Merge remote-tracking branch 'origin/develop' into bug/JAL-2665-2.10.3

[jalview.git] / src / jalview / api / FeatureRenderer.java

diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index 7123b8c..9d2d7f4 100644 (file)
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -60,6 +60,7 @@ public interface FeatureRenderer
    * 
    * @param sequence
    * @param column
+   *          aligned column position (1..)
    * @param g
    * @return
    */
@@ -147,14 +148,27 @@ public interface FeatureRenderer
   void setGroupVisibility(String group, boolean visible);
 
   /**
-   * Returns features at the specified position on the given sequence.
+   * Returns features at the specified aligned column on the given sequence.
+   * Non-positional features are not included. If the column has a gap, then
+   * enclosing features are included (but not contact features).
+   * 
+   * @param sequence
+   * @param column
+   *          aligned column position (1..)
+   * @return
+   */
+  List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column);
+
+  /**
+   * Returns features at the specified residue position on the given sequence.
    * Non-positional features are not included.
    * 
    * @param sequence
-   * @param res
+   * @param resNo
+   *          residue position (start..)
    * @return
    */
-  List<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res);
+  List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence, int resNo);
 
   /**
    * get current displayed types, in ordering of rendering (on top last)
@@ -165,9 +179,9 @@ public interface FeatureRenderer
   List<String> getDisplayedFeatureTypes();
 
   /**
-   * get current displayed groups
+   * Returns a (possibly empty) list of currently visible feature groups
    * 
-   * @return a (possibly empty) list of feature groups
+   * @return
    */
   List<String> getDisplayedFeatureGroups();
 
@@ -200,4 +214,5 @@ public interface FeatureRenderer
    * @return
    */
   float getTransparency();
+
 }