+
+ public List<AlignedCodonFrame> getSequenceMappings()
+ {
+ return seqmappings;
+ }
+
+ /**
+ * quick and dirty route to just highlight all structure positions for a range
+ * of columns
+ *
+ * @param sequencesArray
+ * @param is
+ * start-end columns on sequencesArray
+ * @param source
+ * origin parent AlignmentPanel
+ */
+ public void highlightPositionsOnMany(SequenceI[] sequencesArray, int[] is,
+ Object source)
+ {
+ for (int i = 0; i < listeners.size(); i++)
+ {
+ Object listener = listeners.elementAt(i);
+ if (listener == source)
+ {
+ // TODO listener (e.g. SeqPanel) is never == source (AlignViewport)
+ // Temporary fudge with SequenceListener.getVamsasSource()
+ continue;
+ }
+ if (listener instanceof StructureListener)
+ {
+ highlightStructureRegionsFor((StructureListener) listener,
+ sequencesArray, is);
+ }
+ }
+ }
+
+ public Map<String, String> getPdbFileNameIdMap()
+ {
+ return pdbFileNameId;
+ }
+
+ public Map<String, String> getPdbIdFileNameMap()
+ {
+ return pdbIdFileName;
+ }
+
+ public static void doConfigureStructurePrefs(
+ StructureSelectionManager ssm)
+ {
+ doConfigureStructurePrefs(ssm,
+ Cache.getDefault(Preferences.ADD_SS_ANN, true),
+ Cache.getDefault(Preferences.ADD_TEMPFACT_ANN, true),
+ Cache.getDefault(Preferences.STRUCT_FROM_PDB, true),
+ Cache.getDefault(Preferences.USE_RNAVIEW, false));
+ }
+
+ public static void doConfigureStructurePrefs(
+ StructureSelectionManager ssm, boolean add_ss_ann,
+ boolean add_tempfact_ann, boolean struct_from_pdb,
+ boolean use_rnaview)
+ {
+ if (add_ss_ann)
+ {
+ ssm.setAddTempFacAnnot(add_tempfact_ann);
+ ssm.setProcessSecondaryStructure(struct_from_pdb);
+ // JAL-3915 - RNAView is no longer an option so this has no effect
+ ssm.setSecStructServices(use_rnaview);
+ }
+ else
+ {
+ ssm.setAddTempFacAnnot(false);
+ ssm.setProcessSecondaryStructure(false);
+ ssm.setSecStructServices(false);
+ }
+ }
+