+ /**
+ *
+ * @param flag
+ * indicating if annotation panel shown below alignment
+ *
+ */
+ void setShowAnnotation(boolean b);
+
+ /**
+ * flag indicating if annotation panel shown below alignment
+ *
+ * @return
+ */
+ boolean isShowAnnotation();
+
+ boolean isRightAlignIds();
+
+ void setRightAlignIds(boolean rightAlignIds);
+
+ boolean areFeaturesDisplayed();
+
+ void setShowSequenceFeaturesHeight(boolean selected);
+
+ boolean isShowSequenceFeaturesHeight();
+
+ void setFeaturesDisplayed(FeaturesDisplayedI featuresDisplayedI);
+
+ void alignmentChanged(AlignmentViewPanel ap);
+
+ /**
+ * @return the padGaps
+ */
+ boolean isPadGaps();
+
+ /**
+ * @param padGaps
+ * the padGaps to set
+ */
+ void setPadGaps(boolean padGaps);
+
+ /**
+ * return visible region boundaries within given column range
+ *
+ * @param min
+ * first column (inclusive, from 0)
+ * @param max
+ * last column (exclusive)
+ * @return int[][] range of {start,end} visible positions TODO: change to list
+ * of int ranges
+ */
+ int[][] getVisibleRegionBoundaries(int min, int max);
+
+ /**
+ * This method returns an array of new SequenceI objects derived from the
+ * whole alignment or just the current selection with start and end points
+ * adjusted
+ *
+ * @note if you need references to the actual SequenceI objects in the
+ * alignment or currently selected then use getSequenceSelection()
+ * @return selection as new sequenceI objects
+ */
+ SequenceI[] getSelectionAsNewSequence();
+
+ void invertColumnSelection();
+
+ /**
+ * broadcast selection to any interested parties
+ */
+ void sendSelection();
+
+ /**
+ * calculate the row position for alignmentIndex if all hidden sequences were
+ * shown
+ *
+ * @param alignmentIndex
+ * @return adjusted row position
+ */
+ int adjustForHiddenSeqs(int alignmentIndex);
+
+ boolean hasHiddenRows();
+