+ public void setViewportAndAlignmentPanel(AlignViewportI viewport,
+ AlignmentViewPanel alignPanel);
+
+ /**
+ * Mark columns in the current column selection according to positions of
+ * sequence features
+ *
+ * @param invert
+ * - when set, mark all but columns containing given type
+ * @param extendCurrent
+ * - when set, do not clear existing column selection
+ * @param toggle
+ * - rather than explicitly set, toggle selection state
+ * @param featureType
+ * - feature type string
+ * @return true if operation affected state
+ */
+ boolean markColumnsContainingFeatures(boolean invert,
+ boolean extendCurrent, boolean clearColumns, String featureType);
+
+ /**
+ * sort the alignment or current selection by average score over the given set of features
+ * @param typ list of feature names or null to use currently displayed features
+ */
+ void sortAlignmentByFeatureScore(String[] typ);
+
+ /**
+ * sort the alignment or current selection by distribution of the given set of features
+ * @param typ list of feature names or null to use currently displayed features
+ */
+ void sortAlignmentByFeatureDensity(String[] typ);
+
+ /**
+ * add a features file of some kind to the current view
+ *
+ * @param file
+ * @param protocol
+ * @param relaxedIdMatching
+ * if true, try harder to match up IDs with local sequence data
+ * @return true if parsing resulted in something being imported to the view or
+ * dataset
+ */
+ public boolean parseFeaturesFile(String file, String protocol,
+ boolean relaxedIdMatching);