JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 5a3aafd..0b26564 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -114,9 +114,11 @@ public interface SequenceI extends ASequenceI
    * get a range on the sequence as a string
    * 
    * @param start
-   *          position relative to start of sequence including gaps (from 0)
+   *          (inclusive) position relative to start of sequence including gaps
+   *          (from 0)
    * @param end
-   *          position relative to start of sequence including gaps (from 0)
+   *          (exclusive) position relative to start of sequence including gaps
+   *          (from 0)
    * 
    * @return String containing all gap and symbols in specified range
    */
@@ -218,7 +220,7 @@ public interface SequenceI extends ASequenceI
    *          - last column, base 1
    * @return
    */
-  public Range findPositions(int fromColum, int toColumn);
+  public ContiguousI findPositions(int fromColum, int toColumn);
 
   /**
    * Returns an int array where indices correspond to each residue in the
@@ -582,6 +584,48 @@ 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();
+
+  /**
+   * allows passing the result ArrayList as a parameter to avoid unnecessary
+   * construction
+   * 
+   * @author Bob Hanson 2019.07.30
+   * 
+   * 
+   */
+  List<SequenceFeature> findFeatures(int column, String type,
+          List<SequenceFeature> result);
+
+  /**
+   * allows early intervention for renderer if false
+   * 
+   * @author Bob Hanson 2019.07.30
+   * 
+   */
+  public boolean hasFeatures(String type);
 
 }