Merge remote-tracking branch 'origin/develop' into bug/JAL-2491

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

diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 2dafc0c..fcb6109 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;
@@ -70,6 +72,7 @@ public class Alignment implements AlignmentI
   {
     groups = Collections.synchronizedList(new ArrayList<SequenceGroup>());
     hiddenSequences = new HiddenSequences(this);
+    hiddenCols = new HiddenColumns();
     codonFrameList = new ArrayList<AlignedCodonFrame>();
 
     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);
   }
 
@@ -1327,6 +1330,12 @@ public class Alignment implements AlignmentI
   }
 
   @Override
+  public HiddenColumns getHiddenColumns()
+  {
+    return hiddenCols;
+  }
+
+  @Override
   public CigarArray getCompactAlignment()
   {
     synchronized (sequences)
@@ -1635,10 +1644,6 @@ public class Alignment implements AlignmentI
     return aa;
   }
 
-  /**
-   * Returns an iterable collection of any annotations that match on given
-   * sequence ref, calcId and label (ignoring null values).
-   */
   @Override
   public Iterable<AlignmentAnnotation> findAnnotations(SequenceI seq,
           String calcId, String label)
@@ -1646,9 +1651,11 @@ public class Alignment implements AlignmentI
     ArrayList<AlignmentAnnotation> aa = new ArrayList<AlignmentAnnotation>();
     for (AlignmentAnnotation ann : getAlignmentAnnotation())
     {
-      if (ann.getCalcId() != null && ann.getCalcId().equals(calcId)
-              && ann.sequenceRef != null && ann.sequenceRef == seq
-              && ann.label != null && ann.label.equals(label))
+      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);
       }
@@ -1946,4 +1953,10 @@ public class Alignment implements AlignmentI
     }
     return new int[] { startPos, endPos };
   }
+
+  @Override
+  public void setHiddenColumns(HiddenColumns cols)
+  {
+    hiddenCols = cols;
+  }
 }