+ // TODO: examine each sequence for 'redundancy'\r
+ jalview.datamodel.DBRefEntry[] dbr = retrieved[rs].getDBRef();\r
+ if (dbr != null && dbr.length > 0)\r
+ {\r
+ for (int di = 0; di < dbr.length; di++)\r
+ {\r
+ // find any entry where we should put in the sequence being cross-referenced into the map\r
+ jalview.datamodel.Mapping map = dbr[di].getMap();\r
+ if (map != null)\r
+ {\r
+ if (map.getTo() != null && map.getMap() != null)\r
+ {\r
+ // should search the local dataset to find any existing candidates for To !\r
+ try\r
+ {\r
+ // compare ms with dss and replace with dss in mapping if map is congruent\r
+ SequenceI ms = map.getTo();\r
+ int sf = map.getMap().getToLowest();\r
+ int st = map.getMap().getToHighest();\r
+ SequenceI mappedrg = ms.getSubSequence(sf, st);\r
+ SequenceI loc = dss.getSubSequence(sf, st);\r
+ if (mappedrg.getLength()>0 && mappedrg.getSequenceAsString().equals(\r
+ loc.getSequenceAsString()))\r
+ {\r
+ System.err\r
+ .println("Mapping updated for retrieved crossreference");\r
+ // method to update all refs of existing To on retrieved sequence with dss and merge any props on To onto dss.\r
+ map.setTo(dss);\r
+ }\r
+ } catch (Exception e)\r
+ {\r
+ System.err\r
+ .println("Exception when consolidating Mapped sequence set...");\r
+ e.printStackTrace(System.err);\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+ retrieved[rs].updatePDBIds();\r