X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=d4290a3243ea5de52b50f9ba48f1ef9f8df4c3f3;hb=34e29960cefd8e743de8734ca0ea2778bab12a40;hp=a8577125dd39eda017270013fcaa9964c3928fdc;hpb=fd21ffd2dbeeeaa269b3fc111566db984e1b672c;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index a857712..d4290a3 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -22,10 +22,13 @@ package jalview.datamodel;
 
 import jalview.analysis.AlignSeq;
 import jalview.api.DBRefEntryI;
+import jalview.util.DBRefUtils;
+import jalview.util.MapList;
 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;
@@ -57,8 +60,6 @@ public class Sequence extends ASequence implements SequenceI
 
   String vamsasId;
 
-  DBRefEntryI sourceDBRef;
-
   DBRefEntry[] dbrefs;
 
   RNA rna;
@@ -235,8 +236,6 @@ public class Sequence extends ASequence implements SequenceI
             seq.getEnd());
     }
     description = seq.getDescription();
-    sourceDBRef = seq.getSourceDBRef() == null ? null : new DBRefEntry(
-            seq.getSourceDBRef());
     if (seq != datasetSequence)
     {
       setDatasetSequence(seq.getDatasetSequence());
@@ -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;
   }
 
   /**
@@ -965,7 +961,12 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void addDBRef(DBRefEntry entry)
   {
-    // TODO add to dataset sequence instead if there is one?
+    if (datasetSequence != null)
+    {
+      datasetSequence.addDBRef(entry);
+      return;
+    }
+
     if (dbrefs == null)
     {
       dbrefs = new DBRefEntry[0];
@@ -1225,46 +1226,22 @@ public class Sequence extends ASequence implements SequenceI
     {
       return false;
     }
-    Vector newpdb = new Vector();
-    for (int i = 0; i < dbrefs.length; i++)
-    {
-      if (DBRefSource.PDB.equals(dbrefs[i].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)
+    boolean added = false;
+    for (DBRefEntry dbr : dbrefs)
     {
-      Enumeration en = newpdb.elements();
-      while (en.hasMoreElements())
+      if (DBRefSource.PDB.equals(dbr.getSource()))
       {
-        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
@@ -1394,12 +1371,15 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public PDBEntry getPDBEntry(String pdbIdStr)
   {
-    if (getDatasetSequence() == null
-            || getDatasetSequence().getAllPDBEntries() == null)
+    if (getDatasetSequence() != null)
+    {
+      return getDatasetSequence().getPDBEntry(pdbIdStr);
+    }
+    if (pdbIds == null)
     {
       return null;
     }
-    List<PDBEntry> entries = getDatasetSequence().getAllPDBEntries();
+    List<PDBEntry> entries = getAllPDBEntries();
     for (PDBEntry entry : entries)
     {
       if (entry.getId().equalsIgnoreCase(pdbIdStr))
@@ -1410,16 +1390,65 @@ public class Sequence extends ASequence implements SequenceI
     return null;
   }
 
-  @Override
-  public void setSourceDBRef(DBRefEntryI dbRef)
-  {
-    this.sourceDBRef = dbRef;
-  }
 
   @Override
-  public DBRefEntryI getSourceDBRef()
+  public List<DBRefEntry> getPrimaryDBRefs()
   {
-    return this.sourceDBRef;
+    if (datasetSequence!=null)
+    {
+      return datasetSequence.getPrimaryDBRefs();
+    }
+    if (dbrefs==null || dbrefs.length==0)
+    {
+      return Collections.emptyList();
+    }
+    synchronized (dbrefs)
+    {
+      List<DBRefEntry> primaries = new ArrayList<DBRefEntry>();
+      DBRefEntry[] tmp = new DBRefEntry[1];
+      for (DBRefEntry ref : dbrefs)
+      {
+        if (!ref.isPrimaryCandidate())
+        {
+          continue;
+        }
+        if (ref.hasMap())
+        {
+          MapList mp = ref.getMap().getMap();
+          if (mp.getFromLowest() > start || mp.getFromHighest() < end)
+          {
+            // map only involves a subsequence, so cannot be primary
+            continue;
+          }
+        }
+        // whilst it looks like it is a primary ref, we also sanity check type
+        if (DBRefUtils.getCanonicalName(DBRefSource.PDB).equals(
+                DBRefUtils.getCanonicalName(ref.getSource())))
+        {
+          // PDB dbrefs imply there should be a PDBEntry associated
+          // 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);
+          }
+          continue;
+        }
+        // check standard protein or dna sources
+        tmp[0] = ref;
+        DBRefEntry[] res = DBRefUtils.selectDbRefs(!isProtein(), tmp);
+        if (res != null && res[0] == tmp[0])
+        {
+          primaries.add(ref);
+          continue;
+        }
+      }
+      return primaries;
+    }
   }
 
 }