X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fapi%2FFeatureRenderer.java;h=404c49725c5724ef70ddb46af04b6d5b25098505;hb=09d3b755d9b00f5c3acb44049aedd49361dc0690;hp=baba482566a00fd36cbcde30743c1653ea2b2e83;hpb=23b954d9c84a16a7dc12ab331a01e44d5e0e5cd4;p=jalview.git diff --git a/src/jalview/api/FeatureRenderer.java b/src/jalview/api/FeatureRenderer.java index baba482..404c497 100644 --- a/src/jalview/api/FeatureRenderer.java +++ b/src/jalview/api/FeatureRenderer.java @@ -1,28 +1,33 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) - * 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. * * 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. + * 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 . + * 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 jalview.schemes.GraduatedColor; +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 @@ -33,12 +38,246 @@ import java.awt.Color; 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(); + + /** + * 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 position on the given sequence. + * Non-positional features are not included. + * + * @param sequence + * @param resNo + * residue position (start..) + * @return + */ + List 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 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); }