--- /dev/null
+/*
+ * This class was automatically generated with
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2;
+
+ //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+
+/**
+ * Reference to a viewer showing RNA structure
+ * for this sequence. Schema supports one viewer showing multiple
+ * annotations for multiple sequences, though currently only one
+ * annotation for one sequence (gapped or trimmed) is used
+ *
+ *
+ * @version $Revision$ $Date$
+ */
+public class RnaViewer implements java.io.Serializable {
+
+
+ //--------------------------/
+ //- Class/Member Variables -/
+ //--------------------------/
+
+ /**
+ * Field _title.
+ */
+ private java.lang.String _title;
+
+ /**
+ * An id unique to the RNA viewer panel
+ *
+ */
+ private java.lang.String _viewId;
+
+ /**
+ * horizontal position of split pane divider
+ *
+ */
+ private int _dividerLocation;
+
+ /**
+ * keeps track of state for field: _dividerLocation
+ */
+ private boolean _has_dividerLocation;
+
+ /**
+ * Index of the selected structure in the
+ * viewer panel
+ *
+ */
+ private int _selectedRna;
+
+ /**
+ * keeps track of state for field: _selectedRna
+ */
+ private boolean _has_selectedRna;
+
+ /**
+ * 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 _secondaryStructureList.
+ */
+ private java.util.Vector _secondaryStructureList;
+
+
+ //----------------/
+ //- Constructors -/
+ //----------------/
+
+ public RnaViewer() {
+ super();
+ this._secondaryStructureList = new java.util.Vector();
+ }
+
+
+ //-----------/
+ //- Methods -/
+ //-----------/
+
+ /**
+ *
+ *
+ * @param vSecondaryStructure
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSecondaryStructure(
+ final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
+ throws java.lang.IndexOutOfBoundsException {
+ this._secondaryStructureList.addElement(vSecondaryStructure);
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSecondaryStructure
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void addSecondaryStructure(
+ final int index,
+ final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
+ throws java.lang.IndexOutOfBoundsException {
+ this._secondaryStructureList.add(index, vSecondaryStructure);
+ }
+
+ /**
+ */
+ public void deleteDividerLocation(
+ ) {
+ this._has_dividerLocation= false;
+ }
+
+ /**
+ */
+ public void deleteHeight(
+ ) {
+ this._has_height= false;
+ }
+
+ /**
+ */
+ public void deleteSelectedRna(
+ ) {
+ this._has_selectedRna= false;
+ }
+
+ /**
+ */
+ public void deleteWidth(
+ ) {
+ this._has_width= false;
+ }
+
+ /**
+ */
+ public void deleteXpos(
+ ) {
+ this._has_xpos= false;
+ }
+
+ /**
+ */
+ public void deleteYpos(
+ ) {
+ this._has_ypos= false;
+ }
+
+ /**
+ * Method enumerateSecondaryStructure.
+ *
+ * @return an Enumeration over all
+ * jalview.schemabinding.version2.SecondaryStructure elements
+ */
+ public java.util.Enumeration enumerateSecondaryStructure(
+ ) {
+ return this._secondaryStructureList.elements();
+ }
+
+ /**
+ * Returns the value of field 'dividerLocation'. The field
+ * 'dividerLocation' has the following description: horizontal
+ * position of split pane divider
+ *
+ *
+ * @return the value of field 'DividerLocation'.
+ */
+ public int getDividerLocation(
+ ) {
+ return this._dividerLocation;
+ }
+
+ /**
+ * Returns the value of field 'height'.
+ *
+ * @return the value of field 'Height'.
+ */
+ public int getHeight(
+ ) {
+ return this._height;
+ }
+
+ /**
+ * Method getSecondaryStructure.
+ *
+ * @param index
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ * @return the value of the
+ * jalview.schemabinding.version2.SecondaryStructure at the
+ * given index
+ */
+ public jalview.schemabinding.version2.SecondaryStructure getSecondaryStructure(
+ final int index)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._secondaryStructureList.size()) {
+ throw new IndexOutOfBoundsException("getSecondaryStructure: Index value '" + index + "' not in range [0.." + (this._secondaryStructureList.size() - 1) + "]");
+ }
+
+ return (jalview.schemabinding.version2.SecondaryStructure) _secondaryStructureList.get(index);
+ }
+
+ /**
+ * Method getSecondaryStructure.Returns the contents of the
+ * collection in an Array. <p>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 <i>know</i> that the Array returned is of
+ * exactly the correct length.
+ *
+ * @return this collection as an Array
+ */
+ public jalview.schemabinding.version2.SecondaryStructure[] getSecondaryStructure(
+ ) {
+ jalview.schemabinding.version2.SecondaryStructure[] array = new jalview.schemabinding.version2.SecondaryStructure[0];
+ return (jalview.schemabinding.version2.SecondaryStructure[]) this._secondaryStructureList.toArray(array);
+ }
+
+ /**
+ * Method getSecondaryStructureCount.
+ *
+ * @return the size of this collection
+ */
+ public int getSecondaryStructureCount(
+ ) {
+ return this._secondaryStructureList.size();
+ }
+
+ /**
+ * Returns the value of field 'selectedRna'. The field
+ * 'selectedRna' has the following description: Index of the
+ * selected structure in the
+ * viewer panel
+ *
+ *
+ * @return the value of field 'SelectedRna'.
+ */
+ public int getSelectedRna(
+ ) {
+ return this._selectedRna;
+ }
+
+ /**
+ * 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 'viewId'. The field 'viewId' has
+ * the following description: An id unique to the RNA viewer
+ * panel
+ *
+ *
+ * @return the value of field 'ViewId'.
+ */
+ public java.lang.String getViewId(
+ ) {
+ return this._viewId;
+ }
+
+ /**
+ * 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 hasDividerLocation.
+ *
+ * @return true if at least one DividerLocation has been added
+ */
+ public boolean hasDividerLocation(
+ ) {
+ return this._has_dividerLocation;
+ }
+
+ /**
+ * Method hasHeight.
+ *
+ * @return true if at least one Height has been added
+ */
+ public boolean hasHeight(
+ ) {
+ return this._has_height;
+ }
+
+ /**
+ * Method hasSelectedRna.
+ *
+ * @return true if at least one SelectedRna has been added
+ */
+ public boolean hasSelectedRna(
+ ) {
+ return this._has_selectedRna;
+ }
+
+ /**
+ * 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;
+ }
+
+ /**
+ * 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 removeAllSecondaryStructure(
+ ) {
+ this._secondaryStructureList.clear();
+ }
+
+ /**
+ * Method removeSecondaryStructure.
+ *
+ * @param vSecondaryStructure
+ * @return true if the object was removed from the collection.
+ */
+ public boolean removeSecondaryStructure(
+ final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure) {
+ boolean removed = _secondaryStructureList.remove(vSecondaryStructure);
+ return removed;
+ }
+
+ /**
+ * Method removeSecondaryStructureAt.
+ *
+ * @param index
+ * @return the element removed from the collection
+ */
+ public jalview.schemabinding.version2.SecondaryStructure removeSecondaryStructureAt(
+ final int index) {
+ java.lang.Object obj = this._secondaryStructureList.remove(index);
+ return (jalview.schemabinding.version2.SecondaryStructure) obj;
+ }
+
+ /**
+ * Sets the value of field 'dividerLocation'. The field
+ * 'dividerLocation' has the following description: horizontal
+ * position of split pane divider
+ *
+ *
+ * @param dividerLocation the value of field 'dividerLocation'.
+ */
+ public void setDividerLocation(
+ final int dividerLocation) {
+ this._dividerLocation = dividerLocation;
+ this._has_dividerLocation = 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;
+ }
+
+ /**
+ *
+ *
+ * @param index
+ * @param vSecondaryStructure
+ * @throws java.lang.IndexOutOfBoundsException if the index
+ * given is outside the bounds of the collection
+ */
+ public void setSecondaryStructure(
+ final int index,
+ final jalview.schemabinding.version2.SecondaryStructure vSecondaryStructure)
+ throws java.lang.IndexOutOfBoundsException {
+ // check bounds for index
+ if (index < 0 || index >= this._secondaryStructureList.size()) {
+ throw new IndexOutOfBoundsException("setSecondaryStructure: Index value '" + index + "' not in range [0.." + (this._secondaryStructureList.size() - 1) + "]");
+ }
+
+ this._secondaryStructureList.set(index, vSecondaryStructure);
+ }
+
+ /**
+ *
+ *
+ * @param vSecondaryStructureArray
+ */
+ public void setSecondaryStructure(
+ final jalview.schemabinding.version2.SecondaryStructure[] vSecondaryStructureArray) {
+ //-- copy array
+ _secondaryStructureList.clear();
+
+ for (int i = 0; i < vSecondaryStructureArray.length; i++) {
+ this._secondaryStructureList.add(vSecondaryStructureArray[i]);
+ }
+ }
+
+ /**
+ * Sets the value of field 'selectedRna'. The field
+ * 'selectedRna' has the following description: Index of the
+ * selected structure in the
+ * viewer panel
+ *
+ *
+ * @param selectedRna the value of field 'selectedRna'.
+ */
+ public void setSelectedRna(
+ final int selectedRna) {
+ this._selectedRna = selectedRna;
+ this._has_selectedRna = 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 'viewId'. The field 'viewId' has the
+ * following description: An id unique to the RNA viewer panel
+ *
+ *
+ * @param viewId the value of field 'viewId'.
+ */
+ public void setViewId(
+ final java.lang.String viewId) {
+ this._viewId = viewId;
+ }
+
+ /**
+ * 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.schemabinding.version2.RnaViewer
+ */
+ public static jalview.schemabinding.version2.RnaViewer unmarshal(
+ final java.io.Reader reader)
+ throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+ return (jalview.schemabinding.version2.RnaViewer) Unmarshaller.unmarshal(jalview.schemabinding.version2.RnaViewer.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);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff