+ editGroupMenu.setText(MessageManager.getString("action.edit_group"));
+ }
+
+ if (!forIdPanel)
+ {
+ sequenceMenu.setVisible(false);
+ chooseStructure.setVisible(false);
+ rnaStructureMenu.setVisible(false);
+ }
+
+ addLinksAndFeatures(seq, column);
+ }
+
+ /**
+ * Adds
+ * <ul>
+ * <li>configured sequence database links (ID panel popup menu)</li>
+ * <li>non-positional feature links (ID panel popup menu)</li>
+ * <li>positional feature links (alignment panel popup menu)</li>
+ * <li>feature details links (alignment panel popup menu)</li>
+ * </ul>
+ * If this panel is also showed complementary (CDS/protein) features, then
+ * links to their feature details are also added.
+ *
+ * @param seq
+ * @param column
+ */
+ void addLinksAndFeatures(final SequenceI seq, final int column)
+ {
+ List<SequenceFeature> features = null;
+ if (forIdPanel)
+ {
+ features = sequence.getFeatures().getNonPositionalFeatures();
+ }
+ else
+ {
+ features = ap.getFeatureRenderer().findFeaturesAtColumn(sequence,
+ column + 1);
+ }
+
+ addLinks(seq, features);
+
+ if (!forIdPanel)
+ {
+ addFeatureDetails(features, seq, column);
+ }
+ }
+
+ /**
+ * Add a menu item to show feature details for each sequence feature. Any
+ * linked 'virtual' features (CDS/protein) are also optionally found and
+ * included.
+ *
+ * @param features
+ * @param seq
+ * @param column
+ */
+ protected void addFeatureDetails(List<SequenceFeature> features,
+ final SequenceI seq, final int column)
+ {
+ /*
+ * add features in CDS/protein complement at the corresponding
+ * position if configured to do so
+ */
+ MappedFeatures mf = null;
+ if (ap.av.isShowComplementFeatures())
+ {
+ if (!Comparison.isGap(sequence.getCharAt(column)))
+ {
+ AlignViewportI complement = ap.getAlignViewport()
+ .getCodingComplement();
+ AlignFrame af = Desktop.getAlignFrameFor(complement);
+ FeatureRendererModel fr2 = af.getFeatureRenderer();
+ int seqPos = sequence.findPosition(column);
+ mf = fr2.findComplementFeaturesAtResidue(sequence, seqPos);
+ }
+ }
+
+ if (features.isEmpty() && mf == null)
+ {
+ /*
+ * no features to show at this position
+ */
+ return;
+ }
+
+ JMenu details = new JMenu(
+ MessageManager.getString("label.feature_details"));
+ add(details);
+
+ String name = seq.getName();
+ for (final SequenceFeature sf : features)
+ {
+ addFeatureDetailsMenuItem(details, name, sf, null);
+ }
+
+ if (mf != null)
+ {
+ for (final SequenceFeature sf : mf.features)
+ {
+ addFeatureDetailsMenuItem(details, name, sf, mf);
+ }
+ }
+ }
+
+ /**
+ * A helper method to add one menu item whose action is to show details for
+ * one feature. The menu text includes feature description, but this may be
+ * truncated.
+ *
+ * @param details
+ * @param seqName
+ * @param sf
+ * @param mf
+ */
+ void addFeatureDetailsMenuItem(JMenu details, final String seqName,
+ final SequenceFeature sf, MappedFeatures mf)
+ {
+ int start = sf.getBegin();
+ int end = sf.getEnd();
+ if (mf != null)
+ {
+ /*
+ * show local rather than linked feature coordinates
+ */
+ int[] localRange = mf.getMappedPositions(start, end);
+ if (localRange == null)
+ {
+ // e.g. variant extending to stop codon so not mappable
+ return;
+ }
+ start = localRange[0];
+ end = localRange[localRange.length - 1];
+ }
+ StringBuilder desc = new StringBuilder();
+ desc.append(sf.getType()).append(" ").append(String.valueOf(start));
+ if (start != end)
+ {
+ desc.append(sf.isContactFeature() ? ":" : "-");
+ desc.append(String.valueOf(end));
+ }
+ String description = sf.getDescription();
+ if (description != null)
+ {
+ desc.append(" ");
+ description = StringUtils.stripHtmlTags(description);
+
+ /*
+ * truncate overlong descriptions unless they contain an href
+ * (as truncation could leave corrupted html)
+ */
+ boolean hasLink = description.indexOf("a href") > -1;
+ if (description.length() > FEATURE_DESC_MAX && !hasLink)
+ {
+ description = description.substring(0, FEATURE_DESC_MAX) + "...";
+ }
+ desc.append(description);