+
+ /**
+ * 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.
+ *
+ * @param selectedRegionOnly
+ * @param isExportHiddenSeqs
+ * @return String[]
+ */
+ String[] getViewAsString(boolean selectedRegionOnly, boolean isExportHiddenSeqs);