JAL-2835 spike updated with latest

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

diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index 7123b8c..ef0abbd 100644 (file)
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -22,6 +22,7 @@ package jalview.api;
 
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.util.matcher.KeyedMatcherSetI;
 
 import java.awt.Color;
 import java.awt.Graphics;
@@ -60,6 +61,7 @@ public interface FeatureRenderer
    * 
    * @param sequence
    * @param column
+   *          aligned column position (1..)
    * @param g
    * @return
    */
@@ -131,7 +133,7 @@ public interface FeatureRenderer
   List<String> getGroups(boolean visible);
 
   /**
-   * change visibility for a range of groups
+   * Set visibility for a list of groups
    * 
    * @param toset
    * @param visible
@@ -139,7 +141,7 @@ public interface FeatureRenderer
   void setGroupVisibility(List<String> toset, boolean visible);
 
   /**
-   * change visibiilty of given group
+   * Set visibility of the given feature group
    * 
    * @param group
    * @param visible
@@ -147,14 +149,27 @@ public interface FeatureRenderer
   void setGroupVisibility(String group, boolean visible);
 
   /**
-   * Returns features at the specified position on the given sequence.
+   * Returns visible 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 +180,9 @@ 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 +215,54 @@ public interface FeatureRenderer
    * @return
    */
   float getTransparency();
+
+  /**
+   * Answers the filters applied to the given feature type, or null if none is
+   * set
+   * 
+   * @param featureType
+   * @return
+   */
+  KeyedMatcherSetI getFeatureFilter(String featureType);
+
+  /**
+   * Answers a shallow copy of the feature filters map
+   * 
+   * @return
+   */
+  public Map<String, KeyedMatcherSetI> getFeatureFilters();
+
+  /**
+   * Sets the filters for the feature type, or removes them if a null or empty
+   * filter is passed
+   * 
+   * @param featureType
+   * @param filter
+   */
+  void setFeatureFilter(String featureType, KeyedMatcherSetI filter);
+
+  /**
+   * Replaces all feature filters with the given map
+   * 
+   * @param filters
+   */
+  void setFeatureFilters(Map<String, KeyedMatcherSetI> filters);
+
+  /**
+   * Returns the colour for a particular feature instance. This includes
+   * calculation of 'colour by label', or of a graduated score colour, if
+   * applicable.
+   * <p>
+   * Returns null if
+   * <ul>
+   * <li>feature type is not visible, or</li>
+   * <li>feature group is not visible, or</li>
+   * <li>feature values lie outside any colour threshold, or</li>
+   * <li>feature is excluded by filter conditions</li>
+   * </ul>
+   * 
+   * @param feature
+   * @return
+   */
+  Color getColour(SequenceFeature feature);
 }