X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fapi%2FFeatureRenderer.java;h=8aa28581842e88b557b84de0232f8f269119c32b;hb=ed512fe4ab6c8a61bbf2e3b9d2b09ea9746af78d;hp=debad16c3b8cb1bce84692a2d9098ecbc2743d7d;hpb=25aaaa87042b3f507ad4348120df7dd073182759;p=jalview.git diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java index debad16..8aa2858 100644 --- a/src/jalview/api/FeatureRenderer.java +++ b/src/jalview/api/FeatureRenderer.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1) - * Copyright (C) 2014 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. * @@ -20,11 +20,13 @@ */ 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.util.Hashtable; +import java.awt.Graphics; import java.util.List; import java.util.Map; @@ -37,42 +39,262 @@ import java.util.Map; 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();
- Object getFeatureStyle(String ft);
+ /**
+ *
+ * @param ft
+ * @return display style for a feature
+ */
+ FeatureColourI getFeatureStyle(String ft);
- void setColour(String ft, Object ggc);
+ /**
+ * 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();
- Map
+ * Returns null if
+ *
+ *
+ * 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
+ *
+ *
+ *
+ * @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);
}