/*
* 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 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
* @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