X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FFeatureRenderer.java;h=ef0abbd1b95ea9487f33a1bebf35c3bb293ebb86;hb=f8b17a9e7363b8a9e7cd12d61bc6d611c7c97d7d;hp=f54231e6a07555430ff7b42376e41179e31c08fe;hpb=9a0f307f1fea87200c2ce905073942570795c6cc;p=jalview.git
diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index f54231e..ef0abbd 100644
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -22,8 +22,10 @@ package jalview.api;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.util.matcher.KeyedMatcherSetI;
import java.awt.Color;
+import java.awt.Graphics;
import java.util.List;
import java.util.Map;
@@ -37,18 +39,33 @@ public interface FeatureRenderer
{
/**
- * compute the perceived colour for a given column position in sequenceI,
- * taking transparency and feature visibility into account.
+ * Computes the feature colour for a given sequence and column position,
+ * taking into account sequence feature locations, feature colour schemes,
+ * render ordering, feature and feature group visibility, and transparency.
+ *
+ * The graphics argument should be provided if transparency is applied
+ * (getTransparency() < 1). With feature transparency, visible features are
+ * written to the graphics context and the composite colour may be read off
+ * from it. In this case, the returned feature colour is not the composite
+ * colour but that of the last feature drawn.
+ *
+ * If no transparency applies, then the graphics argument may be null, and the
+ * returned colour is the one that would be drawn for the feature.
+ *
+ * Returns null if there is no visible feature at the position.
+ *
+ * This is provided to support rendering of feature colours other than on the
+ * sequence alignment, including by structure viewers and the overview window.
+ * Note this method takes no account of whether the sequence or column is
+ * hidden.
*
- * @param col
- * - background colour (due to alignment/group shading schemes, etc).
- * @param sequenceI
- * - sequence providing features
- * @param r
- * - column position
+ * @param sequence
+ * @param column
+ * aligned column position (1..)
+ * @param g
* @return
*/
- Color findFeatureColour(Color col, SequenceI sequenceI, int r);
+ Color findFeatureColour(SequenceI sequence, int column, Graphics g);
/**
* trigger the feature discovery process for a newly created feature renderer.
@@ -116,7 +133,7 @@ public interface FeatureRenderer
List getGroups(boolean visible);
/**
- * change visibility for a range of groups
+ * Set visibility for a list of groups
*
* @param toset
* @param visible
@@ -124,7 +141,7 @@ public interface FeatureRenderer
void setGroupVisibility(List toset, boolean visible);
/**
- * change visibiilty of given group
+ * Set visibility of the given feature group
*
* @param group
* @param visible
@@ -132,14 +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 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 findFeaturesAtRes(SequenceI sequence, int res);
+ List findFeaturesAtResidue(SequenceI sequence, int resNo);
/**
* get current displayed types, in ordering of rendering (on top last)
@@ -150,9 +180,9 @@ public interface FeatureRenderer
List 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 getDisplayedFeatureGroups();
@@ -170,4 +200,69 @@ public interface FeatureRenderer
*/
void setVisible(String featureType);
+ /**
+ * Sets the transparency value, between 0 (full transparency) and 1 (no
+ * transparency)
+ *
+ * @param value
+ */
+ void setTransparency(float value);
+
+ /**
+ * Returns the transparency value, between 0 (full transparency) and 1 (no
+ * transparency)
+ *
+ * @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 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 filters);
+
+ /**
+ * Returns the colour for a particular feature instance. This includes
+ * calculation of 'colour by label', or of a graduated score colour, if
+ * applicable.
+ *
+ * Returns null if
+ *
+ * - feature type is not visible, or
+ * - feature group is not visible, or
+ * - feature values lie outside any colour threshold, or
+ * - feature is excluded by filter conditions
+ *
+ *
+ * @param feature
+ * @return
+ */
+ Color getColour(SequenceFeature feature);
}