* 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. 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. 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);
+ String[] getViewAsString(boolean selectedRegionOnly, boolean isExportHiddenSeqs);
void setSelectionGroup(SequenceGroup sg);
*/
void setFollowHighlight(boolean b);
- /**
- * Set whether hidden Sequences should be trimmed off during an export
- * operation.
- *
- * @param isExportHiddenSeqs
- */
- public void setExportHiddenSeqs(boolean isExportHiddenSeqs);
+
+ public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
/**
- * If true hidden Sequences are exported otherwise they aren't
+ * check if current selection group is defined on the view, or is simply a
+ * temporary group.
*
- * @return
+ * @return true if group is defined on the alignment
*/
- public boolean isExportHiddenSeqs();
-
- public void applyFeaturesStyle(FeatureSettingsModelI featureSettings);
+ boolean isSelectionDefinedGroup();
}