X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=89c55e64f273b738e56bd47c1e44e3338e0584b6;hb=1b355b40b6f8db41ced6a05a9eab76b44089f7f1;hp=026061bd00969854e10110d5e861141c52efd762;hpb=8c0019f5e35dcfdb8014f280ba1193db239c92dd;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 026061b..89c55e6 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -21,13 +21,13 @@
 package jalview.datamodel;
 
 import jalview.analysis.AlignSeq;
-import jalview.api.DBRefEntryI;
 import jalview.datamodel.features.SequenceFeatures;
 import jalview.datamodel.features.SequenceFeaturesI;
 import jalview.util.Comparison;
 import jalview.util.DBRefUtils;
 import jalview.util.MapList;
 import jalview.util.StringUtils;
+import jalview.workers.InformationThread;
 
 import java.util.ArrayList;
 import java.util.Arrays;
@@ -47,25 +47,55 @@ import fr.orsay.lri.varna.models.rna.RNA;
  */
 public class Sequence extends ASequence implements SequenceI
 {
+
+  /**
+   * A subclass that gives us access to modCount, which tracks whether there
+   * have been any changes. We use this to update
+   * 
+   * @author hansonr
+   *
+   * @param <T>
+   */
+  @SuppressWarnings("serial")
+  public class DBModList<T> extends ArrayList<DBRefEntry>
+  {
+
+    protected int getModCount()
+    {
+      return modCount;
+    }
+
+  }
+
   SequenceI datasetSequence;
 
-  String name;
+  private String name;
 
   private char[] sequence;
 
-  String description;
+  private String description;
+
+  private int start;
+
+  private int end;
 
-  int start;
+  private Vector<PDBEntry> pdbIds;
 
-  int end;
+  private String vamsasId;
 
-  Vector<PDBEntry> pdbIds;
+  HiddenMarkovModel hmm;
 
-  String vamsasId;
+  boolean isHMMConsensusSequence = false;
+  private DBModList<DBRefEntry> dbrefs; // controlled access
 
-  DBRefEntry[] dbrefs;
+  /**
+   * a flag to let us know that elements have changed in dbrefs
+   * 
+   * @author Bob Hanson
+   */
+  private int refModCount = 0;
 
-  RNA rna;
+  private RNA rna;
 
   /**
    * This annotation is displayed below the alignment but the positions are tied
@@ -73,7 +103,7 @@ public class Sequence extends ASequence implements SequenceI
    *
    * TODO: change to List<>
    */
-  Vector<AlignmentAnnotation> annotation;
+  private Vector<AlignmentAnnotation> annotation;
 
   private SequenceFeaturesI sequenceFeatureStore;
 
@@ -228,6 +258,21 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
+   * Create a new sequence object from a characters array using default values
+   * of 1 and -1 for start and end. The array used to create the sequence is
+   * copied and is not stored internally.
+   * 
+   * @param name
+   *          sequence name
+   * @param sequence
+   *          list of residues
+   */
+  public Sequence(String name, char[] sequence)
+  {
+    this(name, Arrays.copyOf(sequence, sequence.length), 1, -1);
+  }
+
+  /**
    * Creates a new Sequence object with new AlignmentAnnotations but inherits
    * any existing dataset sequence reference. If non exists, everything is
    * copied.
@@ -278,18 +323,18 @@ public class Sequence extends ASequence implements SequenceI
     {
       setDatasetSequence(seq.getDatasetSequence());
     }
-    
+
     /*
      * only copy DBRefs and seqfeatures if we really are a dataset sequence
      */
     if (datasetSequence == null)
     {
-      if (seq.getDBRefs() != null)
+      List<DBRefEntry> dbr = seq.getDBRefs();
+      if (dbr != null)
       {
-        DBRefEntry[] dbr = seq.getDBRefs();
-        for (int i = 0; i < dbr.length; i++)
+        for (int i = 0, n = dbr.size(); i < n; i++)
         {
-          addDBRef(new DBRefEntry(dbr[i]));
+          addDBRef(new DBRefEntry(dbr.get(i)));
         }
       }
 
@@ -335,6 +380,10 @@ public class Sequence extends ASequence implements SequenceI
         this.addPDBId(new PDBEntry(pdb));
       }
     }
+    if (seq.getHMM() != null)
+    {
+      this.hmm = new HiddenMarkovModel(seq.getHMM(), this);
+    }
   }
 
   @Override
@@ -353,8 +402,8 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (sf.getType() == null)
     {
-      System.err.println("SequenceFeature type may not be null: "
-              + sf.toString());
+      System.err.println(
+              "SequenceFeature type may not be null: " + sf.toString());
       return false;
     }
 
@@ -497,6 +546,7 @@ public class Sequence extends ASequence implements SequenceI
   public void setStart(int start)
   {
     this.start = start;
+    sequenceChanged();
   }
 
   /**
@@ -544,6 +594,14 @@ public class Sequence extends ASequence implements SequenceI
     return this.sequence.length;
   }
 
+  @Override
+  public void setSequence(char[] seq)
+  {
+    this.sequence = Arrays.copyOf(seq, seq.length);
+    checkValidRange();
+    sequenceChanged();
+  }
+
   /**
    * DOCUMENT ME!
    * 
@@ -574,8 +632,8 @@ public class Sequence extends ASequence implements SequenceI
   public char[] getSequence()
   {
     // return sequence;
-    return sequence == null ? null : Arrays.copyOf(sequence,
-            sequence.length);
+    return sequence == null ? null
+            : Arrays.copyOf(sequence, sequence.length);
   }
 
   /*
@@ -683,7 +741,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public GeneLociI getGeneLoci()
   {
-    DBRefEntry[] refs = getDBRefs();
+    List<DBRefEntry> refs = getDBRefs();
     if (refs != null)
     {
       for (final DBRefEntry ref : refs)
@@ -853,7 +911,7 @@ public class Sequence extends ASequence implements SequenceI
     {
       return findPosition(column + 1, cursor);
     }
-    
+
     // TODO recode this more naturally i.e. count residues only
     // as they are found, not 'in anticipation'
 
@@ -1042,7 +1100,8 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public ContiguousI findPositions(int fromColumn, int toColumn)
   {
-    if (toColumn < fromColumn || fromColumn < 1)
+    fromColumn = Math.max(fromColumn, 1);
+    if (toColumn < fromColumn)
     {
       return null;
     }
@@ -1158,7 +1217,7 @@ public class Sequence extends ASequence implements SequenceI
   {
     ArrayList<int[]> map = new ArrayList<>();
     int lastj = -1, j = 0;
-    int pos = start;
+    // int pos = start;
     int seqlen = sequence.length;
     while ((j < seqlen))
     {
@@ -1192,7 +1251,7 @@ public class Sequence extends ASequence implements SequenceI
   {
     BitSet map = new BitSet();
     int lastj = -1, j = 0;
-    int pos = start;
+    // int pos = start;
     int seqlen = sequence.length;
     while ((j < seqlen))
     {
@@ -1360,24 +1419,22 @@ public class Sequence extends ASequence implements SequenceI
     vamsasId = id;
   }
 
+  @Deprecated
   @Override
-  public void setDBRefs(DBRefEntry[] dbref)
+  public void setDBRefs(DBModList<DBRefEntry> newDBrefs)
   {
     if (dbrefs == null && datasetSequence != null
             && this != datasetSequence)
     {
-      datasetSequence.setDBRefs(dbref);
+      datasetSequence.setDBRefs(newDBrefs);
       return;
     }
-    dbrefs = dbref;
-    if (dbrefs != null)
-    {
-      DBRefUtils.ensurePrimaries(this);
-    }
+    dbrefs = newDBrefs;
+    refModCount = 0;
   }
 
   @Override
-  public DBRefEntry[] getDBRefs()
+  public DBModList<DBRefEntry> getDBRefs()
   {
     if (dbrefs == null && datasetSequence != null
             && this != datasetSequence)
@@ -1390,6 +1447,7 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void addDBRef(DBRefEntry entry)
   {
+    // TODO JAL-3980 maintain as sorted list
     if (datasetSequence != null)
     {
       datasetSequence.addDBRef(entry);
@@ -1398,12 +1456,13 @@ public class Sequence extends ASequence implements SequenceI
 
     if (dbrefs == null)
     {
-      dbrefs = new DBRefEntry[0];
+      dbrefs = new DBModList<>();
     }
+    // TODO JAL-3979 LOOK UP RATHER THAN SWEEP FOR EFFICIENCY
 
-    for (DBRefEntryI dbr : dbrefs)
+    for (int ib = 0, nb = dbrefs.size(); ib < nb; ib++)
     {
-      if (dbr.updateFrom(entry))
+      if (dbrefs.get(ib).updateFrom(entry))
       {
         /*
          * found a dbref that either matched, or could be
@@ -1413,18 +1472,19 @@ public class Sequence extends ASequence implements SequenceI
       }
     }
 
-    /*
-     * 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;
+    // /// BH OUCH!
+    // /*
+    // * extend the array to make room for one more
+    // */
+    // // TODO use an ArrayList instead
+    // int j = dbrefs.length;
+    // List<DBRefEntry> temp = new DBRefEntry[j + 1];
+    // System.arraycopy(dbrefs, 0, temp, 0, j);
+    // temp[temp.length - 1] = entry;
+    //
+    // dbrefs = temp;
 
-    DBRefUtils.ensurePrimaries(this);
+    dbrefs.add(entry);
   }
 
   @Override
@@ -1537,6 +1597,8 @@ public class Sequence extends ASequence implements SequenceI
 
   private int _seqhash = 0;
 
+  private List<DBRefEntry> primaryRefs;
+
   /**
    * Answers false if the sequence is more than 85% nucleotide (ACGTU), else
    * true
@@ -1554,7 +1616,7 @@ public class Sequence extends ASequence implements SequenceI
       _isNa = Comparison.isNucleotide(this);
     }
     return !_isNa;
-  };
+  }
 
   /*
    * (non-Javadoc)
@@ -1668,13 +1730,14 @@ public class Sequence extends ASequence implements SequenceI
       // TODO: could merge DBRefs
       return datasetSequence.updatePDBIds();
     }
-    if (dbrefs == null || dbrefs.length == 0)
+    if (dbrefs == null || dbrefs.size() == 0)
     {
       return false;
     }
     boolean added = false;
-    for (DBRefEntry dbr : dbrefs)
+    for (int ib = 0, nb = dbrefs.size(); ib < nb; ib++)
     {
+      DBRefEntry dbr = dbrefs.get(ib);
       if (DBRefSource.PDB.equals(dbr.getSource()))
       {
         /*
@@ -1710,8 +1773,9 @@ public class Sequence extends ASequence implements SequenceI
       List<SequenceFeature> sfs = entry.getSequenceFeatures();
       for (SequenceFeature feature : sfs)
       {
-       SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature)
-                : new SequenceFeature[] { new SequenceFeature(feature) };
+        SequenceFeature sf[] = (mp != null) ? mp.locateFeature(feature)
+                : new SequenceFeature[]
+                { new SequenceFeature(feature) };
         if (sf != null)
         {
           for (int sfi = 0; sfi < sf.length; sfi++)
@@ -1733,12 +1797,12 @@ public class Sequence extends ASequence implements SequenceI
       }
     }
     // transfer database references
-    DBRefEntry[] entryRefs = entry.getDBRefs();
+    List<DBRefEntry> entryRefs = entry.getDBRefs();
     if (entryRefs != null)
     {
-      for (int r = 0; r < entryRefs.length; r++)
+      for (int r = 0, n = entryRefs.size(); r < n; r++)
       {
-        DBRefEntry newref = new DBRefEntry(entryRefs[r]);
+        DBRefEntry newref = new DBRefEntry(entryRefs.get(r));
         if (newref.getMap() != null && mp != null)
         {
           // remap ref using our local mapping
@@ -1769,13 +1833,30 @@ public class Sequence extends ASequence implements SequenceI
   public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
           String label)
   {
+    return getAlignmentAnnotations(calcId, label, null, true);
+  }
+
+  @Override
+  public List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label, String description)
+  {
+    return getAlignmentAnnotations(calcId, label, description, false);
+  }
+
+  private List<AlignmentAnnotation> getAlignmentAnnotations(String calcId,
+          String label, String description, boolean ignoreDescription)
+  {
     List<AlignmentAnnotation> result = new ArrayList<>();
     if (this.annotation != null)
     {
       for (AlignmentAnnotation ann : annotation)
       {
-        if (ann.calcId != null && ann.calcId.equals(calcId)
-                && ann.label != null && ann.label.equals(label))
+        String id = ann.getCalcId();
+        if ((id != null && id.equals(calcId))
+                && (ann.label != null && ann.label.equals(label))
+                && ((ignoreDescription && description == null)
+                        || (ann.description != null
+                                && ann.description.equals(description))))
         {
           result.add(ann);
         }
@@ -1812,6 +1893,8 @@ public class Sequence extends ASequence implements SequenceI
     return null;
   }
 
+  private List<DBRefEntry> tmpList;
+
   @Override
   public List<DBRefEntry> getPrimaryDBRefs()
   {
@@ -1819,16 +1902,29 @@ public class Sequence extends ASequence implements SequenceI
     {
       return datasetSequence.getPrimaryDBRefs();
     }
-    if (dbrefs == null || dbrefs.length == 0)
+    if (dbrefs == null || dbrefs.size() == 0)
     {
       return Collections.emptyList();
     }
     synchronized (dbrefs)
     {
-      List<DBRefEntry> primaries = new ArrayList<>();
-      DBRefEntry[] tmp = new DBRefEntry[1];
-      for (DBRefEntry ref : dbrefs)
+      if (refModCount == dbrefs.getModCount() && primaryRefs != null)
       {
+        return primaryRefs; // no changes
+      }
+      refModCount = dbrefs.getModCount();
+      List<DBRefEntry> primaries = (primaryRefs == null
+              ? (primaryRefs = new ArrayList<>())
+              : primaryRefs);
+      primaries.clear();
+      if (tmpList == null)
+      {
+        tmpList = new ArrayList<>();
+        tmpList.add(null); // for replacement
+      }
+      for (int i = 0, n = dbrefs.size(); i < n; i++)
+      {
+        DBRefEntry ref = dbrefs.get(i);
         if (!ref.isPrimaryCandidate())
         {
           continue;
@@ -1843,8 +1939,8 @@ public class Sequence extends ASequence implements SequenceI
           }
         }
         // whilst it looks like it is a primary ref, we also sanity check type
-        if (DBRefUtils.getCanonicalName(DBRefSource.PDB)
-                .equals(DBRefUtils.getCanonicalName(ref.getSource())))
+        if (DBRefSource.PDB_CANONICAL_NAME
+                .equals(ref.getCanonicalSourceName()))
         {
           // PDB dbrefs imply there should be a PDBEntry associated
           // TODO: tighten PDB dbrefs
@@ -1853,25 +1949,59 @@ public class Sequence extends ASequence implements SequenceI
           // 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)
+          if (pdbentry == null || pdbentry.getFile() == null)
           {
-            primaries.add(ref);
+            continue;
           }
-          continue;
         }
-        // check standard protein or dna sources
-        tmp[0] = ref;
-        DBRefEntry[] res = DBRefUtils.selectDbRefs(!isProtein(), tmp);
-        if (res != null && res[0] == tmp[0])
+        else
         {
-          primaries.add(ref);
-          continue;
+          // check standard protein or dna sources
+          tmpList.set(0, ref);
+          List<DBRefEntry> res = DBRefUtils.selectDbRefs(!isProtein(),
+                  tmpList);
+          if (res == null || res.get(0) != tmpList.get(0))
+          {
+            continue;
+          }
         }
+        primaries.add(ref);
       }
+
+      // version must be not null, as otherwise it will not be a candidate,
+      // above
+      DBRefUtils.ensurePrimaries(this, primaries);
       return primaries;
     }
   }
 
+  @Override
+  public HiddenMarkovModel getHMM()
+  {
+    return hmm;
+  }
+
+  @Override
+  public void setHMM(HiddenMarkovModel hmm)
+  {
+    this.hmm = hmm;
+  }
+
+  @Override
+  public boolean hasHMMAnnotation()
+  {
+    if (this.annotation == null) {
+      return false;
+    }
+    for (AlignmentAnnotation ann : annotation)
+    {
+      if (InformationThread.HMM_CALC_ID.equals(ann.getCalcId()))
+      {
+        return true;
+      }
+    }
+    return false;
+  }
   /**
    * {@inheritDoc}
    */
@@ -2036,4 +2166,10 @@ public class Sequence extends ASequence implements SequenceI
     // otherwise, sequence was completely hidden
     return 0;
   }
+
+  @Override
+  public boolean hasHMMProfile()
+  {
+    return hmm != null;
+  }
 }