+ /**
+ *
+ * @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);
+
+ /**
+ * Set visibility for a list of groups
+ *
+ * @param toset
+ * @param visible
+ */
+ void setGroupVisibility(List<String> toset, boolean visible);
+
+ /**
+ * Set visibility of the given feature group
+ *
+ * @param group
+ * @param visible
+ */
+ void setGroupVisibility(String group, boolean visible);
+
+ /**
+ * Returns visible features at the specified aligned column on the given
+ * sequence. Non-positional features are not included. If the column has a gap,
+ * then enclosing features are included (but not contact features).
+ *
+ * @param sequence
+ * @param column
+ * aligned column position (1..)
+ * @return
+ */
+ List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column);
+
+ /**
+ * Returns features at the specified residue position on the given sequence.
+ * Non-positional features are not included.
+ *
+ * @param sequence
+ * @param resNo
+ * residue position (start..)
+ * @return
+ */
+ List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence, int resNo);
+
+ /**
+ * get current displayed types, in ordering of rendering (on top last)
+ *
+ * @return a (possibly empty) list of feature types
+ */
+
+ List<String> getDisplayedFeatureTypes();
+
+ /**
+ * Returns a (possibly empty) list of currently visible feature groups
+ *
+ * @return
+ */
+ List<String> getDisplayedFeatureGroups();
+
+ /**
+ * display all features of these types
+ *
+ * @param featureTypes
+ */
+ void setAllVisible(List<String> featureTypes);
+
+ /**
+ * display featureType
+ *
+ * @param featureType
+ */
+ void setVisible(String featureType);
+
+ /**
+ * Sets the transparency value, between 0 (full transparency) and 1 (no
+ * transparency)
+ *
+ * @param value
+ */
+ void setTransparency(float value);
+
+ /**
+ * Returns the transparency value, between 0 (full transparency) and 1 (no
+ * transparency)
+ *
+ * @return
+ */
+ float getTransparency();
+
+ /**
+ * Answers the filters applied to the given feature type, or null if none is
+ * set
+ *
+ * @param featureType
+ * @return
+ */
+ FeatureMatcherSetI getFeatureFilter(String featureType);
+
+ /**
+ * Answers the feature filters map
+ *
+ * @return
+ */
+ public Map<String, FeatureMatcherSetI> getFeatureFilters();
+
+ /**
+ * Sets the filters for the feature type, or removes them if a null or empty
+ * filter is passed
+ *
+ * @param featureType
+ * @param filter
+ */
+ void setFeatureFilter(String featureType, FeatureMatcherSetI filter);
+
+ /**
+ * Replaces all feature filters with the given map
+ *
+ * @param filters
+ */
+ void setFeatureFilters(Map<String, FeatureMatcherSetI> filters);
+
+ /**
+ * Returns the colour for a particular feature instance. This includes
+ * calculation of 'colour by label', or of a graduated score colour, if
+ * applicable.
+ * <p>
+ * Returns null if
+ * <ul>
+ * <li>feature group is not visible, or</li>
+ * <li>feature values lie outside any colour threshold, or</li>
+ * <li>feature is excluded by filter conditions</li>
+ * </ul>
+ * This method does not check feature type visibility.
+ *
+ * @param feature
+ * @return
+ */
+ Color getColour(SequenceFeature feature);