X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=c8b94cecf83e3d4710d2186fc8d0b4a551b03d4d;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=fbe36701053fbe072192c13aa9849017fc8d00d9;hpb=c1fd773fbb58cc3eaa35b71f390a3cf416b1bdad;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index fbe3670..c8b94ce 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -22,10 +22,14 @@ package jalview.datamodel;
 
 import jalview.analysis.AlignSeq;
 import jalview.api.DBRefEntryI;
+import jalview.util.Comparison;
+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 +61,6 @@ public class Sequence extends ASequence implements SequenceI
 
   String vamsasId;
 
-  DBRefEntryI sourceDBRef;
-
   DBRefEntry[] dbrefs;
 
   RNA rna;
@@ -231,12 +233,9 @@ public class Sequence extends ASequence implements SequenceI
     {
       char[] oseq = seq.getSequence();
       initSeqAndName(seq.getName(), Arrays.copyOf(oseq, oseq.length),
-              seq.getStart(),
-            seq.getEnd());
+              seq.getStart(), seq.getEnd());
     }
     description = seq.getDescription();
-    sourceDBRef = seq.getSourceDBRef() == null ? null : new DBRefEntry(
-            seq.getSourceDBRef());
     if (seq != datasetSequence)
     {
       setDatasetSequence(seq.getDatasetSequence());
@@ -293,22 +292,35 @@ public class Sequence extends ASequence implements SequenceI
     }
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param v
-   *          DOCUMENT ME!
-   */
   @Override
   public void setSequenceFeatures(SequenceFeature[] features)
   {
-    sequenceFeatures = features;
+    if (datasetSequence == null)
+    {
+      sequenceFeatures = features;
+    }
+    else
+    {
+      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);
+    }
   }
 
   @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];
@@ -334,6 +346,10 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (sequenceFeatures == null)
     {
+      if (datasetSequence != null)
+      {
+        datasetSequence.deleteFeature(sf);
+      }
       return;
     }
 
@@ -396,28 +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;
   }
 
   /**
@@ -932,7 +944,17 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void setDBRefs(DBRefEntry[] dbref)
   {
+    if (dbrefs == null && datasetSequence != null
+            && this != datasetSequence)
+    {
+      datasetSequence.setDBRefs(dbref);
+      return;
+    }
     dbrefs = dbref;
+    if (dbrefs != null)
+    {
+      DBRefUtils.ensurePrimaries(this);
+    }
   }
 
   @Override
@@ -949,41 +971,56 @@ 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];
     }
 
-    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;
+
+    DBRefUtils.ensurePrimaries(this);
   }
 
   @Override
   public void setDatasetSequence(SequenceI seq)
   {
-    // TODO check for circular reference before setting?
+    if (seq == this)
+    {
+      throw new IllegalArgumentException(
+              "Implementation Error: self reference passed to SequenceI.setDatasetSequence");
+    }
+    if (seq != null && seq.getDatasetSequence() != null)
+    {
+      throw new IllegalArgumentException(
+              "Implementation error: cascading dataset sequences are not allowed.");
+    }
     datasetSequence = seq;
   }
 
@@ -1056,33 +1093,49 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public SequenceI deriveSequence()
   {
-    SequenceI seq = new Sequence(this);
-    if (datasetSequence != null)
-    {
-      // duplicate current sequence with same dataset
-      seq.setDatasetSequence(datasetSequence);
-    }
-    else
+    Sequence seq = null;
+    if (datasetSequence == null)
     {
       if (isValidDatasetSequence())
       {
         // Use this as dataset sequence
+        seq = new Sequence(getName(), "", 1, -1);
         seq.setDatasetSequence(this);
+        seq.initSeqFrom(this, getAnnotation());
+        return seq;
       }
       else
       {
         // Create a new, valid dataset sequence
-        SequenceI ds = seq;
-        ds.setSequence(AlignSeq.extractGaps(
-                jalview.util.Comparison.GapChars, new String(sequence)));
-        setDatasetSequence(ds);
-        ds.setSequenceFeatures(getSequenceFeatures());
-        seq = this; // and return this sequence as the derived sequence.
+        createDatasetSequence();
       }
     }
-    return seq;
+    return new Sequence(this);
   }
 
+  private boolean _isNa;
+
+  private long _seqhash = 0;
+
+  /**
+   * Answers false if the sequence is more than 85% nucleotide (ACGTU), else
+   * true
+   */
+  @Override
+  public boolean isProtein()
+  {
+    if (datasetSequence != null)
+    {
+      return datasetSequence.isProtein();
+    }
+    if (_seqhash != sequence.hashCode())
+    {
+      _seqhash = sequence.hashCode();
+      _isNa = Comparison.isNucleotide(this);
+    }
+    return !_isNa;
+  };
+
   /*
    * (non-Javadoc)
    * 
@@ -1102,9 +1155,9 @@ public class Sequence extends ASequence implements SequenceI
       dsseq.setDescription(description);
       // move features and database references onto dataset sequence
       dsseq.sequenceFeatures = sequenceFeatures;
-      sequenceFeatures=null;
+      sequenceFeatures = null;
       dsseq.dbrefs = dbrefs;
-      dbrefs=null;
+      dbrefs = null;
       // TODO: search and replace any references to this sequence with
       // references to the dataset sequence in Mappings on dbref
       dsseq.pdbIds = pdbIds;
@@ -1198,46 +1251,22 @@ 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
@@ -1367,12 +1396,15 @@ 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))
@@ -1384,15 +1416,63 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   @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;
+    }
   }
 
 }