X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FStructureState.java;fp=src%2Fjalview%2Fschemabinding%2Fversion2%2FStructureState.java;h=0000000000000000000000000000000000000000;hb=74393b51f368cb9f58589472d432a433d9c4386d;hp=186e4e690ffc30ed2f292c9f9f7ee668faefa59e;hpb=7a0d503181fe41452120a8a02ca63476392aa08c;p=jalview.git diff --git a/src/jalview/schemabinding/version2/StructureState.java b/src/jalview/schemabinding/version2/StructureState.java deleted file mode 100644 index 186e4e6..0000000 --- a/src/jalview/schemabinding/version2/StructureState.java +++ /dev/null @@ -1,706 +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; - -/** - * Class StructureState. - * - * @version $Revision$ $Date$ - */ -public class StructureState implements java.io.Serializable -{ - - // --------------------------/ - // - Class/Member Variables -/ - // --------------------------/ - - /** - * internal content storage - */ - private java.lang.String _content = ""; - - /** - * Field _visible. - */ - private boolean _visible; - - /** - * keeps track of state for field: _visible - */ - private boolean _has_visible; - - /** - * additional identifier which properly disambiguates the structure view from - * any other view with the same attributes. This is not an ID, because it is - * possible to have many references to the same physical structure view from - * different sequences in an alignment. A structureState element citing the - * same viewId will appear for each instance. - * - */ - private java.lang.String _viewId; - - /** - * Flag set if the alignment panel containing this JSeq should be included in - * those used to perform a structure superposition (since Jalview 2.7). - * - */ - private boolean _alignwithAlignPanel = true; - - /** - * keeps track of state for field: _alignwithAlignPanel - */ - private boolean _has_alignwithAlignPanel; - - /** - * Flag set if the alignment panel containing this JSeq should be included in - * those used to colour its associated sequences in this structureState(since - * Jalview 2.7). - * - */ - private boolean _colourwithAlignPanel = false; - - /** - * keeps track of state for field: _colourwithAlignPanel - */ - private boolean _has_colourwithAlignPanel; - - /** - * Flag set if the structure display is coloured by the Jmol state, rather - * than by one or more linked alignment views. - * - */ - private boolean _colourByJmol = true; - - /** - * keeps track of state for field: _colourByJmol - */ - private boolean _has_colourByJmol; - - /** - * An identifier for the viewer type, currently either JMOL or CHIMERA - * - */ - private java.lang.String _type; - - /** - * 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; - - // ----------------/ - // - Constructors -/ - // ----------------/ - - public StructureState() - { - super(); - setContent(""); - } - - // -----------/ - // - Methods -/ - // -----------/ - - /** - */ - public void deleteAlignwithAlignPanel() - { - this._has_alignwithAlignPanel = false; - } - - /** - */ - public void deleteColourByJmol() - { - this._has_colourByJmol = false; - } - - /** - */ - public void deleteColourwithAlignPanel() - { - this._has_colourwithAlignPanel = false; - } - - /** - */ - public void deleteHeight() - { - this._has_height = false; - } - - /** - */ - public void deleteVisible() - { - this._has_visible = 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 'alignwithAlignPanel'. The field - * 'alignwithAlignPanel' has the following description: Flag set if the - * alignment panel containing this JSeq should be included in those used to - * perform a structure superposition (since Jalview 2.7). - * - * - * @return the value of field 'AlignwithAlignPanel'. - */ - public boolean getAlignwithAlignPanel() - { - return this._alignwithAlignPanel; - } - - /** - * Returns the value of field 'colourByJmol'. The field 'colourByJmol' has the - * following description: Flag set if the structure display is coloured by the - * Jmol state, rather than by one or more linked alignment views. - * - * - * @return the value of field 'ColourByJmol'. - */ - public boolean getColourByJmol() - { - return this._colourByJmol; - } - - /** - * Returns the value of field 'colourwithAlignPanel'. The field - * 'colourwithAlignPanel' has the following description: Flag set if the - * alignment panel containing this JSeq should be included in those used to - * colour its associated sequences in this structureState(since Jalview 2.7). - * - * - * @return the value of field 'ColourwithAlignPanel'. - */ - public boolean getColourwithAlignPanel() - { - return this._colourwithAlignPanel; - } - - /** - * Returns the value of field 'content'. The field 'content' has the following - * description: internal content storage - * - * @return the value of field 'Content'. - */ - public java.lang.String getContent() - { - return this._content; - } - - /** - * Returns the value of field 'height'. - * - * @return the value of field 'Height'. - */ - public int getHeight() - { - return this._height; - } - - /** - * Returns the value of field 'type'. The field 'type' has the following - * description: An identifier for the viewer type, currently either JMOL or - * CHIMERA - * - * - * @return the value of field 'Type'. - */ - public java.lang.String getType() - { - return this._type; - } - - /** - * Returns the value of field 'viewId'. The field 'viewId' has the following - * description: additional identifier which properly disambiguates the - * structure view from any other view with the same attributes. This is not an - * ID, because it is possible to have many references to the same physical - * structure view from different sequences in an alignment. A structureState - * element citing the same viewId will appear for each instance. - * - * - * @return the value of field 'ViewId'. - */ - public java.lang.String getViewId() - { - return this._viewId; - } - - /** - * Returns the value of field 'visible'. - * - * @return the value of field 'Visible'. - */ - public boolean getVisible() - { - return this._visible; - } - - /** - * 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 hasAlignwithAlignPanel. - * - * @return true if at least one AlignwithAlignPanel has been added - */ - public boolean hasAlignwithAlignPanel() - { - return this._has_alignwithAlignPanel; - } - - /** - * Method hasColourByJmol. - * - * @return true if at least one ColourByJmol has been added - */ - public boolean hasColourByJmol() - { - return this._has_colourByJmol; - } - - /** - * Method hasColourwithAlignPanel. - * - * @return true if at least one ColourwithAlignPanel has been added - */ - public boolean hasColourwithAlignPanel() - { - return this._has_colourwithAlignPanel; - } - - /** - * Method hasHeight. - * - * @return true if at least one Height has been added - */ - public boolean hasHeight() - { - return this._has_height; - } - - /** - * Method hasVisible. - * - * @return true if at least one Visible has been added - */ - public boolean hasVisible() - { - return this._has_visible; - } - - /** - * 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 'alignwithAlignPanel'. The field - * 'alignwithAlignPanel' has the following description: Flag set if the - * alignment panel containing this JSeq should be included in those used to - * perform a structure superposition (since Jalview 2.7). - * - * - * @return the value of field 'AlignwithAlignPanel'. - */ - public boolean isAlignwithAlignPanel() - { - return this._alignwithAlignPanel; - } - - /** - * Returns the value of field 'colourByJmol'. The field 'colourByJmol' has the - * following description: Flag set if the structure display is coloured by the - * Jmol state, rather than by one or more linked alignment views. - * - * - * @return the value of field 'ColourByJmol'. - */ - public boolean isColourByJmol() - { - return this._colourByJmol; - } - - /** - * Returns the value of field 'colourwithAlignPanel'. The field - * 'colourwithAlignPanel' has the following description: Flag set if the - * alignment panel containing this JSeq should be included in those used to - * colour its associated sequences in this structureState(since Jalview 2.7). - * - * - * @return the value of field 'ColourwithAlignPanel'. - */ - public boolean isColourwithAlignPanel() - { - return this._colourwithAlignPanel; - } - - /** - * 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 'visible'. - * - * @return the value of field 'Visible'. - */ - public boolean isVisible() - { - return this._visible; - } - - /** - * - * - * @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 'alignwithAlignPanel'. The field - * 'alignwithAlignPanel' has the following description: Flag set if the - * alignment panel containing this JSeq should be included in those used to - * perform a structure superposition (since Jalview 2.7). - * - * - * @param alignwithAlignPanel - * the value of field 'alignwithAlignPanel'. - */ - public void setAlignwithAlignPanel(final boolean alignwithAlignPanel) - { - this._alignwithAlignPanel = alignwithAlignPanel; - this._has_alignwithAlignPanel = true; - } - - /** - * Sets the value of field 'colourByJmol'. The field 'colourByJmol' has the - * following description: Flag set if the structure display is coloured by the - * Jmol state, rather than by one or more linked alignment views. - * - * - * @param colourByJmol - * the value of field 'colourByJmol'. - */ - public void setColourByJmol(final boolean colourByJmol) - { - this._colourByJmol = colourByJmol; - this._has_colourByJmol = true; - } - - /** - * Sets the value of field 'colourwithAlignPanel'. The field - * 'colourwithAlignPanel' has the following description: Flag set if the - * alignment panel containing this JSeq should be included in those used to - * colour its associated sequences in this structureState(since Jalview 2.7). - * - * - * @param colourwithAlignPanel - * the value of field 'colourwithAlignPanel'. - */ - public void setColourwithAlignPanel(final boolean colourwithAlignPanel) - { - this._colourwithAlignPanel = colourwithAlignPanel; - this._has_colourwithAlignPanel = true; - } - - /** - * Sets the value of field 'content'. The field 'content' has the following - * description: internal content storage - * - * @param content - * the value of field 'content'. - */ - public void setContent(final java.lang.String content) - { - this._content = content; - } - - /** - * 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 'type'. The field 'type' has the following - * description: An identifier for the viewer type, currently either JMOL or - * CHIMERA - * - * - * @param type - * the value of field 'type'. - */ - public void setType(final java.lang.String type) - { - this._type = type; - } - - /** - * Sets the value of field 'viewId'. The field 'viewId' has the following - * description: additional identifier which properly disambiguates the - * structure view from any other view with the same attributes. This is not an - * ID, because it is possible to have many references to the same physical - * structure view from different sequences in an alignment. A structureState - * element citing the same viewId will appear for each instance. - * - * - * @param viewId - * the value of field 'viewId'. - */ - public void setViewId(final java.lang.String viewId) - { - this._viewId = viewId; - } - - /** - * Sets the value of field 'visible'. - * - * @param visible - * the value of field 'visible'. - */ - public void setVisible(final boolean visible) - { - this._visible = visible; - this._has_visible = true; - } - - /** - * 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.StructureState - */ - public static jalview.schemabinding.version2.StructureState unmarshal( - final java.io.Reader reader) - throws org.exolab.castor.xml.MarshalException, - org.exolab.castor.xml.ValidationException - { - return (jalview.schemabinding.version2.StructureState) Unmarshaller - .unmarshal(jalview.schemabinding.version2.StructureState.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); - } - -}