X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceI.java;h=ca12c8310b692cb4a678d08ddda9f639f06bbd14;hb=08b87509ada06ac8614424247346daef4054b41a;hp=933f33292f8a29c028d3b99e2715fbd438a799dc;hpb=3da878124135ff033f42d19d8733891b09e953cd;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 933f332..ca12c83 100755
--- 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);
@@ -584,6 +590,45 @@ 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
+   * 
+   */
+  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);
 
 }