From: gmungoc
Jalview can
perform PCA analysis on both proteins and nucleotide sequence
alignments. In both cases, components are generated by an
- eigenvector decomposition of the matrix formed from the sum of
- substitution matrix scores at each aligned position between each
- pair of sequences - computed with one of the available score
- matrices, such as BLOSUM62,
+ eigenvector decomposition of the matrix formed from pairwise similarity
+ scores between each pair of sequences. The similarity score model is
+ selected on the calculations dialog, and
+ may use one of the available score matrices, such as
+ BLOSUM62,
PAM250, or the simple single
- nucleotide substitution matrix. The options available for
- calculation are given in the Change
- Parameters menu.
+ nucleotide substitution matrix, or by sequence percentage identity,
+ or sequence feature similarity.
diff --git a/help/html/releases.html b/help/html/releases.html index af417a7..0fba08a 100755 --- a/help/html/releases.html +++ b/help/html/releases.html @@ -71,25 +71,64 @@ li:before {
* Returns null if *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.AnnotationElement[] getAnnotationElement() - { - jalview.binding.AnnotationElement[] array = new jalview.binding.AnnotationElement[0]; - return (jalview.binding.AnnotationElement[]) this._annotationElementList - .toArray(array); - } - - /** - * Method getAnnotationElementCount. - * - * @return the size of this collection - */ - public int getAnnotationElementCount() - { - return this._annotationElementList.size(); - } - - /** - * Returns the value of field 'description'. - * - * @return the value of field 'Description'. - */ - public java.lang.String getDescription() - { - return this._description; - } - - /** - * Returns the value of field 'graph'. - * - * @return the value of field 'Graph'. - */ - public boolean getGraph() - { - return this._graph; - } - - /** - * Returns the value of field 'graphType'. - * - * @return the value of field 'GraphType'. - */ - public int getGraphType() - { - return this._graphType; - } - - /** - * Returns the value of field 'label'. - * - * @return the value of field 'Label'. - */ - public java.lang.String getLabel() - { - return this._label; - } - - /** - * Method hasGraph. - * - * @return true if at least one Graph has been added - */ - public boolean hasGraph() - { - return this._has_graph; - } - - /** - * Method hasGraphType. - * - * @return true if at least one GraphType has been added - */ - public boolean hasGraphType() - { - return this._has_graphType; - } - - /** - * Returns the value of field 'graph'. - * - * @return the value of field 'Graph'. - */ - public boolean isGraph() - { - return this._graph; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllAnnotationElement() - { - this._annotationElementList.clear(); - } - - /** - * Method removeAnnotationElement. - * - * @param vAnnotationElement - * @return true if the object was removed from the collection. - */ - public boolean removeAnnotationElement( - final jalview.binding.AnnotationElement vAnnotationElement) - { - boolean removed = _annotationElementList.remove(vAnnotationElement); - return removed; - } - - /** - * Method removeAnnotationElementAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.AnnotationElement removeAnnotationElementAt( - final int index) - { - java.lang.Object obj = this._annotationElementList.remove(index); - return (jalview.binding.AnnotationElement) obj; - } - - /** - * - * - * @param index - * @param vAnnotationElement - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAnnotationElement(final int index, - final jalview.binding.AnnotationElement vAnnotationElement) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._annotationElementList.size()) - { - throw new IndexOutOfBoundsException( - "setAnnotationElement: Index value '" + index - + "' not in range [0.." - + (this._annotationElementList.size() - 1) + "]"); - } - - this._annotationElementList.set(index, vAnnotationElement); - } - - /** - * - * - * @param vAnnotationElementArray - */ - public void setAnnotationElement( - final jalview.binding.AnnotationElement[] vAnnotationElementArray) - { - // -- copy array - _annotationElementList.clear(); - - for (int i = 0; i < vAnnotationElementArray.length; i++) - { - this._annotationElementList.add(vAnnotationElementArray[i]); - } - } - - /** - * Sets the value of field 'description'. - * - * @param description - * the value of field 'description'. - */ - public void setDescription(final java.lang.String description) - { - this._description = description; - } - - /** - * Sets the value of field 'graph'. - * - * @param graph - * the value of field 'graph'. - */ - public void setGraph(final boolean graph) - { - this._graph = graph; - this._has_graph = true; - } - - /** - * Sets the value of field 'graphType'. - * - * @param graphType - * the value of field 'graphType'. - */ - public void setGraphType(final int graphType) - { - this._graphType = graphType; - this._has_graphType = true; - } - - /** - * Sets the value of field 'label'. - * - * @param label - * the value of field 'label'. - */ - public void setLabel(final java.lang.String label) - { - this._label = label; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Annotation - */ - public static jalview.binding.Annotation unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Annotation) Unmarshaller - .unmarshal(jalview.binding.Annotation.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/AnnotationElement.java b/src/jalview/binding/AnnotationElement.java deleted file mode 100644 index 505d91e..0000000 --- a/src/jalview/binding/AnnotationElement.java +++ /dev/null @@ -1,305 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class 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(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deletePosition() - { - this._has_position = false; - } - - /** - */ - public void deleteValue() - { - this._has_value = false; - } - - /** - * Returns the value of field 'description'. - * - * @return the value of field 'Description'. - */ - public java.lang.String getDescription() - { - return this._description; - } - - /** - * Returns the value of field 'displayCharacter'. - * - * @return the value of field 'DisplayCharacter'. - */ - public java.lang.String getDisplayCharacter() - { - return this._displayCharacter; - } - - /** - * Returns the value of field 'position'. - * - * @return the value of field 'Position'. - */ - public int getPosition() - { - return this._position; - } - - /** - * Returns the value of field 'secondaryStructure'. - * - * @return the value of field 'SecondaryStructure'. - */ - public java.lang.String getSecondaryStructure() - { - return this._secondaryStructure; - } - - /** - * Returns the value of field 'value'. - * - * @return the value of field 'Value'. - */ - public float getValue() - { - return this._value; - } - - /** - * Method hasPosition. - * - * @return true if at least one Position has been added - */ - public boolean hasPosition() - { - return this._has_position; - } - - /** - * Method hasValue. - * - * @return true if at least one Value has been added - */ - public boolean hasValue() - { - return this._has_value; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'description'. - * - * @param description - * the value of field 'description'. - */ - public void setDescription(final java.lang.String description) - { - this._description = description; - } - - /** - * Sets the value of field 'displayCharacter'. - * - * @param displayCharacter - * the value of field 'displayCharacter' - */ - public void setDisplayCharacter(final java.lang.String displayCharacter) - { - this._displayCharacter = displayCharacter; - } - - /** - * Sets the value of field 'position'. - * - * @param position - * the value of field 'position'. - */ - public void setPosition(final int position) - { - this._position = position; - this._has_position = true; - } - - /** - * Sets the value of field 'secondaryStructure'. - * - * @param secondaryStructure - * the value of field 'secondaryStructure'. - */ - public void setSecondaryStructure( - final java.lang.String secondaryStructure) - { - this._secondaryStructure = secondaryStructure; - } - - /** - * Sets the value of field 'value'. - * - * @param value - * the value of field 'value'. - */ - public void setValue(final float value) - { - this._value = value; - this._has_value = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.AnnotationElement - */ - public static jalview.binding.AnnotationElement unmarshal( - final 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); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Colour.java b/src/jalview/binding/Colour.java deleted file mode 100644 index f51e9af..0000000 --- a/src/jalview/binding/Colour.java +++ /dev/null @@ -1,707 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Colour. - * - * @version $Revision$ $Date$ - */ -public class Colour implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Single letter residue code for an alignment colour scheme, or feature type - * for a feature colour scheme - */ - private java.lang.String _name; - - /** - * Field _RGB. - */ - private java.lang.String _RGB; - - /** - * Field _minRGB. - */ - private java.lang.String _minRGB; - - /** - * Field _noValueColour. - */ - private jalview.binding.types.NoValueColour _noValueColour = jalview.binding.types.NoValueColour - .valueOf("Min"); - - /** - * Field _threshType. - */ - private jalview.binding.types.ColourThreshTypeType _threshType; - - /** - * Field _threshold. - */ - private float _threshold; - - /** - * keeps track of state for field: _threshold - */ - private boolean _has_threshold; - - /** - * Field _max. - */ - private float _max; - - /** - * keeps track of state for field: _max - */ - private boolean _has_max; - - /** - * Field _min. - */ - private float _min; - - /** - * keeps track of state for field: _min - */ - private boolean _has_min; - - /** - * Field _colourByLabel. - */ - private boolean _colourByLabel; - - /** - * keeps track of state for field: _colourByLabel - */ - private boolean _has_colourByLabel; - - /** - * Field _autoScale. - */ - private boolean _autoScale; - - /** - * keeps track of state for field: _autoScale - */ - private boolean _has_autoScale; - - /** - * name of feature attribute to colour by, or attribute and sub-attribute - */ - private java.util.Vector _attributeNameList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Colour() - { - super(); - setNoValueColour(jalview.binding.types.NoValueColour.valueOf("Min")); - this._attributeNameList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAttributeName(final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._attributeNameList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addAttributeName has a maximum of 2"); - } - - this._attributeNameList.addElement(vAttributeName); - } - - /** - * - * - * @param index - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAttributeName(final int index, - final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._attributeNameList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addAttributeName has a maximum of 2"); - } - - this._attributeNameList.add(index, vAttributeName); - } - - /** - */ - public void deleteAutoScale() - { - this._has_autoScale = false; - } - - /** - */ - public void deleteColourByLabel() - { - this._has_colourByLabel = false; - } - - /** - */ - public void deleteMax() - { - this._has_max = false; - } - - /** - */ - public void deleteMin() - { - this._has_min = false; - } - - /** - */ - public void deleteThreshold() - { - this._has_threshold = false; - } - - /** - * Method enumerateAttributeName. - * - * @return an Enumeration over all java.lang.String elements - */ - public java.util.Enumeration enumerateAttributeName() - { - return this._attributeNameList.elements(); - } - - /** - * Method getAttributeName. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the java.lang.String at the given index - */ - public java.lang.String getAttributeName(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._attributeNameList.size()) - { - throw new IndexOutOfBoundsException("getAttributeName: Index value '" - + index + "' not in range [0.." - + (this._attributeNameList.size() - 1) + "]"); - } - - return (java.lang.String) _attributeNameList.get(index); - } - - /** - * Method getAttributeName.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public java.lang.String[] getAttributeName() - { - java.lang.String[] array = new java.lang.String[0]; - return (java.lang.String[]) this._attributeNameList.toArray(array); - } - - /** - * Method getAttributeNameCount. - * - * @return the size of this collection - */ - public int getAttributeNameCount() - { - return this._attributeNameList.size(); - } - - /** - * Returns the value of field 'autoScale'. - * - * @return the value of field 'AutoScale'. - */ - public boolean getAutoScale() - { - return this._autoScale; - } - - /** - * Returns the value of field 'colourByLabel'. - * - * @return the value of field 'ColourByLabel'. - */ - public boolean getColourByLabel() - { - return this._colourByLabel; - } - - /** - * Returns the value of field 'max'. - * - * @return the value of field 'Max'. - */ - public float getMax() - { - return this._max; - } - - /** - * Returns the value of field 'min'. - * - * @return the value of field 'Min'. - */ - public float getMin() - { - return this._min; - } - - /** - * Returns the value of field 'minRGB'. - * - * @return the value of field 'MinRGB'. - */ - public java.lang.String getMinRGB() - { - return this._minRGB; - } - - /** - * Returns the value of field 'name'. The field 'name' has the following - * description: Single letter residue code for an alignment colour scheme, or - * feature type for a feature colour scheme - * - * @return the value of field 'Name'. - */ - public java.lang.String getName() - { - return this._name; - } - - /** - * Returns the value of field 'noValueColour'. - * - * @return the value of field 'NoValueColour'. - */ - public jalview.binding.types.NoValueColour getNoValueColour() - { - return this._noValueColour; - } - - /** - * Returns the value of field 'RGB'. - * - * @return the value of field 'RGB'. - */ - public java.lang.String getRGB() - { - return this._RGB; - } - - /** - * Returns the value of field 'threshType'. - * - * @return the value of field 'ThreshType'. - */ - public jalview.binding.types.ColourThreshTypeType getThreshType() - { - return this._threshType; - } - - /** - * Returns the value of field 'threshold'. - * - * @return the value of field 'Threshold'. - */ - public float getThreshold() - { - return this._threshold; - } - - /** - * Method hasAutoScale. - * - * @return true if at least one AutoScale has been added - */ - public boolean hasAutoScale() - { - return this._has_autoScale; - } - - /** - * Method hasColourByLabel. - * - * @return true if at least one ColourByLabel has been added - */ - public boolean hasColourByLabel() - { - return this._has_colourByLabel; - } - - /** - * Method hasMax. - * - * @return true if at least one Max has been added - */ - public boolean hasMax() - { - return this._has_max; - } - - /** - * Method hasMin. - * - * @return true if at least one Min has been added - */ - public boolean hasMin() - { - return this._has_min; - } - - /** - * Method hasThreshold. - * - * @return true if at least one Threshold has been added - */ - public boolean hasThreshold() - { - return this._has_threshold; - } - - /** - * Returns the value of field 'autoScale'. - * - * @return the value of field 'AutoScale'. - */ - public boolean isAutoScale() - { - return this._autoScale; - } - - /** - * Returns the value of field 'colourByLabel'. - * - * @return the value of field 'ColourByLabel'. - */ - public boolean isColourByLabel() - { - return this._colourByLabel; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllAttributeName() - { - this._attributeNameList.clear(); - } - - /** - * Method removeAttributeName. - * - * @param vAttributeName - * @return true if the object was removed from the collection. - */ - public boolean removeAttributeName(final java.lang.String vAttributeName) - { - boolean removed = _attributeNameList.remove(vAttributeName); - return removed; - } - - /** - * Method removeAttributeNameAt. - * - * @param index - * @return the element removed from the collection - */ - public java.lang.String removeAttributeNameAt(final int index) - { - java.lang.Object obj = this._attributeNameList.remove(index); - return (java.lang.String) obj; - } - - /** - * - * - * @param index - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAttributeName(final int index, - final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._attributeNameList.size()) - { - throw new IndexOutOfBoundsException("setAttributeName: Index value '" - + index + "' not in range [0.." - + (this._attributeNameList.size() - 1) + "]"); - } - - this._attributeNameList.set(index, vAttributeName); - } - - /** - * - * - * @param vAttributeNameArray - */ - public void setAttributeName(final java.lang.String[] vAttributeNameArray) - { - // -- copy array - _attributeNameList.clear(); - - for (int i = 0; i < vAttributeNameArray.length; i++) - { - this._attributeNameList.add(vAttributeNameArray[i]); - } - } - - /** - * Sets the value of field 'autoScale'. - * - * @param autoScale - * the value of field 'autoScale'. - */ - public void setAutoScale(final boolean autoScale) - { - this._autoScale = autoScale; - this._has_autoScale = true; - } - - /** - * Sets the value of field 'colourByLabel'. - * - * @param colourByLabel - * the value of field 'colourByLabel'. - */ - public void setColourByLabel(final boolean colourByLabel) - { - this._colourByLabel = colourByLabel; - this._has_colourByLabel = true; - } - - /** - * Sets the value of field 'max'. - * - * @param max - * the value of field 'max'. - */ - public void setMax(final float max) - { - this._max = max; - this._has_max = true; - } - - /** - * Sets the value of field 'min'. - * - * @param min - * the value of field 'min'. - */ - public void setMin(final float min) - { - this._min = min; - this._has_min = true; - } - - /** - * Sets the value of field 'minRGB'. - * - * @param minRGB - * the value of field 'minRGB'. - */ - public void setMinRGB(final java.lang.String minRGB) - { - this._minRGB = minRGB; - } - - /** - * Sets the value of field 'name'. The field 'name' has the following - * description: Single letter residue code for an alignment colour scheme, or - * feature type for a feature colour scheme - * - * @param name - * the value of field 'name'. - */ - public void setName(final java.lang.String name) - { - this._name = name; - } - - /** - * Sets the value of field 'noValueColour'. - * - * @param noValueColour - * the value of field 'noValueColour'. - */ - public void setNoValueColour( - final jalview.binding.types.NoValueColour noValueColour) - { - this._noValueColour = noValueColour; - } - - /** - * Sets the value of field 'RGB'. - * - * @param RGB - * the value of field 'RGB'. - */ - public void setRGB(final java.lang.String RGB) - { - this._RGB = RGB; - } - - /** - * Sets the value of field 'threshType'. - * - * @param threshType - * the value of field 'threshType'. - */ - public void setThreshType( - final jalview.binding.types.ColourThreshTypeType threshType) - { - this._threshType = threshType; - } - - /** - * Sets the value of field 'threshold'. - * - * @param threshold - * the value of field 'threshold'. - */ - public void setThreshold(final float threshold) - { - this._threshold = threshold; - this._has_threshold = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Colour - */ - public static jalview.binding.Colour unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Colour) Unmarshaller - .unmarshal(jalview.binding.Colour.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/CompoundMatcher.java b/src/jalview/binding/CompoundMatcher.java deleted file mode 100644 index a2d1048..0000000 --- a/src/jalview/binding/CompoundMatcher.java +++ /dev/null @@ -1,368 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class CompoundMatcher. - * - * @version $Revision$ $Date$ - */ -public class CompoundMatcher implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * If true, matchers are AND-ed, if false they are OR-ed - */ - private boolean _and; - - /** - * keeps track of state for field: _and - */ - private boolean _has_and; - - /** - * Field _matcherSetList. - */ - private java.util.Vector _matcherSetList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public CompoundMatcher() - { - super(); - this._matcherSetList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vMatcherSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addMatcherSet(final jalview.binding.MatcherSet vMatcherSet) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._matcherSetList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addMatcherSet has a maximum of 2"); - } - - this._matcherSetList.addElement(vMatcherSet); - } - - /** - * - * - * @param index - * @param vMatcherSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addMatcherSet(final int index, - final jalview.binding.MatcherSet vMatcherSet) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._matcherSetList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addMatcherSet has a maximum of 2"); - } - - this._matcherSetList.add(index, vMatcherSet); - } - - /** - */ - public void deleteAnd() - { - this._has_and = false; - } - - /** - * Method enumerateMatcherSet. - * - * @return an Enumeration over all jalview.binding.MatcherSet elements - */ - public java.util.Enumeration enumerateMatcherSet() - { - return this._matcherSetList.elements(); - } - - /** - * Returns the value of field 'and'. The field 'and' has the following - * description: If true, matchers are AND-ed, if false they are OR-ed - * - * @return the value of field 'And'. - */ - public boolean getAnd() - { - return this._and; - } - - /** - * Method getMatcherSet. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.MatcherSet at the given index - */ - public jalview.binding.MatcherSet getMatcherSet(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._matcherSetList.size()) - { - throw new IndexOutOfBoundsException( - "getMatcherSet: Index value '" + index + "' not in range [0.." - + (this._matcherSetList.size() - 1) + "]"); - } - - return (jalview.binding.MatcherSet) _matcherSetList.get(index); - } - - /** - * Method getMatcherSet.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.MatcherSet[] getMatcherSet() - { - jalview.binding.MatcherSet[] array = new jalview.binding.MatcherSet[0]; - return (jalview.binding.MatcherSet[]) this._matcherSetList - .toArray(array); - } - - /** - * Method getMatcherSetCount. - * - * @return the size of this collection - */ - public int getMatcherSetCount() - { - return this._matcherSetList.size(); - } - - /** - * Method hasAnd. - * - * @return true if at least one And has been added - */ - public boolean hasAnd() - { - return this._has_and; - } - - /** - * Returns the value of field 'and'. The field 'and' has the following - * description: If true, matchers are AND-ed, if false they are OR-ed - * - * @return the value of field 'And'. - */ - public boolean isAnd() - { - return this._and; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllMatcherSet() - { - this._matcherSetList.clear(); - } - - /** - * Method removeMatcherSet. - * - * @param vMatcherSet - * @return true if the object was removed from the collection. - */ - public boolean removeMatcherSet( - final jalview.binding.MatcherSet vMatcherSet) - { - boolean removed = _matcherSetList.remove(vMatcherSet); - return removed; - } - - /** - * Method removeMatcherSetAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.MatcherSet removeMatcherSetAt(final int index) - { - java.lang.Object obj = this._matcherSetList.remove(index); - return (jalview.binding.MatcherSet) obj; - } - - /** - * Sets the value of field 'and'. The field 'and' has the following - * description: If true, matchers are AND-ed, if false they are OR-ed - * - * @param and - * the value of field 'and'. - */ - public void setAnd(final boolean and) - { - this._and = and; - this._has_and = true; - } - - /** - * - * - * @param index - * @param vMatcherSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setMatcherSet(final int index, - final jalview.binding.MatcherSet vMatcherSet) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._matcherSetList.size()) - { - throw new IndexOutOfBoundsException( - "setMatcherSet: Index value '" + index + "' not in range [0.." - + (this._matcherSetList.size() - 1) + "]"); - } - - this._matcherSetList.set(index, vMatcherSet); - } - - /** - * - * - * @param vMatcherSetArray - */ - public void setMatcherSet( - final jalview.binding.MatcherSet[] vMatcherSetArray) - { - // -- copy array - _matcherSetList.clear(); - - for (int i = 0; i < vMatcherSetArray.length; i++) - { - this._matcherSetList.add(vMatcherSetArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.CompoundMatcher - */ - public static jalview.binding.CompoundMatcher unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.CompoundMatcher) Unmarshaller - .unmarshal(jalview.binding.CompoundMatcher.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Feature.java b/src/jalview/binding/Feature.java deleted file mode 100644 index d72b29c..0000000 --- a/src/jalview/binding/Feature.java +++ /dev/null @@ -1,304 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Feature. - * - * @version $Revision$ $Date$ - */ -public class Feature implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _begin. - */ - private int _begin; - - /** - * keeps track of state for field: _begin - */ - private boolean _has_begin; - - /** - * Field _end. - */ - private int _end; - - /** - * keeps track of state for field: _end - */ - private boolean _has_end; - - /** - * Field _type. - */ - private java.lang.String _type; - - /** - * Field _description. - */ - private java.lang.String _description; - - /** - * Field _status. - */ - private java.lang.String _status; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Feature() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteBegin() - { - this._has_begin = false; - } - - /** - */ - public void deleteEnd() - { - this._has_end = false; - } - - /** - * Returns the value of field 'begin'. - * - * @return the value of field 'Begin'. - */ - public int getBegin() - { - return this._begin; - } - - /** - * Returns the value of field 'description'. - * - * @return the value of field 'Description'. - */ - public java.lang.String getDescription() - { - return this._description; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd() - { - return this._end; - } - - /** - * Returns the value of field 'status'. - * - * @return the value of field 'Status'. - */ - public java.lang.String getStatus() - { - return this._status; - } - - /** - * Returns the value of field 'type'. - * - * @return the value of field 'Type'. - */ - public java.lang.String getType() - { - return this._type; - } - - /** - * Method hasBegin. - * - * @return true if at least one Begin has been added - */ - public boolean hasBegin() - { - return this._has_begin; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd() - { - return this._has_end; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'begin'. - * - * @param begin - * the value of field 'begin'. - */ - public void setBegin(final int begin) - { - this._begin = begin; - this._has_begin = true; - } - - /** - * Sets the value of field 'description'. - * - * @param description - * the value of field 'description'. - */ - public void setDescription(final java.lang.String description) - { - this._description = description; - } - - /** - * Sets the value of field 'end'. - * - * @param end - * the value of field 'end'. - */ - public void setEnd(final int end) - { - this._end = end; - this._has_end = true; - } - - /** - * Sets the value of field 'status'. - * - * @param status - * the value of field 'status'. - */ - public void setStatus(final java.lang.String status) - { - this._status = status; - } - - /** - * Sets the value of field 'type'. - * - * @param type - * the value of field 'type'. - */ - public void setType(final java.lang.String type) - { - this._type = type; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Feature - */ - public static jalview.binding.Feature unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Feature) Unmarshaller - .unmarshal(jalview.binding.Feature.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/FeatureMatcher.java b/src/jalview/binding/FeatureMatcher.java deleted file mode 100644 index e4e52fb..0000000 --- a/src/jalview/binding/FeatureMatcher.java +++ /dev/null @@ -1,381 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class FeatureMatcher. - * - * @version $Revision$ $Date$ - */ -public class FeatureMatcher implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _by. - */ - private jalview.binding.types.FeatureMatcherByType _by; - - /** - * name of feature attribute to filter on, or attribute and sub-attribute - */ - private java.util.Vector _attributeNameList; - - /** - * Field _condition. - */ - private java.lang.String _condition; - - /** - * Field _value. - */ - private java.lang.String _value; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FeatureMatcher() - { - super(); - this._attributeNameList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAttributeName(final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._attributeNameList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addAttributeName has a maximum of 2"); - } - - this._attributeNameList.addElement(vAttributeName); - } - - /** - * - * - * @param index - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAttributeName(final int index, - final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check for the maximum size - if (this._attributeNameList.size() >= 2) - { - throw new IndexOutOfBoundsException( - "addAttributeName has a maximum of 2"); - } - - this._attributeNameList.add(index, vAttributeName); - } - - /** - * Method enumerateAttributeName. - * - * @return an Enumeration over all java.lang.String elements - */ - public java.util.Enumeration enumerateAttributeName() - { - return this._attributeNameList.elements(); - } - - /** - * Method getAttributeName. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the java.lang.String at the given index - */ - public java.lang.String getAttributeName(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._attributeNameList.size()) - { - throw new IndexOutOfBoundsException("getAttributeName: Index value '" - + index + "' not in range [0.." - + (this._attributeNameList.size() - 1) + "]"); - } - - return (java.lang.String) _attributeNameList.get(index); - } - - /** - * Method getAttributeName.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public java.lang.String[] getAttributeName() - { - java.lang.String[] array = new java.lang.String[0]; - return (java.lang.String[]) this._attributeNameList.toArray(array); - } - - /** - * Method getAttributeNameCount. - * - * @return the size of this collection - */ - public int getAttributeNameCount() - { - return this._attributeNameList.size(); - } - - /** - * Returns the value of field 'by'. - * - * @return the value of field 'By'. - */ - public jalview.binding.types.FeatureMatcherByType getBy() - { - return this._by; - } - - /** - * Returns the value of field 'condition'. - * - * @return the value of field 'Condition'. - */ - public java.lang.String getCondition() - { - return this._condition; - } - - /** - * Returns the value of field 'value'. - * - * @return the value of field 'Value'. - */ - public java.lang.String getValue() - { - return this._value; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllAttributeName() - { - this._attributeNameList.clear(); - } - - /** - * Method removeAttributeName. - * - * @param vAttributeName - * @return true if the object was removed from the collection. - */ - public boolean removeAttributeName(final java.lang.String vAttributeName) - { - boolean removed = _attributeNameList.remove(vAttributeName); - return removed; - } - - /** - * Method removeAttributeNameAt. - * - * @param index - * @return the element removed from the collection - */ - public java.lang.String removeAttributeNameAt(final int index) - { - java.lang.Object obj = this._attributeNameList.remove(index); - return (java.lang.String) obj; - } - - /** - * - * - * @param index - * @param vAttributeName - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAttributeName(final int index, - final java.lang.String vAttributeName) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._attributeNameList.size()) - { - throw new IndexOutOfBoundsException("setAttributeName: Index value '" - + index + "' not in range [0.." - + (this._attributeNameList.size() - 1) + "]"); - } - - this._attributeNameList.set(index, vAttributeName); - } - - /** - * - * - * @param vAttributeNameArray - */ - public void setAttributeName(final java.lang.String[] vAttributeNameArray) - { - // -- copy array - _attributeNameList.clear(); - - for (int i = 0; i < vAttributeNameArray.length; i++) - { - this._attributeNameList.add(vAttributeNameArray[i]); - } - } - - /** - * Sets the value of field 'by'. - * - * @param by - * the value of field 'by'. - */ - public void setBy(final jalview.binding.types.FeatureMatcherByType by) - { - this._by = by; - } - - /** - * Sets the value of field 'condition'. - * - * @param condition - * the value of field 'condition'. - */ - public void setCondition(final java.lang.String condition) - { - this._condition = condition; - } - - /** - * Sets the value of field 'value'. - * - * @param value - * the value of field 'value'. - */ - public void setValue(final java.lang.String value) - { - this._value = value; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.FeatureMatcher - */ - public static jalview.binding.FeatureMatcher unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.FeatureMatcher) Unmarshaller - .unmarshal(jalview.binding.FeatureMatcher.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/FeatureMatcherSet.java b/src/jalview/binding/FeatureMatcherSet.java deleted file mode 100644 index 7ba5f0e..0000000 --- a/src/jalview/binding/FeatureMatcherSet.java +++ /dev/null @@ -1,200 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * A feature match condition, which may be simple or compound - * - * @version $Revision$ $Date$ - */ -public class FeatureMatcherSet implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Internal choice value storage - */ - private java.lang.Object _choiceValue; - - /** - * Field _matchCondition. - */ - private jalview.binding.MatchCondition _matchCondition; - - /** - * Field _compoundMatcher. - */ - private jalview.binding.CompoundMatcher _compoundMatcher; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FeatureMatcherSet() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'choiceValue'. The field 'choiceValue' has the - * following description: Internal choice value storage - * - * @return the value of field 'ChoiceValue'. - */ - public java.lang.Object getChoiceValue() - { - return this._choiceValue; - } - - /** - * Returns the value of field 'compoundMatcher'. - * - * @return the value of field 'CompoundMatcher'. - */ - public jalview.binding.CompoundMatcher getCompoundMatcher() - { - return this._compoundMatcher; - } - - /** - * Returns the value of field 'matchCondition'. - * - * @return the value of field 'MatchCondition'. - */ - public jalview.binding.MatchCondition getMatchCondition() - { - return this._matchCondition; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'compoundMatcher'. - * - * @param compoundMatcher - * the value of field 'compoundMatcher'. - */ - public void setCompoundMatcher( - final jalview.binding.CompoundMatcher compoundMatcher) - { - this._compoundMatcher = compoundMatcher; - this._choiceValue = compoundMatcher; - } - - /** - * Sets the value of field 'matchCondition'. - * - * @param matchCondition - * the value of field 'matchCondition'. - */ - public void setMatchCondition( - final jalview.binding.MatchCondition matchCondition) - { - this._matchCondition = matchCondition; - this._choiceValue = matchCondition; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.FeatureMatcherSet - */ - public static jalview.binding.FeatureMatcherSet unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.FeatureMatcherSet) Unmarshaller - .unmarshal(jalview.binding.FeatureMatcherSet.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/FeatureSettings.java b/src/jalview/binding/FeatureSettings.java deleted file mode 100644 index 321536d..0000000 --- a/src/jalview/binding/FeatureSettings.java +++ /dev/null @@ -1,289 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class FeatureSettings. - * - * @version $Revision$ $Date$ - */ -public class FeatureSettings implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _settingList. - */ - private java.util.Vector _settingList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public FeatureSettings() - { - super(); - this._settingList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vSetting - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSetting(final jalview.binding.Setting vSetting) - throws java.lang.IndexOutOfBoundsException - { - this._settingList.addElement(vSetting); - } - - /** - * - * - * @param index - * @param vSetting - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSetting(final int index, - final jalview.binding.Setting vSetting) - throws java.lang.IndexOutOfBoundsException - { - this._settingList.add(index, vSetting); - } - - /** - * Method enumerateSetting. - * - * @return an Enumeration over all jalview.binding.Setting elements - */ - public java.util.Enumeration enumerateSetting() - { - return this._settingList.elements(); - } - - /** - * Method getSetting. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.Setting at the given index - */ - public jalview.binding.Setting getSetting(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._settingList.size()) - { - throw new IndexOutOfBoundsException( - "getSetting: Index value '" + index + "' not in range [0.." - + (this._settingList.size() - 1) + "]"); - } - - return (jalview.binding.Setting) _settingList.get(index); - } - - /** - * Method getSetting.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.Setting[] getSetting() - { - jalview.binding.Setting[] array = new jalview.binding.Setting[0]; - return (jalview.binding.Setting[]) this._settingList.toArray(array); - } - - /** - * Method getSettingCount. - * - * @return the size of this collection - */ - public int getSettingCount() - { - return this._settingList.size(); - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllSetting() - { - this._settingList.clear(); - } - - /** - * Method removeSetting. - * - * @param vSetting - * @return true if the object was removed from the collection. - */ - public boolean removeSetting(final jalview.binding.Setting vSetting) - { - boolean removed = _settingList.remove(vSetting); - return removed; - } - - /** - * Method removeSettingAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.Setting removeSettingAt(final int index) - { - java.lang.Object obj = this._settingList.remove(index); - return (jalview.binding.Setting) obj; - } - - /** - * - * - * @param index - * @param vSetting - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setSetting(final int index, - final jalview.binding.Setting vSetting) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._settingList.size()) - { - throw new IndexOutOfBoundsException( - "setSetting: Index value '" + index + "' not in range [0.." - + (this._settingList.size() - 1) + "]"); - } - - this._settingList.set(index, vSetting); - } - - /** - * - * - * @param vSettingArray - */ - public void setSetting(final jalview.binding.Setting[] vSettingArray) - { - // -- copy array - _settingList.clear(); - - for (int i = 0; i < vSettingArray.length; i++) - { - this._settingList.add(vSettingArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.FeatureSettings - */ - public static jalview.binding.FeatureSettings unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.FeatureSettings) Unmarshaller - .unmarshal(jalview.binding.FeatureSettings.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Features.java b/src/jalview/binding/Features.java deleted file mode 100644 index bf283df..0000000 --- a/src/jalview/binding/Features.java +++ /dev/null @@ -1,124 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Features. - * - * @version $Revision$ $Date$ - */ -public class Features extends Feature implements java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Features() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Feature - */ - public static jalview.binding.Feature unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Feature) Unmarshaller - .unmarshal(jalview.binding.Features.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Filter.java b/src/jalview/binding/Filter.java deleted file mode 100644 index 687ae91..0000000 --- a/src/jalview/binding/Filter.java +++ /dev/null @@ -1,180 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Filter. - * - * @version $Revision$ $Date$ - */ -public class Filter implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _featureType. - */ - private java.lang.String _featureType; - - /** - * Field _matcherSet. - */ - private jalview.binding.MatcherSet _matcherSet; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Filter() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'featureType'. - * - * @return the value of field 'FeatureType'. - */ - public java.lang.String getFeatureType() - { - return this._featureType; - } - - /** - * Returns the value of field 'matcherSet'. - * - * @return the value of field 'MatcherSet'. - */ - public jalview.binding.MatcherSet getMatcherSet() - { - return this._matcherSet; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'featureType'. - * - * @param featureType - * the value of field 'featureType'. - */ - public void setFeatureType(final java.lang.String featureType) - { - this._featureType = featureType; - } - - /** - * Sets the value of field 'matcherSet'. - * - * @param matcherSet - * the value of field 'matcherSet'. - */ - public void setMatcherSet(final jalview.binding.MatcherSet matcherSet) - { - this._matcherSet = matcherSet; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Filter - */ - public static jalview.binding.Filter unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Filter) Unmarshaller - .unmarshal(jalview.binding.Filter.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/JGroup.java b/src/jalview/binding/JGroup.java deleted file mode 100644 index 555c2fd..0000000 --- a/src/jalview/binding/JGroup.java +++ /dev/null @@ -1,761 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class 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(); - this._seqList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vSeq - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSeq(final int vSeq) - throws java.lang.IndexOutOfBoundsException - { - this._seqList.addElement(new java.lang.Integer(vSeq)); - } - - /** - * - * - * @param index - * @param vSeq - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSeq(final int index, final int vSeq) - throws java.lang.IndexOutOfBoundsException - { - this._seqList.add(index, new java.lang.Integer(vSeq)); - } - - /** - */ - public void deleteColourText() - { - this._has_colourText = false; - } - - /** - */ - public void deleteConsThreshold() - { - this._has_consThreshold = false; - } - - /** - */ - public void deleteDisplayBoxes() - { - this._has_displayBoxes = false; - } - - /** - */ - public void deleteDisplayText() - { - this._has_displayText = false; - } - - /** - */ - public void deleteEnd() - { - this._has_end = false; - } - - /** - */ - public void deleteOutlineColour() - { - this._has_outlineColour = false; - } - - /** - */ - public void deletePidThreshold() - { - this._has_pidThreshold = false; - } - - /** - */ - public void deleteStart() - { - this._has_start = false; - } - - /** - * Method enumerateSeq. - * - * @return an Enumeration over all int elements - */ - public java.util.Enumeration enumerateSeq() - { - return this._seqList.elements(); - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public java.lang.String getColour() - { - return this._colour; - } - - /** - * Returns the value of field 'colourText'. - * - * @return the value of field 'ColourText'. - */ - public boolean getColourText() - { - return this._colourText; - } - - /** - * Returns the value of field 'consThreshold'. - * - * @return the value of field 'ConsThreshold'. - */ - public int getConsThreshold() - { - return this._consThreshold; - } - - /** - * Returns the value of field 'displayBoxes'. - * - * @return the value of field 'DisplayBoxes'. - */ - public boolean getDisplayBoxes() - { - return this._displayBoxes; - } - - /** - * Returns the value of field 'displayText'. - * - * @return the value of field 'DisplayText'. - */ - public boolean getDisplayText() - { - return this._displayText; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd() - { - return this._end; - } - - /** - * Returns the value of field 'name'. - * - * @return the value of field 'Name'. - */ - public java.lang.String getName() - { - return this._name; - } - - /** - * Returns the value of field 'outlineColour'. - * - * @return the value of field 'OutlineColour'. - */ - public int getOutlineColour() - { - return this._outlineColour; - } - - /** - * Returns the value of field 'pidThreshold'. - * - * @return the value of field 'PidThreshold'. - */ - public int getPidThreshold() - { - return this._pidThreshold; - } - - /** - * Method getSeq. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the int at the given index - */ - public int getSeq(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._seqList.size()) - { - throw new IndexOutOfBoundsException("getSeq: Index value '" + index - + "' not in range [0.." + (this._seqList.size() - 1) + "]"); - } - - return ((java.lang.Integer) _seqList.get(index)).intValue(); - } - - /** - * Method getSeq.Returns the contents of the collection in an Array. - * - * @return this collection as an Array - */ - public int[] getSeq() - { - int size = this._seqList.size(); - int[] array = new int[size]; - java.util.Iterator iter = _seqList.iterator(); - for (int index = 0; index < size; index++) - { - array[index] = ((java.lang.Integer) iter.next()).intValue(); - } - return array; - } - - /** - * Method getSeqCount. - * - * @return the size of this collection - */ - public int getSeqCount() - { - return this._seqList.size(); - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart() - { - return this._start; - } - - /** - * Method hasColourText. - * - * @return true if at least one ColourText has been added - */ - public boolean hasColourText() - { - return this._has_colourText; - } - - /** - * Method hasConsThreshold. - * - * @return true if at least one ConsThreshold has been added - */ - public boolean hasConsThreshold() - { - return this._has_consThreshold; - } - - /** - * Method hasDisplayBoxes. - * - * @return true if at least one DisplayBoxes has been added - */ - public boolean hasDisplayBoxes() - { - return this._has_displayBoxes; - } - - /** - * Method hasDisplayText. - * - * @return true if at least one DisplayText has been added - */ - public boolean hasDisplayText() - { - return this._has_displayText; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd() - { - return this._has_end; - } - - /** - * Method hasOutlineColour. - * - * @return true if at least one OutlineColour has been added - */ - public boolean hasOutlineColour() - { - return this._has_outlineColour; - } - - /** - * Method hasPidThreshold. - * - * @return true if at least one PidThreshold has been added - */ - public boolean hasPidThreshold() - { - return this._has_pidThreshold; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart() - { - return this._has_start; - } - - /** - * Returns the value of field 'colourText'. - * - * @return the value of field 'ColourText'. - */ - public boolean isColourText() - { - return this._colourText; - } - - /** - * Returns the value of field 'displayBoxes'. - * - * @return the value of field 'DisplayBoxes'. - */ - public boolean isDisplayBoxes() - { - return this._displayBoxes; - } - - /** - * Returns the value of field 'displayText'. - * - * @return the value of field 'DisplayText'. - */ - public boolean isDisplayText() - { - return this._displayText; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllSeq() - { - this._seqList.clear(); - } - - /** - * Method removeSeq. - * - * @param vSeq - * @return true if the object was removed from the collection. - */ - public boolean removeSeq(final int vSeq) - { - boolean removed = _seqList.remove(new java.lang.Integer(vSeq)); - return removed; - } - - /** - * Method removeSeqAt. - * - * @param index - * @return the element removed from the collection - */ - public int removeSeqAt(final int index) - { - java.lang.Object obj = this._seqList.remove(index); - return ((java.lang.Integer) obj).intValue(); - } - - /** - * Sets the value of field 'colour'. - * - * @param colour - * the value of field 'colour'. - */ - public void setColour(final java.lang.String colour) - { - this._colour = colour; - } - - /** - * Sets the value of field 'colourText'. - * - * @param colourText - * the value of field 'colourText'. - */ - public void setColourText(final boolean colourText) - { - this._colourText = colourText; - this._has_colourText = true; - } - - /** - * Sets the value of field 'consThreshold'. - * - * @param consThreshold - * the value of field 'consThreshold'. - */ - public void setConsThreshold(final int consThreshold) - { - this._consThreshold = consThreshold; - this._has_consThreshold = true; - } - - /** - * Sets the value of field 'displayBoxes'. - * - * @param displayBoxes - * the value of field 'displayBoxes'. - */ - public void setDisplayBoxes(final boolean displayBoxes) - { - this._displayBoxes = displayBoxes; - this._has_displayBoxes = true; - } - - /** - * Sets the value of field 'displayText'. - * - * @param displayText - * the value of field 'displayText'. - */ - public void setDisplayText(final boolean displayText) - { - this._displayText = displayText; - this._has_displayText = true; - } - - /** - * Sets the value of field 'end'. - * - * @param end - * the value of field 'end'. - */ - public void setEnd(final int end) - { - this._end = end; - this._has_end = true; - } - - /** - * Sets the value of field 'name'. - * - * @param name - * the value of field 'name'. - */ - public void setName(final java.lang.String name) - { - this._name = name; - } - - /** - * Sets the value of field 'outlineColour'. - * - * @param outlineColour - * the value of field 'outlineColour'. - */ - public void setOutlineColour(final int outlineColour) - { - this._outlineColour = outlineColour; - this._has_outlineColour = true; - } - - /** - * Sets the value of field 'pidThreshold'. - * - * @param pidThreshold - * the value of field 'pidThreshold'. - */ - public void setPidThreshold(final int pidThreshold) - { - this._pidThreshold = pidThreshold; - this._has_pidThreshold = true; - } - - /** - * - * - * @param index - * @param vSeq - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setSeq(final int index, final int vSeq) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._seqList.size()) - { - throw new IndexOutOfBoundsException("setSeq: Index value '" + index - + "' not in range [0.." + (this._seqList.size() - 1) + "]"); - } - - this._seqList.set(index, new java.lang.Integer(vSeq)); - } - - /** - * - * - * @param vSeqArray - */ - public void setSeq(final int[] vSeqArray) - { - // -- copy array - _seqList.clear(); - - for (int i = 0; i < vSeqArray.length; i++) - { - this._seqList.add(new java.lang.Integer(vSeqArray[i])); - } - } - - /** - * Sets the value of field 'start'. - * - * @param start - * the value of field 'start'. - */ - public void setStart(final int start) - { - this._start = start; - this._has_start = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.JGroup - */ - public static jalview.binding.JGroup unmarshal( - final 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); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/JSeq.java b/src/jalview/binding/JSeq.java deleted file mode 100644 index 49334e1..0000000 --- a/src/jalview/binding/JSeq.java +++ /dev/null @@ -1,645 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class 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; - - /** - * Field _featuresList. - */ - private java.util.Vector _featuresList; - - /** - * Field _pdbidsList. - */ - private java.util.Vector _pdbidsList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JSeq() - { - super(); - this._featuresList = new java.util.Vector(); - this._pdbidsList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vFeatures - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addFeatures(final jalview.binding.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - this._featuresList.addElement(vFeatures); - } - - /** - * - * - * @param index - * @param vFeatures - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addFeatures(final int index, - final jalview.binding.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - this._featuresList.add(index, vFeatures); - } - - /** - * - * - * @param vPdbids - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addPdbids(final jalview.binding.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException - { - this._pdbidsList.addElement(vPdbids); - } - - /** - * - * - * @param index - * @param vPdbids - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addPdbids(final int index, - final jalview.binding.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException - { - this._pdbidsList.add(index, vPdbids); - } - - /** - */ - public void deleteColour() - { - this._has_colour = false; - } - - /** - */ - public void deleteEnd() - { - this._has_end = false; - } - - /** - */ - public void deleteId() - { - this._has_id = false; - } - - /** - */ - public void deleteStart() - { - this._has_start = false; - } - - /** - * Method enumerateFeatures. - * - * @return an Enumeration over all jalview.binding.Features elements - */ - public java.util.Enumeration enumerateFeatures() - { - return this._featuresList.elements(); - } - - /** - * Method enumeratePdbids. - * - * @return an Enumeration over all jalview.binding.Pdbids elements - */ - public java.util.Enumeration enumeratePdbids() - { - return this._pdbidsList.elements(); - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public int getColour() - { - return this._colour; - } - - /** - * Returns the value of field 'end'. - * - * @return the value of field 'End'. - */ - public int getEnd() - { - return this._end; - } - - /** - * Method getFeatures. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.Features at the given index - */ - public jalview.binding.Features getFeatures(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._featuresList.size()) - { - throw new IndexOutOfBoundsException( - "getFeatures: Index value '" + index + "' not in range [0.." - + (this._featuresList.size() - 1) + "]"); - } - - return (jalview.binding.Features) _featuresList.get(index); - } - - /** - * Method getFeatures.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.Features[] getFeatures() - { - jalview.binding.Features[] array = new jalview.binding.Features[0]; - return (jalview.binding.Features[]) this._featuresList.toArray(array); - } - - /** - * Method getFeaturesCount. - * - * @return the size of this collection - */ - public int getFeaturesCount() - { - return this._featuresList.size(); - } - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public int getId() - { - return this._id; - } - - /** - * Method getPdbids. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.Pdbids at the given index - */ - public jalview.binding.Pdbids getPdbids(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._pdbidsList.size()) - { - throw new IndexOutOfBoundsException( - "getPdbids: Index value '" + index + "' not in range [0.." - + (this._pdbidsList.size() - 1) + "]"); - } - - return (jalview.binding.Pdbids) _pdbidsList.get(index); - } - - /** - * Method getPdbids.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.Pdbids[] getPdbids() - { - jalview.binding.Pdbids[] array = new jalview.binding.Pdbids[0]; - return (jalview.binding.Pdbids[]) this._pdbidsList.toArray(array); - } - - /** - * Method getPdbidsCount. - * - * @return the size of this collection - */ - public int getPdbidsCount() - { - return this._pdbidsList.size(); - } - - /** - * Returns the value of field 'start'. - * - * @return the value of field 'Start'. - */ - public int getStart() - { - return this._start; - } - - /** - * Method hasColour. - * - * @return true if at least one Colour has been added - */ - public boolean hasColour() - { - return this._has_colour; - } - - /** - * Method hasEnd. - * - * @return true if at least one End has been added - */ - public boolean hasEnd() - { - return this._has_end; - } - - /** - * Method hasId. - * - * @return true if at least one Id has been added - */ - public boolean hasId() - { - return this._has_id; - } - - /** - * Method hasStart. - * - * @return true if at least one Start has been added - */ - public boolean hasStart() - { - return this._has_start; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllFeatures() - { - this._featuresList.clear(); - } - - /** - */ - public void removeAllPdbids() - { - this._pdbidsList.clear(); - } - - /** - * Method removeFeatures. - * - * @param vFeatures - * @return true if the object was removed from the collection. - */ - public boolean removeFeatures(final jalview.binding.Features vFeatures) - { - boolean removed = _featuresList.remove(vFeatures); - return removed; - } - - /** - * Method removeFeaturesAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.Features removeFeaturesAt(final int index) - { - java.lang.Object obj = this._featuresList.remove(index); - return (jalview.binding.Features) obj; - } - - /** - * Method removePdbids. - * - * @param vPdbids - * @return true if the object was removed from the collection. - */ - public boolean removePdbids(final jalview.binding.Pdbids vPdbids) - { - boolean removed = _pdbidsList.remove(vPdbids); - return removed; - } - - /** - * Method removePdbidsAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.Pdbids removePdbidsAt(final int index) - { - java.lang.Object obj = this._pdbidsList.remove(index); - return (jalview.binding.Pdbids) obj; - } - - /** - * Sets the value of field 'colour'. - * - * @param colour - * the value of field 'colour'. - */ - public void setColour(final int colour) - { - this._colour = colour; - this._has_colour = true; - } - - /** - * Sets the value of field 'end'. - * - * @param end - * the value of field 'end'. - */ - public void setEnd(final int end) - { - this._end = end; - this._has_end = true; - } - - /** - * - * - * @param index - * @param vFeatures - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setFeatures(final int index, - final jalview.binding.Features vFeatures) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._featuresList.size()) - { - throw new IndexOutOfBoundsException( - "setFeatures: Index value '" + index + "' not in range [0.." - + (this._featuresList.size() - 1) + "]"); - } - - this._featuresList.set(index, vFeatures); - } - - /** - * - * - * @param vFeaturesArray - */ - public void setFeatures(final jalview.binding.Features[] vFeaturesArray) - { - // -- copy array - _featuresList.clear(); - - for (int i = 0; i < vFeaturesArray.length; i++) - { - this._featuresList.add(vFeaturesArray[i]); - } - } - - /** - * Sets the value of field 'id'. - * - * @param id - * the value of field 'id'. - */ - public void setId(final int id) - { - this._id = id; - this._has_id = true; - } - - /** - * - * - * @param index - * @param vPdbids - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setPdbids(final int index, - final jalview.binding.Pdbids vPdbids) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._pdbidsList.size()) - { - throw new IndexOutOfBoundsException( - "setPdbids: Index value '" + index + "' not in range [0.." - + (this._pdbidsList.size() - 1) + "]"); - } - - this._pdbidsList.set(index, vPdbids); - } - - /** - * - * - * @param vPdbidsArray - */ - public void setPdbids(final jalview.binding.Pdbids[] vPdbidsArray) - { - // -- copy array - _pdbidsList.clear(); - - for (int i = 0; i < vPdbidsArray.length; i++) - { - this._pdbidsList.add(vPdbidsArray[i]); - } - } - - /** - * Sets the value of field 'start'. - * - * @param start - * the value of field 'start'. - */ - public void setStart(final int start) - { - this._start = start; - this._has_start = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.JSeq - */ - public static jalview.binding.JSeq unmarshal(final 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); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/JalviewModel.java b/src/jalview/binding/JalviewModel.java deleted file mode 100644 index 28645e0..0000000 --- a/src/jalview/binding/JalviewModel.java +++ /dev/null @@ -1,233 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class JalviewModel. - * - * @version $Revision$ $Date$ - */ -public class JalviewModel implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _creationDate. - */ - private java.util.Date _creationDate; - - /** - * Field _version. - */ - private java.lang.String _version; - - /** - * Field _vamsasModel. - */ - private jalview.binding.VamsasModel _vamsasModel; - - /** - * Field _jalviewModelSequence. - */ - private jalview.binding.JalviewModelSequence _jalviewModelSequence; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JalviewModel() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'creationDate'. - * - * @return the value of field 'CreationDate'. - */ - public java.util.Date getCreationDate() - { - return this._creationDate; - } - - /** - * Returns the value of field 'jalviewModelSequence'. - * - * @return the value of field 'JalviewModelSequence'. - */ - public jalview.binding.JalviewModelSequence getJalviewModelSequence() - { - return this._jalviewModelSequence; - } - - /** - * Returns the value of field 'vamsasModel'. - * - * @return the value of field 'VamsasModel'. - */ - public jalview.binding.VamsasModel getVamsasModel() - { - return this._vamsasModel; - } - - /** - * Returns the value of field 'version'. - * - * @return the value of field 'Version'. - */ - public java.lang.String getVersion() - { - return this._version; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'creationDate'. - * - * @param creationDate - * the value of field 'creationDate'. - */ - public void setCreationDate(final java.util.Date creationDate) - { - this._creationDate = creationDate; - } - - /** - * Sets the value of field 'jalviewModelSequence'. - * - * @param jalviewModelSequence - * the value of field 'jalviewModelSequence'. - */ - public void setJalviewModelSequence( - final jalview.binding.JalviewModelSequence jalviewModelSequence) - { - this._jalviewModelSequence = jalviewModelSequence; - } - - /** - * Sets the value of field 'vamsasModel'. - * - * @param vamsasModel - * the value of field 'vamsasModel'. - */ - public void setVamsasModel(final jalview.binding.VamsasModel vamsasModel) - { - this._vamsasModel = vamsasModel; - } - - /** - * Sets the value of field 'version'. - * - * @param version - * the value of field 'version'. - */ - public void setVersion(final java.lang.String version) - { - this._version = version; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.JalviewModel - */ - public static jalview.binding.JalviewModel unmarshal( - final 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); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/JalviewModelSequence.java b/src/jalview/binding/JalviewModelSequence.java deleted file mode 100644 index 9020ce2..0000000 --- a/src/jalview/binding/JalviewModelSequence.java +++ /dev/null @@ -1,955 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class JalviewModelSequence. - * - * @version $Revision$ $Date$ - */ -public class JalviewModelSequence implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _JSeqList. - */ - private java.util.Vector _JSeqList; - - /** - * Field _JGroupList. - */ - private java.util.Vector _JGroupList; - - /** - * Field _viewportList. - */ - private java.util.Vector _viewportList; - - /** - * Field _userColoursList. - */ - private java.util.Vector _userColoursList; - - /** - * Field _treeList. - */ - private java.util.Vector _treeList; - - /** - * Field _featureSettings. - */ - private jalview.binding.FeatureSettings _featureSettings; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JalviewModelSequence() - { - super(); - this._JSeqList = new java.util.Vector(); - this._JGroupList = new java.util.Vector(); - this._viewportList = new java.util.Vector(); - this._userColoursList = new java.util.Vector(); - this._treeList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vJGroup - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addJGroup(final jalview.binding.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException - { - this._JGroupList.addElement(vJGroup); - } - - /** - * - * - * @param index - * @param vJGroup - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addJGroup(final int index, - final jalview.binding.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException - { - this._JGroupList.add(index, vJGroup); - } - - /** - * - * - * @param vJSeq - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addJSeq(final jalview.binding.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException - { - this._JSeqList.addElement(vJSeq); - } - - /** - * - * - * @param index - * @param vJSeq - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addJSeq(final int index, final jalview.binding.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException - { - this._JSeqList.add(index, vJSeq); - } - - /** - * - * - * @param vTree - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addTree(final jalview.binding.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - this._treeList.addElement(vTree); - } - - /** - * - * - * @param index - * @param vTree - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addTree(final int index, final jalview.binding.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - this._treeList.add(index, vTree); - } - - /** - * - * - * @param vUserColours - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addUserColours(final jalview.binding.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException - { - this._userColoursList.addElement(vUserColours); - } - - /** - * - * - * @param index - * @param vUserColours - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addUserColours(final int index, - final jalview.binding.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException - { - this._userColoursList.add(index, vUserColours); - } - - /** - * - * - * @param vViewport - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addViewport(final jalview.binding.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - this._viewportList.addElement(vViewport); - } - - /** - * - * - * @param index - * @param vViewport - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addViewport(final int index, - final jalview.binding.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - this._viewportList.add(index, vViewport); - } - - /** - * Method enumerateJGroup. - * - * @return an Enumeration over all jalview.binding.JGroup elements - */ - public java.util.Enumeration enumerateJGroup() - { - return this._JGroupList.elements(); - } - - /** - * Method enumerateJSeq. - * - * @return an Enumeration over all jalview.binding.JSeq elements - */ - public java.util.Enumeration enumerateJSeq() - { - return this._JSeqList.elements(); - } - - /** - * Method enumerateTree. - * - * @return an Enumeration over all jalview.binding.Tree elements - */ - public java.util.Enumeration enumerateTree() - { - return this._treeList.elements(); - } - - /** - * Method enumerateUserColours. - * - * @return an Enumeration over all jalview.binding.UserColours elements - */ - public java.util.Enumeration enumerateUserColours() - { - return this._userColoursList.elements(); - } - - /** - * Method enumerateViewport. - * - * @return an Enumeration over all jalview.binding.Viewport elements - */ - public java.util.Enumeration enumerateViewport() - { - return this._viewportList.elements(); - } - - /** - * Returns the value of field 'featureSettings'. - * - * @return the value of field 'FeatureSettings'. - */ - public jalview.binding.FeatureSettings getFeatureSettings() - { - return this._featureSettings; - } - - /** - * Method getJGroup. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.JGroup at the given index - */ - public jalview.binding.JGroup getJGroup(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._JGroupList.size()) - { - throw new IndexOutOfBoundsException( - "getJGroup: Index value '" + index + "' not in range [0.." - + (this._JGroupList.size() - 1) + "]"); - } - - return (jalview.binding.JGroup) _JGroupList.get(index); - } - - /** - * Method getJGroup.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.JGroup[] getJGroup() - { - jalview.binding.JGroup[] array = new jalview.binding.JGroup[0]; - return (jalview.binding.JGroup[]) this._JGroupList.toArray(array); - } - - /** - * Method getJGroupCount. - * - * @return the size of this collection - */ - public int getJGroupCount() - { - return this._JGroupList.size(); - } - - /** - * Method getJSeq. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.JSeq at the given index - */ - public jalview.binding.JSeq getJSeq(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._JSeqList.size()) - { - throw new IndexOutOfBoundsException("getJSeq: Index value '" + index - + "' not in range [0.." + (this._JSeqList.size() - 1) + "]"); - } - - return (jalview.binding.JSeq) _JSeqList.get(index); - } - - /** - * Method getJSeq.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.JSeq[] getJSeq() - { - jalview.binding.JSeq[] array = new jalview.binding.JSeq[0]; - return (jalview.binding.JSeq[]) this._JSeqList.toArray(array); - } - - /** - * Method getJSeqCount. - * - * @return the size of this collection - */ - public int getJSeqCount() - { - return this._JSeqList.size(); - } - - /** - * Method getTree. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.Tree at the given index - */ - public jalview.binding.Tree getTree(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._treeList.size()) - { - throw new IndexOutOfBoundsException("getTree: Index value '" + index - + "' not in range [0.." + (this._treeList.size() - 1) + "]"); - } - - return (jalview.binding.Tree) _treeList.get(index); - } - - /** - * Method getTree.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.Tree[] getTree() - { - jalview.binding.Tree[] array = new jalview.binding.Tree[0]; - return (jalview.binding.Tree[]) this._treeList.toArray(array); - } - - /** - * Method getTreeCount. - * - * @return the size of this collection - */ - public int getTreeCount() - { - return this._treeList.size(); - } - - /** - * Method getUserColours. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.UserColours at the given index - */ - public jalview.binding.UserColours getUserColours(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._userColoursList.size()) - { - throw new IndexOutOfBoundsException("getUserColours: Index value '" - + index + "' not in range [0.." - + (this._userColoursList.size() - 1) + "]"); - } - - return (jalview.binding.UserColours) _userColoursList.get(index); - } - - /** - * Method getUserColours.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.UserColours[] getUserColours() - { - jalview.binding.UserColours[] array = new jalview.binding.UserColours[0]; - return (jalview.binding.UserColours[]) this._userColoursList - .toArray(array); - } - - /** - * Method getUserColoursCount. - * - * @return the size of this collection - */ - public int getUserColoursCount() - { - return this._userColoursList.size(); - } - - /** - * Method getViewport. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.Viewport at the given index - */ - public jalview.binding.Viewport getViewport(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._viewportList.size()) - { - throw new IndexOutOfBoundsException( - "getViewport: Index value '" + index + "' not in range [0.." - + (this._viewportList.size() - 1) + "]"); - } - - return (jalview.binding.Viewport) _viewportList.get(index); - } - - /** - * Method getViewport.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.Viewport[] getViewport() - { - jalview.binding.Viewport[] array = new jalview.binding.Viewport[0]; - return (jalview.binding.Viewport[]) this._viewportList.toArray(array); - } - - /** - * Method getViewportCount. - * - * @return the size of this collection - */ - public int getViewportCount() - { - return this._viewportList.size(); - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllJGroup() - { - this._JGroupList.clear(); - } - - /** - */ - public void removeAllJSeq() - { - this._JSeqList.clear(); - } - - /** - */ - public void removeAllTree() - { - this._treeList.clear(); - } - - /** - */ - public void removeAllUserColours() - { - this._userColoursList.clear(); - } - - /** - */ - public void removeAllViewport() - { - this._viewportList.clear(); - } - - /** - * Method removeJGroup. - * - * @param vJGroup - * @return true if the object was removed from the collection. - */ - public boolean removeJGroup(final jalview.binding.JGroup vJGroup) - { - boolean removed = _JGroupList.remove(vJGroup); - return removed; - } - - /** - * Method removeJGroupAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.JGroup removeJGroupAt(final int index) - { - java.lang.Object obj = this._JGroupList.remove(index); - return (jalview.binding.JGroup) obj; - } - - /** - * Method removeJSeq. - * - * @param vJSeq - * @return true if the object was removed from the collection. - */ - public boolean removeJSeq(final jalview.binding.JSeq vJSeq) - { - boolean removed = _JSeqList.remove(vJSeq); - return removed; - } - - /** - * Method removeJSeqAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.JSeq removeJSeqAt(final int index) - { - java.lang.Object obj = this._JSeqList.remove(index); - return (jalview.binding.JSeq) obj; - } - - /** - * Method removeTree. - * - * @param vTree - * @return true if the object was removed from the collection. - */ - public boolean removeTree(final jalview.binding.Tree vTree) - { - boolean removed = _treeList.remove(vTree); - return removed; - } - - /** - * Method removeTreeAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.Tree removeTreeAt(final int index) - { - java.lang.Object obj = this._treeList.remove(index); - return (jalview.binding.Tree) obj; - } - - /** - * Method removeUserColours. - * - * @param vUserColours - * @return true if the object was removed from the collection. - */ - public boolean removeUserColours( - final jalview.binding.UserColours vUserColours) - { - boolean removed = _userColoursList.remove(vUserColours); - return removed; - } - - /** - * Method removeUserColoursAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.UserColours removeUserColoursAt(final int index) - { - java.lang.Object obj = this._userColoursList.remove(index); - return (jalview.binding.UserColours) obj; - } - - /** - * Method removeViewport. - * - * @param vViewport - * @return true if the object was removed from the collection. - */ - public boolean removeViewport(final jalview.binding.Viewport vViewport) - { - boolean removed = _viewportList.remove(vViewport); - return removed; - } - - /** - * Method removeViewportAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.Viewport removeViewportAt(final int index) - { - java.lang.Object obj = this._viewportList.remove(index); - return (jalview.binding.Viewport) obj; - } - - /** - * Sets the value of field 'featureSettings'. - * - * @param featureSettings - * the value of field 'featureSettings'. - */ - public void setFeatureSettings( - final jalview.binding.FeatureSettings featureSettings) - { - this._featureSettings = featureSettings; - } - - /** - * - * - * @param index - * @param vJGroup - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setJGroup(final int index, - final jalview.binding.JGroup vJGroup) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._JGroupList.size()) - { - throw new IndexOutOfBoundsException( - "setJGroup: Index value '" + index + "' not in range [0.." - + (this._JGroupList.size() - 1) + "]"); - } - - this._JGroupList.set(index, vJGroup); - } - - /** - * - * - * @param vJGroupArray - */ - public void setJGroup(final jalview.binding.JGroup[] vJGroupArray) - { - // -- copy array - _JGroupList.clear(); - - for (int i = 0; i < vJGroupArray.length; i++) - { - this._JGroupList.add(vJGroupArray[i]); - } - } - - /** - * - * - * @param index - * @param vJSeq - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setJSeq(final int index, final jalview.binding.JSeq vJSeq) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._JSeqList.size()) - { - throw new IndexOutOfBoundsException("setJSeq: Index value '" + index - + "' not in range [0.." + (this._JSeqList.size() - 1) + "]"); - } - - this._JSeqList.set(index, vJSeq); - } - - /** - * - * - * @param vJSeqArray - */ - public void setJSeq(final jalview.binding.JSeq[] vJSeqArray) - { - // -- copy array - _JSeqList.clear(); - - for (int i = 0; i < vJSeqArray.length; i++) - { - this._JSeqList.add(vJSeqArray[i]); - } - } - - /** - * - * - * @param index - * @param vTree - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setTree(final int index, final jalview.binding.Tree vTree) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._treeList.size()) - { - throw new IndexOutOfBoundsException("setTree: Index value '" + index - + "' not in range [0.." + (this._treeList.size() - 1) + "]"); - } - - this._treeList.set(index, vTree); - } - - /** - * - * - * @param vTreeArray - */ - public void setTree(final jalview.binding.Tree[] vTreeArray) - { - // -- copy array - _treeList.clear(); - - for (int i = 0; i < vTreeArray.length; i++) - { - this._treeList.add(vTreeArray[i]); - } - } - - /** - * - * - * @param index - * @param vUserColours - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setUserColours(final int index, - final jalview.binding.UserColours vUserColours) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._userColoursList.size()) - { - throw new IndexOutOfBoundsException("setUserColours: Index value '" - + index + "' not in range [0.." - + (this._userColoursList.size() - 1) + "]"); - } - - this._userColoursList.set(index, vUserColours); - } - - /** - * - * - * @param vUserColoursArray - */ - public void setUserColours( - final jalview.binding.UserColours[] vUserColoursArray) - { - // -- copy array - _userColoursList.clear(); - - for (int i = 0; i < vUserColoursArray.length; i++) - { - this._userColoursList.add(vUserColoursArray[i]); - } - } - - /** - * - * - * @param index - * @param vViewport - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setViewport(final int index, - final jalview.binding.Viewport vViewport) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._viewportList.size()) - { - throw new IndexOutOfBoundsException( - "setViewport: Index value '" + index + "' not in range [0.." - + (this._viewportList.size() - 1) + "]"); - } - - this._viewportList.set(index, vViewport); - } - - /** - * - * - * @param vViewportArray - */ - public void setViewport(final jalview.binding.Viewport[] vViewportArray) - { - // -- copy array - _viewportList.clear(); - - for (int i = 0; i < vViewportArray.length; i++) - { - this._viewportList.add(vViewportArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.JalviewModelSequence - */ - public static jalview.binding.JalviewModelSequence unmarshal( - final 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); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/JalviewUserColours.java b/src/jalview/binding/JalviewUserColours.java deleted file mode 100644 index 67ee5a2..0000000 --- a/src/jalview/binding/JalviewUserColours.java +++ /dev/null @@ -1,503 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class JalviewUserColours. - * - * @version $Revision$ $Date$ - */ -public class JalviewUserColours implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _schemeName. - */ - private java.lang.String _schemeName; - - /** - * Jalview colour scheme document version. - * - */ - private java.lang.String _version; - - /** - * Field _colourList. - */ - private java.util.Vector _colourList; - - /** - * Field _filterList. - */ - private java.util.Vector _filterList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public JalviewUserColours() - { - super(); - this._colourList = new java.util.Vector(); - this._filterList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vColour - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addColour(final Colour vColour) - throws java.lang.IndexOutOfBoundsException - { - this._colourList.addElement(vColour); - } - - /** - * - * - * @param index - * @param vColour - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addColour(final int index, final Colour vColour) - throws java.lang.IndexOutOfBoundsException - { - this._colourList.add(index, vColour); - } - - /** - * - * - * @param vFilter - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addFilter(final Filter vFilter) - throws java.lang.IndexOutOfBoundsException - { - this._filterList.addElement(vFilter); - } - - /** - * - * - * @param index - * @param vFilter - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addFilter(final int index, final Filter vFilter) - throws java.lang.IndexOutOfBoundsException - { - this._filterList.add(index, vFilter); - } - - /** - * Method enumerateColour. - * - * @return an Enumeration over all Colour elements - */ - public java.util.Enumeration enumerateColour() - { - return this._colourList.elements(); - } - - /** - * Method enumerateFilter. - * - * @return an Enumeration over all Filter elements - */ - public java.util.Enumeration enumerateFilter() - { - return this._filterList.elements(); - } - - /** - * Method getColour. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the Colour at the given index - */ - public Colour getColour(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._colourList.size()) - { - throw new IndexOutOfBoundsException( - "getColour: Index value '" + index + "' not in range [0.." - + (this._colourList.size() - 1) + "]"); - } - - return (Colour) _colourList.get(index); - } - - /** - * Method getColour.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public Colour[] getColour() - { - Colour[] array = new Colour[0]; - return (Colour[]) this._colourList.toArray(array); - } - - /** - * Method getColourCount. - * - * @return the size of this collection - */ - public int getColourCount() - { - return this._colourList.size(); - } - - /** - * Method getFilter. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the Filter at the given index - */ - public Filter getFilter(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._filterList.size()) - { - throw new IndexOutOfBoundsException( - "getFilter: Index value '" + index + "' not in range [0.." - + (this._filterList.size() - 1) + "]"); - } - - return (Filter) _filterList.get(index); - } - - /** - * Method getFilter.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public Filter[] getFilter() - { - Filter[] array = new Filter[0]; - return (Filter[]) this._filterList.toArray(array); - } - - /** - * Method getFilterCount. - * - * @return the size of this collection - */ - public int getFilterCount() - { - return this._filterList.size(); - } - - /** - * Returns the value of field 'schemeName'. - * - * @return the value of field 'SchemeName'. - */ - public java.lang.String getSchemeName() - { - return this._schemeName; - } - - /** - * Returns the value of field 'version'. The field 'version' has the following - * description: Jalview colour scheme document version. - * - * - * @return the value of field 'Version'. - */ - public java.lang.String getVersion() - { - return this._version; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllColour() - { - this._colourList.clear(); - } - - /** - */ - public void removeAllFilter() - { - this._filterList.clear(); - } - - /** - * Method removeColour. - * - * @param vColour - * @return true if the object was removed from the collection. - */ - public boolean removeColour(final Colour vColour) - { - boolean removed = _colourList.remove(vColour); - return removed; - } - - /** - * Method removeColourAt. - * - * @param index - * @return the element removed from the collection - */ - public Colour removeColourAt(final int index) - { - java.lang.Object obj = this._colourList.remove(index); - return (Colour) obj; - } - - /** - * Method removeFilter. - * - * @param vFilter - * @return true if the object was removed from the collection. - */ - public boolean removeFilter(final Filter vFilter) - { - boolean removed = _filterList.remove(vFilter); - return removed; - } - - /** - * Method removeFilterAt. - * - * @param index - * @return the element removed from the collection - */ - public Filter removeFilterAt(final int index) - { - java.lang.Object obj = this._filterList.remove(index); - return (Filter) obj; - } - - /** - * - * - * @param index - * @param vColour - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setColour(final int index, final Colour vColour) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._colourList.size()) - { - throw new IndexOutOfBoundsException( - "setColour: Index value '" + index + "' not in range [0.." - + (this._colourList.size() - 1) + "]"); - } - - this._colourList.set(index, vColour); - } - - /** - * - * - * @param vColourArray - */ - public void setColour(final Colour[] vColourArray) - { - // -- copy array - _colourList.clear(); - - for (int i = 0; i < vColourArray.length; i++) - { - this._colourList.add(vColourArray[i]); - } - } - - /** - * - * - * @param index - * @param vFilter - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setFilter(final int index, final Filter vFilter) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._filterList.size()) - { - throw new IndexOutOfBoundsException( - "setFilter: Index value '" + index + "' not in range [0.." - + (this._filterList.size() - 1) + "]"); - } - - this._filterList.set(index, vFilter); - } - - /** - * - * - * @param vFilterArray - */ - public void setFilter(final Filter[] vFilterArray) - { - // -- copy array - _filterList.clear(); - - for (int i = 0; i < vFilterArray.length; i++) - { - this._filterList.add(vFilterArray[i]); - } - } - - /** - * Sets the value of field 'schemeName'. - * - * @param schemeName - * the value of field 'schemeName'. - */ - public void setSchemeName(final java.lang.String schemeName) - { - this._schemeName = schemeName; - } - - /** - * Sets the value of field 'version'. The field 'version' has the following - * description: Jalview colour scheme document version. - * - * - * @param version - * the value of field 'version'. - */ - public void setVersion(final java.lang.String version) - { - this._version = version; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.JalviewUserColours - */ - public static jalview.binding.JalviewUserColours unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.JalviewUserColours) Unmarshaller - .unmarshal(jalview.binding.JalviewUserColours.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/MatchCondition.java b/src/jalview/binding/MatchCondition.java deleted file mode 100644 index 44a3d3e..0000000 --- a/src/jalview/binding/MatchCondition.java +++ /dev/null @@ -1,125 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class MatchCondition. - * - * @version $Revision$ $Date$ - */ -public class MatchCondition extends FeatureMatcher - implements java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MatchCondition() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.FeatureMatcher - */ - public static jalview.binding.FeatureMatcher unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.FeatureMatcher) Unmarshaller - .unmarshal(jalview.binding.MatchCondition.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/MatcherSet.java b/src/jalview/binding/MatcherSet.java deleted file mode 100644 index 756d93a..0000000 --- a/src/jalview/binding/MatcherSet.java +++ /dev/null @@ -1,125 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class MatcherSet. - * - * @version $Revision$ $Date$ - */ -public class MatcherSet extends FeatureMatcherSet - implements java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public MatcherSet() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.FeatureMatcherSet - */ - public static jalview.binding.FeatureMatcherSet unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.FeatureMatcherSet) Unmarshaller - .unmarshal(jalview.binding.MatcherSet.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Pdbentry.java b/src/jalview/binding/Pdbentry.java deleted file mode 100644 index 77bb446..0000000 --- a/src/jalview/binding/Pdbentry.java +++ /dev/null @@ -1,344 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Pdbentry. - * - * @version $Revision$ $Date$ - */ -public class Pdbentry implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _type. - */ - private java.lang.String _type; - - /** - * Field _items. - */ - private java.util.Vector _items; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Pdbentry() - { - super(); - this._items = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vPdbentryItem - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addPdbentryItem( - final jalview.binding.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - this._items.addElement(vPdbentryItem); - } - - /** - * - * - * @param index - * @param vPdbentryItem - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addPdbentryItem(final int index, - final jalview.binding.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - this._items.add(index, vPdbentryItem); - } - - /** - * Method enumeratePdbentryItem. - * - * @return an Enumeration over all jalview.binding.PdbentryItem elements - */ - public java.util.Enumeration enumeratePdbentryItem() - { - return this._items.elements(); - } - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * Method getPdbentryItem. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.PdbentryItem at the given index - */ - public jalview.binding.PdbentryItem getPdbentryItem(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._items.size()) - { - throw new IndexOutOfBoundsException("getPdbentryItem: Index value '" - + index + "' not in range [0.." + (this._items.size() - 1) - + "]"); - } - - return (jalview.binding.PdbentryItem) _items.get(index); - } - - /** - * Method getPdbentryItem.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.PdbentryItem[] getPdbentryItem() - { - jalview.binding.PdbentryItem[] array = new jalview.binding.PdbentryItem[0]; - return (jalview.binding.PdbentryItem[]) this._items.toArray(array); - } - - /** - * Method getPdbentryItemCount. - * - * @return the size of this collection - */ - public int getPdbentryItemCount() - { - return this._items.size(); - } - - /** - * Returns the value of field 'type'. - * - * @return the value of field 'Type'. - */ - public java.lang.String getType() - { - return this._type; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllPdbentryItem() - { - this._items.clear(); - } - - /** - * Method removePdbentryItem. - * - * @param vPdbentryItem - * @return true if the object was removed from the collection. - */ - public boolean removePdbentryItem( - final jalview.binding.PdbentryItem vPdbentryItem) - { - boolean removed = _items.remove(vPdbentryItem); - return removed; - } - - /** - * Method removePdbentryItemAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.PdbentryItem removePdbentryItemAt(final int index) - { - java.lang.Object obj = this._items.remove(index); - return (jalview.binding.PdbentryItem) obj; - } - - /** - * Sets the value of field 'id'. - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * - * - * @param index - * @param vPdbentryItem - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setPdbentryItem(final int index, - final jalview.binding.PdbentryItem vPdbentryItem) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._items.size()) - { - throw new IndexOutOfBoundsException("setPdbentryItem: Index value '" - + index + "' not in range [0.." + (this._items.size() - 1) - + "]"); - } - - this._items.set(index, vPdbentryItem); - } - - /** - * - * - * @param vPdbentryItemArray - */ - public void setPdbentryItem( - final jalview.binding.PdbentryItem[] vPdbentryItemArray) - { - // -- copy array - _items.clear(); - - for (int i = 0; i < vPdbentryItemArray.length; i++) - { - this._items.add(vPdbentryItemArray[i]); - } - } - - /** - * Sets the value of field 'type'. - * - * @param type - * the value of field 'type'. - */ - public void setType(final java.lang.String type) - { - this._type = type; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Pdbentry - */ - public static jalview.binding.Pdbentry unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Pdbentry) Unmarshaller - .unmarshal(jalview.binding.Pdbentry.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/PdbentryItem.java b/src/jalview/binding/PdbentryItem.java deleted file mode 100644 index 30a0512..0000000 --- a/src/jalview/binding/PdbentryItem.java +++ /dev/null @@ -1,196 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -/** - * Class PdbentryItem. - * - * @version $Revision$ $Date$ - */ -public class PdbentryItem implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _propertyList. - */ - private java.util.Vector _propertyList; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public PdbentryItem() - { - super(); - this._propertyList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vProperty - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addProperty(final jalview.binding.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - this._propertyList.addElement(vProperty); - } - - /** - * - * - * @param index - * @param vProperty - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addProperty(final int index, - final jalview.binding.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - this._propertyList.add(index, vProperty); - } - - /** - * Method enumerateProperty. - * - * @return an Enumeration over all jalview.binding.Property elements - */ - public java.util.Enumeration enumerateProperty() - { - return this._propertyList.elements(); - } - - /** - * Method getProperty. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.Property at the given index - */ - public jalview.binding.Property getProperty(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._propertyList.size()) - { - throw new IndexOutOfBoundsException( - "getProperty: Index value '" + index + "' not in range [0.." - + (this._propertyList.size() - 1) + "]"); - } - - return (jalview.binding.Property) _propertyList.get(index); - } - - /** - * Method getProperty.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.Property[] getProperty() - { - jalview.binding.Property[] array = new jalview.binding.Property[0]; - return (jalview.binding.Property[]) this._propertyList.toArray(array); - } - - /** - * Method getPropertyCount. - * - * @return the size of this collection - */ - public int getPropertyCount() - { - return this._propertyList.size(); - } - - /** - */ - public void removeAllProperty() - { - this._propertyList.clear(); - } - - /** - * Method removeProperty. - * - * @param vProperty - * @return true if the object was removed from the collection. - */ - public boolean removeProperty(final jalview.binding.Property vProperty) - { - boolean removed = _propertyList.remove(vProperty); - return removed; - } - - /** - * Method removePropertyAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.Property removePropertyAt(final int index) - { - java.lang.Object obj = this._propertyList.remove(index); - return (jalview.binding.Property) obj; - } - - /** - * - * - * @param index - * @param vProperty - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setProperty(final int index, - final jalview.binding.Property vProperty) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._propertyList.size()) - { - throw new IndexOutOfBoundsException( - "setProperty: Index value '" + index + "' not in range [0.." - + (this._propertyList.size() - 1) + "]"); - } - - this._propertyList.set(index, vProperty); - } - - /** - * - * - * @param vPropertyArray - */ - public void setProperty(final jalview.binding.Property[] vPropertyArray) - { - // -- copy array - _propertyList.clear(); - - for (int i = 0; i < vPropertyArray.length; i++) - { - this._propertyList.add(vPropertyArray[i]); - } - } - -} diff --git a/src/jalview/binding/Pdbids.java b/src/jalview/binding/Pdbids.java deleted file mode 100644 index 79cae6c..0000000 --- a/src/jalview/binding/Pdbids.java +++ /dev/null @@ -1,124 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Pdbids. - * - * @version $Revision$ $Date$ - */ -public class Pdbids extends Pdbentry implements java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Pdbids() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Pdbentry - */ - public static jalview.binding.Pdbentry unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Pdbentry) Unmarshaller - .unmarshal(jalview.binding.Pdbids.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Property.java b/src/jalview/binding/Property.java deleted file mode 100644 index 5823fed..0000000 --- a/src/jalview/binding/Property.java +++ /dev/null @@ -1,180 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Property. - * - * @version $Revision$ $Date$ - */ -public class Property implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _name. - */ - private java.lang.String _name; - - /** - * Field _value. - */ - private java.lang.String _value; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Property() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'name'. - * - * @return the value of field 'Name'. - */ - public java.lang.String getName() - { - return this._name; - } - - /** - * Returns the value of field 'value'. - * - * @return the value of field 'Value'. - */ - public java.lang.String getValue() - { - return this._value; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'name'. - * - * @param name - * the value of field 'name'. - */ - public void setName(final java.lang.String name) - { - this._name = name; - } - - /** - * Sets the value of field 'value'. - * - * @param value - * the value of field 'value'. - */ - public void setValue(final java.lang.String value) - { - this._value = value; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Property - */ - public static jalview.binding.Property unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Property) Unmarshaller - .unmarshal(jalview.binding.Property.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Sequence.java b/src/jalview/binding/Sequence.java deleted file mode 100644 index 845f224..0000000 --- a/src/jalview/binding/Sequence.java +++ /dev/null @@ -1,124 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Sequence. - * - * @version $Revision$ $Date$ - */ -public class Sequence extends SequenceType implements java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Sequence() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.SequenceType - */ - public static jalview.binding.SequenceType unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.SequenceType) Unmarshaller - .unmarshal(jalview.binding.Sequence.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/SequenceSet.java b/src/jalview/binding/SequenceSet.java deleted file mode 100644 index 3d81bae..0000000 --- a/src/jalview/binding/SequenceSet.java +++ /dev/null @@ -1,538 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class 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(); - this._sequenceList = new java.util.Vector(); - this._annotationList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vAnnotation - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAnnotation(final jalview.binding.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException - { - this._annotationList.addElement(vAnnotation); - } - - /** - * - * - * @param index - * @param vAnnotation - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAnnotation(final int index, - final jalview.binding.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException - { - this._annotationList.add(index, vAnnotation); - } - - /** - * - * - * @param vSequence - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSequence(final jalview.binding.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - this._sequenceList.addElement(vSequence); - } - - /** - * - * - * @param index - * @param vSequence - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSequence(final int index, - final jalview.binding.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - this._sequenceList.add(index, vSequence); - } - - /** - */ - public void deleteAligned() - { - this._has_aligned = false; - } - - /** - * Method enumerateAnnotation. - * - * @return an Enumeration over all jalview.binding.Annotation elements - */ - public java.util.Enumeration enumerateAnnotation() - { - return this._annotationList.elements(); - } - - /** - * Method enumerateSequence. - * - * @return an Enumeration over all jalview.binding.Sequence elements - */ - public java.util.Enumeration enumerateSequence() - { - return this._sequenceList.elements(); - } - - /** - * Returns the value of field 'aligned'. - * - * @return the value of field 'Aligned'. - */ - public boolean getAligned() - { - return this._aligned; - } - - /** - * Method getAnnotation. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.Annotation at the given index - */ - public jalview.binding.Annotation getAnnotation(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._annotationList.size()) - { - throw new IndexOutOfBoundsException( - "getAnnotation: Index value '" + index + "' not in range [0.." - + (this._annotationList.size() - 1) + "]"); - } - - return (jalview.binding.Annotation) _annotationList.get(index); - } - - /** - * Method getAnnotation.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.Annotation[] getAnnotation() - { - jalview.binding.Annotation[] array = new jalview.binding.Annotation[0]; - return (jalview.binding.Annotation[]) this._annotationList - .toArray(array); - } - - /** - * Method getAnnotationCount. - * - * @return the size of this collection - */ - public int getAnnotationCount() - { - return this._annotationList.size(); - } - - /** - * Returns the value of field 'gapChar'. - * - * @return the value of field 'GapChar'. - */ - public java.lang.String getGapChar() - { - return this._gapChar; - } - - /** - * Method getSequence. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the jalview.binding.Sequence at the given index - */ - public jalview.binding.Sequence getSequence(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._sequenceList.size()) - { - throw new IndexOutOfBoundsException( - "getSequence: Index value '" + index + "' not in range [0.." - + (this._sequenceList.size() - 1) + "]"); - } - - return (jalview.binding.Sequence) _sequenceList.get(index); - } - - /** - * Method getSequence.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public jalview.binding.Sequence[] getSequence() - { - jalview.binding.Sequence[] array = new jalview.binding.Sequence[0]; - return (jalview.binding.Sequence[]) this._sequenceList.toArray(array); - } - - /** - * Method getSequenceCount. - * - * @return the size of this collection - */ - public int getSequenceCount() - { - return this._sequenceList.size(); - } - - /** - * Method hasAligned. - * - * @return true if at least one Aligned has been added - */ - public boolean hasAligned() - { - return this._has_aligned; - } - - /** - * Returns the value of field 'aligned'. - * - * @return the value of field 'Aligned'. - */ - public boolean isAligned() - { - return this._aligned; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - */ - public void removeAllAnnotation() - { - this._annotationList.clear(); - } - - /** - */ - public void removeAllSequence() - { - this._sequenceList.clear(); - } - - /** - * Method removeAnnotation. - * - * @param vAnnotation - * @return true if the object was removed from the collection. - */ - public boolean removeAnnotation( - final jalview.binding.Annotation vAnnotation) - { - boolean removed = _annotationList.remove(vAnnotation); - return removed; - } - - /** - * Method removeAnnotationAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.Annotation removeAnnotationAt(final int index) - { - java.lang.Object obj = this._annotationList.remove(index); - return (jalview.binding.Annotation) obj; - } - - /** - * Method removeSequence. - * - * @param vSequence - * @return true if the object was removed from the collection. - */ - public boolean removeSequence(final jalview.binding.Sequence vSequence) - { - boolean removed = _sequenceList.remove(vSequence); - return removed; - } - - /** - * Method removeSequenceAt. - * - * @param index - * @return the element removed from the collection - */ - public jalview.binding.Sequence removeSequenceAt(final int index) - { - java.lang.Object obj = this._sequenceList.remove(index); - return (jalview.binding.Sequence) obj; - } - - /** - * Sets the value of field 'aligned'. - * - * @param aligned - * the value of field 'aligned'. - */ - public void setAligned(final boolean aligned) - { - this._aligned = aligned; - this._has_aligned = true; - } - - /** - * - * - * @param index - * @param vAnnotation - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setAnnotation(final int index, - final jalview.binding.Annotation vAnnotation) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._annotationList.size()) - { - throw new IndexOutOfBoundsException( - "setAnnotation: Index value '" + index + "' not in range [0.." - + (this._annotationList.size() - 1) + "]"); - } - - this._annotationList.set(index, vAnnotation); - } - - /** - * - * - * @param vAnnotationArray - */ - public void setAnnotation( - final jalview.binding.Annotation[] vAnnotationArray) - { - // -- copy array - _annotationList.clear(); - - for (int i = 0; i < vAnnotationArray.length; i++) - { - this._annotationList.add(vAnnotationArray[i]); - } - } - - /** - * Sets the value of field 'gapChar'. - * - * @param gapChar - * the value of field 'gapChar'. - */ - public void setGapChar(final java.lang.String gapChar) - { - this._gapChar = gapChar; - } - - /** - * - * - * @param index - * @param vSequence - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void setSequence(final int index, - final jalview.binding.Sequence vSequence) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._sequenceList.size()) - { - throw new IndexOutOfBoundsException( - "setSequence: Index value '" + index + "' not in range [0.." - + (this._sequenceList.size() - 1) + "]"); - } - - this._sequenceList.set(index, vSequence); - } - - /** - * - * - * @param vSequenceArray - */ - public void setSequence(final jalview.binding.Sequence[] vSequenceArray) - { - // -- copy array - _sequenceList.clear(); - - for (int i = 0; i < vSequenceArray.length; i++) - { - this._sequenceList.add(vSequenceArray[i]); - } - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.SequenceSet - */ - public static jalview.binding.SequenceSet unmarshal( - final 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); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/SequenceType.java b/src/jalview/binding/SequenceType.java deleted file mode 100644 index 7f10bca..0000000 --- a/src/jalview/binding/SequenceType.java +++ /dev/null @@ -1,206 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class 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(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * Returns the value of field 'name'. - * - * @return the value of field 'Name'. - */ - public java.lang.String getName() - { - return this._name; - } - - /** - * Returns the value of field 'sequence'. - * - * @return the value of field 'Sequence'. - */ - public java.lang.String getSequence() - { - return this._sequence; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'id'. - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * Sets the value of field 'name'. - * - * @param name - * the value of field 'name'. - */ - public void setName(final java.lang.String name) - { - this._name = name; - } - - /** - * Sets the value of field 'sequence'. - * - * @param sequence - * the value of field 'sequence'. - */ - public void setSequence(final java.lang.String sequence) - { - this._sequence = sequence; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.SequenceType - */ - public static jalview.binding.SequenceType unmarshal( - final 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); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Setting.java b/src/jalview/binding/Setting.java deleted file mode 100644 index d098303..0000000 --- a/src/jalview/binding/Setting.java +++ /dev/null @@ -1,262 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Setting. - * - * @version $Revision$ $Date$ - */ -public class Setting implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _type. - */ - private java.lang.String _type; - - /** - * Field _colour. - */ - private int _colour; - - /** - * keeps track of state for field: _colour - */ - private boolean _has_colour; - - /** - * Field _display. - */ - private boolean _display; - - /** - * keeps track of state for field: _display - */ - private boolean _has_display; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Setting() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteColour() - { - this._has_colour = false; - } - - /** - */ - public void deleteDisplay() - { - this._has_display = false; - } - - /** - * Returns the value of field 'colour'. - * - * @return the value of field 'Colour'. - */ - public int getColour() - { - return this._colour; - } - - /** - * Returns the value of field 'display'. - * - * @return the value of field 'Display'. - */ - public boolean getDisplay() - { - return this._display; - } - - /** - * Returns the value of field 'type'. - * - * @return the value of field 'Type'. - */ - public java.lang.String getType() - { - return this._type; - } - - /** - * Method hasColour. - * - * @return true if at least one Colour has been added - */ - public boolean hasColour() - { - return this._has_colour; - } - - /** - * Method hasDisplay. - * - * @return true if at least one Display has been added - */ - public boolean hasDisplay() - { - return this._has_display; - } - - /** - * Returns the value of field 'display'. - * - * @return the value of field 'Display'. - */ - public boolean isDisplay() - { - return this._display; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'colour'. - * - * @param colour - * the value of field 'colour'. - */ - public void setColour(final int colour) - { - this._colour = colour; - this._has_colour = true; - } - - /** - * Sets the value of field 'display'. - * - * @param display - * the value of field 'display'. - */ - public void setDisplay(final boolean display) - { - this._display = display; - this._has_display = true; - } - - /** - * Sets the value of field 'type'. - * - * @param type - * the value of field 'type'. - */ - public void setType(final java.lang.String type) - { - this._type = type; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Setting - */ - public static jalview.binding.Setting unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Setting) Unmarshaller - .unmarshal(jalview.binding.Setting.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/Tree.java b/src/jalview/binding/Tree.java deleted file mode 100644 index 7005c93..0000000 --- a/src/jalview/binding/Tree.java +++ /dev/null @@ -1,843 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class Tree. - * - * @version $Revision$ $Date$ - */ -public class Tree implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * 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 _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 _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; - - /** - * Field _threshold. - */ - private float _threshold; - - /** - * keeps track of state for field: _threshold - */ - private boolean _has_threshold; - - /** - * Field _showBootstrap. - */ - private boolean _showBootstrap; - - /** - * keeps track of state for field: _showBootstrap - */ - private boolean _has_showBootstrap; - - /** - * Field _showDistances. - */ - private boolean _showDistances; - - /** - * keeps track of state for field: _showDistances - */ - private boolean _has_showDistances; - - /** - * Field _markUnlinked. - */ - private boolean _markUnlinked; - - /** - * keeps track of state for field: _markUnlinked - */ - private boolean _has_markUnlinked; - - /** - * Field _fitToWindow. - */ - private boolean _fitToWindow; - - /** - * keeps track of state for field: _fitToWindow - */ - private boolean _has_fitToWindow; - - /** - * Field _currentTree. - */ - private boolean _currentTree; - - /** - * keeps track of state for field: _currentTree - */ - private boolean _has_currentTree; - - /** - * Field _title. - */ - private java.lang.String _title; - - /** - * Field _newick. - */ - private java.lang.String _newick; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public Tree() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteCurrentTree() - { - this._has_currentTree = false; - } - - /** - */ - public void deleteFitToWindow() - { - this._has_fitToWindow = false; - } - - /** - */ - public void deleteFontSize() - { - this._has_fontSize = false; - } - - /** - */ - public void deleteFontStyle() - { - this._has_fontStyle = false; - } - - /** - */ - public void deleteHeight() - { - this._has_height = false; - } - - /** - */ - public void deleteMarkUnlinked() - { - this._has_markUnlinked = false; - } - - /** - */ - public void deleteShowBootstrap() - { - this._has_showBootstrap = false; - } - - /** - */ - public void deleteShowDistances() - { - this._has_showDistances = false; - } - - /** - */ - public void deleteThreshold() - { - this._has_threshold = false; - } - - /** - */ - public void deleteWidth() - { - this._has_width = false; - } - - /** - */ - public void deleteXpos() - { - this._has_xpos = false; - } - - /** - */ - public void deleteYpos() - { - this._has_ypos = false; - } - - /** - * Returns the value of field 'currentTree'. - * - * @return the value of field 'CurrentTree'. - */ - public boolean getCurrentTree() - { - return this._currentTree; - } - - /** - * Returns the value of field 'fitToWindow'. - * - * @return the value of field 'FitToWindow'. - */ - public boolean getFitToWindow() - { - return this._fitToWindow; - } - - /** - * Returns the value of field 'fontName'. - * - * @return the value of field 'FontName'. - */ - public java.lang.String getFontName() - { - return this._fontName; - } - - /** - * Returns the value of field 'fontSize'. - * - * @return the value of field 'FontSize'. - */ - public int getFontSize() - { - return this._fontSize; - } - - /** - * Returns the value of field 'fontStyle'. - * - * @return the value of field 'FontStyle'. - */ - public int getFontStyle() - { - return this._fontStyle; - } - - /** - * Returns the value of field 'height'. - * - * @return the value of field 'Height'. - */ - public int getHeight() - { - return this._height; - } - - /** - * Returns the value of field 'markUnlinked'. - * - * @return the value of field 'MarkUnlinked'. - */ - public boolean getMarkUnlinked() - { - return this._markUnlinked; - } - - /** - * Returns the value of field 'newick'. - * - * @return the value of field 'Newick'. - */ - public java.lang.String getNewick() - { - return this._newick; - } - - /** - * Returns the value of field 'showBootstrap'. - * - * @return the value of field 'ShowBootstrap'. - */ - public boolean getShowBootstrap() - { - return this._showBootstrap; - } - - /** - * Returns the value of field 'showDistances'. - * - * @return the value of field 'ShowDistances'. - */ - public boolean getShowDistances() - { - return this._showDistances; - } - - /** - * Returns the value of field 'threshold'. - * - * @return the value of field 'Threshold'. - */ - public float getThreshold() - { - return this._threshold; - } - - /** - * Returns the value of field 'title'. - * - * @return the value of field 'Title'. - */ - public java.lang.String getTitle() - { - return this._title; - } - - /** - * Returns the value of field 'width'. - * - * @return the value of field 'Width'. - */ - public int getWidth() - { - return this._width; - } - - /** - * Returns the value of field 'xpos'. - * - * @return the value of field 'Xpos'. - */ - public int getXpos() - { - return this._xpos; - } - - /** - * Returns the value of field 'ypos'. - * - * @return the value of field 'Ypos'. - */ - public int getYpos() - { - return this._ypos; - } - - /** - * Method hasCurrentTree. - * - * @return true if at least one CurrentTree has been added - */ - public boolean hasCurrentTree() - { - return this._has_currentTree; - } - - /** - * Method hasFitToWindow. - * - * @return true if at least one FitToWindow has been added - */ - public boolean hasFitToWindow() - { - return this._has_fitToWindow; - } - - /** - * Method hasFontSize. - * - * @return true if at least one FontSize has been added - */ - public boolean hasFontSize() - { - return this._has_fontSize; - } - - /** - * Method hasFontStyle. - * - * @return true if at least one FontStyle has been added - */ - public boolean hasFontStyle() - { - return this._has_fontStyle; - } - - /** - * Method hasHeight. - * - * @return true if at least one Height has been added - */ - public boolean hasHeight() - { - return this._has_height; - } - - /** - * Method hasMarkUnlinked. - * - * @return true if at least one MarkUnlinked has been added - */ - public boolean hasMarkUnlinked() - { - return this._has_markUnlinked; - } - - /** - * Method hasShowBootstrap. - * - * @return true if at least one ShowBootstrap has been added - */ - public boolean hasShowBootstrap() - { - return this._has_showBootstrap; - } - - /** - * Method hasShowDistances. - * - * @return true if at least one ShowDistances has been added - */ - public boolean hasShowDistances() - { - return this._has_showDistances; - } - - /** - * Method hasThreshold. - * - * @return true if at least one Threshold has been added - */ - public boolean hasThreshold() - { - return this._has_threshold; - } - - /** - * Method hasWidth. - * - * @return true if at least one Width has been added - */ - public boolean hasWidth() - { - return this._has_width; - } - - /** - * Method hasXpos. - * - * @return true if at least one Xpos has been added - */ - public boolean hasXpos() - { - return this._has_xpos; - } - - /** - * Method hasYpos. - * - * @return true if at least one Ypos has been added - */ - public boolean hasYpos() - { - return this._has_ypos; - } - - /** - * Returns the value of field 'currentTree'. - * - * @return the value of field 'CurrentTree'. - */ - public boolean isCurrentTree() - { - return this._currentTree; - } - - /** - * Returns the value of field 'fitToWindow'. - * - * @return the value of field 'FitToWindow'. - */ - public boolean isFitToWindow() - { - return this._fitToWindow; - } - - /** - * Returns the value of field 'markUnlinked'. - * - * @return the value of field 'MarkUnlinked'. - */ - public boolean isMarkUnlinked() - { - return this._markUnlinked; - } - - /** - * Returns the value of field 'showBootstrap'. - * - * @return the value of field 'ShowBootstrap'. - */ - public boolean isShowBootstrap() - { - return this._showBootstrap; - } - - /** - * Returns the value of field 'showDistances'. - * - * @return the value of field 'ShowDistances'. - */ - public boolean isShowDistances() - { - return this._showDistances; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'currentTree'. - * - * @param currentTree - * the value of field 'currentTree'. - */ - public void setCurrentTree(final boolean currentTree) - { - this._currentTree = currentTree; - this._has_currentTree = true; - } - - /** - * Sets the value of field 'fitToWindow'. - * - * @param fitToWindow - * the value of field 'fitToWindow'. - */ - public void setFitToWindow(final boolean fitToWindow) - { - this._fitToWindow = fitToWindow; - this._has_fitToWindow = true; - } - - /** - * Sets the value of field 'fontName'. - * - * @param fontName - * the value of field 'fontName'. - */ - public void setFontName(final java.lang.String fontName) - { - this._fontName = fontName; - } - - /** - * Sets the value of field 'fontSize'. - * - * @param fontSize - * the value of field 'fontSize'. - */ - public void setFontSize(final int fontSize) - { - this._fontSize = fontSize; - this._has_fontSize = true; - } - - /** - * Sets the value of field 'fontStyle'. - * - * @param fontStyle - * the value of field 'fontStyle'. - */ - public void setFontStyle(final int fontStyle) - { - this._fontStyle = fontStyle; - this._has_fontStyle = true; - } - - /** - * Sets the value of field 'height'. - * - * @param height - * the value of field 'height'. - */ - public void setHeight(final int height) - { - this._height = height; - this._has_height = true; - } - - /** - * Sets the value of field 'markUnlinked'. - * - * @param markUnlinked - * the value of field 'markUnlinked'. - */ - public void setMarkUnlinked(final boolean markUnlinked) - { - this._markUnlinked = markUnlinked; - this._has_markUnlinked = true; - } - - /** - * Sets the value of field 'newick'. - * - * @param newick - * the value of field 'newick'. - */ - public void setNewick(final java.lang.String newick) - { - this._newick = newick; - } - - /** - * Sets the value of field 'showBootstrap'. - * - * @param showBootstrap - * the value of field 'showBootstrap'. - */ - public void setShowBootstrap(final boolean showBootstrap) - { - this._showBootstrap = showBootstrap; - this._has_showBootstrap = true; - } - - /** - * Sets the value of field 'showDistances'. - * - * @param showDistances - * the value of field 'showDistances'. - */ - public void setShowDistances(final boolean showDistances) - { - this._showDistances = showDistances; - this._has_showDistances = true; - } - - /** - * Sets the value of field 'threshold'. - * - * @param threshold - * the value of field 'threshold'. - */ - public void setThreshold(final float threshold) - { - this._threshold = threshold; - this._has_threshold = true; - } - - /** - * Sets the value of field 'title'. - * - * @param title - * the value of field 'title'. - */ - public void setTitle(final java.lang.String title) - { - this._title = title; - } - - /** - * Sets the value of field 'width'. - * - * @param width - * the value of field 'width'. - */ - public void setWidth(final int width) - { - this._width = width; - this._has_width = true; - } - - /** - * Sets the value of field 'xpos'. - * - * @param xpos - * the value of field 'xpos'. - */ - public void setXpos(final int xpos) - { - this._xpos = xpos; - this._has_xpos = true; - } - - /** - * Sets the value of field 'ypos'. - * - * @param ypos - * the value of field 'ypos'. - */ - public void setYpos(final int ypos) - { - this._ypos = ypos; - this._has_ypos = true; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.Tree - */ - public static jalview.binding.Tree unmarshal(final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.Tree) Unmarshaller - .unmarshal(jalview.binding.Tree.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/UserColourScheme.java b/src/jalview/binding/UserColourScheme.java deleted file mode 100644 index e1a1a2f..0000000 --- a/src/jalview/binding/UserColourScheme.java +++ /dev/null @@ -1,125 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class UserColourScheme. - * - * @version $Revision$ $Date$ - */ -public class UserColourScheme extends JalviewUserColours - implements java.io.Serializable -{ - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public UserColourScheme() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.JalviewUserColours - */ - public static jalview.binding.JalviewUserColours unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.JalviewUserColours) Unmarshaller - .unmarshal(jalview.binding.UserColourScheme.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/UserColours.java b/src/jalview/binding/UserColours.java deleted file mode 100644 index 9dbcc9e..0000000 --- a/src/jalview/binding/UserColours.java +++ /dev/null @@ -1,181 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class UserColours. - * - * @version $Revision$ $Date$ - */ -public class UserColours implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * Field _id. - */ - private java.lang.String _id; - - /** - * Field _userColourScheme. - */ - private jalview.binding.UserColourScheme _userColourScheme; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public UserColours() - { - super(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * Returns the value of field 'id'. - * - * @return the value of field 'Id'. - */ - public java.lang.String getId() - { - return this._id; - } - - /** - * Returns the value of field 'userColourScheme'. - * - * @return the value of field 'UserColourScheme'. - */ - public jalview.binding.UserColourScheme getUserColourScheme() - { - return this._userColourScheme; - } - - /** - * Method isValid. - * - * @return true if this object is valid according to the schema - */ - public boolean isValid() - { - try - { - validate(); - } catch (org.exolab.castor.xml.ValidationException vex) - { - return false; - } - return true; - } - - /** - * - * - * @param out - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void marshal(final java.io.Writer out) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, out); - } - - /** - * - * - * @param handler - * @throws java.io.IOException - * if an IOException occurs during marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - */ - public void marshal(final org.xml.sax.ContentHandler handler) - throws java.io.IOException, - org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - Marshaller.marshal(this, handler); - } - - /** - * Sets the value of field 'id'. - * - * @param id - * the value of field 'id'. - */ - public void setId(final java.lang.String id) - { - this._id = id; - } - - /** - * Sets the value of field 'userColourScheme'. - * - * @param userColourScheme - * the value of field 'userColourScheme' - */ - public void setUserColourScheme( - final jalview.binding.UserColourScheme userColourScheme) - { - this._userColourScheme = userColourScheme; - } - - /** - * Method unmarshal. - * - * @param reader - * @throws org.exolab.castor.xml.MarshalException - * if object is null or if any SAXException is thrown during - * marshaling - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - * @return the unmarshaled jalview.binding.UserColours - */ - public static jalview.binding.UserColours unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.binding.UserColours) Unmarshaller - .unmarshal(jalview.binding.UserColours.class, reader); - } - - /** - * - * - * @throws org.exolab.castor.xml.ValidationException - * if this object is an invalid instance according to the schema - */ - public void validate() throws org.exolab.castor.xml.ValidationException - { - org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator(); - validator.validate(this); - } - -} diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java deleted file mode 100644 index b5a32da..0000000 --- a/src/jalview/binding/VAMSAS.java +++ /dev/null @@ -1,605 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, using an XML - * Schema. - * $Id$ - */ - -package jalview.binding; - -//---------------------------------/ -//- Imported classes and packages -/ -//---------------------------------/ - -import org.exolab.castor.xml.Marshaller; -import org.exolab.castor.xml.Unmarshaller; - -/** - * Class 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(); - this._alignmentList = new java.util.Vector(); - this._treeList = new java.util.Vector(); - this._sequenceSetList = new java.util.Vector(); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - * - * - * @param vAlignment - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlignment(final Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - this._alignmentList.addElement(vAlignment); - } - - /** - * - * - * @param index - * @param vAlignment - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addAlignment(final int index, final Alignment vAlignment) - throws java.lang.IndexOutOfBoundsException - { - this._alignmentList.add(index, vAlignment); - } - - /** - * - * - * @param vSequenceSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSequenceSet(final SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - this._sequenceSetList.addElement(vSequenceSet); - } - - /** - * - * - * @param index - * @param vSequenceSet - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addSequenceSet(final int index, - final SequenceSet vSequenceSet) - throws java.lang.IndexOutOfBoundsException - { - this._sequenceSetList.add(index, vSequenceSet); - } - - /** - * - * - * @param vTree - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addTree(final java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - this._treeList.addElement(vTree); - } - - /** - * - * - * @param index - * @param vTree - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - */ - public void addTree(final int index, final java.lang.String vTree) - throws java.lang.IndexOutOfBoundsException - { - this._treeList.add(index, vTree); - } - - /** - * Method enumerateAlignment. - * - * @return an Enumeration over all Alignment elements - */ - public java.util.Enumeration enumerateAlignment() - { - return this._alignmentList.elements(); - } - - /** - * Method enumerateSequenceSet. - * - * @return an Enumeration over all SequenceSet elements - */ - public java.util.Enumeration enumerateSequenceSet() - { - return this._sequenceSetList.elements(); - } - - /** - * Method enumerateTree. - * - * @return an Enumeration over all java.lang.String elements - */ - public java.util.Enumeration enumerateTree() - { - return this._treeList.elements(); - } - - /** - * Method getAlignment. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the Alignment at the given index - */ - public Alignment getAlignment(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._alignmentList.size()) - { - throw new IndexOutOfBoundsException( - "getAlignment: Index value '" + index + "' not in range [0.." - + (this._alignmentList.size() - 1) + "]"); - } - - return (Alignment) _alignmentList.get(index); - } - - /** - * Method getAlignment.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public Alignment[] getAlignment() - { - Alignment[] array = new Alignment[0]; - return (Alignment[]) this._alignmentList.toArray(array); - } - - /** - * Method getAlignmentCount. - * - * @return the size of this collection - */ - public int getAlignmentCount() - { - return this._alignmentList.size(); - } - - /** - * Method getSequenceSet. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the SequenceSet at the given index - */ - public SequenceSet getSequenceSet(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._sequenceSetList.size()) - { - throw new IndexOutOfBoundsException("getSequenceSet: Index value '" - + index + "' not in range [0.." - + (this._sequenceSetList.size() - 1) + "]"); - } - - return (SequenceSet) _sequenceSetList.get(index); - } - - /** - * Method getSequenceSet.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread, - * we pass a 0-length Array of the correct type into the API call. This way we - * know that the Array returned is of exactly the correct length. - * - * @return this collection as an Array - */ - public SequenceSet[] getSequenceSet() - { - SequenceSet[] array = new SequenceSet[0]; - return (SequenceSet[]) this._sequenceSetList.toArray(array); - } - - /** - * Method getSequenceSetCount. - * - * @return the size of this collection - */ - public int getSequenceSetCount() - { - return this._sequenceSetList.size(); - } - - /** - * Method getTree. - * - * @param index - * @throws java.lang.IndexOutOfBoundsException - * if the index given is outside the bounds of the collection - * @return the value of the java.lang.String at the given index - */ - public java.lang.String getTree(final int index) - throws java.lang.IndexOutOfBoundsException - { - // check bounds for index - if (index < 0 || index >= this._treeList.size()) - { - throw new IndexOutOfBoundsException("getTree: Index value '" + index - + "' not in range [0.." + (this._treeList.size() - 1) + "]"); - } - - return (java.lang.String) _treeList.get(index); - } - - /** - * Method getTree.Returns the contents of the collection in an Array. - *
- * Note: Just in case the collection contents are changing in another thread,
- * we pass a 0-length Array of the correct type into the API call. This way we
- * know that the Array returned is of exactly the correct length.
- *
- * @return this collection as an Array
- */
- public java.lang.String[] getTree()
- {
- java.lang.String[] array = new java.lang.String[0];
- return (java.lang.String[]) this._treeList.toArray(array);
- }
-
- /**
- * Method getTreeCount.
- *
- * @return the size of this collection
- */
- public int getTreeCount()
- {
- return this._treeList.size();
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Method removeAlignment.
- *
- * @param vAlignment
- * @return true if the object was removed from the collection.
- */
- public boolean removeAlignment(final Alignment vAlignment)
- {
- boolean removed = _alignmentList.remove(vAlignment);
- return removed;
- }
-
- /**
- * Method removeAlignmentAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public Alignment removeAlignmentAt(final int index)
- {
- java.lang.Object obj = this._alignmentList.remove(index);
- return (Alignment) obj;
- }
-
- /**
- */
- public void removeAllAlignment()
- {
- this._alignmentList.clear();
- }
-
- /**
- */
- public void removeAllSequenceSet()
- {
- this._sequenceSetList.clear();
- }
-
- /**
- */
- public void removeAllTree()
- {
- this._treeList.clear();
- }
-
- /**
- * Method removeSequenceSet.
- *
- * @param vSequenceSet
- * @return true if the object was removed from the collection.
- */
- public boolean removeSequenceSet(final SequenceSet vSequenceSet)
- {
- boolean removed = _sequenceSetList.remove(vSequenceSet);
- return removed;
- }
-
- /**
- * Method removeSequenceSetAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public SequenceSet removeSequenceSetAt(final int index)
- {
- java.lang.Object obj = this._sequenceSetList.remove(index);
- return (SequenceSet) obj;
- }
-
- /**
- * Method removeTree.
- *
- * @param vTree
- * @return true if the object was removed from the collection.
- */
- public boolean removeTree(final java.lang.String vTree)
- {
- boolean removed = _treeList.remove(vTree);
- return removed;
- }
-
- /**
- * Method removeTreeAt.
- *
- * @param index
- * @return the element removed from the collection
- */
- public java.lang.String removeTreeAt(final int index)
- {
- java.lang.Object obj = this._treeList.remove(index);
- return (java.lang.String) obj;
- }
-
- /**
- *
- *
- * @param index
- * @param vAlignment
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setAlignment(final int index, final Alignment vAlignment)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._alignmentList.size())
- {
- throw new IndexOutOfBoundsException(
- "setAlignment: Index value '" + index + "' not in range [0.."
- + (this._alignmentList.size() - 1) + "]");
- }
-
- this._alignmentList.set(index, vAlignment);
- }
-
- /**
- *
- *
- * @param vAlignmentArray
- */
- public void setAlignment(final Alignment[] vAlignmentArray)
- {
- // -- copy array
- _alignmentList.clear();
-
- for (int i = 0; i < vAlignmentArray.length; i++)
- {
- this._alignmentList.add(vAlignmentArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vSequenceSet
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setSequenceSet(final int index,
- final SequenceSet vSequenceSet)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._sequenceSetList.size())
- {
- throw new IndexOutOfBoundsException("setSequenceSet: Index value '"
- + index + "' not in range [0.."
- + (this._sequenceSetList.size() - 1) + "]");
- }
-
- this._sequenceSetList.set(index, vSequenceSet);
- }
-
- /**
- *
- *
- * @param vSequenceSetArray
- */
- public void setSequenceSet(final SequenceSet[] vSequenceSetArray)
- {
- // -- copy array
- _sequenceSetList.clear();
-
- for (int i = 0; i < vSequenceSetArray.length; i++)
- {
- this._sequenceSetList.add(vSequenceSetArray[i]);
- }
- }
-
- /**
- *
- *
- * @param index
- * @param vTree
- * @throws java.lang.IndexOutOfBoundsException
- * if the index given is outside the bounds of the collection
- */
- public void setTree(final int index, final java.lang.String vTree)
- throws java.lang.IndexOutOfBoundsException
- {
- // check bounds for index
- if (index < 0 || index >= this._treeList.size())
- {
- throw new IndexOutOfBoundsException("setTree: Index value '" + index
- + "' not in range [0.." + (this._treeList.size() - 1) + "]");
- }
-
- this._treeList.set(index, vTree);
- }
-
- /**
- *
- *
- * @param vTreeArray
- */
- public void setTree(final java.lang.String[] vTreeArray)
- {
- // -- copy array
- _treeList.clear();
-
- for (int i = 0; i < vTreeArray.length; i++)
- {
- this._treeList.add(vTreeArray[i]);
- }
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.VAMSAS
- */
- public static jalview.binding.VAMSAS unmarshal(
- final 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);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
-
-}
diff --git a/src/jalview/binding/VamsasModel.java b/src/jalview/binding/VamsasModel.java
deleted file mode 100644
index d3c90cf..0000000
--- a/src/jalview/binding/VamsasModel.java
+++ /dev/null
@@ -1,124 +0,0 @@
-/*
- * This class was automatically generated with
- * Castor 1.1, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.binding;
-
-//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-
-/**
- * Class VamsasModel.
- *
- * @version $Revision$ $Date$
- */
-public class VamsasModel extends VAMSAS implements java.io.Serializable
-{
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- public VamsasModel()
- {
- super();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
- }
- return true;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.VAMSAS
- */
- public static jalview.binding.VAMSAS unmarshal(
- final java.io.Reader reader)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- return (jalview.binding.VAMSAS) Unmarshaller
- .unmarshal(jalview.binding.VamsasModel.class, reader);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
-
-}
diff --git a/src/jalview/binding/Viewport.java b/src/jalview/binding/Viewport.java
deleted file mode 100644
index 183e048..0000000
--- a/src/jalview/binding/Viewport.java
+++ /dev/null
@@ -1,1463 +0,0 @@
-/*
- * This class was automatically generated with
- * Castor 1.1, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.binding;
-
-//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import org.exolab.castor.xml.Marshaller;
-import org.exolab.castor.xml.Unmarshaller;
-
-/**
- * Class 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();
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- */
- public void deleteConsThreshold()
- {
- this._has_consThreshold = false;
- }
-
- /**
- */
- public void deleteConservationSelected()
- {
- this._has_conservationSelected = false;
- }
-
- /**
- */
- public void deleteFontSize()
- {
- this._has_fontSize = false;
- }
-
- /**
- */
- public void deleteFontStyle()
- {
- this._has_fontStyle = false;
- }
-
- /**
- */
- public void deleteHeight()
- {
- this._has_height = false;
- }
-
- /**
- */
- public void deletePidSelected()
- {
- this._has_pidSelected = false;
- }
-
- /**
- */
- public void deletePidThreshold()
- {
- this._has_pidThreshold = false;
- }
-
- /**
- */
- public void deleteRenderGaps()
- {
- this._has_renderGaps = false;
- }
-
- /**
- */
- public void deleteShowAnnotation()
- {
- this._has_showAnnotation = false;
- }
-
- /**
- */
- public void deleteShowBoxes()
- {
- this._has_showBoxes = false;
- }
-
- /**
- */
- public void deleteShowColourText()
- {
- this._has_showColourText = false;
- }
-
- /**
- */
- public void deleteShowConservation()
- {
- this._has_showConservation = false;
- }
-
- /**
- */
- public void deleteShowFullId()
- {
- this._has_showFullId = false;
- }
-
- /**
- */
- public void deleteShowIdentity()
- {
- this._has_showIdentity = false;
- }
-
- /**
- */
- public void deleteShowQuality()
- {
- this._has_showQuality = false;
- }
-
- /**
- */
- public void deleteShowSequenceFeatures()
- {
- this._has_showSequenceFeatures = false;
- }
-
- /**
- */
- public void deleteShowText()
- {
- this._has_showText = false;
- }
-
- /**
- */
- public void deleteStartRes()
- {
- this._has_startRes = false;
- }
-
- /**
- */
- public void deleteStartSeq()
- {
- this._has_startSeq = false;
- }
-
- /**
- */
- public void deleteWidth()
- {
- this._has_width = false;
- }
-
- /**
- */
- public void deleteWrapAlignment()
- {
- this._has_wrapAlignment = false;
- }
-
- /**
- */
- public void deleteXpos()
- {
- this._has_xpos = false;
- }
-
- /**
- */
- public void deleteYpos()
- {
- this._has_ypos = false;
- }
-
- /**
- * Returns the value of field 'bgColour'.
- *
- * @return the value of field 'BgColour'.
- */
- public java.lang.String getBgColour()
- {
- return this._bgColour;
- }
-
- /**
- * Returns the value of field 'consThreshold'.
- *
- * @return the value of field 'ConsThreshold'.
- */
- public int getConsThreshold()
- {
- return this._consThreshold;
- }
-
- /**
- * Returns the value of field 'conservationSelected'.
- *
- * @return the value of field 'ConservationSelected'.
- */
- public boolean getConservationSelected()
- {
- return this._conservationSelected;
- }
-
- /**
- * Returns the value of field 'fontName'.
- *
- * @return the value of field 'FontName'.
- */
- public java.lang.String getFontName()
- {
- return this._fontName;
- }
-
- /**
- * Returns the value of field 'fontSize'.
- *
- * @return the value of field 'FontSize'.
- */
- public int getFontSize()
- {
- return this._fontSize;
- }
-
- /**
- * Returns the value of field 'fontStyle'.
- *
- * @return the value of field 'FontStyle'.
- */
- public int getFontStyle()
- {
- return this._fontStyle;
- }
-
- /**
- * Returns the value of field 'height'.
- *
- * @return the value of field 'Height'.
- */
- public int getHeight()
- {
- return this._height;
- }
-
- /**
- * Returns the value of field 'pidSelected'.
- *
- * @return the value of field 'PidSelected'.
- */
- public boolean getPidSelected()
- {
- return this._pidSelected;
- }
-
- /**
- * Returns the value of field 'pidThreshold'.
- *
- * @return the value of field 'PidThreshold'.
- */
- public int getPidThreshold()
- {
- return this._pidThreshold;
- }
-
- /**
- * Returns the value of field 'renderGaps'.
- *
- * @return the value of field 'RenderGaps'.
- */
- public boolean getRenderGaps()
- {
- return this._renderGaps;
- }
-
- /**
- * Returns the value of field 'showAnnotation'.
- *
- * @return the value of field 'ShowAnnotation'.
- */
- public boolean getShowAnnotation()
- {
- return this._showAnnotation;
- }
-
- /**
- * Returns the value of field 'showBoxes'.
- *
- * @return the value of field 'ShowBoxes'.
- */
- public boolean getShowBoxes()
- {
- return this._showBoxes;
- }
-
- /**
- * Returns the value of field 'showColourText'.
- *
- * @return the value of field 'ShowColourText'.
- */
- public boolean getShowColourText()
- {
- return this._showColourText;
- }
-
- /**
- * Returns the value of field 'showConservation'.
- *
- * @return the value of field 'ShowConservation'.
- */
- public boolean getShowConservation()
- {
- return this._showConservation;
- }
-
- /**
- * Returns the value of field 'showFullId'.
- *
- * @return the value of field 'ShowFullId'.
- */
- public boolean getShowFullId()
- {
- return this._showFullId;
- }
-
- /**
- * Returns the value of field 'showIdentity'.
- *
- * @return the value of field 'ShowIdentity'.
- */
- public boolean getShowIdentity()
- {
- return this._showIdentity;
- }
-
- /**
- * Returns the value of field 'showQuality'.
- *
- * @return the value of field 'ShowQuality'.
- */
- public boolean getShowQuality()
- {
- return this._showQuality;
- }
-
- /**
- * Returns the value of field 'showSequenceFeatures'.
- *
- * @return the value of field 'ShowSequenceFeatures'.
- */
- public boolean getShowSequenceFeatures()
- {
- return this._showSequenceFeatures;
- }
-
- /**
- * Returns the value of field 'showText'.
- *
- * @return the value of field 'ShowText'.
- */
- public boolean getShowText()
- {
- return this._showText;
- }
-
- /**
- * Returns the value of field 'startRes'.
- *
- * @return the value of field 'StartRes'.
- */
- public int getStartRes()
- {
- return this._startRes;
- }
-
- /**
- * Returns the value of field 'startSeq'.
- *
- * @return the value of field 'StartSeq'.
- */
- public int getStartSeq()
- {
- return this._startSeq;
- }
-
- /**
- * Returns the value of field 'title'.
- *
- * @return the value of field 'Title'.
- */
- public java.lang.String getTitle()
- {
- return this._title;
- }
-
- /**
- * Returns the value of field 'width'.
- *
- * @return the value of field 'Width'.
- */
- public int getWidth()
- {
- return this._width;
- }
-
- /**
- * Returns the value of field 'wrapAlignment'.
- *
- * @return the value of field 'WrapAlignment'.
- */
- public boolean getWrapAlignment()
- {
- return this._wrapAlignment;
- }
-
- /**
- * Returns the value of field 'xpos'.
- *
- * @return the value of field 'Xpos'.
- */
- public int getXpos()
- {
- return this._xpos;
- }
-
- /**
- * Returns the value of field 'ypos'.
- *
- * @return the value of field 'Ypos'.
- */
- public int getYpos()
- {
- return this._ypos;
- }
-
- /**
- * Method hasConsThreshold.
- *
- * @return true if at least one ConsThreshold has been added
- */
- public boolean hasConsThreshold()
- {
- return this._has_consThreshold;
- }
-
- /**
- * Method hasConservationSelected.
- *
- * @return true if at least one ConservationSelected has been added
- */
- public boolean hasConservationSelected()
- {
- return this._has_conservationSelected;
- }
-
- /**
- * Method hasFontSize.
- *
- * @return true if at least one FontSize has been added
- */
- public boolean hasFontSize()
- {
- return this._has_fontSize;
- }
-
- /**
- * Method hasFontStyle.
- *
- * @return true if at least one FontStyle has been added
- */
- public boolean hasFontStyle()
- {
- return this._has_fontStyle;
- }
-
- /**
- * Method hasHeight.
- *
- * @return true if at least one Height has been added
- */
- public boolean hasHeight()
- {
- return this._has_height;
- }
-
- /**
- * Method hasPidSelected.
- *
- * @return true if at least one PidSelected has been added
- */
- public boolean hasPidSelected()
- {
- return this._has_pidSelected;
- }
-
- /**
- * Method hasPidThreshold.
- *
- * @return true if at least one PidThreshold has been added
- */
- public boolean hasPidThreshold()
- {
- return this._has_pidThreshold;
- }
-
- /**
- * Method hasRenderGaps.
- *
- * @return true if at least one RenderGaps has been added
- */
- public boolean hasRenderGaps()
- {
- return this._has_renderGaps;
- }
-
- /**
- * Method hasShowAnnotation.
- *
- * @return true if at least one ShowAnnotation has been added
- */
- public boolean hasShowAnnotation()
- {
- return this._has_showAnnotation;
- }
-
- /**
- * Method hasShowBoxes.
- *
- * @return true if at least one ShowBoxes has been added
- */
- public boolean hasShowBoxes()
- {
- return this._has_showBoxes;
- }
-
- /**
- * Method hasShowColourText.
- *
- * @return true if at least one ShowColourText has been added
- */
- public boolean hasShowColourText()
- {
- return this._has_showColourText;
- }
-
- /**
- * Method hasShowConservation.
- *
- * @return true if at least one ShowConservation has been added
- */
- public boolean hasShowConservation()
- {
- return this._has_showConservation;
- }
-
- /**
- * Method hasShowFullId.
- *
- * @return true if at least one ShowFullId has been added
- */
- public boolean hasShowFullId()
- {
- return this._has_showFullId;
- }
-
- /**
- * Method hasShowIdentity.
- *
- * @return true if at least one ShowIdentity has been added
- */
- public boolean hasShowIdentity()
- {
- return this._has_showIdentity;
- }
-
- /**
- * Method hasShowQuality.
- *
- * @return true if at least one ShowQuality has been added
- */
- public boolean hasShowQuality()
- {
- return this._has_showQuality;
- }
-
- /**
- * Method hasShowSequenceFeatures.
- *
- * @return true if at least one ShowSequenceFeatures has been added
- */
- public boolean hasShowSequenceFeatures()
- {
- return this._has_showSequenceFeatures;
- }
-
- /**
- * Method hasShowText.
- *
- * @return true if at least one ShowText has been added
- */
- public boolean hasShowText()
- {
- return this._has_showText;
- }
-
- /**
- * Method hasStartRes.
- *
- * @return true if at least one StartRes has been added
- */
- public boolean hasStartRes()
- {
- return this._has_startRes;
- }
-
- /**
- * Method hasStartSeq.
- *
- * @return true if at least one StartSeq has been added
- */
- public boolean hasStartSeq()
- {
- return this._has_startSeq;
- }
-
- /**
- * Method hasWidth.
- *
- * @return true if at least one Width has been added
- */
- public boolean hasWidth()
- {
- return this._has_width;
- }
-
- /**
- * Method hasWrapAlignment.
- *
- * @return true if at least one WrapAlignment has been added
- */
- public boolean hasWrapAlignment()
- {
- return this._has_wrapAlignment;
- }
-
- /**
- * Method hasXpos.
- *
- * @return true if at least one Xpos has been added
- */
- public boolean hasXpos()
- {
- return this._has_xpos;
- }
-
- /**
- * Method hasYpos.
- *
- * @return true if at least one Ypos has been added
- */
- public boolean hasYpos()
- {
- return this._has_ypos;
- }
-
- /**
- * Returns the value of field 'conservationSelected'.
- *
- * @return the value of field 'ConservationSelected'.
- */
- public boolean isConservationSelected()
- {
- return this._conservationSelected;
- }
-
- /**
- * Returns the value of field 'pidSelected'.
- *
- * @return the value of field 'PidSelected'.
- */
- public boolean isPidSelected()
- {
- return this._pidSelected;
- }
-
- /**
- * Returns the value of field 'renderGaps'.
- *
- * @return the value of field 'RenderGaps'.
- */
- public boolean isRenderGaps()
- {
- return this._renderGaps;
- }
-
- /**
- * Returns the value of field 'showAnnotation'.
- *
- * @return the value of field 'ShowAnnotation'.
- */
- public boolean isShowAnnotation()
- {
- return this._showAnnotation;
- }
-
- /**
- * Returns the value of field 'showBoxes'.
- *
- * @return the value of field 'ShowBoxes'.
- */
- public boolean isShowBoxes()
- {
- return this._showBoxes;
- }
-
- /**
- * Returns the value of field 'showColourText'.
- *
- * @return the value of field 'ShowColourText'.
- */
- public boolean isShowColourText()
- {
- return this._showColourText;
- }
-
- /**
- * Returns the value of field 'showConservation'.
- *
- * @return the value of field 'ShowConservation'.
- */
- public boolean isShowConservation()
- {
- return this._showConservation;
- }
-
- /**
- * Returns the value of field 'showFullId'.
- *
- * @return the value of field 'ShowFullId'.
- */
- public boolean isShowFullId()
- {
- return this._showFullId;
- }
-
- /**
- * Returns the value of field 'showIdentity'.
- *
- * @return the value of field 'ShowIdentity'.
- */
- public boolean isShowIdentity()
- {
- return this._showIdentity;
- }
-
- /**
- * Returns the value of field 'showQuality'.
- *
- * @return the value of field 'ShowQuality'.
- */
- public boolean isShowQuality()
- {
- return this._showQuality;
- }
-
- /**
- * Returns the value of field 'showSequenceFeatures'.
- *
- * @return the value of field 'ShowSequenceFeatures'.
- */
- public boolean isShowSequenceFeatures()
- {
- return this._showSequenceFeatures;
- }
-
- /**
- * Returns the value of field 'showText'.
- *
- * @return the value of field 'ShowText'.
- */
- public boolean isShowText()
- {
- return this._showText;
- }
-
- /**
- * Method isValid.
- *
- * @return true if this object is valid according to the schema
- */
- public boolean isValid()
- {
- try
- {
- validate();
- } catch (org.exolab.castor.xml.ValidationException vex)
- {
- return false;
- }
- return true;
- }
-
- /**
- * Returns the value of field 'wrapAlignment'.
- *
- * @return the value of field 'WrapAlignment'.
- */
- public boolean isWrapAlignment()
- {
- return this._wrapAlignment;
- }
-
- /**
- *
- *
- * @param out
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void marshal(final java.io.Writer out)
- throws org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, out);
- }
-
- /**
- *
- *
- * @param handler
- * @throws java.io.IOException
- * if an IOException occurs during marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- */
- public void marshal(final org.xml.sax.ContentHandler handler)
- throws java.io.IOException,
- org.exolab.castor.xml.MarshalException,
- org.exolab.castor.xml.ValidationException
- {
- Marshaller.marshal(this, handler);
- }
-
- /**
- * Sets the value of field 'bgColour'.
- *
- * @param bgColour
- * the value of field 'bgColour'.
- */
- public void setBgColour(final java.lang.String bgColour)
- {
- this._bgColour = bgColour;
- }
-
- /**
- * Sets the value of field 'consThreshold'.
- *
- * @param consThreshold
- * the value of field 'consThreshold'.
- */
- public void setConsThreshold(final int consThreshold)
- {
- this._consThreshold = consThreshold;
- this._has_consThreshold = true;
- }
-
- /**
- * Sets the value of field 'conservationSelected'.
- *
- * @param conservationSelected
- * the value of field 'conservationSelected'.
- */
- public void setConservationSelected(final boolean conservationSelected)
- {
- this._conservationSelected = conservationSelected;
- this._has_conservationSelected = true;
- }
-
- /**
- * Sets the value of field 'fontName'.
- *
- * @param fontName
- * the value of field 'fontName'.
- */
- public void setFontName(final java.lang.String fontName)
- {
- this._fontName = fontName;
- }
-
- /**
- * Sets the value of field 'fontSize'.
- *
- * @param fontSize
- * the value of field 'fontSize'.
- */
- public void setFontSize(final int fontSize)
- {
- this._fontSize = fontSize;
- this._has_fontSize = true;
- }
-
- /**
- * Sets the value of field 'fontStyle'.
- *
- * @param fontStyle
- * the value of field 'fontStyle'.
- */
- public void setFontStyle(final int fontStyle)
- {
- this._fontStyle = fontStyle;
- this._has_fontStyle = true;
- }
-
- /**
- * Sets the value of field 'height'.
- *
- * @param height
- * the value of field 'height'.
- */
- public void setHeight(final int height)
- {
- this._height = height;
- this._has_height = true;
- }
-
- /**
- * Sets the value of field 'pidSelected'.
- *
- * @param pidSelected
- * the value of field 'pidSelected'.
- */
- public void setPidSelected(final boolean pidSelected)
- {
- this._pidSelected = pidSelected;
- this._has_pidSelected = true;
- }
-
- /**
- * Sets the value of field 'pidThreshold'.
- *
- * @param pidThreshold
- * the value of field 'pidThreshold'.
- */
- public void setPidThreshold(final int pidThreshold)
- {
- this._pidThreshold = pidThreshold;
- this._has_pidThreshold = true;
- }
-
- /**
- * Sets the value of field 'renderGaps'.
- *
- * @param renderGaps
- * the value of field 'renderGaps'.
- */
- public void setRenderGaps(final boolean renderGaps)
- {
- this._renderGaps = renderGaps;
- this._has_renderGaps = true;
- }
-
- /**
- * Sets the value of field 'showAnnotation'.
- *
- * @param showAnnotation
- * the value of field 'showAnnotation'.
- */
- public void setShowAnnotation(final boolean showAnnotation)
- {
- this._showAnnotation = showAnnotation;
- this._has_showAnnotation = true;
- }
-
- /**
- * Sets the value of field 'showBoxes'.
- *
- * @param showBoxes
- * the value of field 'showBoxes'.
- */
- public void setShowBoxes(final boolean showBoxes)
- {
- this._showBoxes = showBoxes;
- this._has_showBoxes = true;
- }
-
- /**
- * Sets the value of field 'showColourText'.
- *
- * @param showColourText
- * the value of field 'showColourText'.
- */
- public void setShowColourText(final boolean showColourText)
- {
- this._showColourText = showColourText;
- this._has_showColourText = true;
- }
-
- /**
- * Sets the value of field 'showConservation'.
- *
- * @param showConservation
- * the value of field 'showConservation'
- */
- public void setShowConservation(final boolean showConservation)
- {
- this._showConservation = showConservation;
- this._has_showConservation = true;
- }
-
- /**
- * Sets the value of field 'showFullId'.
- *
- * @param showFullId
- * the value of field 'showFullId'.
- */
- public void setShowFullId(final boolean showFullId)
- {
- this._showFullId = showFullId;
- this._has_showFullId = true;
- }
-
- /**
- * Sets the value of field 'showIdentity'.
- *
- * @param showIdentity
- * the value of field 'showIdentity'.
- */
- public void setShowIdentity(final boolean showIdentity)
- {
- this._showIdentity = showIdentity;
- this._has_showIdentity = true;
- }
-
- /**
- * Sets the value of field 'showQuality'.
- *
- * @param showQuality
- * the value of field 'showQuality'.
- */
- public void setShowQuality(final boolean showQuality)
- {
- this._showQuality = showQuality;
- this._has_showQuality = true;
- }
-
- /**
- * Sets the value of field 'showSequenceFeatures'.
- *
- * @param showSequenceFeatures
- * the value of field 'showSequenceFeatures'.
- */
- public void setShowSequenceFeatures(final boolean showSequenceFeatures)
- {
- this._showSequenceFeatures = showSequenceFeatures;
- this._has_showSequenceFeatures = true;
- }
-
- /**
- * Sets the value of field 'showText'.
- *
- * @param showText
- * the value of field 'showText'.
- */
- public void setShowText(final boolean showText)
- {
- this._showText = showText;
- this._has_showText = true;
- }
-
- /**
- * Sets the value of field 'startRes'.
- *
- * @param startRes
- * the value of field 'startRes'.
- */
- public void setStartRes(final int startRes)
- {
- this._startRes = startRes;
- this._has_startRes = true;
- }
-
- /**
- * Sets the value of field 'startSeq'.
- *
- * @param startSeq
- * the value of field 'startSeq'.
- */
- public void setStartSeq(final int startSeq)
- {
- this._startSeq = startSeq;
- this._has_startSeq = true;
- }
-
- /**
- * Sets the value of field 'title'.
- *
- * @param title
- * the value of field 'title'.
- */
- public void setTitle(final java.lang.String title)
- {
- this._title = title;
- }
-
- /**
- * Sets the value of field 'width'.
- *
- * @param width
- * the value of field 'width'.
- */
- public void setWidth(final int width)
- {
- this._width = width;
- this._has_width = true;
- }
-
- /**
- * Sets the value of field 'wrapAlignment'.
- *
- * @param wrapAlignment
- * the value of field 'wrapAlignment'.
- */
- public void setWrapAlignment(final boolean wrapAlignment)
- {
- this._wrapAlignment = wrapAlignment;
- this._has_wrapAlignment = true;
- }
-
- /**
- * Sets the value of field 'xpos'.
- *
- * @param xpos
- * the value of field 'xpos'.
- */
- public void setXpos(final int xpos)
- {
- this._xpos = xpos;
- this._has_xpos = true;
- }
-
- /**
- * Sets the value of field 'ypos'.
- *
- * @param ypos
- * the value of field 'ypos'.
- */
- public void setYpos(final int ypos)
- {
- this._ypos = ypos;
- this._has_ypos = true;
- }
-
- /**
- * Method unmarshal.
- *
- * @param reader
- * @throws org.exolab.castor.xml.MarshalException
- * if object is null or if any SAXException is thrown during
- * marshaling
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- * @return the unmarshaled jalview.binding.Viewport
- */
- public static jalview.binding.Viewport unmarshal(
- final 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);
- }
-
- /**
- *
- *
- * @throws org.exolab.castor.xml.ValidationException
- * if this object is an invalid instance according to the schema
- */
- public void validate() throws org.exolab.castor.xml.ValidationException
- {
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
- validator.validate(this);
- }
-
-}
diff --git a/src/jalview/binding/types/ColourThreshTypeType.java b/src/jalview/binding/types/ColourThreshTypeType.java
deleted file mode 100644
index 024f2c0..0000000
--- a/src/jalview/binding/types/ColourThreshTypeType.java
+++ /dev/null
@@ -1,168 +0,0 @@
-/*
- * This class was automatically generated with
- * Castor 1.1, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.binding.types;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.util.Hashtable;
-
-/**
- * Class ColourThreshTypeType.
- *
- * @version $Revision$ $Date$
- */
-public class ColourThreshTypeType implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * The NONE type
- */
- public static final int NONE_TYPE = 0;
-
- /**
- * The instance of the NONE type
- */
- public static final ColourThreshTypeType NONE = new ColourThreshTypeType(NONE_TYPE, "NONE");
-
- /**
- * The ABOVE type
- */
- public static final int ABOVE_TYPE = 1;
-
- /**
- * The instance of the ABOVE type
- */
- public static final ColourThreshTypeType ABOVE = new ColourThreshTypeType(ABOVE_TYPE, "ABOVE");
-
- /**
- * The BELOW type
- */
- public static final int BELOW_TYPE = 2;
-
- /**
- * The instance of the BELOW type
- */
- public static final ColourThreshTypeType BELOW = new ColourThreshTypeType(BELOW_TYPE, "BELOW");
-
- /**
- * Field _memberTable.
- */
- private static java.util.Hashtable _memberTable = init();
-
- /**
- * Field type.
- */
- private int type = -1;
-
- /**
- * Field stringValue.
- */
- private java.lang.String stringValue = null;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- private ColourThreshTypeType(final int type, final java.lang.String value) {
- super();
- this.type = type;
- this.stringValue = value;
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method enumerate.Returns an enumeration of all possible
- * instances of ColourThreshTypeType
- *
- * @return an Enumeration over all possible instances of
- * ColourThreshTypeType
- */
- public static java.util.Enumeration enumerate(
- ) {
- return _memberTable.elements();
- }
-
- /**
- * Method getType.Returns the type of this ColourThreshTypeType
- *
- * @return the type of this ColourThreshTypeType
- */
- public int getType(
- ) {
- return this.type;
- }
-
- /**
- * Method init.
- *
- * @return the initialized Hashtable for the member table
- */
- private static java.util.Hashtable init(
- ) {
- Hashtable members = new Hashtable();
- members.put("NONE", NONE);
- members.put("ABOVE", ABOVE);
- members.put("BELOW", BELOW);
- return members;
- }
-
- /**
- * Method readResolve. will be called during deserialization to
- * replace the deserialized object with the correct constant
- * instance.
- *
- * @return this deserialized object
- */
- private java.lang.Object readResolve(
- ) {
- return valueOf(this.stringValue);
- }
-
- /**
- * Method toString.Returns the String representation of this
- * ColourThreshTypeType
- *
- * @return the String representation of this ColourThreshTypeTyp
- */
- public java.lang.String toString(
- ) {
- return this.stringValue;
- }
-
- /**
- * Method valueOf.Returns a new ColourThreshTypeType based on
- * the given String value.
- *
- * @param string
- * @return the ColourThreshTypeType value of parameter 'string'
- */
- public static jalview.binding.types.ColourThreshTypeType valueOf(
- final java.lang.String string) {
- java.lang.Object obj = null;
- if (string != null) {
- obj = _memberTable.get(string);
- }
- if (obj == null) {
- String err = "" + string + " is not a valid ColourThreshTypeType";
- throw new IllegalArgumentException(err);
- }
- return (ColourThreshTypeType) obj;
- }
-
-}
diff --git a/src/jalview/binding/types/FeatureMatcherByType.java b/src/jalview/binding/types/FeatureMatcherByType.java
deleted file mode 100644
index 2185bba..0000000
--- a/src/jalview/binding/types/FeatureMatcherByType.java
+++ /dev/null
@@ -1,168 +0,0 @@
-/*
- * This class was automatically generated with
- * Castor 1.1, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.binding.types;
-
- //---------------------------------/
- //- Imported classes and packages -/
-//---------------------------------/
-
-import java.util.Hashtable;
-
-/**
- * Class FeatureMatcherByType.
- *
- * @version $Revision$ $Date$
- */
-public class FeatureMatcherByType implements java.io.Serializable {
-
-
- //--------------------------/
- //- Class/Member Variables -/
- //--------------------------/
-
- /**
- * The byLabel type
- */
- public static final int BYLABEL_TYPE = 0;
-
- /**
- * The instance of the byLabel type
- */
- public static final FeatureMatcherByType BYLABEL = new FeatureMatcherByType(BYLABEL_TYPE, "byLabel");
-
- /**
- * The byScore type
- */
- public static final int BYSCORE_TYPE = 1;
-
- /**
- * The instance of the byScore type
- */
- public static final FeatureMatcherByType BYSCORE = new FeatureMatcherByType(BYSCORE_TYPE, "byScore");
-
- /**
- * The byAttribute type
- */
- public static final int BYATTRIBUTE_TYPE = 2;
-
- /**
- * The instance of the byAttribute type
- */
- public static final FeatureMatcherByType BYATTRIBUTE = new FeatureMatcherByType(BYATTRIBUTE_TYPE, "byAttribute");
-
- /**
- * Field _memberTable.
- */
- private static java.util.Hashtable _memberTable = init();
-
- /**
- * Field type.
- */
- private int type = -1;
-
- /**
- * Field stringValue.
- */
- private java.lang.String stringValue = null;
-
-
- //----------------/
- //- Constructors -/
- //----------------/
-
- private FeatureMatcherByType(final int type, final java.lang.String value) {
- super();
- this.type = type;
- this.stringValue = value;
- }
-
-
- //-----------/
- //- Methods -/
- //-----------/
-
- /**
- * Method enumerate.Returns an enumeration of all possible
- * instances of FeatureMatcherByType
- *
- * @return an Enumeration over all possible instances of
- * FeatureMatcherByType
- */
- public static java.util.Enumeration enumerate(
- ) {
- return _memberTable.elements();
- }
-
- /**
- * Method getType.Returns the type of this FeatureMatcherByType
- *
- * @return the type of this FeatureMatcherByType
- */
- public int getType(
- ) {
- return this.type;
- }
-
- /**
- * Method init.
- *
- * @return the initialized Hashtable for the member table
- */
- private static java.util.Hashtable init(
- ) {
- Hashtable members = new Hashtable();
- members.put("byLabel", BYLABEL);
- members.put("byScore", BYSCORE);
- members.put("byAttribute", BYATTRIBUTE);
- return members;
- }
-
- /**
- * Method readResolve. will be called during deserialization to
- * replace the deserialized object with the correct constant
- * instance.
- *
- * @return this deserialized object
- */
- private java.lang.Object readResolve(
- ) {
- return valueOf(this.stringValue);
- }
-
- /**
- * Method toString.Returns the String representation of this
- * FeatureMatcherByType
- *
- * @return the String representation of this FeatureMatcherByTyp
- */
- public java.lang.String toString(
- ) {
- return this.stringValue;
- }
-
- /**
- * Method valueOf.Returns a new FeatureMatcherByType based on
- * the given String value.
- *
- * @param string
- * @return the FeatureMatcherByType value of parameter 'string'
- */
- public static jalview.binding.types.FeatureMatcherByType valueOf(
- final java.lang.String string) {
- java.lang.Object obj = null;
- if (string != null) {
- obj = _memberTable.get(string);
- }
- if (obj == null) {
- String err = "" + string + " is not a valid FeatureMatcherByType";
- throw new IllegalArgumentException(err);
- }
- return (FeatureMatcherByType) obj;
- }
-
-}
diff --git a/src/jalview/binding/types/NoValueColour.java b/src/jalview/binding/types/NoValueColour.java
deleted file mode 100644
index c1540f6..0000000
--- a/src/jalview/binding/types/NoValueColour.java
+++ /dev/null
@@ -1,169 +0,0 @@
-/*
- * This class was automatically generated with
- * Castor 1.1, using an XML
- * Schema.
- * $Id$
- */
-
-package jalview.binding.types;
-
-//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import java.util.Hashtable;
-
-/**
- * Graduated feature colour if no score (or attribute) value
- *
- * @version $Revision$ $Date$
- */
-public class NoValueColour implements java.io.Serializable
-{
-
- // --------------------------/
- // - Class/Member Variables -/
- // --------------------------/
-
- /**
- * The None type
- */
- public static final int NONE_TYPE = 0;
-
- /**
- * The instance of the None type
- */
- public static final NoValueColour NONE = new NoValueColour(NONE_TYPE,
- "None");
-
- /**
- * The Min type
- */
- public static final int MIN_TYPE = 1;
-
- /**
- * The instance of the Min type
- */
- public static final NoValueColour MIN = new NoValueColour(MIN_TYPE,
- "Min");
-
- /**
- * The Max type
- */
- public static final int MAX_TYPE = 2;
-
- /**
- * The instance of the Max type
- */
- public static final NoValueColour MAX = new NoValueColour(MAX_TYPE,
- "Max");
-
- /**
- * Field _memberTable.
- */
- private static java.util.Hashtable _memberTable = init();
-
- /**
- * Field type.
- */
- private int type = -1;
-
- /**
- * Field stringValue.
- */
- private java.lang.String stringValue = null;
-
- // ----------------/
- // - Constructors -/
- // ----------------/
-
- private NoValueColour(final int type, final java.lang.String value)
- {
- super();
- this.type = type;
- this.stringValue = value;
- }
-
- // -----------/
- // - Methods -/
- // -----------/
-
- /**
- * Method enumerate.Returns an enumeration of all possible instances of
- * NoValueColour
- *
- * @return an Enumeration over all possible instances of NoValueColour
- */
- public static java.util.Enumeration enumerate()
- {
- return _memberTable.elements();
- }
-
- /**
- * Method getType.Returns the type of this NoValueColour
- *
- * @return the type of this NoValueColour
- */
- public int getType()
- {
- return this.type;
- }
-
- /**
- * Method init.
- *
- * @return the initialized Hashtable for the member table
- */
- private static java.util.Hashtable init()
- {
- Hashtable members = new Hashtable();
- members.put("None", NONE);
- members.put("Min", MIN);
- members.put("Max", MAX);
- return members;
- }
-
- /**
- * Method readResolve. will be called during deserialization to replace the
- * deserialized object with the correct constant instance.
- *
- * @return this deserialized object
- */
- private java.lang.Object readResolve()
- {
- return valueOf(this.stringValue);
- }
-
- /**
- * Method toString.Returns the String representation of this NoValueColour
- *
- * @return the String representation of this NoValueColour
- */
- public java.lang.String toString()
- {
- return this.stringValue;
- }
-
- /**
- * Method valueOf.Returns a new NoValueColour based on the given String value.
- *
- * @param string
- * @return the NoValueColour value of parameter 'string'
- */
- public static jalview.binding.types.NoValueColour valueOf(
- final java.lang.String string)
- {
- java.lang.Object obj = null;
- if (string != null)
- {
- obj = _memberTable.get(string);
- }
- if (obj == null)
- {
- String err = "" + string + " is not a valid NoValueColour";
- throw new IllegalArgumentException(err);
- }
- return (NoValueColour) obj;
- }
-
-}
diff --git a/src/jalview/commands/EditCommand.java b/src/jalview/commands/EditCommand.java
index cac843f..b9d32f7 100644
--- a/src/jalview/commands/EditCommand.java
+++ b/src/jalview/commands/EditCommand.java
@@ -20,12 +20,17 @@
*/
package jalview.commands;
+import jalview.analysis.AlignSeq;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.Annotation;
+import jalview.datamodel.ContiguousI;
+import jalview.datamodel.Range;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeaturesI;
+import jalview.util.Comparison;
import jalview.util.ReverseListIterator;
import jalview.util.StringUtils;
@@ -114,7 +119,7 @@ public class EditCommand implements CommandI
public abstract Action getUndoAction();
};
- private List
- * We assume here that for each range, start <= end. Behaviour for reverse
- * ordered ranges is undefined.
- *
- * @param ranges
- */
- public NCList(List
- * Each subrange must lie within start-end (inclusive). Subranges must be
- * ordered by start position ascending.
- *
- *
- * @param start
- * @param end
- * @return
- */
- boolean isValid(final int start, final int end)
- {
- int lastStart = start;
- for (NCNode
+ * (This test was needed when fetching transcript features as GFF. As we are
+ * now fetching as JSON, all features have type 'transcript' so the check for
+ * NMD_transcript_variant is redundant. Left in for any future case arising.)
*
* @param featureType
* @return
diff --git a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
index 9e3fef4..4da0e3c 100644
--- a/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
+++ b/src/jalview/ext/ensembl/EnsemblSequenceFetcher.java
@@ -20,6 +20,7 @@
*/
package jalview.ext.ensembl;
+import jalview.analysis.AlignmentUtils;
import jalview.bin.Cache;
import jalview.datamodel.DBRefSource;
import jalview.ws.seqfetcher.DbSourceProxyImpl;
@@ -64,7 +65,7 @@ abstract class EnsemblSequenceFetcher extends DbSourceProxyImpl
protected static final String PARENT = "Parent";
- protected static final String JSON_ID = "id";
+ protected static final String JSON_ID = AlignmentUtils.VARIANT_ID; // "id";
protected static final String OBJECT_TYPE = "object_type";
diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java
index 8832278..a5b1110 100644
--- a/src/jalview/ext/jmol/JalviewJmolBinding.java
+++ b/src/jalview/ext/jmol/JalviewJmolBinding.java
@@ -1254,7 +1254,10 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel
return chainNames;
}
- protected abstract IProgressIndicator getIProgressIndicator();
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ return null;
+ }
public void notifyNewPickingModeMeasurement(int iatom, String strMeasure)
{
diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 94b38ed..606e2e7 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -64,6 +64,7 @@ import jalview.gui.ColourMenuHelper.ColourChangeListener;
import jalview.gui.ViewSelectionMenu.ViewSetProvider;
import jalview.io.AlignmentProperties;
import jalview.io.AnnotationFile;
+import jalview.io.BackupFiles;
import jalview.io.BioJsHTMLOutput;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
@@ -733,9 +734,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
int aSize = alignPanels.size();
- tabbedPane.setVisible(aSize > 1 || ap.av.viewName != null);
+ tabbedPane.setVisible(aSize > 1 || ap.av.getViewName() != null);
- if (aSize == 1 && ap.av.viewName == null)
+ if (aSize == 1 && ap.av.getViewName() == null)
{
this.getContentPane().add(ap, BorderLayout.CENTER);
}
@@ -748,7 +749,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
expandViews.setEnabled(true);
gatherViews.setEnabled(true);
- tabbedPane.addTab(ap.av.viewName, ap);
+ tabbedPane.addTab(ap.av.getViewName(), ap);
ap.setVisible(false);
}
@@ -771,7 +772,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
gatherViews.setEnabled(true);
tabbedPane.setVisible(true);
AlignmentPanel first = alignPanels.get(0);
- tabbedPane.addTab(first.av.viewName, first);
+ tabbedPane.addTab(first.av.getViewName(), first);
this.getContentPane().add(tabbedPane, BorderLayout.CENTER);
}
@@ -872,7 +873,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
* @param av
* AlignViewport
*/
- void setMenusFromViewport(AlignViewport av)
+ public void setMenusFromViewport(AlignViewport av)
{
padGapsMenuitem.setSelected(av.isPadGaps());
colourTextMenuItem.setSelected(av.isShowColourText());
@@ -963,6 +964,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
return progressBar.operationInProgress();
}
+ /**
+ * Sets the text of the status bar. Note that setting a null or empty value
+ * will cause the status bar to be hidden, with possibly undesirable flicker
+ * of the screen layout.
+ */
@Override
public void setStatus(String text)
{
@@ -1154,7 +1160,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
shortName.lastIndexOf(java.io.File.separatorChar) + 1);
}
- success = new Jalview2XML().saveAlignment(this, file, shortName);
+ success = new jalview.project.Jalview2XML().saveAlignment(this, file,
+ shortName);
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
@@ -1186,9 +1193,13 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
}
else
{
+ // create backupfiles object and get new temp filename destination
+ BackupFiles backupfiles = new BackupFiles(file);
+
try
{
- PrintWriter out = new PrintWriter(new FileWriter(file));
+ PrintWriter out = new PrintWriter(
+ new FileWriter(backupfiles.getTempFilePath()));
out.print(output);
out.close();
@@ -1201,6 +1212,11 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
success = false;
ex.printStackTrace();
}
+
+ backupfiles.setWriteSuccess(success);
+ // do the backup file roll and rename the temp file to actual file
+ success = backupfiles.rollBackupsAndRenameTempFile();
+
}
}
@@ -2397,15 +2413,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
@Override
public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)
{
- SequenceGroup sg = new SequenceGroup();
-
- for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)
- {
- sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);
- }
+ SequenceGroup sg = new SequenceGroup(
+ viewport.getAlignment().getSequences());
sg.setEndRes(viewport.getAlignment().getWidth() - 1);
viewport.setSelectionGroup(sg);
+ viewport.isSelectionGroupChanged(true);
viewport.sendSelection();
// JAL-2034 - should delegate to
// alignPanel to decide if overview needs
@@ -2701,7 +2714,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
/*
* Create a new AlignmentPanel (with its own, new Viewport)
*/
- AlignmentPanel newap = new Jalview2XML().copyAlignPanel(alignPanel);
+ AlignmentPanel newap = new jalview.project.Jalview2XML()
+ .copyAlignPanel(alignPanel);
if (!copyAnnotation)
{
/*
@@ -2713,10 +2727,10 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
newap.av.setGatherViewsHere(false);
- if (viewport.viewName == null)
+ if (viewport.getViewName() == null)
{
- viewport.viewName = MessageManager
- .getString("label.view_name_original");
+ viewport.setViewName(MessageManager
+ .getString("label.view_name_original"));
}
/*
@@ -2740,7 +2754,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
newap.refresh(true); // adjust layout of annotations
}
- newap.av.viewName = getNewViewName(viewTitle);
+ newap.av.setViewName(getNewViewName(viewTitle));
addAlignmentPanel(newap, true);
newap.alignmentChanged();
@@ -2803,9 +2817,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (comp instanceof AlignmentPanel)
{
AlignmentPanel ap = (AlignmentPanel) comp;
- if (!existingNames.contains(ap.av.viewName))
+ if (!existingNames.contains(ap.av.getViewName()))
{
- existingNames.add(ap.av.viewName);
+ existingNames.add(ap.av.getViewName());
}
}
}
@@ -2888,7 +2902,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
viewport.setFollowHighlight(state);
if (state)
{
- alignPanel.scrollToPosition(viewport.getSearchResults(), false);
+ alignPanel.scrollToPosition(viewport.getSearchResults());
}
}
@@ -3597,9 +3611,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
frameTitle += " from ";
- if (viewport.viewName != null)
+ if (viewport.getViewName() != null)
{
- frameTitle += viewport.viewName + " of ";
+ frameTitle += viewport.getViewName() + " of ";
}
frameTitle += this.title;
@@ -4767,7 +4781,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (reply != null)
{
- viewport.viewName = reply;
+ viewport.setViewName(reply);
// TODO warn if reply is in getExistingViewNames()?
tabbedPane.setTitleAt(tabbedPane.getSelectedIndex(), reply);
}
@@ -5399,7 +5413,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
*/
public List extends AlignmentViewPanel> getAlignPanels()
{
- return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ // alignPanels is never null
+ // return alignPanels == null ? Arrays.asList(alignPanel) : alignPanels;
+ return alignPanels;
}
/**
diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 7e77bec..f94b74d 100644
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -79,7 +79,7 @@ public class AlignViewport extends AlignmentViewport
private Rectangle explodedGeometry;
- String viewName;
+ private String viewName;
/*
* Flag set true on the view that should 'gather' multiple views of the same
@@ -795,7 +795,7 @@ public class AlignViewport extends AlignmentViewport
AlignFrame newAlignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
AlignFrame.DEFAULT_HEIGHT);
newAlignFrame.setTitle(title);
- newAlignFrame.statusBar.setText(MessageManager
+ newAlignFrame.setStatus(MessageManager
.formatMessage("label.successfully_loaded_file", new Object[]
{ title }));
@@ -1032,4 +1032,14 @@ public class AlignViewport extends AlignmentViewport
}
fr.setTransparency(featureSettings.getTransparency());
}
+
+ public String getViewName()
+ {
+ return viewName;
+ }
+
+ public void setViewName(String viewName)
+ {
+ this.viewName = viewName;
+ }
}
diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java
index 60ef480..82e2113 100644
--- a/src/jalview/gui/AlignmentPanel.java
+++ b/src/jalview/gui/AlignmentPanel.java
@@ -328,12 +328,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
}
/**
- * Highlight the given results on the alignment.
+ * Highlight the given results on the alignment
*
*/
public void highlightSearchResults(SearchResultsI results)
{
- boolean scrolled = scrollToPosition(results, 0, true, false);
+ boolean scrolled = scrollToPosition(results, 0, false);
boolean noFastPaint = scrolled && av.getWrapAlignment();
@@ -345,13 +345,11 @@ public class AlignmentPanel extends GAlignmentPanel implements
* (if any)
*
* @param searchResults
- * @param redrawOverview
* @return
*/
- public boolean scrollToPosition(SearchResultsI searchResults,
- boolean redrawOverview)
+ public boolean scrollToPosition(SearchResultsI searchResults)
{
- return scrollToPosition(searchResults, 0, redrawOverview, false);
+ return scrollToPosition(searchResults, 0, false);
}
/**
@@ -364,14 +362,12 @@ public class AlignmentPanel extends GAlignmentPanel implements
* @param verticalOffset
* if greater than zero, allows scrolling to a position below the
* first displayed sequence
- * @param redrawOverview
- * - when set, the overview will be recalculated (takes longer)
* @param centre
* if true, try to centre the search results horizontally in the view
* @return
*/
protected boolean scrollToPosition(SearchResultsI results,
- int verticalOffset, boolean redrawOverview, boolean centre)
+ int verticalOffset, boolean centre)
{
int startv, endv, starts, ends;
ViewportRanges ranges = av.getRanges();
@@ -477,7 +473,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
scrollNeeded = ranges.scrollToWrappedVisible(start);
}
- paintAlignment(redrawOverview, false);
+ paintAlignment(false, false);
return scrollNeeded;
}
@@ -1567,7 +1563,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
@Override
public String getViewName()
{
- return av.viewName;
+ return av.getViewName();
}
/**
@@ -1698,7 +1694,7 @@ public class AlignmentPanel extends GAlignmentPanel implements
*/
protected void scrollToCentre(SearchResultsI sr, int verticalOffset)
{
- scrollToPosition(sr, verticalOffset, true, true);
+ scrollToPosition(sr, verticalOffset, true);
}
/**
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 6f8b225..6da6cc3 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -51,12 +51,9 @@ import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.awt.geom.AffineTransform;
-import java.awt.image.BufferedImage;
-import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.Iterator;
-import java.util.regex.Pattern;
import javax.swing.JCheckBoxMenuItem;
import javax.swing.JMenuItem;
@@ -73,6 +70,10 @@ import javax.swing.ToolTipManager;
public class AnnotationLabels extends JPanel
implements MouseListener, MouseMotionListener, ActionListener
{
+ private static final String HTML_END_TAG = "
+ *
+ *
+ * @param command
+ * the Cut command
+ * @param seq
+ * the sequence the Cut applied to
+ * @param start
+ * the start residue position of the cut
+ * @param length
+ * the number of residues cut
+ * @param sameDatasetSequence
+ * true if dataset sequence and frame of reference were left
+ * unchanged by the Cut
+ */
+ final static void undoCutFeatures(Edit command, SequenceI seq,
+ final int start, final int length, boolean sameDatasetSequence)
{
- SequenceI seq = command.seqs[index];
SequenceI sequence = seq.getDatasetSequence();
if (sequence == null)
{
sequence = seq;
}
- if (insert)
+ /*
+ * shift right features that lie to the right of the restored cut (but not
+ * if dataset sequence unchanged - so coordinates were changed by Cut)
+ */
+ if (!sameDatasetSequence)
{
- if (command.editedFeatures != null
- && command.editedFeatures.containsKey(seq))
+ /*
+ * shift right all features right of and not
+ * contiguous with the cut position
+ */
+ seq.getFeatures().shiftFeatures(start + 1, length);
+
+ /*
+ * shift right any features that start at the cut position,
+ * unless they were truncated
+ */
+ List
+ *
+ *
+ * @param command
+ * @param seq
+ * @param fromPosition
+ * @param toPosition
+ * @param cutIsInternal
+ */
+ protected static void cutFeatures(Edit command, SequenceI seq,
+ int fromPosition, int toPosition, boolean cutIsInternal)
+ {
+ /*
+ * if the cut is at start or end of sequence
+ * then we don't modify the sequence feature store
+ */
+ if (!cutIsInternal)
+ {
+ return;
+ }
+ List
- * Nested Containment List (NCList): a new algorithm for accelerating
- * interval query of genome alignment and interval databases
- * - Alexander V. Alekseyenko, Christopher J. Lee
- * https://doi.org/10.1093/bioinformatics/btl647
- *
- */
-public class NCList
- * [1-100 [10-30 [10-20]], 15-30 [20-20]]
- *
- */
- @Override
- public String toString()
- {
- return subranges.toString();
- }
-
- /**
- * Returns a string representation of the data where containment is shown by
- * indentation on new lines
- *
- * @return
- */
- public String prettyPrint()
- {
- StringBuilder sb = new StringBuilder(512);
- int offset = 0;
- int indent = 2;
- prettyPrint(sb, offset, indent);
- sb.append(System.lineSeparator());
- return sb.toString();
- }
-
- /**
- * @param sb
- * @param offset
- * @param indent
- */
- void prettyPrint(StringBuilder sb, int offset, int indent)
- {
- boolean first = true;
- for (NCNode
- * [1-100 [10-30 [10-20]], 15-30 [20-20]]
- *
- */
- @Override
- public String toString() {
- StringBuilder sb = new StringBuilder(10 * size);
- sb.append(region.getBegin()).append("-").append(region.getEnd());
- if (subregions != null)
- {
- sb.append(" ").append(subregions.toString());
- }
- return sb.toString();
- }
-
- void prettyPrint(StringBuilder sb, int offset, int indent) {
- for (int i = 0 ; i < offset ; i++) {
- sb.append(" ");
- }
- sb.append(region.getBegin()).append("-").append(region.getEnd());
- if (subregions != null)
- {
- sb.append(System.lineSeparator());
- subregions.prettyPrint(sb, offset + 2, indent);
- }
- }
- /**
- * Add any ranges that overlap the from-to range to the result list
- *
- * @param from
- * @param to
- * @param result
- */
- void findOverlaps(long from, long to, List