+ /*
+ * positional features within groups
+ */
+ foundSome |= outputFeaturesByGroup(out, sortedGroups, types, sequences);
+
+ return foundSome ? out.toString() : "No Features Visible";
+ }
+
+ /**
+ * Outputs any feature filters defined for visible feature types, sandwiched by
+ * STARTFILTERS and ENDFILTERS lines
+ *
+ * @param out
+ * @param visible
+ * @param featureFilters
+ */
+ void outputFeatureFilters(StringBuilder out,
+ Map<String, FeatureColourI> visible,
+ Map<String, FeatureMatcherSetI> featureFilters)
+ {
+ if (visible == null || featureFilters == null
+ || featureFilters.isEmpty())
+ {
+ return;
+ }
+
+ boolean first = true;
+ for (String featureType : visible.keySet())
+ {
+ FeatureMatcherSetI filter = featureFilters.get(featureType);
+ if (filter != null)
+ {
+ if (first)
+ {
+ first = false;
+ out.append(newline).append(STARTFILTERS).append(newline);
+ }
+ out.append(featureType).append(TAB).append(filter.toStableString())
+ .append(newline);
+ }
+ }
+ if (!first)
+ {
+ out.append(ENDFILTERS).append(newline).append(newline);
+ }
+
+ }
+
+ /**
+ * Appends output of sequence features within feature groups to the output
+ * buffer. Groups other than the null or empty group are sandwiched by
+ * STARTGROUP and ENDGROUP lines.
+ *
+ * @param out
+ * @param groups
+ * @param featureTypes
+ * @param sequences
+ * @return
+ */
+ private boolean outputFeaturesByGroup(StringBuilder out,
+ List<String> groups, String[] featureTypes, SequenceI[] sequences)
+ {
+ boolean foundSome = false;
+ for (String group : groups)