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.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. + *
+ * 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.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); + } }