-/**
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
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;
/**
* 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.
+ * <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 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<String, FeatureColourI> 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<String, FeatureColourI> getDisplayedFeatureCols();
+
+ /**
+ * get all registered groups
+ *
+ * @return
+ */
+ List<String> getFeatureGroups();
+
+ /**
+ * get groups that are visible/invisible
+ *
+ * @param visible
+ * @return
+ */
+ List<String> getGroups(boolean visible);
+
+ /**
+ * Set visibility for a list of groups
+ *
+ * @param toset
+ * @param visible
+ */
+ void setGroupVisibility(List<String> 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<SequenceFeature> findFeaturesAtColumn(SequenceI sequence, int column);
+
+ /**
+ * Returns features at the specified residue position on the given sequence.
+ * Non-positional features are not included.
+ *
+ * @param sequence
+ * @param resNo
+ * residue position (start..)
+ * @return
+ */
+ List<SequenceFeature> findFeaturesAtResidue(SequenceI sequence, int resNo);
+
+ /**
+ * get current displayed types, in ordering of rendering (on top last)
+ *
+ * @return a (possibly empty) list of feature types
+ */
+
+ List<String> getDisplayedFeatureTypes();
+
+ /**
+ * Returns a (possibly empty) list of currently visible feature groups
+ *
+ * @return
+ */
+ List<String> getDisplayedFeatureGroups();
+
+ /**
+ * display all features of these types
+ *
+ * @param featureTypes
+ */
+ void setAllVisible(List<String> 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<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);
}
git://source.jalview.org / jalview.git / blobdiff