JAL-3383 removing colour caching (to a separate branch)

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index 7624d2c..6c0e528 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -1612,7 +1612,7 @@ public class Sequence extends ASequence implements SequenceI
       _isNa = Comparison.isNucleotide(this);
     }
     return !_isNa;
-  };
+  }
 
   /*
    * (non-Javadoc)
@@ -1967,15 +1967,6 @@ 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, 
@@ -2026,7 +2017,6 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void sequenceChanged()
   {
-    argb = null;
     changeCount++;
   }
 
@@ -2129,42 +2119,24 @@ public class Sequence extends ASequence implements SequenceI
     return 0;
   }
 
-  private int[] argb;
-
-  @Override
-  public int getColor(int i)
-  {
-    return argb == null ? 0 : argb[i];
-  }
-
-  @Override
-  public int setColor(int i, int rgb)
-  {
-    if (argb == null)
-    {
-      argb = new int[this.sequence.length];
-    }
-    return (argb[i] = rgb);
-  }
-
-  @Override
-  public void resetColors()
-  {
-    argb = null;
-  }
-
   /**
-   * @author Bob Hanson 2019.07.30
-   * 
-   * allows passing the result ArrayList as a parameter to avoid unnecessary construction
-   * 
+   * 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 void findFeatures(int column, String type,
+  public List<SequenceFeature> findFeatures(int column, String type,
           List<SequenceFeature> result)
   {
-    getFeatures().findFeatures(findPosition(column - 1), type, result);
+    return getFeatures().findFeatures(findPosition(column - 1), type,
+            result);
   }
 
+  @Override
+  public boolean hasFeatures(String type)
+  {
+    return getFeatures().hasFeatures(type);
+  }
 
 }