/*
* 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.ext.rbvi.chimera;
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.MappedFeatures;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.Desktop;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.ColorUtils;
import jalview.util.StructureCommands;
import java.awt.Color;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
/**
* Routines for generating Chimera commands for Jalview/Chimera binding
*
* @author JimP
*
*/
public class ChimeraCommands extends StructureCommands
{
public static final String NAMESPACE_PREFIX = "jv_";
/*
* colour for residues shown in structure but hidden in alignment
*/
private static final String COLOR_GRAY_HEX = "color "
+ ColorUtils.toTkCode(Color.GRAY);
/**
* Constructs Chimera commands to colour residues as per the Jalview alignment
*
* @param colourMap
* @param binding
* @return
*/
public static String[] getColourBySequenceCommand(
Map