._showConservation; + } //-- boolean getShowConservation() + + /** + * Returns the value of field 'showFullId'. + * + * @return boolean + * @return the value of field 'showFullId'. + */ + public boolean getShowFullId() + { + return this._showFullId; + } //-- boolean getShowFullId() + + /** + * Returns the value of field 'showIdentity'. + * + * @return boolean + * @return the value of field 'showIdentity'. + */ + public boolean getShowIdentity() + { + return this._showIdentity; + } //-- boolean getShowIdentity() + + /** + * Returns the value of field 'showQuality'. + * + * @return boolean + * @return the value of field 'showQuality'. + */ + public boolean getShowQuality() + { + return this._showQuality; + } //-- boolean getShowQuality() + + /** + * Returns the value of field 'showSequenceFeatures'. + * + * @return boolean + * @return the value of field 'showSequenceFeatures'. + */ + public boolean getShowSequenceFeatures() + { + return this._showSequenceFeatures; + } //-- boolean getShowSequenceFeatures() + + /** + * Returns the value of field 'showText'. + * + * @return boolean + * @return the value of field 'showText'. + */ + public boolean getShowText() + { + return this._showText; + } //-- boolean getShowText() + + /** + * Returns the value of field 'startRes'. + * + * @return int + * @return the value of field 'startRes'. + */ + public int getStartRes() + { + return this._startRes; + } //-- int getStartRes() + + /** + * Returns the value of field 'startSeq'. + * + * @return int + * @return the value of field 'startSeq'. + */ + public int getStartSeq() + { + return this._startSeq; + } //-- int getStartSeq() + + /** + * Returns the value of field 'title'. + * + * @return String + * @return the value of field 'title'. + */ + public java.lang.String getTitle() + { + return this._title; + } //-- java.lang.String getTitle() + + /** + * Returns the value of field 'width'. + * + * @return int + * @return the value of field 'width'. + */ + public int getWidth() + { + return this._width; + } //-- int getWidth() + + /** + * Returns the value of field 'wrapAlignment'. + * + * @return boolean + * @return the value of field 'wrapAlignment'. + */ + public boolean getWrapAlignment() + { + return this._wrapAlignment; + } //-- boolean getWrapAlignment() + + /** + * Returns the value of field 'xpos'. + * + * @return int + * @return the value of field 'xpos'. + */ + public int getXpos() + { + return this._xpos; + } //-- int getXpos() + + /** + * Returns the value of field 'ypos'. + * + * @return int + * @return the value of field 'ypos'. + */ + public int getYpos() + { + return this._ypos; + } //-- int getYpos() + + /** + * Method hasConsThreshold + * + * + * + * @return boolean + */ + public boolean hasConsThreshold() + { + return this._has_consThreshold; + } //-- boolean hasConsThreshold() + + /** + * Method hasConservationSelected + * + * + * + * @return boolean + */ + public boolean hasConservationSelected() + { + return this._has_conservationSelected; + } //-- boolean hasConservationSelected() + + /** + * Method hasFontSize + * + * + * + * @return boolean + */ + public boolean hasFontSize() + { + return this._has_fontSize; + } //-- boolean hasFontSize() + + /** + * Method hasFontStyle + * + * + * + * @return boolean + */ + public boolean hasFontStyle() + { + return this._has_fontStyle; + } //-- boolean hasFontStyle() + + /** + * Method hasHeight + * + * + * + * @return boolean + */ + public boolean hasHeight() + { + return this._has_height; + } //-- boolean hasHeight() + + /** + * Method hasPidSelected + * + * + * + * @return boolean + */ + public boolean hasPidSelected() + { + return this._has_pidSelected; + } //-- boolean hasPidSelected() + + /** + * Method hasPidThreshold + * + * + * + * @return boolean + */ + public boolean hasPidThreshold() + { + return this._has_pidThreshold; + } //-- boolean hasPidThreshold() + + /** + * Method hasRenderGaps + * + * + * + * @return boolean + */ + public boolean hasRenderGaps() + { + return this._has_renderGaps; + } //-- boolean hasRenderGaps() + + /** + * Method hasShowAnnotation + * + * + * + * @return boolean + */ + public boolean hasShowAnnotation() + { + return this._has_showAnnotation; + } //-- boolean hasShowAnnotation() + + /** + * Method hasShowBoxes + * + * + * + * @return boolean + */ + public boolean hasShowBoxes() + { + return this._has_showBoxes; + } //-- boolean hasShowBoxes() + + /** + * Method hasShowColourText + * + * + * + * @return boolean + */ + public boolean hasShowColourText() + { + return this._has_showColourText; + } //-- boolean hasShowColourText() + + /** + * Method hasShowConservation + * + * + * + * @return boolean + */ + public boolean hasShowConservation() + { + return this._has_showConservation; + } //-- boolean hasShowConservation() + + /** + * Method hasShowFullId + * + * + * + * @return boolean + */ + public boolean hasShowFullId() + { + return this._has_showFullId; + } //-- boolean hasShowFullId() + + /** + * Method hasShowIdentity + * + * + * + * @return boolean + */ + public boolean hasShowIdentity() + { + return this._has_showIdentity; + } //-- boolean hasShowIdentity() + + /** + * Method hasShowQuality + * + * + * + * @return boolean + */ + public boolean hasShowQuality() + { + return this._has_showQuality; + } //-- boolean hasShowQuality() + + /** + * Method hasShowSequenceFeatures + * + * + * + * @return boolean + */ + public boolean hasShowSequenceFeatures() + { + return this._has_showSequenceFeatures; + } //-- boolean hasShowSequenceFeatures() + + /** + * Method hasShowText + * + * + * + * @return boolean + */ + public boolean hasShowText() + { + return this._has_showText; + } //-- boolean hasShowText() + + /** + * Method hasStartRes + * + * + * + * @return boolean + */ + public boolean hasStartRes() + { + return this._has_startRes; + } //-- boolean hasStartRes() + + /** + * Method hasStartSeq + * + * + * + * @return boolean + */ + public boolean hasStartSeq() + { + return this._has_startSeq; + } //-- boolean hasStartSeq() + + /** + * Method hasWidth + * + * + * + * @return boolean + */ + public boolean hasWidth() + { + return this._has_width; + } //-- boolean hasWidth() + + /** + * Method hasWrapAlignment + * + * + * + * @return boolean + */ + public boolean hasWrapAlignment() + { + return this._has_wrapAlignment; + } //-- boolean hasWrapAlignment() + + /** + * Method hasXpos + * + * + * + * @return boolean + */ + public boolean hasXpos() + { + return this._has_xpos; + } //-- boolean hasXpos() + + /** + * Method hasYpos + * + * + * + * @return boolean + */ + public boolean hasYpos() + { + return this._has_ypos; + } //-- boolean hasYpos() + + /** + * 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) + + /** + * Sets the value of field 'bgColour'. + * + * @param bgColour the value of field 'bgColour'. + */ + public void setBgColour(java.lang.String bgColour) + { + this._bgColour = bgColour; + } //-- void setBgColour(java.lang.String) + + /** + * Sets the value of field 'consThreshold'. + * + * @param consThreshold the value of field 'consThreshold'. + */ + public void setConsThreshold(int consThreshold) + { + this._consThreshold = consThreshold; + this._has_consThreshold = true; + } //-- void setConsThreshold(int) + + /** + * Sets the value of field 'conservationSelected'. + * + * @param conservationSelected the value of field + * 'conservationSelected'. + */ + public void setConservationSelected(boolean conservationSelected) + { + this._conservationSelected = conservationSelected; + this._has_conservationSelected = true; + } //-- void setConservationSelected(boolean) + + /** + * Sets the value of field 'fontName'. + * + * @param fontName the value of field 'fontName'. + */ + public void setFontName(java.lang.String fontName) + { + this._fontName = fontName; + } //-- void setFontName(java.lang.String) + + /** + * Sets the value of field 'fontSize'. + * + * @param fontSize the value of field 'fontSize'. + */ + public void setFontSize(int fontSize) + { + this._fontSize = fontSize; + this._has_fontSize = true; + } //-- void setFontSize(int) + + /** + * Sets the value of field 'fontStyle'. + * + * @param fontStyle the value of field 'fontStyle'. + */ + public void setFontStyle(int fontStyle) + { + this._fontStyle = fontStyle; + this._has_fontStyle = true; + } //-- void setFontStyle(int) + + /** + * Sets the value of field 'height'. + * + * @param height the value of field 'height'. + */ + public void setHeight(int height) + { + this._height = height; + this._has_height = true; + } //-- void setHeight(int) + + /** + * Sets the value of field 'pidSelected'. + * + * @param pidSelected the value of field 'pidSelected'. + */ + public void setPidSelected(boolean pidSelected) + { + this._pidSelected = pidSelected; + this._has_pidSelected = true; + } //-- void setPidSelected(boolean) + + /** + * Sets the value of field 'pidThreshold'. + * + * @param pidThreshold the value of field 'pidThreshold'. + */ + public void setPidThreshold(int pidThreshold) + { + this._pidThreshold = pidThreshold; + this._has_pidThreshold = true; + } //-- void setPidThreshold(int) + + /** + * Sets the value of field 'renderGaps'. + * + * @param renderGaps the value of field 'renderGaps'. + */ + public void setRenderGaps(boolean renderGaps) + { + this._renderGaps = renderGaps; + this._has_renderGaps = true; + } //-- void setRenderGaps(boolean) + + /** + * Sets the value of field 'showAnnotation'. + * + * @param showAnnotation the value of field 'showAnnotation'. + */ + public void setShowAnnotation(boolean showAnnotation) + { + this._showAnnotation = showAnnotation; + this._has_showAnnotation = true; + } //-- void setShowAnnotation(boolean) + + /** + * Sets the value of field 'showBoxes'. + * + * @param showBoxes the value of field 'showBoxes'. + */ + public void setShowBoxes(boolean showBoxes) + { + this._showBoxes = showBoxes; + this._has_showBoxes = true; + } //-- void setShowBoxes(boolean) + + /** + * Sets the value of field 'showColourText'. + * + * @param showColourText the value of field 'showColourText'. + */ + public void setShowColourText(boolean showColourText) + { + this._showColourText = showColourText; + this._has_showColourText = true; + } //-- void setShowColourText(boolean) + + /** + * Sets the value of field 'showConservation'. + * + * @param showConservation the value of field 'showConservation' + */ + public void setShowConservation(boolean showConservation) + { + this._showConservation = showConservation; + this._has_showConservation = true; + } //-- void setShowConservation(boolean) + + /** + * Sets the value of field 'showFullId'. + * + * @param showFullId the value of field 'showFullId'. + */ + public void setShowFullId(boolean showFullId) + { + this._showFullId = showFullId; + this._has_showFullId = true; + } //-- void setShowFullId(boolean) + + /** + * Sets the value of field 'showIdentity'. + * + * @param showIdentity the value of field 'showIdentity'. + */ + public void setShowIdentity(boolean showIdentity) + { + this._showIdentity = showIdentity; + this._has_showIdentity = true; + } //-- void setShowIdentity(boolean) + + /** + * Sets the value of field 'showQuality'. + * + * @param showQuality the value of field 'showQuality'. + */ + public void setShowQuality(boolean showQuality) + { + this._showQuality = showQuality; + this._has_showQuality = true; + } //-- void setShowQuality(boolean) + + /** + * Sets the value of field 'showSequenceFeatures'. + * + * @param showSequenceFeatures the value of field + * 'showSequenceFeatures'. + */ + public void setShowSequenceFeatures(boolean showSequenceFeatures) + { + this._showSequenceFeatures = showSequenceFeatures; + this._has_showSequenceFeatures = true; + } //-- void setShowSequenceFeatures(boolean) + + /** + * Sets the value of field 'showText'. + * + * @param showText the value of field 'showText'. + */ + public void setShowText(boolean showText) + { + this._showText = showText; + this._has_showText = true; + } //-- void setShowText(boolean) + + /** + * Sets the value of field 'startRes'. + * + * @param startRes the value of field 'startRes'. + */ + public void setStartRes(int startRes) + { + this._startRes = startRes; + this._has_startRes = true; + } //-- void setStartRes(int) + + /** + * Sets the value of field 'startSeq'. + * + * @param startSeq the value of field 'startSeq'. + */ + public void setStartSeq(int startSeq) + { + this._startSeq = startSeq; + this._has_startSeq = true; + } //-- void setStartSeq(int) + + /** + * Sets the value of field 'title'. + * + * @param title the value of field 'title'. + */ + public void setTitle(java.lang.String title) + { + this._title = title; + } //-- void setTitle(java.lang.String) + + /** + * Sets the value of field 'width'. + * + * @param width the value of field 'width'. + */ + public void setWidth(int width) + { + this._width = width; + this._has_width = true; + } //-- void setWidth(int) + + /** + * Sets the value of field 'wrapAlignment'. + * + * @param wrapAlignment the value of field 'wrapAlignment'. + */ + public void setWrapAlignment(boolean wrapAlignment) + { + this._wrapAlignment = wrapAlignment; + this._has_wrapAlignment = true; + } //-- void setWrapAlignment(boolean) + + /** + * Sets the value of field 'xpos'. + * + * @param xpos the value of field 'xpos'. + */ + public void setXpos(int xpos) + { + this._xpos = xpos; + this._has_xpos = true; + } //-- void setXpos(int) + + /** + * Sets the value of field 'ypos'. + * + * @param ypos the value of field 'ypos'. + */ + public void setYpos(int ypos) + { + this._ypos = ypos; + this._has_ypos = true; + } //-- void setYpos(int) + + /** + * 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.Viewport) Unmarshaller.unmarshal(jalview.binding.Viewport.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() } -- 1.7.10.2