/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.api;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-
import java.awt.Color;
+import java.awt.Graphics;
+import java.beans.PropertyChangeListener;
import java.util.List;
import java.util.Map;
+import jalview.datamodel.MappedFeatures;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.FeatureMatcherSetI;
+
/**
* Abstract feature renderer interface
*
{
/**
- * 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.
+ * <p>
+ * 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.
+ * <p>
+ * 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.
+ * <p>
+ * Returns null if there is no visible feature at the position.
+ * <p>
+ * 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.
* @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();
*
* @return
*/
- Map<String, Object> getFeatureColours();
+ Map<String, FeatureColourI> getFeatureColours();
/**
* query the alignment view to find all features
*
* @return
*/
- Map<String, Object> getDisplayedFeatureCols();
+ Map<String, FeatureColourI> getDisplayedFeatureCols();
/**
* get all registered groups
List<String> getGroups(boolean visible);
/**
- * change visibility for a range of groups
+ * Set visibility for a list of groups
*
* @param toset
* @param visible
void setGroupVisibility(List<String> toset, boolean visible);
/**
- * change visibiilty of given group
+ * Set visibility of the given feature group
*
* @param group
* @param visible
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<SequenceFeature> findFeaturesAtRes(SequenceI sequence, int res);
+ List<SequenceFeature> findFeaturesAtColumn(SequenceI sequence,
+ int column);
/**
+ * Returns features at the specified residue positions on the given sequence.
+ * Non-positional features are not included. Features are returned in render
+ * order of their feature type (last is on top). Within feature type, ordering
+ * is undefined.
*
- * @return true if the rendering platform supports transparency
+ * @param sequence
+ * @param fromResNo
+ * @param toResNo
+ * @return
*/
- boolean isTransparencyAvailable();
+ List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence,
+ int fromResNo, int toResNo);
/**
- * 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<String> getDisplayedFeatureTypes();
/**
- * get current displayed groups
+ * Returns a (possibly empty) list of currently visible feature groups
*
* @return
*/
- String[] getDisplayedFeatureGroups();
+ List<String> getDisplayedFeatureGroups();
/**
* display all features of these types
*/
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<String, FeatureMatcherSetI> 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<String, FeatureMatcherSetI> 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 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>
+ * This method does not check feature type visibility.
+ *
+ * @param feature
+ * @return
+ */
+ Color getColour(SequenceFeature feature);
+
+ /**
+ * Answers true if feature would be shown, else false. A feature is shown if
+ * <ul>
+ * <li>its feature type is set to visible</li>
+ * <li>its feature group is either null, or set to visible</li>
+ * <li>it is not excluded by a colour threshold on score or other numeric
+ * attribute</li>
+ * <li>it is not excluded by a filter condition</li>
+ * </ul>
+ *
+ * @param feature
+ * @return
+ */
+ boolean isVisible(SequenceFeature feature);
+
+ /**
+ * Answers a bean containing a mapping, and a list of visible features in this
+ * alignment at a position (or range) which is mappable from the given
+ * sequence residue position in a mapped alignment. Features are returned in
+ * render order of feature type (on top last), with order within feature type
+ * undefined. If no features or mapping are found, answers null.
+ *
+ * @param sequence
+ * @param pos
+ * @return
+ */
+ MappedFeatures findComplementFeaturesAtResidue(SequenceI sequence,
+ int pos);
+
+ /**
+ * Sends a message to let any registered parties know that something about
+ * feature rendering has changed
+ */
+ void notifyFeaturesChanged();
+
+ /**
+ * register as a listener for notifyFeaturesChanged events
+ *
+ * @param ourListener
+ */
+ void addPropertyChangeListener(PropertyChangeListener ourListener);
+
+ /**
+ * remove a listener for notifyFeaturesChanged events
+ *
+ * @param ourListener
+ */
+ void removePropertyChangeListener(PropertyChangeListener ourListener);
+
+ /**
+ *
+ * @return associated alignment panel for this feature renderer (may return
+ * null)
+ */
+ AlignmentViewPanel getAlignPanel();
+
}