+ }
+
+ return count;
+ }
+
+ /**
+ * Answers a list of mapped features visible in the (CDS/protein) complement,
+ * with feature positions translated to local sequence coordinates
+ *
+ * @param seq
+ * @param fr2
+ * @return
+ */
+ protected List<SequenceFeature> findComplementaryFeatures(SequenceI seq,
+ FeatureRenderer fr2)
+ {
+ /*
+ * avoid duplication of features (e.g. peptide feature
+ * at all 3 mapped codon positions)
+ */
+ List<SequenceFeature> found = new ArrayList<>();
+ List<SequenceFeature> complementary = new ArrayList<>();
+
+ for (int pos = seq.getStart(); pos <= seq.getEnd(); pos++)
+ {
+ MappedFeatures mf = fr2.findComplementFeaturesAtResidue(seq, pos);
+
+ if (mf != null)
+ {
+ for (SequenceFeature sf : mf.features)
+ {
+ /*
+ * make a virtual feature with local coordinates
+ */
+ if (!found.contains(sf))
+ {
+ String group = sf.getFeatureGroup();
+ if (group == null)
+ {
+ group = "";
+ }
+ found.add(sf);
+ int begin = sf.getBegin();
+ int end = sf.getEnd();
+ int[] range = mf.getMappedPositions(begin, end);
+ SequenceFeature sf2 = new SequenceFeature(sf, range[0],
+ range[1], group, sf.getScore());
+ complementary.add(sf2);
+ }
+ }
+ }
+ }
+
+ return complementary;
+ }
+
+ /**
+ * 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);
+ }
+
+ }
+
+ /**
+ * Appends output of visible sequence features within feature groups to the
+ * output buffer. Groups other than the null or empty group are sandwiched by
+ * STARTGROUP and ENDGROUP lines. Answers the number of features written.
+ *
+ * @param out
+ * @param fr
+ * @param featureTypes
+ * @param sequences
+ * @param includeNonPositional
+ * @return
+ */
+ private int outputFeaturesByGroup(StringBuilder out, FeatureRenderer fr,
+ String[] featureTypes, SequenceI[] sequences,
+ boolean includeNonPositional)
+ {
+ List<String> featureGroups = fr.getFeatureGroups();
+
+ /*
+ * sort groups alphabetically, and ensure that features with a
+ * null or empty group are output after those in named groups
+ */
+ List<String> sortedGroups = new ArrayList<>(featureGroups);
+ sortedGroups.remove(null);
+ sortedGroups.remove("");
+ Collections.sort(sortedGroups);
+ sortedGroups.add(null);
+ sortedGroups.add("");
+
+ int count = 0;
+ List<String> visibleGroups = fr.getDisplayedFeatureGroups();
+
+ /*
+ * loop over all groups (may be visible or not);
+ * non-positional features are output even if group is not visible
+ */
+ for (String group : sortedGroups)
+ {
+ boolean firstInGroup = true;
+ boolean isNullGroup = group == null || "".equals(group);