JAL-3210 Barebones gradle/buildship/eclipse. See README

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index bad33d1..ca2b6d4 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -392,10 +392,6 @@ public class Sequence extends ASequence implements SequenceI
     return sequenceFeatureStore.add(sf);
   }
 
-  /**
-   * @param sf
-   *          A known feature of this featureStore
-   */
   @Override
   public void deleteFeature(SequenceFeature sf)
   {
@@ -1971,15 +1967,15 @@ 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 (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, 
@@ -2030,7 +2026,6 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void sequenceChanged()
   {
-    argb = null;
     changeCount++;
   }
 
@@ -2132,54 +2127,4 @@ public class Sequence extends ASequence implements SequenceI
     // otherwise, sequence was completely hidden
     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
-   * @return result (JavaScript) or new ArrayList (Java -- see FeatureRender)
-   * 
-   */
-  @Override
-  public List<SequenceFeature> findFeatures(int column, String type,
-          List<SequenceFeature> result)
-  {
-    return getFeatures().findFeatures(findPosition(column - 1), type,
-            result);
-  }
-
-  /**
-   * allows early intervention for renderer if this returns false
-   */
-  @Override
-  public boolean hasFeatures(String type)
-  {
-    return getFeatures().hasFeatures(type);
-  }
-
 }