Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[jalview.git] / src / jalview / datamodel / Alignment.java

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 93ad332..5232f8e 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -47,7 +47,7 @@ import java.util.Vector;
  * @author JimP
  * 
  */
-public class Alignment implements AlignmentI
+public class Alignment implements AlignmentI, AutoCloseable
 {
   private Alignment dataset;
 
@@ -195,6 +195,7 @@ public class Alignment implements AlignmentI
   {
     synchronized (sequences)
     {
+
       if (i > -1 && i < sequences.size())
       {
         return sequences.get(i);
@@ -291,6 +292,32 @@ public class Alignment implements AlignmentI
   }
 
   /**
+   * Inserts a sequence at a point in the alignment.
+   * 
+   * @param i
+   *          the index of the position the sequence is to be inserted in.
+   */
+  @Override
+  public void insertSequenceAt(int i, SequenceI snew)
+  {
+    synchronized (sequences)
+    {
+      if (sequences.size() > i)
+      {
+        sequences.add(i, snew);
+        return;
+
+      }
+      else
+      {
+        sequences.add(snew);
+        hiddenSequences.adjustHeightSequenceAdded();
+      }
+      return;
+    }
+  }
+
+  /**
    * DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
@@ -302,15 +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();
   }
 
   /**
@@ -585,15 +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)
         {
@@ -606,7 +640,7 @@ public class Alignment implements AlignmentI
         i = 0;
       }
     }
-    while (i < sequences.size())
+    while (i < nseq)
     {
       sq = getSequenceAt(i);
       sqname = sq.getName();
@@ -709,7 +743,7 @@ public class Alignment implements AlignmentI
   public int getWidth()
   {
     int maxLength = -1;
-  
+
     for (int i = 0; i < sequences.size(); i++)
     {
       maxLength = Math.max(maxLength, getSequenceAt(i).getLength());
@@ -717,6 +751,17 @@ public class Alignment implements AlignmentI
     return maxLength;
   }
 
+  @Override
+  public int getVisibleWidth()
+  {
+    int w = getWidth();
+    if (hiddenCols != null)
+    {
+      w -= hiddenCols.getSize();
+    }
+    return w;
+  }
+
   /**
    * DOCUMENT ME!
    * 
@@ -1177,7 +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--)
@@ -1194,7 +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();
@@ -1586,34 +1632,50 @@ 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);
     }
-    AlignmentAnnotation annot = new AlignmentAnnotation(name, name,
-            new Annotation[1], 0f, 0f, AlignmentAnnotation.BAR_GRAPH);
-    annot.hasText = false;
-    if (calcId != null)
+    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.setCalcId(new String(calcId));
+      annot = new AlignmentAnnotation(ala);
+      addAnnotation(annot);
     }
-    annot.autoCalculated = autoCalc;
-    if (seqRef != null)
+    else
     {
-      annot.setSequenceRef(seqRef);
+      annot.updateAlignmentAnnotationFrom(ala);
     }
-    annot.groupRef = groupRef;
-    addAnnotation(annot);
-
+    validateAnnotation(annot);
     return annot;
   }
 
@@ -1893,9 +1955,12 @@ 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
@@ -2010,4 +2075,18 @@ public class Alignment implements AlignmentI
     }
   }
 
+  @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())
+      {
+        result.add(seq);
+      }
+    }
+    return result;
+  }
 }