JAL-3383 JAL-3253-applet Allows for possibility of a sequence caching

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

diff --git a/src/jalview/datamodel/SequenceI.java b/src/jalview/datamodel/SequenceI.java
index 5a3aafd..5e2355d 100755 (executable)
--- a/src/jalview/datamodel/SequenceI.java
+++ b/src/jalview/datamodel/SequenceI.java
@@ -25,6 +25,7 @@ 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;
@@ -114,9 +115,11 @@ 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 +221,7 @@ 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 +585,11 @@ public interface SequenceI extends ASequenceI
    */
   public int firstResidueOutsideIterator(Iterator<int[]> it);
 
+  public Color getColor(int i);
+
+  public Color setColor(int i, Color c);
+
+  public void resetColors();
 
 }