From: jprocter <Jim Procter>
Date: Mon, 12 Nov 2007 16:35:50 +0000 (+0000)
Subject: crossrefs have properly updated pdbId lists
X-Git-Tag: Release_2_4~188
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=ce886100c1eae01eac7d59c961e694f4493d4bcb;p=jalview.git

crossrefs have properly updated pdbId lists
---

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index d2f0358..3e046c2 100644
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -40,8 +40,8 @@ public class CrossRef
     {
       rfs = jalview.util.DBRefUtils.selectRefs(rfs,
               DBRefSource.DNACODINGDBS); // could attempt to find other cross
-                                          // refs and return here - ie PDB xrefs
-                                          // (not dna, not protein seq)
+      // refs and return here - ie PDB xrefs
+      // (not dna, not protein seq)
     }
     return rfs;
   }
@@ -216,13 +216,13 @@ public class CrossRef
       {
         System.out.println("Attempting to find ds Xrefs refs.");
         DBRefEntry[] lrfs = CrossRef.findXDbRefs(!dna, seqs[s].getDBRef()); // less
-                                                                            // ambiguous
-                                                                            // would
-                                                                            // be a
-                                                                            // 'find
-                                                                            // primary
-                                                                            // dbRefEntry'
-                                                                            // method.
+        // ambiguous
+        // would
+        // be a
+        // 'find
+        // primary
+        // dbRefEntry'
+        // method.
         // filter for desired source xref here
         found = CrossRef.searchDatasetXrefs(dss, !dna, lrfs, dataset,
                 rseqs, cf);
@@ -305,7 +305,7 @@ public class CrossRef
             xrfs = t;
             try
             {
-              retrieved = sftch.getSequences(xrfs);
+              retrieved = sftch.getSequences(xrfs); // problem here is we don't know which of xrfs resulted in which retrieved element
             } catch (Exception e)
             {
               System.err
@@ -317,6 +317,46 @@ public class CrossRef
             {
               for (int rs = 0; rs < retrieved.length; rs++)
               {
+                // TODO: examine each sequence for 'redundancy'
+                jalview.datamodel.DBRefEntry[] dbr = retrieved[rs].getDBRef();
+                if (dbr != null && dbr.length > 0)
+                {
+                  for (int di = 0; di < dbr.length; di++)
+                  {
+                    // find any entry where we should put in the sequence being cross-referenced into the map
+                    jalview.datamodel.Mapping map = dbr[di].getMap();
+                    if (map != null)
+                    {
+                      if (map.getTo() != null && map.getMap() != null)
+                      {
+                        // should search the local dataset to find any existing candidates for To !
+                        try
+                        {
+                          // compare ms with dss and replace with dss in mapping if map is congruent
+                          SequenceI ms = map.getTo();
+                          int sf = map.getMap().getToLowest();
+                          int st = map.getMap().getToHighest();
+                          SequenceI mappedrg = ms.getSubSequence(sf, st);
+                          SequenceI loc = dss.getSubSequence(sf, st);
+                          if (mappedrg.getLength()>0 && mappedrg.getSequenceAsString().equals(
+                                  loc.getSequenceAsString()))
+                          {
+                            System.err
+                                    .println("Mapping updated for retrieved crossreference");
+                            // method to update all refs of existing To on retrieved sequence with dss and merge any props on To onto dss.
+                            map.setTo(dss);
+                          }
+                        } catch (Exception e)
+                        {
+                          System.err
+                                  .println("Exception when consolidating Mapped sequence set...");
+                          e.printStackTrace(System.err);
+                        }
+                      }
+                    }
+                  }
+                }
+                retrieved[rs].updatePDBIds();
                 rseqs.addElement(retrieved[rs]);
               }
             }
@@ -442,7 +482,7 @@ public class CrossRef
             {
               rseqs.addElement(nxt);
               boolean foundmap = cf != null; // don't search if we aren't given
-                                              // a codon map object
+              // a codon map object
               for (int r = 0; foundmap && r < cands.length; r++)
               {
                 if (cands[r].hasMap())