+ * 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;
+ }
+
+ /**