+ if (forIdPanel)
+ {
+ addDisplayColumnsMenu();
+ }
+
+ addLinksAndFeatures(seq, column);
+ }
+
+ void addDisplayColumnsMenu()
+ {
+ JMenu dis_cols = new JMenu(
+ MessageManager.getString("action.displayed_columns"));
+ final IdColumns id_cols = ap.av.getIdColumns();
+ id_cols.updateTypeList();
+ for (final IdColumn col : id_cols.getIdColumns())
+ {
+ JMenuItem col_entry = new JCheckBoxMenuItem(col.getLabel(),
+ col.isVisible());
+ col_entry.addActionListener(new ActionListener()
+ {
+
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ id_cols.toggleVisible(col.getLabel());
+ }
+ });
+ dis_cols.add(col_entry);
+ }
+ add(dis_cols);
+ }
+
+ /**
+ * 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)