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

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 013897d..851ef79 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -386,6 +386,12 @@ public interface SequenceI extends ASequenceI
    */
   public boolean addSequenceFeature(SequenceFeature sf);
 
+  /**
+   * Deletes the feature from the sequence (if found). To be precise, deletes
+   * the first feature {@code f} found where {@code f.equals(sf)}.
+   * 
+   * @param sf
+   */
   public void deleteFeature(SequenceFeature sf);
 
   public void setDatasetSequence(SequenceI seq);
@@ -585,36 +591,20 @@ public interface SequenceI extends ASequenceI
   public int firstResidueOutsideIterator(Iterator<int[]> it);
 
   /**
-   * @author Bob Hanson 2019.07.30
-   * 
-   * get a 4-byte color, with caching
-   * 
-   */
-  public int getColor(int i);
-
-  /**
-   * @author Bob Hanson 2019.07.30
-   * 
-   * set a 4-byte color, with caching
-   * 
+   * 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.
    */
-  public int setColor(int i, int argb);
+  List<SequenceFeature> findFeatures(int column, String type,
+          List<SequenceFeature> result);
 
   /**
-   * @author Bob Hanson 2019.07.30
-   * 
-   * allows resetting the color cache
-   * 
-   */
-  public void resetColors();
-
-  /**
-   * @author Bob Hanson 2019.07.30
-   * 
-   * allows passing the result ArrayList as a parameter to avoid unnecessary construction
+   * Answers true if this store contains at least one feature, else false
    * 
+   * @return
    */
-  void findFeatures(int column, String type, List<SequenceFeature> result);
+  public boolean hasFeatures(String type);
 
 }