+ * 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;
+ }
+
+ /**