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

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 5e2355d..ca12c83 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -25,7 +25,6 @@ import jalview.datamodel.features.SequenceFeaturesI;
 import jalview.util.MapList;
 import jalview.ws.params.InvalidArgumentException;
 
-import java.awt.Color;
 import java.util.BitSet;
 import java.util.Iterator;
 import java.util.List;
@@ -387,6 +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);
@@ -585,11 +590,45 @@ public interface SequenceI extends ASequenceI
    */
   public int firstResidueOutsideIterator(Iterator<int[]> it);
 
-  public Color getColor(int i);
+  /**
+   * @author Bob Hanson 2019.07.30
+   * 
+   * get a 4-byte color, with caching
+   * 
+   */
+  public int getColor(int i);
 
-  public Color setColor(int i, Color c);
+  /**
+   * @author Bob Hanson 2019.07.30
+   * 
+   * set a 4-byte color, with caching
+   * 
+   */
+  public int setColor(int i, int argb);
 
+  /**
+   * @author Bob Hanson 2019.07.30
+   * 
+   * allows resetting the color cache
+   * 
+   */
   public void resetColors();
 
+  /**
+   * 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.
+   */
+  List<SequenceFeature> findFeatures(int column, String type,
+          List<SequenceFeature> result);
+
+  /**
+   * Answers true if this store contains at least one feature, else false
+   * 
+   * @return
+   */
+  public boolean hasFeatures(String type);
+
 }