From 124589ea0c58cbb7b3788bbf13b687a0ece3c9e0 Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Thu, 19 May 2005 17:46:40 +0000 Subject: [PATCH] Created by Castor --- src/jalview/binding/Alignment.java | 173 +++ src/jalview/binding/Annotation.java | 379 +++++++ src/jalview/binding/AnnotationElement.java | 306 ++++++ src/jalview/binding/JGroup.java | 750 +++++++++++++ src/jalview/binding/JSeq.java | 333 ++++++ src/jalview/binding/JalviewModel.java | 201 ++++ src/jalview/binding/JalviewModelSequence.java | 576 ++++++++++ src/jalview/binding/JalviewState.java | 301 ++++++ src/jalview/binding/Sequence.java | 118 ++ src/jalview/binding/SequenceSet.java | 504 +++++++++ src/jalview/binding/SequenceType.java | 199 ++++ src/jalview/binding/VAMSAS.java | 576 ++++++++++ src/jalview/binding/VamsasModel.java | 118 ++ src/jalview/binding/Viewport.java | 1420 +++++++++++++++++++++++++ 14 files changed, 5954 insertions(+) create mode 100755 src/jalview/binding/Alignment.java create mode 100755 src/jalview/binding/Annotation.java create mode 100755 src/jalview/binding/AnnotationElement.java create mode 100755 src/jalview/binding/JGroup.java create mode 100755 src/jalview/binding/JSeq.java create mode 100755 src/jalview/binding/JalviewModel.java create mode 100755 src/jalview/binding/JalviewModelSequence.java create mode 100755 src/jalview/binding/JalviewState.java create mode 100755 src/jalview/binding/Sequence.java create mode 100755 src/jalview/binding/SequenceSet.java create mode 100755 src/jalview/binding/SequenceType.java create mode 100755 src/jalview/binding/VAMSAS.java create mode 100755 src/jalview/binding/VamsasModel.java create mode 100755 src/jalview/binding/Viewport.java diff --git a/src/jalview/binding/Alignment.java b/src/jalview/binding/Alignment.java new file mode 100755 index 0000000..9a38f10 --- /dev/null +++ b/src/jalview/binding/Alignment.java @@ -0,0 +1,173 @@ +/* + * This class was automatically generated with + * Castor 0.9.6, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- 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 -/ + //--------------------------/ + + /** + * Field _annotation + */ + private jalview.binding.Annotation _annotation; + + /** + * Field _sequenceSet + */ + private jalview.binding.SequenceSet _sequenceSet; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Alignment() { + super(); + } //-- jalview.binding.Alignment() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * 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() + + /** + * 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() + + /** + * 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 'annotation'. + * + * @param annotation the value of field 'annotation'. + */ + public void setAnnotation(jalview.binding.Annotation annotation) + { + this._annotation = 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) + + /** + * 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.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 + { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } //-- void validate() + +} diff --git a/src/jalview/binding/Annotation.java b/src/jalview/binding/Annotation.java new file mode 100755 index 0000000..fefdd12 --- /dev/null +++ b/src/jalview/binding/Annotation.java @@ -0,0 +1,379 @@ +/* + * This class was automatically generated with + * Castor 0.9.6, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- Imported classes and packages -/ +//---------------------------------/ + +import java.io.IOException; +import java.io.Reader; +import java.io.Serializable; +import java.io.Writer; +import java.util.Enumeration; +import java.util.Vector; +import org.exolab.castor.xml.MarshalException; +import org.exolab.castor.xml.Marshaller; +import org.exolab.castor.xml.Unmarshaller; +import org.exolab.castor.xml.ValidationException; +import org.xml.sax.ContentHandler; + +/** + * Class Annotation. + * + * @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())) { + throw new IndexOutOfBoundsException(); + } + + return (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index); + } //-- jalview.binding.AnnotationElement getAnnotationElement(int) + + /** + * Method getAnnotationElement + * + * + * + * @return AnnotationElement + */ + public jalview.binding.AnnotationElement[] getAnnotationElement() + { + int size = _annotationElementList.size(); + jalview.binding.AnnotationElement[] mArray = new jalview.binding.AnnotationElement[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (jalview.binding.AnnotationElement) _annotationElementList.elementAt(index); + } + return mArray; + } //-- jalview.binding.AnnotationElement[] getAnnotationElement() + + /** + * Method getAnnotationElementCount + * + * + * + * @return int + */ + public int getAnnotationElementCount() + { + return _annotationElementList.size(); + } //-- int getAnnotationElementCount() + + /** + * Returns the value of field 'description'. + * + * @return String + * @return the value of field 'description'. + */ + public java.lang.String getDescription() + { + return this._description; + } //-- java.lang.String getDescription() + + /** + * Returns the value of field 'graph'. + * + * @return boolean + * @return the value of field 'graph'. + */ + public boolean getGraph() + { + return this._graph; + } //-- boolean getGraph() + + /** + * Returns the value of field 'label'. + * + * @return String + * @return the value of field 'label'. + */ + public java.lang.String getLabel() + { + return this._label; + } //-- java.lang.String getLabel() + + /** + * Method hasGraph + * + * + * + * @return boolean + */ + public boolean hasGraph() + { + return this._has_graph; + } //-- boolean hasGraph() + + /** + * Method isValid + * + * + * + * @return boolean + */ + public boolean isValid() + { + try { + validate(); + } + catch (org.exolab.castor.xml.ValidationException vex) { + return false; + } + return true; + } //-- boolean isValid() + + /** + * Method marshal + * + * + * + * @param out + */ + public void marshal(java.io.Writer out) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + + Marshaller.marshal(this, out); + } //-- void marshal(java.io.Writer) + + /** + * Method marshal + * + * + * + * @param handler + */ + public void marshal(org.xml.sax.ContentHandler handler) + throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + + Marshaller.marshal(this, handler); + } //-- void marshal(org.xml.sax.ContentHandler) + + /** + * Method removeAllAnnotationElement + * + */ + public void removeAllAnnotationElement() + { + _annotationElementList.removeAllElements(); + } //-- void removeAllAnnotationElement() + + /** + * Method removeAnnotationElement + * + * + * + * @param index + * @return AnnotationElement + */ + public jalview.binding.AnnotationElement removeAnnotationElement(int index) + { + java.lang.Object obj = _annotationElementList.elementAt(index); + _annotationElementList.removeElementAt(index); + return (jalview.binding.AnnotationElement) obj; + } //-- jalview.binding.AnnotationElement removeAnnotationElement(int) + + /** + * Method setAnnotationElement + * + * + * + * @param index + * @param vAnnotationElement + */ + public void setAnnotationElement(int index, jalview.binding.AnnotationElement vAnnotationElement) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _annotationElementList.size())) { + throw new IndexOutOfBoundsException(); + } + _annotationElementList.setElementAt(vAnnotationElement, index); + } //-- void setAnnotationElement(int, jalview.binding.AnnotationElement) + + /** + * Method setAnnotationElement + * + * + * + * @param annotationElementArray + */ + public void setAnnotationElement(jalview.binding.AnnotationElement[] annotationElementArray) + { + //-- copy array + _annotationElementList.removeAllElements(); + for (int i = 0; i < annotationElementArray.length; i++) { + _annotationElementList.addElement(annotationElementArray[i]); + } + } //-- void setAnnotationElement(jalview.binding.AnnotationElement) + + /** + * Sets the value of field 'description'. + * + * @param description the value of field 'description'. + */ + public void setDescription(java.lang.String description) + { + this._description = description; + } //-- void setDescription(java.lang.String) + + /** + * Sets the value of field 'graph'. + * + * @param graph the value of field 'graph'. + */ + public void setGraph(boolean graph) + { + this._graph = graph; + this._has_graph = true; + } //-- void setGraph(boolean) + + /** + * Sets the value of field 'label'. + * + * @param label the value of field 'label'. + */ + public void setLabel(java.lang.String label) + { + this._label = label; + } //-- void setLabel(java.lang.String) + + /** + * Method unmarshal + * + * + * + * @param reader + * @return Object + */ + public static java.lang.Object unmarshal(java.io.Reader reader) + throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException + { + return (jalview.binding.Annotation) Unmarshaller.unmarshal(jalview.binding.Annotation.class, reader); + } //-- java.lang.Object unmarshal(java.io.Reader) + + /** + * Method validate + * + */ + public void validate() + throws org.exolab.castor.xml.ValidationException + { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } //-- void validate() + +} diff --git a/src/jalview/binding/AnnotationElement.java b/src/jalview/binding/AnnotationElement.java new file mode 100755 index 0000000..e4aec31 --- /dev/null +++ b/src/jalview/binding/AnnotationElement.java @@ -0,0 +1,306 @@ +/* + * This class was automatically generated with + * Castor 0.9.6, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- 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 -/ + //--------------------------/ + + /** + * Field _position + */ + private int _position; + + /** + * keeps track of state for field: _position + */ + private boolean _has_position; + + /** + * Field _displayCharacter + */ + private java.lang.String _displayCharacter; + + /** + * Field _description + */ + private java.lang.String _description; + + /** + * Field _secondaryStructure + */ + private java.lang.String _secondaryStructure; + + /** + * Field _value + */ + private float _value; + + /** + * keeps track of state for field: _value + */ + private boolean _has_value; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public AnnotationElement() { + super(); + } //-- jalview.binding.AnnotationElement() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method deletePosition + * + */ + public void deletePosition() + { + this._has_position= false; + } //-- void deletePosition() + + /** + * Method deleteValue + * + */ + public 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() + + /** + * 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() + + /** + * Returns the value of field 'position'. + * + * @return int + * @return the value of field 'position'. + */ + public int getPosition() + { + return this._position; + } //-- 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() + + /** + * Returns the value of field 'value'. + * + * @return float + * @return the value of field 'value'. + */ + public float getValue() + { + return this._value; + } //-- float getValue() + + /** + * Method hasPosition + * + * + * + * @return boolean + */ + public boolean hasPosition() + { + return this._has_position; + } //-- boolean hasPosition() + + /** + * Method hasValue + * + * + * + * @return boolean + */ + public boolean hasValue() + { + return this._has_value; + } //-- boolean hasValue() + + /** + * 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 '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 'displayCharacter'. + * + * @param displayCharacter the value of field 'displayCharacter' + */ + public void setDisplayCharacter(java.lang.String displayCharacter) + { + this._displayCharacter = displayCharacter; + } //-- 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) + + /** + * 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) + + /** + * 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) + + /** + * 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.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 + { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } //-- void validate() + +} diff --git a/src/jalview/binding/JGroup.java b/src/jalview/binding/JGroup.java new file mode 100755 index 0000000..6473149 --- /dev/null +++ b/src/jalview/binding/JGroup.java @@ -0,0 +1,750 @@ +/* + * This class was automatically generated with + * Castor 0.9.6, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- 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 -/ + //--------------------------/ + + /** + * Field _start + */ + private int _start; + + /** + * keeps track of state for field: _start + */ + private boolean _has_start; + + /** + * Field _end + */ + private int _end; + + /** + * keeps track of state for field: _end + */ + private boolean _has_end; + + /** + * Field _name + */ + private java.lang.String _name; + + /** + * Field _colour + */ + private java.lang.String _colour; + + /** + * 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 _outlineColour + */ + private int _outlineColour; + + /** + * keeps track of state for field: _outlineColour + */ + private boolean _has_outlineColour; + + /** + * Field _displayBoxes + */ + private boolean _displayBoxes; + + /** + * keeps track of state for field: _displayBoxes + */ + private boolean _has_displayBoxes; + + /** + * Field _displayText + */ + private boolean _displayText; + + /** + * keeps track of state for field: _displayText + */ + private boolean _has_displayText; + + /** + * Field _colourText + */ + private boolean _colourText; + + /** + * keeps track of state for field: _colourText + */ + private boolean _has_colourText; + + /** + * Field _seqList + */ + private java.util.Vector _seqList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JGroup() { + super(); + _seqList = new Vector(); + } //-- jalview.binding.JGroup() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method addSeq + * + * + * + * @param vSeq + */ + public void addSeq(int vSeq) + throws java.lang.IndexOutOfBoundsException + { + _seqList.addElement(new java.lang.Integer(vSeq)); + } //-- void addSeq(int) + + /** + * Method addSeq + * + * + * + * @param index + * @param vSeq + */ + public void addSeq(int index, int vSeq) + throws java.lang.IndexOutOfBoundsException + { + _seqList.insertElementAt(new java.lang.Integer(vSeq), index); + } //-- void addSeq(int, int) + + /** + * Method deleteColourText + * + */ + public void deleteColourText() + { + this._has_colourText= false; + } //-- void deleteColourText() + + /** + * Method deleteConsThreshold + * + */ + public void deleteConsThreshold() + { + this._has_consThreshold= false; + } //-- void deleteConsThreshold() + + /** + * Method deleteDisplayBoxes + * + */ + public void deleteDisplayBoxes() + { + this._has_displayBoxes= false; + } //-- void deleteDisplayBoxes() + + /** + * Method deleteDisplayText + * + */ + public void deleteDisplayText() + { + this._has_displayText= false; + } //-- void deleteDisplayText() + + /** + * Method deleteEnd + * + */ + public void deleteEnd() + { + this._has_end= false; + } //-- void deleteEnd() + + /** + * Method deleteOutlineColour + * + */ + public void deleteOutlineColour() + { + this._has_outlineColour= false; + } //-- void deleteOutlineColour() + + /** + * Method deletePidThreshold + * + */ + public void deletePidThreshold() + { + this._has_pidThreshold= false; + } //-- void deletePidThreshold() + + /** + * Method deleteStart + * + */ + public void deleteStart() + { + this._has_start= false; + } //-- void deleteStart() + + /** + * Method enumerateSeq + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateSeq() + { + return _seqList.elements(); + } //-- 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() + + /** + * Returns the value of field 'colourText'. + * + * @return boolean + * @return the value of field 'colourText'. + */ + public boolean getColourText() + { + return this._colourText; + } //-- boolean getColourText() + + /** + * 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 'displayBoxes'. + * + * @return boolean + * @return the value of field 'displayBoxes'. + */ + public boolean getDisplayBoxes() + { + return this._displayBoxes; + } //-- boolean getDisplayBoxes() + + /** + * Returns the value of field 'displayText'. + * + * @return boolean + * @return the value of field 'displayText'. + */ + public boolean getDisplayText() + { + return this._displayText; + } //-- boolean getDisplayText() + + /** + * Returns the value of field 'end'. + * + * @return int + * @return the value of field 'end'. + */ + public int getEnd() + { + return this._end; + } //-- 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() + + /** + * Returns the value of field 'outlineColour'. + * + * @return int + * @return the value of field 'outlineColour'. + */ + public int getOutlineColour() + { + return this._outlineColour; + } //-- int getOutlineColour() + + /** + * Returns the value of field 'pidThreshold'. + * + * @return int + * @return the value of field 'pidThreshold'. + */ + public int getPidThreshold() + { + return this._pidThreshold; + } //-- int getPidThreshold() + + /** + * Method getSeq + * + * + * + * @param index + * @return int + */ + public int getSeq(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _seqList.size())) { + throw new IndexOutOfBoundsException(); + } + + 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(); + } + return mArray; + } //-- int[] getSeq() + + /** + * Method getSeqCount + * + * + * + * @return int + */ + public int getSeqCount() + { + return _seqList.size(); + } //-- int getSeqCount() + + /** + * Returns the value of field 'start'. + * + * @return int + * @return the value of field 'start'. + */ + public int getStart() + { + return this._start; + } //-- int getStart() + + /** + * Method hasColourText + * + * + * + * @return boolean + */ + public boolean hasColourText() + { + return this._has_colourText; + } //-- boolean hasColourText() + + /** + * Method hasConsThreshold + * + * + * + * @return boolean + */ + public boolean hasConsThreshold() + { + return this._has_consThreshold; + } //-- boolean hasConsThreshold() + + /** + * Method hasDisplayBoxes + * + * + * + * @return boolean + */ + public boolean hasDisplayBoxes() + { + return this._has_displayBoxes; + } //-- boolean hasDisplayBoxes() + + /** + * Method hasDisplayText + * + * + * + * @return boolean + */ + public boolean hasDisplayText() + { + return this._has_displayText; + } //-- boolean hasDisplayText() + + /** + * Method hasEnd + * + * + * + * @return boolean + */ + public boolean hasEnd() + { + return this._has_end; + } //-- boolean hasEnd() + + /** + * Method hasOutlineColour + * + * + * + * @return boolean + */ + public boolean hasOutlineColour() + { + return this._has_outlineColour; + } //-- boolean hasOutlineColour() + + /** + * Method hasPidThreshold + * + * + * + * @return boolean + */ + public boolean hasPidThreshold() + { + return this._has_pidThreshold; + } //-- boolean hasPidThreshold() + + /** + * Method hasStart + * + * + * + * @return boolean + */ + public boolean hasStart() + { + return this._has_start; + } //-- boolean hasStart() + + /** + * 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 removeAllSeq + * + */ + public void removeAllSeq() + { + _seqList.removeAllElements(); + } //-- void removeAllSeq() + + /** + * Method removeSeq + * + * + * + * @param index + * @return int + */ + public int removeSeq(int index) + { + java.lang.Object obj = _seqList.elementAt(index); + _seqList.removeElementAt(index); + 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) + + /** + * 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) + + /** + * 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 'displayBoxes'. + * + * @param displayBoxes the value of field 'displayBoxes'. + */ + public void setDisplayBoxes(boolean displayBoxes) + { + this._displayBoxes = displayBoxes; + this._has_displayBoxes = true; + } //-- 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) + + /** + * 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) + + /** + * 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 'outlineColour'. + * + * @param outlineColour the value of field 'outlineColour'. + */ + public void setOutlineColour(int outlineColour) + { + this._outlineColour = outlineColour; + this._has_outlineColour = true; + } //-- 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) + + /** + * Method setSeq + * + * + * + * @param index + * @param vSeq + */ + public void setSeq(int index, int vSeq) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _seqList.size())) { + throw new IndexOutOfBoundsException(); + } + _seqList.setElementAt(new java.lang.Integer(vSeq), index); + } //-- 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++) { + _seqList.addElement(new java.lang.Integer(seqArray[i])); + } + } //-- 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) + + /** + * 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.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 + { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } //-- void validate() + +} diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java new file mode 100755 index 0000000..751409f --- /dev/null +++ b/src/jalview/binding/JSeq.java @@ -0,0 +1,333 @@ +/* + * This class was automatically generated with + * Castor 0.9.6, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- 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 -/ + //--------------------------/ + + /** + * Field _colour + */ + private int _colour; + + /** + * keeps track of state for field: _colour + */ + private boolean _has_colour; + + /** + * Field _start + */ + private int _start; + + /** + * keeps track of state for field: _start + */ + private boolean _has_start; + + /** + * Field _end + */ + private int _end; + + /** + * keeps track of state for field: _end + */ + private boolean _has_end; + + /** + * Field _id + */ + private int _id; + + /** + * keeps track of state for field: _id + */ + private boolean _has_id; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JSeq() { + super(); + } //-- jalview.binding.JSeq() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method deleteColour + * + */ + public void deleteColour() + { + this._has_colour= false; + } //-- void deleteColour() + + /** + * Method deleteEnd + * + */ + public void deleteEnd() + { + this._has_end= false; + } //-- void deleteEnd() + + /** + * Method deleteId + * + */ + public void deleteId() + { + this._has_id= false; + } //-- void deleteId() + + /** + * Method deleteStart + * + */ + public 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() + + /** + * Returns the value of field 'end'. + * + * @return int + * @return the value of field 'end'. + */ + public int getEnd() + { + return this._end; + } //-- int getEnd() + + /** + * Returns the value of field 'id'. + * + * @return int + * @return the value of field 'id'. + */ + public int getId() + { + return this._id; + } //-- int getId() + + /** + * Returns the value of field 'start'. + * + * @return int + * @return the value of field 'start'. + */ + public int getStart() + { + return this._start; + } //-- int getStart() + + /** + * Method hasColour + * + * + * + * @return boolean + */ + public boolean hasColour() + { + return this._has_colour; + } //-- boolean hasColour() + + /** + * Method hasEnd + * + * + * + * @return boolean + */ + public boolean hasEnd() + { + return this._has_end; + } //-- boolean hasEnd() + + /** + * Method hasId + * + * + * + * @return boolean + */ + public boolean hasId() + { + return this._has_id; + } //-- boolean hasId() + + /** + * Method hasStart + * + * + * + * @return boolean + */ + public boolean hasStart() + { + return this._has_start; + } //-- boolean hasStart() + + /** + * 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 'colour'. + * + * @param colour the value of field 'colour'. + */ + public void setColour(int colour) + { + this._colour = colour; + this._has_colour = true; + } //-- 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) + + /** + * 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) + + /** + * 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) + + /** + * 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.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 + { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } //-- void validate() + +} diff --git a/src/jalview/binding/JalviewModel.java b/src/jalview/binding/JalviewModel.java new file mode 100755 index 0000000..a558b10 --- /dev/null +++ b/src/jalview/binding/JalviewModel.java @@ -0,0 +1,201 @@ +/* + * This class was automatically generated with + * Castor 0.9.6, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- 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 -/ + //--------------------------/ + + /** + * Field _creationDate + */ + private java.util.Date _creationDate; + + /** + * Field _vamsasModel + */ + private jalview.binding.VamsasModel _vamsasModel; + + /** + * Field _jalviewModelSequence + */ + private jalview.binding.JalviewModelSequence _jalviewModelSequence; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JalviewModel() { + super(); + } //-- jalview.binding.JalviewModel() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * 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() + + /** + * 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() + + /** + * 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() + + /** + * 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 'creationDate'. + * + * @param creationDate the value of field 'creationDate'. + */ + public void setCreationDate(java.util.Date creationDate) + { + this._creationDate = creationDate; + } //-- 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) + { + this._jalviewModelSequence = 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) + + /** + * 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.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 + { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } //-- void validate() + +} diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java new file mode 100755 index 0000000..7f17893 --- /dev/null +++ b/src/jalview/binding/JalviewModelSequence.java @@ -0,0 +1,576 @@ +/* + * This class was automatically generated with + * Castor 0.9.6, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- 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 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; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JalviewModelSequence() { + super(); + _JSeqList = new Vector(); + _JGroupList = new Vector(); + _viewportList = 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 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 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 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 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 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 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/JalviewState.java b/src/jalview/binding/JalviewState.java new file mode 100755 index 0000000..ad9d1b3 --- /dev/null +++ b/src/jalview/binding/JalviewState.java @@ -0,0 +1,301 @@ +/* + * This class was automatically generated with + * Castor 0.9.6, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- 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 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 JalviewState. + * + * @version $Revision$ $Date$ + */ +public class JalviewState implements java.io.Serializable { + + + //--------------------------/ + //- Class/Member Variables -/ + //--------------------------/ + + /** + * Field _creationDate + */ + private java.util.Date _creationDate; + + /** + * Field _fileList + */ + private java.util.Vector _fileList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public JalviewState() { + super(); + _fileList = new Vector(); + } //-- jalview.binding.JalviewState() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method addFile + * + * + * + * @param vFile + */ + public void addFile(java.lang.String vFile) + throws java.lang.IndexOutOfBoundsException + { + _fileList.addElement(vFile); + } //-- void addFile(java.lang.String) + + /** + * Method addFile + * + * + * + * @param index + * @param vFile + */ + public void addFile(int index, java.lang.String vFile) + throws java.lang.IndexOutOfBoundsException + { + _fileList.insertElementAt(vFile, index); + } //-- void addFile(int, java.lang.String) + + /** + * Method enumerateFile + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateFile() + { + return _fileList.elements(); + } //-- java.util.Enumeration enumerateFile() + + /** + * 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() + + /** + * Method getFile + * + * + * + * @param index + * @return String + */ + public java.lang.String getFile(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _fileList.size())) { + throw new IndexOutOfBoundsException(); + } + + return (String)_fileList.elementAt(index); + } //-- java.lang.String getFile(int) + + /** + * Method getFile + * + * + * + * @return String + */ + public java.lang.String[] getFile() + { + int size = _fileList.size(); + java.lang.String[] mArray = new java.lang.String[size]; + for (int index = 0; index < size; index++) { + mArray[index] = (String)_fileList.elementAt(index); + } + return mArray; + } //-- java.lang.String[] getFile() + + /** + * Method getFileCount + * + * + * + * @return int + */ + public int getFileCount() + { + return _fileList.size(); + } //-- int getFileCount() + + /** + * 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 removeAllFile + * + */ + public void removeAllFile() + { + _fileList.removeAllElements(); + } //-- void removeAllFile() + + /** + * Method removeFile + * + * + * + * @param index + * @return String + */ + public java.lang.String removeFile(int index) + { + java.lang.Object obj = _fileList.elementAt(index); + _fileList.removeElementAt(index); + return (String)obj; + } //-- java.lang.String removeFile(int) + + /** + * 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) + + /** + * Method setFile + * + * + * + * @param index + * @param vFile + */ + public void setFile(int index, java.lang.String vFile) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _fileList.size())) { + throw new IndexOutOfBoundsException(); + } + _fileList.setElementAt(vFile, index); + } //-- void setFile(int, java.lang.String) + + /** + * Method setFile + * + * + * + * @param fileArray + */ + public void setFile(java.lang.String[] fileArray) + { + //-- copy array + _fileList.removeAllElements(); + for (int i = 0; i < fileArray.length; i++) { + _fileList.addElement(fileArray[i]); + } + } //-- void setFile(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.JalviewState) Unmarshaller.unmarshal(jalview.binding.JalviewState.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/Sequence.java b/src/jalview/binding/Sequence.java new file mode 100755 index 0000000..f3fd4e4 --- /dev/null +++ b/src/jalview/binding/Sequence.java @@ -0,0 +1,118 @@ +/* + * This class was automatically generated with + * Castor 0.9.6, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- 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 Sequence. + * + * @version $Revision$ $Date$ + */ +public class Sequence extends SequenceType +implements java.io.Serializable +{ + + + //----------------/ + //- Constructors -/ + //----------------/ + + public Sequence() { + super(); + } //-- jalview.binding.Sequence() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * 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 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() + +} diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java new file mode 100755 index 0000000..7ed3b52 --- /dev/null +++ b/src/jalview/binding/SequenceSet.java @@ -0,0 +1,504 @@ +/* + * This class was automatically generated with + * Castor 0.9.6, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- 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 -/ + //--------------------------/ + + /** + * Field _gapChar + */ + private java.lang.String _gapChar; + + /** + * Field _aligned + */ + private boolean _aligned; + + /** + * keeps track of state for field: _aligned + */ + private boolean _has_aligned; + + /** + * Field _sequenceList + */ + private java.util.Vector _sequenceList; + + /** + * Field _annotationList + */ + private java.util.Vector _annotationList; + + + //----------------/ + //- Constructors -/ + //----------------/ + + public SequenceSet() { + super(); + _sequenceList = new Vector(); + _annotationList = new Vector(); + } //-- jalview.binding.SequenceSet() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * Method addAnnotation + * + * + * + * @param vAnnotation + */ + public void addAnnotation(jalview.binding.Annotation vAnnotation) + throws java.lang.IndexOutOfBoundsException + { + _annotationList.addElement(vAnnotation); + } //-- void addAnnotation(jalview.binding.Annotation) + + /** + * Method addAnnotation + * + * + * + * @param index + * @param vAnnotation + */ + public void addAnnotation(int index, jalview.binding.Annotation vAnnotation) + throws java.lang.IndexOutOfBoundsException + { + _annotationList.insertElementAt(vAnnotation, index); + } //-- 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) + + /** + * Method addSequence + * + * + * + * @param index + * @param vSequence + */ + public void addSequence(int index, jalview.binding.Sequence vSequence) + throws java.lang.IndexOutOfBoundsException + { + _sequenceList.insertElementAt(vSequence, index); + } //-- void addSequence(int, jalview.binding.Sequence) + + /** + * Method deleteAligned + * + */ + public void deleteAligned() + { + this._has_aligned= false; + } //-- void deleteAligned() + + /** + * Method enumerateAnnotation + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateAnnotation() + { + return _annotationList.elements(); + } //-- java.util.Enumeration enumerateAnnotation() + + /** + * Method enumerateSequence + * + * + * + * @return Enumeration + */ + public java.util.Enumeration enumerateSequence() + { + return _sequenceList.elements(); + } //-- 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() + + /** + * Method getAnnotation + * + * + * + * @param index + * @return Annotation + */ + public jalview.binding.Annotation getAnnotation(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _annotationList.size())) { + throw new IndexOutOfBoundsException(); + } + + return (jalview.binding.Annotation) _annotationList.elementAt(index); + } //-- 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++) { + mArray[index] = (jalview.binding.Annotation) _annotationList.elementAt(index); + } + return mArray; + } //-- jalview.binding.Annotation[] getAnnotation() + + /** + * Method getAnnotationCount + * + * + * + * @return int + */ + public int getAnnotationCount() + { + return _annotationList.size(); + } //-- 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() + + /** + * Method getSequence + * + * + * + * @param index + * @return Sequence + */ + public jalview.binding.Sequence getSequence(int index) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _sequenceList.size())) { + throw new IndexOutOfBoundsException(); + } + + return (jalview.binding.Sequence) _sequenceList.elementAt(index); + } //-- 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++) { + mArray[index] = (jalview.binding.Sequence) _sequenceList.elementAt(index); + } + return mArray; + } //-- jalview.binding.Sequence[] getSequence() + + /** + * Method getSequenceCount + * + * + * + * @return int + */ + public int getSequenceCount() + { + return _sequenceList.size(); + } //-- int getSequenceCount() + + /** + * Method hasAligned + * + * + * + * @return boolean + */ + public boolean hasAligned() + { + return this._has_aligned; + } //-- boolean hasAligned() + + /** + * 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 removeAllAnnotation + * + */ + public void removeAllAnnotation() + { + _annotationList.removeAllElements(); + } //-- void removeAllAnnotation() + + /** + * Method removeAllSequence + * + */ + public void removeAllSequence() + { + _sequenceList.removeAllElements(); + } //-- void removeAllSequence() + + /** + * Method removeAnnotation + * + * + * + * @param index + * @return Annotation + */ + public jalview.binding.Annotation removeAnnotation(int index) + { + java.lang.Object obj = _annotationList.elementAt(index); + _annotationList.removeElementAt(index); + return (jalview.binding.Annotation) obj; + } //-- jalview.binding.Annotation removeAnnotation(int) + + /** + * Method removeSequence + * + * + * + * @param index + * @return Sequence + */ + public jalview.binding.Sequence removeSequence(int index) + { + java.lang.Object obj = _sequenceList.elementAt(index); + _sequenceList.removeElementAt(index); + return (jalview.binding.Sequence) obj; + } //-- 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) + + /** + * Method setAnnotation + * + * + * + * @param index + * @param vAnnotation + */ + public void setAnnotation(int index, jalview.binding.Annotation vAnnotation) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _annotationList.size())) { + throw new IndexOutOfBoundsException(); + } + _annotationList.setElementAt(vAnnotation, index); + } //-- 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++) { + _annotationList.addElement(annotationArray[i]); + } + } //-- 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) + + /** + * Method setSequence + * + * + * + * @param index + * @param vSequence + */ + public void setSequence(int index, jalview.binding.Sequence vSequence) + throws java.lang.IndexOutOfBoundsException + { + //-- check bounds for index + if ((index < 0) || (index > _sequenceList.size())) { + throw new IndexOutOfBoundsException(); + } + _sequenceList.setElementAt(vSequence, index); + } //-- 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++) { + _sequenceList.addElement(sequenceArray[i]); + } + } //-- 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 + { + 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 + { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } //-- void validate() + +} diff --git a/src/jalview/binding/SequenceType.java b/src/jalview/binding/SequenceType.java new file mode 100755 index 0000000..3a935e4 --- /dev/null +++ b/src/jalview/binding/SequenceType.java @@ -0,0 +1,199 @@ +/* + * This class was automatically generated with + * Castor 0.9.6, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- 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 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 { + 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 + { + 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() + +} diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java new file mode 100755 index 0000000..b4237b8 --- /dev/null +++ b/src/jalview/binding/VAMSAS.java @@ -0,0 +1,576 @@ +/* + * This class was automatically generated with + * Castor 0.9.6, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- 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 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() + +} diff --git a/src/jalview/binding/VamsasModel.java b/src/jalview/binding/VamsasModel.java new file mode 100755 index 0000000..a4d4362 --- /dev/null +++ b/src/jalview/binding/VamsasModel.java @@ -0,0 +1,118 @@ +/* + * This class was automatically generated with + * Castor 0.9.6, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- 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 +{ + + + //----------------/ + //- Constructors -/ + //----------------/ + + public VamsasModel() { + super(); + } //-- jalview.binding.VamsasModel() + + + //-----------/ + //- Methods -/ + //-----------/ + + /** + * 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 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.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 + { + org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); + validator.validate(this); + } //-- void validate() + +} diff --git a/src/jalview/binding/Viewport.java b/src/jalview/binding/Viewport.java new file mode 100755 index 0000000..911061b --- /dev/null +++ b/src/jalview/binding/Viewport.java @@ -0,0 +1,1420 @@ +/* + * This class was automatically generated with + * Castor 0.9.6, using an XML + * Schema. + * $Id$ + */ + +package jalview.binding; + + //---------------------------------/ + //- 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 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() + +} -- 1.7.10.2