X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FFeatureRenderer.java;h=cf3c8da9513d718ea8e3212e1a9fbe157eb17754;hb=a4f2a7f356b8edab17a9a5bb6f2e71a1419792a9;hp=0d0adaa333c678b460c0761259a07dfe652846ca;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git
diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index 0d0adaa..cf3c8da 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.datamodel.features.FeatureMatcherSetI;
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.
@@ -60,17 +77,15 @@ public interface FeatureRenderer
* @param ft
* @return display style for a feature
*/
- Object getFeatureStyle(String ft);
+ FeatureColourI getFeatureStyle(String ft);
/**
* update the feature style for a particular feature
*
* @param ft
* @param ggc
- * - currently allows java.awt.Color and
- * jalview.schemes.GraduatedColor
*/
- void setColour(String ft, Object ggc);
+ void setColour(String ft, FeatureColourI ggc);
AlignViewportI getViewport();
@@ -85,7 +100,7 @@ public interface FeatureRenderer
*
* @return
*/
- Map getFeatureColours();
+ Map getFeatureColours();
/**
* query the alignment view to find all features
@@ -100,7 +115,7 @@ public interface FeatureRenderer
*
* @return
*/
- Map getDisplayedFeatureCols();
+ Map getDisplayedFeatureCols();
/**
* get all registered groups
@@ -118,7 +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
@@ -126,7 +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
@@ -134,34 +149,42 @@ public interface FeatureRenderer
void setGroupVisibility(String group, boolean visible);
/**
- * locate features at a particular 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 res
+ * @param column
+ * aligned column position (1..)
* @return
*/
- List findFeaturesAtRes(SequenceI sequence, int res);
+ List findFeaturesAtColumn(SequenceI sequence, int column);
/**
+ * Returns features at the specified residue position on the given sequence.
+ * Non-positional features are not included.
*
- * @return true if the rendering platform supports transparency
+ * @param sequence
+ * @param resNo
+ * residue position (start..)
+ * @return
*/
- boolean isTransparencyAvailable();
+ List findFeaturesAtResidue(SequenceI sequence, int resNo);
/**
- * get current displayed types
+ * get current displayed types, in ordering of rendering (on top last)
*
- * @return
+ * @return a (possibly empty) list of feature types
*/
- String[] getDisplayedFeatureTypes();
+ List getDisplayedFeatureTypes();
/**
- * get current displayed groups
+ * Returns a (possibly empty) list of currently visible feature groups
*
* @return
*/
- String[] getDisplayedFeatureGroups();
+ List getDisplayedFeatureGroups();
/**
* display all features of these types
@@ -177,4 +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
+ */
+ FeatureMatcherSetI getFeatureFilter(String featureType);
+
+ /**
+ * Answers 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, FeatureMatcherSetI 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);
}