crossrefs have properly updated pdbId lists

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index d2f0358..3e046c2 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -40,8 +40,8 @@ public class CrossRef
     {\r
       rfs = jalview.util.DBRefUtils.selectRefs(rfs,\r
               DBRefSource.DNACODINGDBS); // could attempt to find other cross\r
-                                          // refs and return here - ie PDB xrefs\r
-                                          // (not dna, not protein seq)\r
+      // refs and return here - ie PDB xrefs\r
+      // (not dna, not protein seq)\r
     }\r
     return rfs;\r
   }\r
@@ -216,13 +216,13 @@ public class CrossRef
       {\r
         System.out.println("Attempting to find ds Xrefs refs.");\r
         DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRef()); // less\r
-                                                                            // ambiguous\r
-                                                                            // would\r
-                                                                            // be a\r
-                                                                            // 'find\r
-                                                                            // primary\r
-                                                                            // dbRefEntry'\r
-                                                                            // method.\r
+        // ambiguous\r
+        // would\r
+        // be a\r
+        // 'find\r
+        // primary\r
+        // dbRefEntry'\r
+        // method.\r
         // filter for desired source xref here\r
         found = CrossRef.searchDatasetXrefs(dss, !dna, lrfs, dataset,\r
                 rseqs, cf);\r
@@ -305,7 +305,7 @@ public class CrossRef
             xrfs = t;\r
             try\r
             {\r
-              retrieved = sftch.getSequences(xrfs);\r
+              retrieved = sftch.getSequences(xrfs); // problem here is we don't know which of xrfs resulted in which retrieved element\r
             } catch (Exception e)\r
             {\r
               System.err\r
@@ -317,6 +317,46 @@ public class CrossRef
             {\r
               for (int rs = 0; rs < retrieved.length; rs++)\r
               {\r
+                // 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
                 rseqs.addElement(retrieved[rs]);\r
               }\r
             }\r
@@ -442,7 +482,7 @@ public class CrossRef
             {\r
               rseqs.addElement(nxt);\r
               boolean foundmap = cf != null; // don't search if we aren't given\r
-                                              // a codon map object\r
+              // a codon map object\r
               for (int r = 0; foundmap && r < cands.length; r++)\r
               {\r
                 if (cands[r].hasMap())\r