2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ext.rbvi.chimera;
23 import jalview.api.FeatureRenderer;
24 import jalview.api.SequenceRenderer;
25 import jalview.datamodel.AlignmentI;
26 import jalview.datamodel.SequenceI;
27 import jalview.structure.StructureMapping;
28 import jalview.structure.StructureMappingcommandSet;
29 import jalview.structure.StructureSelectionManager;
30 import jalview.util.ColorUtils;
31 import jalview.util.Comparison;
33 import java.awt.Color;
34 import java.util.ArrayList;
35 import java.util.LinkedHashMap;
36 import java.util.List;
38 import java.util.TreeMap;
41 * Routines for generating Chimera commands for Jalview/Chimera binding
46 public class ChimeraCommands
50 * utility to construct the commands to colour chains by the given alignment
51 * for passing to Chimera
53 * @returns Object[] { Object[] { <model being coloured>,
56 public static StructureMappingcommandSet[] getColourBySequenceCommand(
57 StructureSelectionManager ssm, String[] files,
58 SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
61 Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap = buildColoursMap(
62 ssm, files, sequence, sr, fr, alignment);
64 List<String> colourCommands = buildColourCommands(colourMap);
66 StructureMappingcommandSet cs = new StructureMappingcommandSet(
67 ChimeraCommands.class, null,
68 colourCommands.toArray(new String[0]));
70 return new StructureMappingcommandSet[]
75 * Traverse the map of colours/models/chains/positions to construct a list of
76 * 'color' commands (one per distinct colour used). The format of each command
79 * <blockquote> color colorname #modelnumber:range.chain e.g. color #00ff00
80 * #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
83 * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec
89 protected static List<String> buildColourCommands(
90 Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap)
93 * This version concatenates all commands into a single String (semi-colon
94 * delimited). If length limit issues arise, refactor to return one color
97 List<String> commands = new ArrayList<String>();
98 StringBuilder sb = new StringBuilder(256);
99 boolean firstColour = true;
100 for (Color colour : colourMap.keySet())
102 String colourCode = ColorUtils.toTkCode(colour);
107 sb.append("color ").append(colourCode).append(" ");
109 boolean firstModelForColour = true;
110 final Map<Integer, Map<String, List<int[]>>> colourData = colourMap.get(colour);
111 for (Integer model : colourData.keySet())
113 boolean firstPositionForModel = true;
114 if (!firstModelForColour)
118 firstModelForColour = false;
119 sb.append("#").append(model).append(":");
121 final Map<String, List<int[]>> modelData = colourData.get(model);
122 for (String chain : modelData.keySet())
124 for (int[] range : modelData.get(chain))
126 if (!firstPositionForModel)
130 if (range[0] == range[1])
136 sb.append(range[0]).append("-").append(range[1]);
138 sb.append(".").append(chain);
139 firstPositionForModel = false;
144 commands.add(sb.toString());
150 * Build a data structure which maps contiguous subsequences for each colour.
151 * This generates a data structure from which we can easily generate the
152 * Chimera command for colour by sequence.
156 * list of start/end ranges
157 * Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
160 protected static Map<Color, Map<Integer, Map<String, List<int[]>>>> buildColoursMap(
161 StructureSelectionManager ssm, String[] files,
162 SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
163 AlignmentI alignment)
165 Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap = new LinkedHashMap<Color, Map<Integer, Map<String, List<int[]>>>>();
166 Color lastColour = null;
167 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
169 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
171 if (mapping == null || mapping.length < 1)
176 int startPos = -1, lastPos = -1;
177 String lastChain = "";
178 for (int s = 0; s < sequence[pdbfnum].length; s++)
180 for (int sp, m = 0; m < mapping.length; m++)
182 final SequenceI seq = sequence[pdbfnum][s];
183 if (mapping[m].getSequence() == seq
184 && (sp = alignment.findIndex(seq)) > -1)
186 SequenceI asp = alignment.getSequenceAt(sp);
187 for (int r = 0; r < asp.getLength(); r++)
189 // no mapping to gaps in sequence
190 if (Comparison.isGap(asp.getCharAt(r)))
194 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
196 if (pos < 1 || pos == lastPos)
201 Color colour = sr.getResidueColour(seq, r, fr);
202 final String chain = mapping[m].getChain();
205 * Just keep incrementing the end position for this colour range
206 * _unless_ colour, PDB model or chain has changed, or there is a
207 * gap in the mapped residue sequence
209 final boolean newColour = !colour.equals(lastColour);
210 final boolean nonContig = lastPos + 1 != pos;
211 final boolean newChain = !chain.equals(lastChain);
212 if (newColour || nonContig || newChain)
216 addColourRange(colourMap, lastColour, pdbfnum, startPos,
225 // final colour range
226 if (lastColour != null)
228 addColourRange(colourMap, lastColour, pdbfnum, startPos,
240 * Helper method to add one contiguous colour range to the colour map.
249 protected static void addColourRange(
250 Map<Color, Map<Integer, Map<String, List<int[]>>>> colourMap,
251 Color colour, int model, int startPos, int endPos, String chain)
254 * Get/initialize map of data for the colour
256 Map<Integer, Map<String, List<int[]>>> colourData = colourMap
258 if (colourData == null)
262 colourData = new TreeMap<Integer, Map<String, List<int[]>>>());
266 * Get/initialize map of data for the colour and model
268 Map<String, List<int[]>> modelData = colourData.get(model);
269 if (modelData == null)
271 colourData.put(model, modelData = new TreeMap<String, List<int[]>>());
275 * Get/initialize map of data for colour, model and chain
277 List<int[]> chainData = modelData.get(chain);
278 if (chainData == null)
280 modelData.put(chain, chainData = new ArrayList<int[]>());
284 * Add the start/end positions
286 chainData.add(new int[]
287 { startPos, endPos });