JAL-3397 impl.IntervalStore and nonc.IntervalStore unified api

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 4219c8e..47a7ead 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -118,6 +118,11 @@ public class Sequence extends ASequence implements SequenceI
    */
   private int changeCount;
 
+  /*
+   * cached rgb colours for each position of the aligned sequence (column)
+   */
+  private int[] argb;
+
   /**
    * Creates a new Sequence object.
    * 
@@ -1612,7 +1617,7 @@ public class Sequence extends ASequence implements SequenceI
       _isNa = Comparison.isNucleotide(this);
     }
     return !_isNa;
-  };
+  }
 
   /*
    * (non-Javadoc)
@@ -1967,15 +1972,6 @@ public class Sequence extends ASequence implements SequenceI
 
     List<SequenceFeature> result = getFeatures().findFeatures(startPos,
             endPos, types);
-    // if (datasetSequence != null)
-    // {
-    // result = datasetSequence.getFeatures().findFeatures(startPos, endPos,
-    // types);
-    // }
-    // else
-    // {
-    // result = sequenceFeatureStore.findFeatures(startPos, endPos, types);
-    // }
 
     /*
      * if end column is gapped, endPos may be to the right, 
@@ -2129,8 +2125,6 @@ public class Sequence extends ASequence implements SequenceI
     return 0;
   }
 
-  private int[] argb;
-
   @Override
   public int getColor(int i)
   {
@@ -2154,12 +2148,10 @@ public class Sequence extends ASequence implements SequenceI
   }
 
   /**
-   * @author Bob Hanson 2019.07.30
-   * 
-   *         allows passing the result ArrayList as a parameter to avoid
-   *         unnecessary construction
-   * @return result (JavaScript) or new ArrayList (Java -- see FeatureRender)
-   * 
+   * Answers a (possibly empty) list of features of the specified type that
+   * overlap the specified column position. If parameter {@code result} is not
+   * null, features are appended to it and the (possibly extended) list is
+   * returned.
    */
   @Override
   public List<SequenceFeature> findFeatures(int column, String type,
@@ -2169,9 +2161,6 @@ public class Sequence extends ASequence implements SequenceI
             result);
   }
 
-  /**
-   * allows early intervention for renderer if this returns false
-   */
   @Override
   public boolean hasFeatures(String type)
   {