/* * 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 { /** * 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 *

* 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); /** * Sends a message to let any registered parties know that something about * feature rendering has changed */ void notifyFeaturesChanged(); }