+ /**
+ *
+ * @param ft
+ * @return display style for a feature
+ */
+ FeatureColourI getFeatureStyle(String ft);
+
+ /**
+ * update the feature style for a particular feature
+ *
+ * @param ft
+ * @param ggc
+ */
+ void setColour(String ft, FeatureColourI ggc);
+
+ AlignViewportI getViewport();
+
+ /**
+ *
+ * @return container managing list of feature types and their visibility
+ */
+ FeaturesDisplayedI getFeaturesDisplayed();
+
+ /**
+ * get display style for all features types - visible or invisible
+ *
+ * @return
+ */
+ Map<String, FeatureColourI> getFeatureColours();
+
+ /**
+ * query the alignment view to find all features
+ *
+ * @param newMadeVisible
+ * - when true, automatically make newly discovered types visible
+ */
+ void findAllFeatures(boolean newMadeVisible);
+
+ /**
+ * get display style for all features types currently visible
+ *
+ * @return
+ */
+ Map<String, FeatureColourI> getDisplayedFeatureCols();
+
+ /**
+ * get all registered groups
+ *
+ * @return
+ */
+ List<String> getFeatureGroups();
+
+ /**
+ * get groups that are visible/invisible
+ *
+ * @param visible
+ * @return
+ */
+ List<String> getGroups(boolean visible);
+
+ /**
+ * change visibility for a range of groups
+ *
+ * @param toset
+ * @param visible
+ */
+ void setGroupVisibility(List<String> toset, boolean visible);
+
+ /**
+ * change visibiilty of given group
+ *
+ * @param group
+ * @param visible
+ */
+ void setGroupVisibility(String group, boolean visible);
+
+ /**
+ * locate features at a particular position on the given sequence
+ *
+ * @param sequence
+ * @param res
+ * @return
+ */
+ List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res);
+
+ /**
+ *
+ * @return true if the rendering platform supports transparency
+ */
+ boolean isTransparencyAvailable();
+
+ /**
+ * get current displayed types
+ *
+ * @return
+ */
+
+ String[] getDisplayedFeatureTypes();
+
+ /**
+ * get current displayed groups
+ *
+ * @return
+ */
+ String[] getDisplayedFeatureGroups();
+
+ /**
+ * display all features of these types
+ *
+ * @param featureTypes
+ */
+ void setAllVisible(List<String> featureTypes);
+
+ /**
+ * display featureType
+ *
+ * @param featureType
+ */
+ void setVisible(String featureType);
+