package jalview.schemabinding.version2;
- //---------------------------------/
- //- Imported classes and packages -/
+//---------------------------------/
+//- 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
- *
+ * 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);
- }
+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