X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fapi%2FFeatureRenderer.java;h=cf98b2f38d27ef62f69699200cbf597a570fea14;hb=604a94b849bcf1ddb14407418a465c9d134cd6ab;hp=22b0a457a2268a50a9b258eb87682c2fc133aee8;hpb=bcec956c0817f71f72a80a02066f1b57672304df;p=jalview.git
diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java
index 22b0a45..cf98b2f 100644
--- a/src/jalview/api/FeatureRenderer.java
+++ b/src/jalview/api/FeatureRenderer.java
@@ -1,20 +1,180 @@
-/**
+/*
+ * 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.SequenceFeature;
import jalview.datamodel.SequenceI;
import java.awt.Color;
+import java.util.List;
+import java.util.Map;
/**
* Abstract feature renderer interface
+ *
* @author JimP
- *
+ *
*/
public interface FeatureRenderer
{
+ /**
+ * compute the perceived colour for a given column position in sequenceI,
+ * taking transparency and feature visibility into account.
+ *
+ * @param col
+ * - background colour (due to alignment/group shading schemes, etc).
+ * @param sequenceI
+ * - sequence providing features
+ * @param r
+ * - column position
+ * @return
+ */
Color findFeatureColour(Color col, SequenceI sequenceI, int r);
+ /**
+ * trigger the feature discovery process for a newly created feature renderer.
+ */
+ void featuresAdded();
+
+ /**
+ *
+ * @param ft
+ * @return display style for a feature
+ */
+ Object 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);
+
+ 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);
+
+ /**
+ * change visibility for a range of groups
+ *
+ * @param toset
+ * @param visible
+ */
+ void setGroupVisibility(List toset, boolean visible);
+
+ /**
+ * change visibiilty of given group
+ *
+ * @param group
+ * @param visible
+ */
+ void setGroupVisibility(String group, boolean visible);
+
+ /**
+ * locate features at a particular position on the given sequence
+ *
+ * @param sequence
+ * @param res
+ * @return
+ */
+ List findFeaturesAtRes(SequenceI sequence, int res);
+
+ /**
+ *
+ * @return true if the rendering platform supports transparency
+ */
+ boolean isTransparencyAvailable();
+
+ /**
+ * get current displayed types
+ *
+ * @return
+ */
+
+ String[] getDisplayedFeatureTypes();
+
+ /**
+ * get current displayed groups
+ *
+ * @return
+ */
+ String[] getDisplayedFeatureGroups();
+
+ /**
+ * display all features of these types
+ *
+ * @param featureTypes
+ */
+ void setAllVisible(List featureTypes);
+
+ /**
+ * display featureType
+ *
+ * @param featureType
+ */
+ void setVisible(String featureType);
+
}