-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package jalview.schemabinding.version2;\r
-\r
- //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.IOException;\r
-import java.io.Reader;\r
-import java.io.Serializable;\r
-import java.io.Writer;\r
-import org.exolab.castor.xml.MarshalException;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-import org.exolab.castor.xml.ValidationException;\r
-import org.xml.sax.ContentHandler;\r
-\r
-/**\r
- * Class StructureState.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class StructureState implements java.io.Serializable {\r
-\r
-\r
- //--------------------------/\r
- //- Class/Member Variables -/\r
- //--------------------------/\r
-\r
- /**\r
- * internal content storage\r
- */\r
- private java.lang.String _content = "";\r
-\r
- /**\r
- * Field _visible\r
- */\r
- private boolean _visible;\r
-\r
- /**\r
- * keeps track of state for field: _visible\r
- */\r
- private boolean _has_visible;\r
-\r
- /**\r
- * Field _xpos\r
- */\r
- private int _xpos;\r
-\r
- /**\r
- * keeps track of state for field: _xpos\r
- */\r
- private boolean _has_xpos;\r
-\r
- /**\r
- * Field _ypos\r
- */\r
- private int _ypos;\r
-\r
- /**\r
- * keeps track of state for field: _ypos\r
- */\r
- private boolean _has_ypos;\r
-\r
- /**\r
- * Field _width\r
- */\r
- private int _width;\r
-\r
- /**\r
- * keeps track of state for field: _width\r
- */\r
- private boolean _has_width;\r
-\r
- /**\r
- * Field _height\r
- */\r
- private int _height;\r
-\r
- /**\r
- * keeps track of state for field: _height\r
- */\r
- private boolean _has_height;\r
-\r
-\r
- //----------------/\r
- //- Constructors -/\r
- //----------------/\r
-\r
- public StructureState() {\r
- super();\r
- setContent("");\r
- } //-- jalview.schemabinding.version2.StructureState()\r
-\r
-\r
- //-----------/\r
- //- Methods -/\r
- //-----------/\r
-\r
- /**\r
- * Method deleteHeight\r
- * \r
- */\r
- public void deleteHeight()\r
- {\r
- this._has_height= false;\r
- } //-- void deleteHeight() \r
-\r
- /**\r
- * Method deleteVisible\r
- * \r
- */\r
- public void deleteVisible()\r
- {\r
- this._has_visible= false;\r
- } //-- void deleteVisible() \r
-\r
- /**\r
- * Method deleteWidth\r
- * \r
- */\r
- public void deleteWidth()\r
- {\r
- this._has_width= false;\r
- } //-- void deleteWidth() \r
-\r
- /**\r
- * Method deleteXpos\r
- * \r
- */\r
- public void deleteXpos()\r
- {\r
- this._has_xpos= false;\r
- } //-- void deleteXpos() \r
-\r
- /**\r
- * Method deleteYpos\r
- * \r
- */\r
- public void deleteYpos()\r
- {\r
- this._has_ypos= false;\r
- } //-- void deleteYpos() \r
-\r
- /**\r
- * Returns the value of field 'content'. The field 'content'\r
- * has the following description: internal content storage\r
- * \r
- * @return String\r
- * @return the value of field 'content'.\r
- */\r
- public java.lang.String getContent()\r
- {\r
- return this._content;\r
- } //-- java.lang.String getContent() \r
-\r
- /**\r
- * Returns the value of field 'height'.\r
- * \r
- * @return int\r
- * @return the value of field 'height'.\r
- */\r
- public int getHeight()\r
- {\r
- return this._height;\r
- } //-- int getHeight() \r
-\r
- /**\r
- * Returns the value of field 'visible'.\r
- * \r
- * @return boolean\r
- * @return the value of field 'visible'.\r
- */\r
- public boolean getVisible()\r
- {\r
- return this._visible;\r
- } //-- boolean getVisible() \r
-\r
- /**\r
- * Returns the value of field 'width'.\r
- * \r
- * @return int\r
- * @return the value of field 'width'.\r
- */\r
- public int getWidth()\r
- {\r
- return this._width;\r
- } //-- int getWidth() \r
-\r
- /**\r
- * Returns the value of field 'xpos'.\r
- * \r
- * @return int\r
- * @return the value of field 'xpos'.\r
- */\r
- public int getXpos()\r
- {\r
- return this._xpos;\r
- } //-- int getXpos() \r
-\r
- /**\r
- * Returns the value of field 'ypos'.\r
- * \r
- * @return int\r
- * @return the value of field 'ypos'.\r
- */\r
- public int getYpos()\r
- {\r
- return this._ypos;\r
- } //-- int getYpos() \r
-\r
- /**\r
- * Method hasHeight\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasHeight()\r
- {\r
- return this._has_height;\r
- } //-- boolean hasHeight() \r
-\r
- /**\r
- * Method hasVisible\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasVisible()\r
- {\r
- return this._has_visible;\r
- } //-- boolean hasVisible() \r
-\r
- /**\r
- * Method hasWidth\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasWidth()\r
- {\r
- return this._has_width;\r
- } //-- boolean hasWidth() \r
-\r
- /**\r
- * Method hasXpos\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasXpos()\r
- {\r
- return this._has_xpos;\r
- } //-- boolean hasXpos() \r
-\r
- /**\r
- * Method hasYpos\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean hasYpos()\r
- {\r
- return this._has_ypos;\r
- } //-- boolean hasYpos() \r
-\r
- /**\r
- * Method isValid\r
- * \r
- * \r
- * \r
- * @return boolean\r
- */\r
- public boolean isValid()\r
- {\r
- try {\r
- validate();\r
- }\r
- catch (org.exolab.castor.xml.ValidationException vex) {\r
- return false;\r
- }\r
- return true;\r
- } //-- boolean isValid() \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param out\r
- */\r
- public void marshal(java.io.Writer out)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, out);\r
- } //-- void marshal(java.io.Writer) \r
-\r
- /**\r
- * Method marshal\r
- * \r
- * \r
- * \r
- * @param handler\r
- */\r
- public void marshal(org.xml.sax.ContentHandler handler)\r
- throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- \r
- Marshaller.marshal(this, handler);\r
- } //-- void marshal(org.xml.sax.ContentHandler) \r
-\r
- /**\r
- * Sets the value of field 'content'. The field 'content' has\r
- * the following description: internal content storage\r
- * \r
- * @param content the value of field 'content'.\r
- */\r
- public void setContent(java.lang.String content)\r
- {\r
- this._content = content;\r
- } //-- void setContent(java.lang.String) \r
-\r
- /**\r
- * Sets the value of field 'height'.\r
- * \r
- * @param height the value of field 'height'.\r
- */\r
- public void setHeight(int height)\r
- {\r
- this._height = height;\r
- this._has_height = true;\r
- } //-- void setHeight(int) \r
-\r
- /**\r
- * Sets the value of field 'visible'.\r
- * \r
- * @param visible the value of field 'visible'.\r
- */\r
- public void setVisible(boolean visible)\r
- {\r
- this._visible = visible;\r
- this._has_visible = true;\r
- } //-- void setVisible(boolean) \r
-\r
- /**\r
- * Sets the value of field 'width'.\r
- * \r
- * @param width the value of field 'width'.\r
- */\r
- public void setWidth(int width)\r
- {\r
- this._width = width;\r
- this._has_width = true;\r
- } //-- void setWidth(int) \r
-\r
- /**\r
- * Sets the value of field 'xpos'.\r
- * \r
- * @param xpos the value of field 'xpos'.\r
- */\r
- public void setXpos(int xpos)\r
- {\r
- this._xpos = xpos;\r
- this._has_xpos = true;\r
- } //-- void setXpos(int) \r
-\r
- /**\r
- * Sets the value of field 'ypos'.\r
- * \r
- * @param ypos the value of field 'ypos'.\r
- */\r
- public void setYpos(int ypos)\r
- {\r
- this._ypos = ypos;\r
- this._has_ypos = true;\r
- } //-- void setYpos(int) \r
-\r
- /**\r
- * Method unmarshal\r
- * \r
- * \r
- * \r
- * @param reader\r
- * @return Object\r
- */\r
- public static java.lang.Object unmarshal(java.io.Reader reader)\r
- throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
- {\r
- return (jalview.schemabinding.version2.StructureState) Unmarshaller.unmarshal(jalview.schemabinding.version2.StructureState.class, reader);\r
- } //-- java.lang.Object unmarshal(java.io.Reader) \r
-\r
- /**\r
- * Method validate\r
- * \r
- */\r
- public void validate()\r
- throws org.exolab.castor.xml.ValidationException\r
- {\r
- org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
- validator.validate(this);\r
- } //-- void validate() \r
-\r
-}\r
+/*
+ * 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;
+
+/**
+ * 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);
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff