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/features/featuresFormat.html b/help/html/features/featuresFormat.html index fd6b99f..4d13dcd 100755 --- a/help/html/features/featuresFormat.html +++ b/help/html/features/featuresFormat.html @@ -60,7 +60,10 @@ contains tab separated text fields. No comments are allowed.
-The first set of lines contain type definitions: +
+ Feature Colours +
+The first set of lines contain feature type definitions and their colours:
Feature label Feature Colour @@ -72,21 +75,37 @@
-[label|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<thresholdtype>|[<threshold value>]] +[label or score or attribute|attName|]<mincolor>|<maxcolor>|[absolute|]<minvalue>|<maxvalue>[|<novalue>][|<thresholdtype>|[<threshold value>]]The fields are as follows:
+ Feature Filters +
+This section is optional, and allows one or more filters to be defined for each feature type.
+
Only features that satisfy the filter conditions will be displayed.
+
Begin with a line which is just STARTFILTERS, and end with a line which is just ENDFILTERS.
+
Each line has the format:
+
featureType <tab> (filtercondition1) [and|or] (filtercondition2) [and|or]...+ The parentheses are not needed if there is only one condition. + Combine multiple conditions with either and or or (but not a mixture). +
Label or Score or AttributeName condition [value]+ where either the label (description), (numeric) score, or (text or numeric) attribute is tested against the condition. +
+ Feature Instances +
+The remaining lines in the file are the sequence annotation definitions, where the now defined features are attached to regions on particular sequences. Each feature can optionally include some descriptive text which is displayed in a tooltip when the mouse is - near the feature on that sequence (and can also be used to generate - a colour the feature).
+ near the feature on that sequence (and may also be used to generate + a colour for the feature).If your sequence annotation is already available in GFF2 (http://gmod.org/wiki/GFF2) or @@ -204,6 +262,13 @@ signal peptide 0,155,165 helix ff0000 strand 00ff00 coil cccccc +kdHydrophobicity ccffcc|333300|-3.9|4.5|above|-2.0 + +STARTFILTERS +metal ion-binding site Label Contains sulfur +kdHydrophobicity (Score LT 1.5) OR (Score GE 2.8) +ENDFILTERS + Your Own description here FER_CAPAA -1 3 93 domain Your Own description here FER_CAPAN -1 48 144 chain Your Own description here FER_CAPAN -1 50 140 domain @@ -211,10 +276,16 @@ Your Own description here FER_CAPAN -1 136 136 modified residue Your Own description here FER1_LYCES -1 1 47 transit peptide Your Own description here Q93XJ9_SOLTU -1 1 48 signal peptide Your Own description here Q93XJ9_SOLTU -1 49 144 chain -startgroup secondarystucture + +STARTGROUP secondarystucture PDB secondary structure annotation FER1_SPIOL -1 52 59 strand PDB secondary structure annotation FER1_SPIOL -1 74 80 helix -endgroup secondarystructure +ENDGROUP secondarystructure + +STARTGROUP kd +Hydrophobicity score by kD Q93XJ9_SOLTU -1 48 48 kdHydrophobicity 1.8 +ENDGROUP kd + GFF FER_CAPAA GffGroup domain 3 93 . . 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 {
+ * Answers false if not a graduated colour, or no threshold is set, or value + * is not outwith the threshold, or value is null or non-numeric. + * + * @param sf + * @return + */ + boolean isOutwithThreshold(SequenceFeature sf); } diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java index cf3c8da..404c497 100644 --- a/src/jalview/api/FeatureRenderer.java +++ b/src/jalview/api/FeatureRenderer.java @@ -255,14 +255,29 @@ public interface FeatureRenderer *
* 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/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 6fefbd0..fac531e 100644
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -20,11 +20,10 @@
*/
package jalview.gui;
-import jalview.api.FeatureColourI;
+import jalview.api.FeatureRenderer;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.FeatureMatcherSetI;
import jalview.io.AnnotationFile;
import jalview.io.FeaturesFile;
import jalview.io.JalviewFileChooser;
@@ -38,8 +37,6 @@ import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.io.FileWriter;
import java.io.PrintWriter;
-import java.util.List;
-import java.util.Map;
import javax.swing.BorderFactory;
import javax.swing.ButtonGroup;
@@ -214,24 +211,18 @@ public class AnnotationExporter extends JPanel
{
String text;
SequenceI[] sequences = ap.av.getAlignment().getSequencesArray();
- Map
+ *
+ *
+ * @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