X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FAlignment.java;h=5232f8e4370609161f49d1d83e1b5e849e64a1f4;hb=45d7b8f24253fa1c49977feedfe8a0f2f7cea85e;hp=40e3230ab1a8a4888463310d17cab588cadbd2b4;hpb=cef7be0f9008ff15318e3479a5de35e127071ef3;p=jalview.git

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 40e3230..5232f8e 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -28,10 +28,13 @@ import jalview.util.LinkedIdentityHashSet;
 import jalview.util.MessageManager;
 
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
 import java.util.Collections;
 import java.util.Enumeration;
 import java.util.HashSet;
 import java.util.Hashtable;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
@@ -44,11 +47,11 @@ import java.util.Vector;
  * @author JimP
  * 
  */
-public class Alignment implements AlignmentI
+public class Alignment implements AlignmentI, AutoCloseable
 {
   private Alignment dataset;
 
-  protected List<SequenceI> sequences;
+  private List<SequenceI> sequences;
 
   protected List<SequenceGroup> groups;
 
@@ -192,11 +195,13 @@ public class Alignment implements AlignmentI
   {
     synchronized (sequences)
     {
+
       if (i > -1 && i < sequences.size())
       {
         return sequences.get(i);
       }
     }
+
     return null;
   }
 
@@ -324,15 +329,20 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public void finalize() throws Throwable
+  public void close()
   {
     if (getDataset() != null)
     {
-      getDataset().removeAlignmentRef();
+      try
+      {
+        getDataset().removeAlignmentRef();
+      } catch (Throwable e)
+      {
+        e.printStackTrace();
+      }
     }
 
     nullReferences();
-    super.finalize();
   }
 
   /**
@@ -607,15 +617,17 @@ public class Alignment implements AlignmentI
   @Override
   public SequenceI findName(SequenceI startAfter, String token, boolean b)
   {
-
+    if (token == null)
+      return null;
     int i = 0;
     SequenceI sq = null;
     String sqname = null;
+    int nseq = sequences.size();
     if (startAfter != null)
     {
       // try to find the sequence in the alignment
       boolean matched = false;
-      while (i < sequences.size())
+      while (i < nseq)
       {
         if (getSequenceAt(i++) == startAfter)
         {
@@ -628,7 +640,7 @@ public class Alignment implements AlignmentI
         i = 0;
       }
     }
-    while (i < sequences.size())
+    while (i < nseq)
     {
       sq = getSequenceAt(i);
       sqname = sq.getName();
@@ -734,15 +746,22 @@ public class Alignment implements AlignmentI
 
     for (int i = 0; i < sequences.size(); i++)
     {
-      if (getSequenceAt(i).getLength() > maxLength)
-      {
-        maxLength = getSequenceAt(i).getLength();
-      }
+      maxLength = Math.max(maxLength, getSequenceAt(i).getLength());
     }
-
     return maxLength;
   }
 
+  @Override
+  public int getVisibleWidth()
+  {
+    int w = getWidth();
+    if (hiddenCols != null)
+    {
+      w -= hiddenCols.getSize();
+    }
+    return w;
+  }
+
   /**
    * DOCUMENT ME!
    * 
@@ -1203,7 +1222,8 @@ public class Alignment implements AlignmentI
     int maxLength = -1;
 
     SequenceI current;
-    for (int i = 0; i < sequences.size(); i++)
+    int nseq = sequences.size();
+    for (int i = 0; i < nseq; i++)
     {
       current = getSequenceAt(i);
       for (int j = current.getLength(); j > maxLength; j--)
@@ -1220,7 +1240,7 @@ public class Alignment implements AlignmentI
     maxLength++;
 
     int cLength;
-    for (int i = 0; i < sequences.size(); i++)
+    for (int i = 0; i < nseq; i++)
     {
       current = getSequenceAt(i);
       cLength = current.getLength();
@@ -1497,8 +1517,8 @@ public class Alignment implements AlignmentI
   {
     // TODO JAL-1270 needs test coverage
     // currently tested for use in jalview.gui.SequenceFetcher
-    boolean samegap = toappend.getGapCharacter() == getGapCharacter();
     char oldc = toappend.getGapCharacter();
+    boolean samegap = oldc == getGapCharacter();
     boolean hashidden = toappend.getHiddenSequences() != null
             && toappend.getHiddenSequences().hiddenSequences != null;
     // get all sequences including any hidden ones
@@ -1516,14 +1536,7 @@ public class Alignment implements AlignmentI
         {
           if (!samegap)
           {
-            char[] oldseq = addedsq.getSequence();
-            for (int c = 0; c < oldseq.length; c++)
-            {
-              if (oldseq[c] == oldc)
-              {
-                oldseq[c] = gapCharacter;
-              }
-            }
+            addedsq.replace(oldc, gapCharacter);
           }
           toappendsq.add(addedsq);
         }
@@ -1619,71 +1632,71 @@ public class Alignment implements AlignmentI
           String calcId, boolean autoCalc, SequenceI seqRef,
           SequenceGroup groupRef)
   {
-    if (annotations != null)
+    AlignmentAnnotation annot = annotations == null ? null
+            : AlignmentAnnotation.findFirstAnnotation(
+              Arrays.asList(getAlignmentAnnotation()), name, calcId,
+              autoCalc, seqRef, groupRef);
+
+    if (annot == null)
     {
-      for (AlignmentAnnotation annot : getAlignmentAnnotation())
+
+      annot = new AlignmentAnnotation(name, name, new Annotation[1], 0f, 0f,
+              AlignmentAnnotation.BAR_GRAPH);
+      annot.hasText = false;
+      if (calcId != null)
       {
-        if (annot.autoCalculated == autoCalc && (name.equals(annot.label))
-                && (calcId == null || annot.getCalcId().equals(calcId))
-                && annot.sequenceRef == seqRef
-                && annot.groupRef == groupRef)
-        {
-          return annot;
-        }
+        annot.setCalcId(calcId);
       }
+      annot.autoCalculated = autoCalc;
+      if (seqRef != null)
+      {
+        annot.setSequenceRef(seqRef);
+      }
+      annot.groupRef = groupRef;
+      addAnnotation(annot);
+    }
+    return annot;
+  }
+
+
+  @Override
+  public AlignmentAnnotation updateFromOrCopyAnnotation(
+          AlignmentAnnotation ala)
+  {
+    AlignmentAnnotation annot = AlignmentAnnotation.findFirstAnnotation(
+            Arrays.asList(getAlignmentAnnotation()), ala.label, ala.calcId,
+            ala.autoCalculated, ala.sequenceRef, ala.groupRef);
+    if (annot == null)
+    {
+      annot = new AlignmentAnnotation(ala);
+      addAnnotation(annot);
     }
-    AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
-            new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
-    annot.hasText = false;
-    annot.setCalcId(new String(calcId));
-    annot.autoCalculated = autoCalc;
-    if (seqRef != null)
+    else
     {
-      annot.setSequenceRef(seqRef);
+      annot.updateAlignmentAnnotationFrom(ala);
     }
-    annot.groupRef = groupRef;
-    addAnnotation(annot);
-
+    validateAnnotation(annot);
     return annot;
   }
 
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    List<AlignmentAnnotation> aa = new ArrayList<>();
     AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
     if (alignmentAnnotation != null)
     {
-      for (AlignmentAnnotation a : alignmentAnnotation)
-      {
-        if (a.getCalcId() == calcId || (a.getCalcId() != null
-                && calcId != null && a.getCalcId().equals(calcId)))
-        {
-          aa.add(a);
-        }
-      }
+      return AlignmentAnnotation.findAnnotation(
+              Arrays.asList(getAlignmentAnnotation()), calcId);
     }
-    return aa;
+    return Arrays.asList(new AlignmentAnnotation[] {});
   }
 
   @Override
   public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
-    for (AlignmentAnnotation ann : getAlignmentAnnotation())
-    {
-      if ((calcId == null || (ann.getCalcId() != null
-              && ann.getCalcId().equals(calcId)))
-              && (seq == null || (ann.sequenceRef != null
-                      && ann.sequenceRef == seq))
-              && (label == null
-                      || (ann.label != null && ann.label.equals(label))))
-      {
-        aa.add(ann);
-      }
-    }
-    return aa;
+    return AlignmentAnnotation.findAnnotations(
+            Arrays.asList(getAlignmentAnnotation()), seq, calcId, label);
   }
 
   @Override
@@ -1942,51 +1955,138 @@ public class Alignment implements AlignmentI
   }
 
   @Override
-  public void setHiddenColumns(HiddenColumns cols)
+  public boolean setHiddenColumns(HiddenColumns cols)
   {
+    boolean changed = cols == null ? hiddenCols != null
+            : !cols.equals(hiddenCols);
     hiddenCols = cols;
+    return changed;
+  }
+
+  @Override
+  public void setupJPredAlignment()
+  {
+    SequenceI repseq = getSequenceAt(0);
+    setSeqrep(repseq);
+    HiddenColumns cs = new HiddenColumns();
+    cs.hideList(repseq.getInsertions());
+    setHiddenColumns(cs);
+  }
+
+  @Override
+  public HiddenColumns propagateInsertions(SequenceI profileseq,
+          AlignmentView input)
+  {
+    int profsqpos = 0;
+
+    char gc = getGapCharacter();
+    Object[] alandhidden = input.getAlignmentAndHiddenColumns(gc);
+    HiddenColumns nview = (HiddenColumns) alandhidden[1];
+    SequenceI origseq = ((SequenceI[]) alandhidden[0])[profsqpos];
+    return propagateInsertions(profileseq, origseq, nview);
   }
 
   /**
-   * Returns all HMM consensus sequences. This will not return real sequences
-   * with HMMs. If remove is set to true, the consensus sequences will be
-   * removed from the alignment.
+   * 
+   * @param profileseq
+   *          sequence in al which corresponds to origseq
+   * @param al
+   *          alignment which is to have gaps inserted into it
+   * @param origseq
+   *          sequence corresponding to profileseq which defines gap map for
+   *          modifying al
    */
-  @Override // TODO make this more efficient.
-  public List<SequenceI> getHMMConsensusSequences(boolean remove)
+  private HiddenColumns propagateInsertions(SequenceI profileseq,
+          SequenceI origseq, HiddenColumns hc)
   {
-    List<SequenceI> seqs = new ArrayList<>();
-    int position = 0;
-    int seqsRemoved = 0;
-    boolean endReached = false;
+    // take the set of hidden columns, and the set of gaps in origseq,
+    // and remove all the hidden gaps from hiddenColumns
+
+    // first get the gaps as a Bitset
+    // then calculate hidden ^ not(gap)
+    BitSet gaps = origseq.gapBitset();
+    hc.andNot(gaps);
+
+    // for each sequence in the alignment, except the profile sequence,
+    // insert gaps corresponding to each hidden region but where each hidden
+    // column region is shifted backwards by the number of preceding visible
+    // gaps update hidden columns at the same time
+    HiddenColumns newhidden = new HiddenColumns();
 
-    while (!endReached)
+    int numGapsBefore = 0;
+    int gapPosition = 0;
+    Iterator<int[]> it = hc.iterator();
+    while (it.hasNext())
     {
-      SequenceI seq = sequences.get(position);
-      if (seq.isHMMConsensusSequence())
+      int[] region = it.next();
+
+      // get region coordinates accounting for gaps
+      // we can rely on gaps not being *in* hidden regions because we already
+      // removed those
+      while (gapPosition < region[0])
       {
-        if (remove)
+        gapPosition++;
+        if (gaps.get(gapPosition))
         {
-          sequences.remove(position);
-          seqsRemoved++;
-          seq.setPreviousPosition(seqsRemoved + position - 1);
+          numGapsBefore++;
         }
-        else
-        {
-          position++;
-        }
-        seqs.add(seq);
       }
-      else
+
+      int left = region[0] - numGapsBefore;
+      int right = region[1] - numGapsBefore;
+
+      newhidden.hideColumns(left, right);
+      padGaps(left, right, profileseq);
+    }
+    return newhidden;
+  }
+
+  /**
+   * Pad gaps in all sequences in alignment except profileseq
+   * 
+   * @param left
+   *          position of first gap to insert
+   * @param right
+   *          position of last gap to insert
+   * @param profileseq
+   *          sequence not to pad
+   */
+  private void padGaps(int left, int right, SequenceI profileseq)
+  {
+    char gc = getGapCharacter();
+
+    // make a string with number of gaps = length of hidden region
+    StringBuilder sb = new StringBuilder();
+    for (int g = 0; g < right - left + 1; g++)
+    {
+      sb.append(gc);
+    }
+
+    // loop over the sequences and pad with gaps where required
+    for (int s = 0, ns = getHeight(); s < ns; s++)
+    {
+      SequenceI sqobj = getSequenceAt(s);
+      if ((sqobj != profileseq) && (sqobj.getLength() >= left))
       {
-        position++;
+        String sq = sqobj.getSequenceAsString();
+        sqobj.setSequence(
+                sq.substring(0, left) + sb.toString() + sq.substring(left));
       }
+    }
+  }
 
-      if (position >= sequences.size())
+  @Override
+  public List<SequenceI> getHmmSequences()
+  {
+    List<SequenceI> result = new ArrayList<>();
+    for (int i = 0; i < sequences.size(); i++)
+    {
+      SequenceI seq = sequences.get(i);
+      if (seq.hasHMMProfile())
       {
-        endReached = true;
+        result.add(seq);
       }
     }
-    return seqs;
+    return result;
   }
 }