X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=2bbc278ba8396491b70feaf11a6e6ccba30cd315;hb=5665f47f06e60c4a3c2715fde7adc02ab4c0186f;hp=5bfdb04946a25dfa30ad01c208c3c35bd16586d6;hpb=6819fa797b45769bb38a80230e5961e09582ed9e;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 5bfdb04..2bbc278 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -22,6 +22,8 @@ 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;
@@ -57,8 +59,6 @@ public class Sequence extends ASequence implements SequenceI
 
   String vamsasId;
 
-  DBRefEntryI sourceDBRef;
-
   DBRefEntry[] dbrefs;
 
   RNA rna;
@@ -235,8 +235,6 @@ 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());
@@ -303,8 +301,14 @@ public class Sequence extends ASequence implements SequenceI
     }
     else
     {
-      System.err
-              .println("Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment");
+      if (datasetSequence.getSequenceFeatures() != features
+              && datasetSequence.getSequenceFeatures() != null
+              && datasetSequence.getSequenceFeatures().length > 0)
+      {
+        new Exception(
+                "Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment")
+                .printStackTrace();
+      }
       datasetSequence.setSequenceFeatures(features);
     }
   }
@@ -312,7 +316,11 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public synchronized void addSequenceFeature(SequenceFeature sf)
   {
-    // TODO add to dataset sequence instead if there is one?
+    if (sequenceFeatures==null && datasetSequence != null)
+    {
+      datasetSequence.addSequenceFeature(sf);
+      return;
+    }
     if (sequenceFeatures == null)
     {
       sequenceFeatures = new SequenceFeature[0];
@@ -338,6 +346,9 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (sequenceFeatures == null)
     {
+      if (datasetSequence!=null) {
+    	  datasetSequence.deleteFeature(sf);
+      }
       return;
     }
 
@@ -959,26 +970,25 @@ public class Sequence extends ASequence implements SequenceI
       dbrefs = new DBRefEntry[0];
     }
 
-    int i, iSize = dbrefs.length;
-
-    for (i = 0; i < iSize; i++)
+    for (DBRefEntryI dbr : dbrefs)
     {
-      if (dbrefs[i].equalRef(entry))
+      if (dbr.updateFrom(entry))
       {
-        if (entry.getMap() != null)
-        {
-          if (dbrefs[i].getMap() == null)
-          {
-            // overwrite with 'superior' entry that contains a mapping.
-            dbrefs[i] = entry;
-          }
-        }
+        /*
+         * found a dbref that either matched, or could be
+         * updated from, the new entry - no need to add it
+         */
         return;
       }
     }
 
-    DBRefEntry[] temp = new DBRefEntry[iSize + 1];
-    System.arraycopy(dbrefs, 0, temp, 0, iSize);
+    /*
+     * extend the array to make room for one more
+     */
+    // TODO use an ArrayList instead
+    int j = dbrefs.length;
+    DBRefEntry[] temp = new DBRefEntry[j + 1];
+    System.arraycopy(dbrefs, 0, temp, 0, j);
     temp[temp.length - 1] = entry;
 
     dbrefs = temp;
@@ -1080,6 +1090,25 @@ public class Sequence extends ASequence implements SequenceI
     return new Sequence(this);
   }
 
+  private boolean _isNa;
+
+  private long _seqhash = 0;
+
+  @Override
+  public boolean isProtein()
+  {
+    if (datasetSequence != null)
+    {
+      return datasetSequence.isProtein();
+    }
+    if (_seqhash != sequence.hashCode())
+    {
+      _seqhash = sequence.hashCode();
+      _isNa=jalview.util.Comparison.isNucleotide(new SequenceI[] { this });
+    }
+    return !_isNa;
+  };
+
   /*
    * (non-Javadoc)
    * 
@@ -1364,12 +1393,15 @@ 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))
@@ -1380,16 +1412,66 @@ 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 Arrays.asList(new DBRefEntry[0]);
+    }
+    synchronized (dbrefs)
+    {
+      List<DBRefEntry> primaries = new ArrayList<DBRefEntry>();
+      DBRefEntry tmp[] = new DBRefEntry[1], res[] = null;
+      for (DBRefEntry ref : dbrefs)
+      {
+        if (!ref.isPrimary())
+        {
+          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 downlaoded 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.getType() != null
+                  && pdbentry.getType().equalsIgnoreCase("PDB"))
+          {
+            primaries.add(ref);
+          }
+          continue;
+        }
+        // check standard protein or dna sources
+        tmp[0] = ref;
+        res = DBRefUtils.selectDbRefs(!isProtein(), tmp);
+        if (res != null && res[0] == tmp[0])
+        {
+          primaries.add(ref);
+          continue;
+        }
+      }
+      return primaries;
+    }
   }
 
 }