JAL-2598 Sequence.getSequence return a copy of the char array

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 8371036..5553840 100755 (executable)
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -62,6 +62,8 @@ public class Alignment implements AlignmentI
 
   HiddenSequences hiddenSequences;
 
+  HiddenColumns hiddenCols;
+
   public Hashtable alignmentProperties;
 
   private List<AlignedCodonFrame> codonFrameList;
@@ -70,7 +72,8 @@ public class Alignment implements AlignmentI
   {
     groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
     hiddenSequences = new HiddenSequences(this);
-    codonFrameList = new ArrayList<AlignedCodonFrame>();
+    hiddenCols = new HiddenColumns();
+    codonFrameList = new ArrayList<>();
 
     nucleotide = Comparison.isNucleotide(seqs);
 
@@ -125,7 +128,7 @@ public class Alignment implements AlignmentI
   public Alignment(SeqCigar[] alseqs)
   {
     SequenceI[] seqs = SeqCigar.createAlignmentSequences(alseqs,
-            gapCharacter, new ColumnSelection(), null);
+            gapCharacter, new HiddenColumns(), null);
     initAlignment(seqs);
   }
 
@@ -402,7 +405,7 @@ public class Alignment implements AlignmentI
   @Override
   public SequenceGroup[] findAllGroups(SequenceI s)
   {
-    ArrayList<SequenceGroup> temp = new ArrayList<SequenceGroup>();
+    ArrayList<SequenceGroup> temp = new ArrayList<>();
 
     synchronized (groups)
     {
@@ -453,7 +456,7 @@ public class Alignment implements AlignmentI
             return;
           }
         }
-        sg.setContext(this);
+        sg.setContext(this, true);
         groups.add(sg);
       }
     }
@@ -530,7 +533,7 @@ public class Alignment implements AlignmentI
       }
       for (SequenceGroup sg : groups)
       {
-        sg.setContext(null);
+        sg.setContext(null, false);
       }
       groups.clear();
     }
@@ -546,7 +549,7 @@ public class Alignment implements AlignmentI
       {
         removeAnnotationForGroup(g);
         groups.remove(g);
-        g.setContext(null);
+        g.setContext(null, false);
       }
     }
   }
@@ -1064,21 +1067,18 @@ public class Alignment implements AlignmentI
         currentSeq = currentSeq.createDatasetSequence();
       }
     }
-    if (seqs.contains(currentSeq))
-    {
-      return;
-    }
-    List<SequenceI> toProcess = new ArrayList<SequenceI>();
+
+    List<SequenceI> toProcess = new ArrayList<>();
     toProcess.add(currentSeq);
     while (toProcess.size() > 0)
     {
       // use a queue ?
       SequenceI curDs = toProcess.remove(0);
-      if (seqs.contains(curDs))
+
+      if (!seqs.add(curDs))
       {
         continue;
       }
-      seqs.add(curDs);
       // iterate over database references, making sure we add forward referenced
       // sequences
       if (curDs.getDBRefs() != null)
@@ -1121,7 +1121,7 @@ public class Alignment implements AlignmentI
       return;
     }
     // try to avoid using SequenceI.equals at this stage, it will be expensive
-    Set<SequenceI> seqs = new LinkedIdentityHashSet<SequenceI>();
+    Set<SequenceI> seqs = new LinkedIdentityHashSet<>();
 
     for (int i = 0; i < getHeight(); i++)
     {
@@ -1327,6 +1327,12 @@ public class Alignment implements AlignmentI
   }
 
   @Override
+  public HiddenColumns getHiddenColumns()
+  {
+    return hiddenCols;
+  }
+
+  @Override
   public CigarArray getCompactAlignment()
   {
     synchronized (sequences)
@@ -1400,7 +1406,7 @@ public class Alignment implements AlignmentI
     {
       return null;
     }
-    List<AlignedCodonFrame> cframes = new ArrayList<AlignedCodonFrame>();
+    List<AlignedCodonFrame> cframes = new ArrayList<>();
     for (AlignedCodonFrame acf : getCodonFrames())
     {
       if (acf.involvesSequence(seq))
@@ -1467,8 +1473,8 @@ 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
@@ -1477,21 +1483,14 @@ public class Alignment implements AlignmentI
     if (sqs != null)
     {
       // avoid self append deadlock by
-      List<SequenceI> toappendsq = new ArrayList<SequenceI>();
+      List<SequenceI> toappendsq = new ArrayList<>();
       synchronized (sqs)
       {
         for (SequenceI addedsq : sqs)
         {
           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);
         }
@@ -1618,7 +1617,7 @@ public class Alignment implements AlignmentI
   @Override
   public Iterable<AlignmentAnnotation> findAnnotation(String calcId)
   {
-    List<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    List<AlignmentAnnotation> aa = new ArrayList<>();
     AlignmentAnnotation[] alignmentAnnotation = getAlignmentAnnotation();
     if (alignmentAnnotation != null)
     {
@@ -1639,7 +1638,7 @@ public class Alignment implements AlignmentI
   public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label)
   {
-    ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
+    ArrayList<AlignmentAnnotation> aa = new ArrayList<>();
     for (AlignmentAnnotation ann : getAlignmentAnnotation())
     {
       if ((calcId == null || (ann.getCalcId() != null && ann.getCalcId()
@@ -1844,7 +1843,7 @@ public class Alignment implements AlignmentI
   @Override
   public Set<String> getSequenceNames()
   {
-    Set<String> names = new HashSet<String>();
+    Set<String> names = new HashSet<>();
     for (SequenceI seq : getSequences())
     {
       names.add(seq.getName());
@@ -1944,4 +1943,10 @@ public class Alignment implements AlignmentI
     }
     return new int[] { startPos, endPos };
   }
+
+  @Override
+  public void setHiddenColumns(HiddenColumns cols)
+  {
+    hiddenCols = cols;
+  }
 }