* This method returns the visible alignment as text, as seen on the GUI, ie
* if columns are hidden they will not be returned in the result. Use this for
* calculating trees, PCA, redundancy etc on views which contain hidden
- * columns.
- *
+ * columns. This method doesn't exclude hidden sequences from the output.
+ *
+ * @param selectedRegionOnly
+ * - determines if only the selected region or entire alignment is
+ * exported
* @return String[]
*/
String[] getViewAsString(boolean selectedRegionOnly);
/**
* This method returns the visible alignment as text, as seen on the GUI, ie
- * if columns are hidden they will not be returned in the result. However, If
- * there are hidden sequences, isExportHiddenSeqs flag decides if they would
- * be exported or not. Use this for calculating trees, PCA, redundancy etc on
- * views which contain hidden columns.
+ * if columns are hidden they will not be returned in the result. Use this for
+ * calculating trees, PCA, redundancy etc on views which contain hidden
+ * columns.
*
* @param selectedRegionOnly
+ * - determines if only the selected region or entire alignment is
+ * exported
* @param isExportHiddenSeqs
+ * - determines if hidden sequences would be exported or not.
+ *
* @return String[]
*/
String[] getViewAsString(boolean selectedRegionOnly, boolean isExportHiddenSeqs);
public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
+
+ /**
+ * check if current selection group is defined on the view, or is simply a
+ * temporary group.
+ *
+ * @return true if group is defined on the alignment
+ */
+ boolean isSelectionDefinedGroup();
}