X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fapi%2FFeatureRenderer.java;h=54303037f19109bc4c17c3c8ddbb2c5e54249a6a;hb=155a17a423e980849fd4dc5f857da1a72b0010b9;hp=22b0a457a2268a50a9b258eb87682c2fc133aee8;hpb=bcec956c0817f71f72a80a02066f1b57672304df;p=jalview.git
diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index 22b0a45..5430303 100644
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -1,20 +1,309 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.api;
+import jalview.datamodel.MappedFeatures;
+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;
/**
* Abstract feature renderer interface
+ *
* @author JimP
- *
+ *
*/
public interface FeatureRenderer
{
- Color findFeatureColour(Color col, SequenceI sequenceI, int r);
+ /**
+ * 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 sequence
+ * @param column
+ * aligned column position (1..)
+ * @param g
+ * @return
+ */
+ Color findFeatureColour(SequenceI sequence, int column, Graphics g);
+
+ /**
+ * trigger the feature discovery process for a newly created feature renderer.
+ */
+ void featuresAdded();
+
+ /**
+ *
+ * @param ft
+ * @return display style for a feature
+ */
+ FeatureColourI getFeatureStyle(String ft);
+
+ /**
+ * update the feature style for a particular feature
+ *
+ * @param ft
+ * @param ggc
+ */
+ void setColour(String ft, FeatureColourI ggc);
+
+ AlignViewportI getViewport();
+
+ /**
+ *
+ * @return container managing list of feature types and their visibility
+ */
+ FeaturesDisplayedI getFeaturesDisplayed();
+
+ /**
+ * get display style for all features types - visible or invisible
+ *
+ * @return
+ */
+ Map getFeatureColours();
+
+ /**
+ * query the alignment view to find all features
+ *
+ * @param newMadeVisible
+ * - when true, automatically make newly discovered types visible
+ */
+ void findAllFeatures(boolean newMadeVisible);
+
+ /**
+ * get display style for all features types currently visible
+ *
+ * @return
+ */
+ Map getDisplayedFeatureCols();
+
+ /**
+ * get all registered groups
+ *
+ * @return
+ */
+ List getFeatureGroups();
+
+ /**
+ * get groups that are visible/invisible
+ *
+ * @param visible
+ * @return
+ */
+ List getGroups(boolean visible);
+
+ /**
+ * Set visibility for a list of groups
+ *
+ * @param toset
+ * @param visible
+ */
+ void setGroupVisibility(List toset, boolean visible);
+
+ /**
+ * Set visibility of the given feature group
+ *
+ * @param group
+ * @param visible
+ */
+ void setGroupVisibility(String group, boolean visible);
+
+ /**
+ * 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 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.
+ *
+ * @param sequence
+ * @param fromResNo
+ * @param toResNo
+ * @return
+ */
+ List findFeaturesAtResidue(SequenceI sequence,
+ int fromResNo, int toResNo);
+
+ /**
+ * get current displayed types, in ordering of rendering (on top last)
+ *
+ * @return a (possibly empty) list of feature types
+ */
+
+ List getDisplayedFeatureTypes();
+
+ /**
+ * Returns a (possibly empty) list of currently visible feature groups
+ *
+ * @return
+ */
+ List getDisplayedFeatureGroups();
+
+ /**
+ * display all features of these types
+ *
+ * @param featureTypes
+ */
+ void setAllVisible(List featureTypes);
+
+ /**
+ * display featureType
+ *
+ * @param featureType
+ */
+ 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 group is not visible, or
+ * - feature values lie outside any colour threshold, or
+ * - feature is excluded by filter conditions
+ *
+ * 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
+ *
+ * - its feature type is set to visible
+ * - its feature group is either null, or set to visible
+ * - it is not excluded by a colour threshold on score or other numeric
+ * attribute
+ * - it is not excluded by a filter condition
+ *
+ *
+ * @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();
}