private boolean _has_visible;
/**
- * Field _xpos.
+ * 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 int _xpos;
+ private java.lang.String _viewId;
/**
- * keeps track of state for field: _xpos
+ * 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 _has_xpos;
+ private boolean _alignwithAlignPanel = true;
/**
- * Field _ypos.
+ * keeps track of state for field: _alignwithAlignPanel
*/
- private int _ypos;
+ private boolean _has_alignwithAlignPanel;
/**
- * keeps track of state for field: _ypos
+ * 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 _has_ypos;
+ private boolean _colourwithAlignPanel = false;
/**
- * Field _width.
+ * keeps track of state for field: _colourwithAlignPanel
*/
- private int _width;
+ private boolean _has_colourwithAlignPanel;
/**
- * keeps track of state for field: _width
+ * Flag
+ * set
+ * if
+ * the
+ * structure
+ * display
+ * is
+ * coloured
+ * by
+ * the
+ * Jmol
+ * state,
+ * rather
+ * than
+ * by
+ * one
+ * or
+ * more
+ * linked
+ * alignment
+ * views.
+ *
*/
- private boolean _has_width;
+ private boolean _colourByJmol = true;
/**
- * Field _height.
+ * keeps track of state for field: _colourByJmol
*/
- private int _height;
+ private boolean _has_colourByJmol;
/**
- * keeps track of state for field: _height
+ * An
+ * identifier
+ * for
+ * the
+ * viewer
+ * type,
+ * currently
+ * either
+ * JMOL
+ * or
+ * CHIMERA
+ *
*/
- private boolean _has_height;
+ private java.lang.String _type;
/**
- * 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.
+ * Field _width.
*/
- private java.lang.String _viewId;
+ private int _width;
/**
- * Flag set if the alignment panel containing this JSeq should
- * be included in those used to perform a structure
- * superposition (since Jalview 2.7).
- *
+ * keeps track of state for field: _width
*/
- private boolean _alignwithAlignPanel = true;
+ private boolean _has_width;
/**
- * keeps track of state for field: _alignwithAlignPanel
+ * Field _height.
*/
- private boolean _has_alignwithAlignPanel;
+ private int _height;
/**
- * 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).
- *
+ * keeps track of state for field: _height
*/
- private boolean _colourwithAlignPanel = false;
+ private boolean _has_height;
/**
- * keeps track of state for field: _colourwithAlignPanel
+ * Field _xpos.
*/
- private boolean _has_colourwithAlignPanel;
+ private int _xpos;
/**
- * Flag set if the structure display is coloured by the Jmol
- * state, rather than by one or more linked alignment views.
- *
+ * keeps track of state for field: _xpos
*/
- private boolean _colourByJmol = true;
+ private boolean _has_xpos;
/**
- * keeps track of state for field: _colourByJmol
+ * Field _ypos.
*/
- private boolean _has_colourByJmol;
+ private int _ypos;
+
+ /**
+ * keeps track of state for field: _ypos
+ */
+ private boolean _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).
+ * 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'.
/**
* 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.
+ * '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'.
/**
* 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).
+ * 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'.
}
/**
+ * 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.
+ * 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'.
*/
/**
* 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).
+ * 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'.
/**
* 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.
+ * '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'.
/**
* 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).
+ * 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'.
/**
* 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).
+ * 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
/**
* 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.
+ * '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'.
/**
* 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).
+ * 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
}
/**
+ * 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.
+ * 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'.
*/
git://source.jalview.org / jalview.git / blobdiff