X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=44522a85d0977ecc5bbd5fd8ad1042b626507a51;hb=33ad2b9a53a0e7faec7afddf91de829d98df07bc;hp=ec8aa81a1c598f4876984ec79d0cc0b9222e482e;hpb=af2dbf10bbcc54d9b9e4d398e9283b3c4a758e06;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index ec8aa81..44522a8 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -28,6 +28,7 @@ import jalview.util.StringUtils;
 
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.Enumeration;
 import java.util.List;
 import java.util.Vector;
@@ -59,8 +60,6 @@ public class Sequence extends ASequence implements SequenceI
 
   String vamsasId;
 
-  DBRefEntryI sourceDBRef;
-
   DBRefEntry[] dbrefs;
 
   RNA rna;
@@ -307,8 +306,9 @@ public class Sequence extends ASequence implements SequenceI
               && datasetSequence.getSequenceFeatures() != null
               && datasetSequence.getSequenceFeatures().length > 0)
       {
-        System.err
-              .println("Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment");
+        new Exception(
+                "Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment")
+                .printStackTrace();
       }
       datasetSequence.setSequenceFeatures(features);
     }
@@ -412,28 +412,24 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   @Override
-  public void addPDBId(PDBEntry entry)
+  public boolean addPDBId(PDBEntry entry)
   {
     if (pdbIds == null)
     {
       pdbIds = new Vector<PDBEntry>();
+      pdbIds.add(entry);
+      return true;
     }
-    if (pdbIds.contains(entry))
-    {
-      updatePDBEntry(pdbIds.get(pdbIds.indexOf(entry)), entry);
-    }
-    else
-    {
-      pdbIds.addElement(entry);
-    }
-  }
 
-  private static void updatePDBEntry(PDBEntry oldEntry, PDBEntry newEntry)
-  {
-    if (newEntry.getFile() != null)
+    for (PDBEntry pdbe : pdbIds)
     {
-      oldEntry.setFile(newEntry.getFile());
+      if (pdbe.updateFrom(entry))
+      {
+        return false;
+      }
     }
+    pdbIds.addElement(entry);
+    return true;
   }
 
   /**
@@ -1225,46 +1221,22 @@ public class Sequence extends ASequence implements SequenceI
     {
       return false;
     }
-    Vector newpdb = new Vector();
-    for (int i = 0; i < dbrefs.length; i++)
+    boolean added = false;
+    for (DBRefEntry dbr : dbrefs)
     {
-      if (DBRefSource.PDB.equals(dbrefs[i].getSource()))
+      if (DBRefSource.PDB.equals(dbr.getSource()))
       {
-        PDBEntry pdbe = new PDBEntry();
-        pdbe.setId(dbrefs[i].getAccessionId());
-        if (pdbIds == null || pdbIds.size() == 0)
-        {
-          newpdb.addElement(pdbe);
-        }
-        else
-        {
-          Enumeration en = pdbIds.elements();
-          boolean matched = false;
-          while (!matched && en.hasMoreElements())
-          {
-            PDBEntry anentry = (PDBEntry) en.nextElement();
-            if (anentry.getId().equals(pdbe.getId()))
-            {
-              matched = true;
-            }
-          }
-          if (!matched)
-          {
-            newpdb.addElement(pdbe);
-          }
-        }
-      }
-    }
-    if (newpdb.size() > 0)
-    {
-      Enumeration en = newpdb.elements();
-      while (en.hasMoreElements())
-      {
-        addPDBId((PDBEntry) en.nextElement());
+        /*
+         * 'Add' any PDB dbrefs as a PDBEntry - add is only performed if the
+         * PDB id is not already present in a 'matching' PDBEntry
+         * Constructor parses out a chain code if appended to the accession id
+         * (a fudge used to 'store' the chain code in the DBRef)
+         */
+        PDBEntry pdbe = new PDBEntry(dbr);
+        added |= addPDBId(pdbe);
       }
-      return true;
     }
-    return false;
+    return added;
   }
 
   @Override
@@ -1423,15 +1395,15 @@ public class Sequence extends ASequence implements SequenceI
     }
     if (dbrefs==null || dbrefs.length==0)
     {
-      return Arrays.asList(new DBRefEntry[0]);
+      return Collections.emptyList();
     }
     synchronized (dbrefs)
     {
       List<DBRefEntry> primaries = new ArrayList<DBRefEntry>();
-      DBRefEntry tmp[] = new DBRefEntry[1], res[] = null;
+      DBRefEntry[] tmp = new DBRefEntry[1];
       for (DBRefEntry ref : dbrefs)
       {
-        if (!ref.isPrimary())
+        if (!ref.isPrimaryCandidate())
         {
           continue;
         }
@@ -1449,7 +1421,13 @@ public class Sequence extends ASequence implements SequenceI
                 DBRefUtils.getCanonicalName(ref.getSource())))
         {
           // PDB dbrefs imply there should be a PDBEntry associated
-          if (getPDBEntry(ref.getAccessionId()) != null)
+          // TODO: tighten PDB dbrefs
+          // formally imply Jalview has actually downloaded and
+          // parsed the pdb file. That means there should be a cached file
+          // handle on the PDBEntry, and a real mapping between sequence and
+          // extracted sequence from PDB file
+          PDBEntry pdbentry = getPDBEntry(ref.getAccessionId());
+          if (pdbentry != null && pdbentry.getFile() != null)
           {
             primaries.add(ref);
           }
@@ -1457,7 +1435,7 @@ public class Sequence extends ASequence implements SequenceI
         }
         // check standard protein or dna sources
         tmp[0] = ref;
-        res = DBRefUtils.selectDbRefs(!isProtein(), tmp);
+        DBRefEntry[] res = DBRefUtils.selectDbRefs(!isProtein(), tmp);
         if (res != null && res[0] == tmp[0])
         {
           primaries.add(ref);