X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FRnaViewer.java;fp=src%2Fjalview%2Fschemabinding%2Fversion2%2FRnaViewer.java;h=0000000000000000000000000000000000000000;hb=116f357c7b1056f7c20dd0f7ecbcb50ea50e4e72;hp=543d053971d5b08583d9dabafd0f292db4903dc0;hpb=3997675132f682a045f2074c31dceedfbc1a3895;p=jalview.git diff --git a/src/jalview/schemabinding/version2/RnaViewer.java b/src/jalview/schemabinding/version2/RnaViewer.java deleted file mode 100644 index 543d053..0000000 --- a/src/jalview/schemabinding/version2/RnaViewer.java +++ /dev/null @@ -1,668 +0,0 @@ -/* - * This class was automatically generated with - * Castor 1.1, 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. - *

- * 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); - } - -}