+ void setSequenceColour(SequenceI seq, Color col);
+
+ Color getSequenceColour(SequenceI seq);
+
+ void updateSequenceIdColours();
+
+ SequenceGroup getSelectionGroup();
+
+ SequenceI[] getSequenceSelection();
+
+ void clearSequenceColours();
+
+ CigarArray getViewAsCigars(boolean selectedRegionOnly);
+
+ AlignmentView getAlignmentView(boolean selectedOnly);
+
+ AlignmentView getAlignmentView(boolean selectedOnly, boolean markGroups);
+
+ String[] getViewAsString(boolean selectedRegionOnly);
+
+ void setSelectionGroup(SequenceGroup sg);
+
+ char getGapCharacter();
+
+ void setColumnSelection(ColumnSelection cs);
+
+ void setConservation(Conservation cons);
+
+ /**
+ * get a copy of the currently visible alignment annotation
+ * @param selectedOnly if true - trim to selected regions on the alignment
+ * @return an empty list or new alignment annotation objects shown only visible columns trimmed to selected region only
+ */
+ List<AlignmentAnnotation> getVisibleAlignmentAnnotation(
+ boolean selectedOnly);
+