2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ 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.SequenceFeature;
27 import jalview.datamodel.SequenceI;
28 import jalview.structure.StructureMapping;
29 import jalview.structure.StructureMappingcommandSet;
30 import jalview.structure.StructureSelectionManager;
31 import jalview.util.ColorUtils;
32 import jalview.util.Comparison;
34 import java.awt.Color;
35 import java.util.ArrayList;
36 import java.util.HashMap;
37 import java.util.LinkedHashMap;
38 import java.util.List;
41 import MCview.PDBChain;
44 * Routines for generating Chimera commands for Jalview/Chimera binding
49 public class ChimeraCommands
52 public static final String NAMESPACE_PREFIX = "jv_";
55 * Constructs Chimera commands to colour residues as per the Jalview alignment
65 public static StructureMappingcommandSet getColourBySequenceCommand(
66 StructureSelectionManager ssm, String[] files,
67 SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
70 Map<Object, AtomSpecModel> colourMap = buildColoursMap(
71 ssm, files, sequence, sr, fr, alignment);
73 List<String> colourCommands = buildColourCommands(colourMap);
75 StructureMappingcommandSet cs = new StructureMappingcommandSet(
76 ChimeraCommands.class, null,
77 colourCommands.toArray(new String[colourCommands.size()]));
83 * Traverse the map of colours/models/chains/positions to construct a list of
84 * 'color' commands (one per distinct colour used). The format of each command
89 * color colorname #modelnumber:range.chain
90 * e.g. color #00ff00 #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
97 protected static List<String> buildColourCommands(
98 Map<Object, AtomSpecModel> colourMap)
101 * This version concatenates all commands into a single String (semi-colon
102 * delimited). If length limit issues arise, refactor to return one color
103 * command per colour.
105 List<String> commands = new ArrayList<String>();
106 StringBuilder sb = new StringBuilder(256);
107 boolean firstColour = true;
108 for (Object key : colourMap.keySet())
110 Color colour = (Color) key;
111 String colourCode = ColorUtils.toTkCode(colour);
116 sb.append("color ").append(colourCode).append(" ");
118 final AtomSpecModel colourData = colourMap
120 sb.append(colourData.getAtomSpec());
122 commands.add(sb.toString());
127 * Traverses a map of { modelNumber, {chain, {list of from-to ranges} } } and
128 * builds a Chimera format atom spec
130 * @param modelAndChainRanges
132 protected static String getAtomSpec(
133 Map<Integer, Map<String, List<int[]>>> modelAndChainRanges)
135 StringBuilder sb = new StringBuilder(128);
136 boolean firstModelForColour = true;
137 for (Integer model : modelAndChainRanges.keySet())
139 boolean firstPositionForModel = true;
140 if (!firstModelForColour)
144 firstModelForColour = false;
145 sb.append("#").append(model).append(":");
147 final Map<String, List<int[]>> modelData = modelAndChainRanges
149 for (String chain : modelData.keySet())
151 boolean hasChain = !"".equals(chain.trim());
152 for (int[] range : modelData.get(chain))
154 if (!firstPositionForModel)
158 if (range[0] == range[1])
164 sb.append(range[0]).append("-").append(range[1]);
168 sb.append(".").append(chain);
170 firstPositionForModel = false;
174 return sb.toString();
179 * Build a data structure which maps contiguous subsequences for each colour.
180 * This generates a data structure from which we can easily generate the
181 * Chimera command for colour by sequence.
185 * list of start/end ranges
186 * Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
189 protected static Map<Object, AtomSpecModel> buildColoursMap(
190 StructureSelectionManager ssm, String[] files,
191 SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
192 AlignmentI alignment)
194 Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<Object, AtomSpecModel>();
195 Color lastColour = null;
196 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
198 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
200 if (mapping == null || mapping.length < 1)
205 int startPos = -1, lastPos = -1;
206 String lastChain = "";
207 for (int s = 0; s < sequence[pdbfnum].length; s++)
209 for (int sp, m = 0; m < mapping.length; m++)
211 final SequenceI seq = sequence[pdbfnum][s];
212 if (mapping[m].getSequence() == seq
213 && (sp = alignment.findIndex(seq)) > -1)
215 SequenceI asp = alignment.getSequenceAt(sp);
216 for (int r = 0; r < asp.getLength(); r++)
218 // no mapping to gaps in sequence
219 if (Comparison.isGap(asp.getCharAt(r)))
223 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
225 if (pos < 1 || pos == lastPos)
230 Color colour = sr.getResidueColour(seq, r, fr);
231 final String chain = mapping[m].getChain();
234 * Just keep incrementing the end position for this colour range
235 * _unless_ colour, PDB model or chain has changed, or there is a
236 * gap in the mapped residue sequence
238 final boolean newColour = !colour.equals(lastColour);
239 final boolean nonContig = lastPos + 1 != pos;
240 final boolean newChain = !chain.equals(lastChain);
241 if (newColour || nonContig || newChain)
245 addRange(colourMap, lastColour, pdbfnum, startPos,
254 // final colour range
255 if (lastColour != null)
257 addRange(colourMap, lastColour, pdbfnum, startPos,
269 * Helper method to add one contiguous colour range to the colour map.
278 protected static void addRange(Map<Object, AtomSpecModel> map,
279 Object key, int model, int startPos, int endPos, String chain)
282 * Get/initialize map of data for the colour
284 AtomSpecModel atomSpec = map.get(key);
285 if (atomSpec == null)
287 atomSpec = new AtomSpecModel();
288 map.put(key, atomSpec);
291 atomSpec.addRange(model, startPos, endPos, chain);
295 * Constructs and returns Chimera commands to set attributes on residues
296 * corresponding to features in Jalview. Attribute names are the Jalview
297 * feature type, with a "jv_" prefix.
306 public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
307 StructureSelectionManager ssm, String[] files,
308 SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
310 Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
311 ssm, files, seqs, fr, alignment);
313 List<String> commands = buildSetAttributeCommands(featureMap);
315 StructureMappingcommandSet cs = new StructureMappingcommandSet(
316 ChimeraCommands.class, null,
317 commands.toArray(new String[commands.size()]));
324 * Helper method to build a map of
325 * { featureType, { feature value, AtomSpecModel } }
335 protected static Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
336 StructureSelectionManager ssm, String[] files,
337 SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
339 Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
341 List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
342 if (visibleFeatures.isEmpty())
347 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
349 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
351 if (mapping == null || mapping.length < 1)
356 for (int seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++)
358 for (int m = 0; m < mapping.length; m++)
360 final SequenceI seq = seqs[pdbfnum][seqNo];
361 int sp = alignment.findIndex(seq);
362 if (mapping[m].getSequence() == seq && sp > -1)
365 * found a sequence with a mapping to a structure;
366 * now scan its features
368 SequenceI asp = alignment.getSequenceAt(sp);
370 scanSequenceFeatures(visibleFeatures, mapping[m], asp, theMap,
380 * Inspect features on the sequence; for each feature that is visible,
381 * determine its mapped ranges in the structure (if any) according to the
382 * given mapping, and add them to the map
384 * @param visibleFeatures
390 protected static void scanSequenceFeatures(List<String> visibleFeatures,
391 StructureMapping mapping, SequenceI seq,
392 Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
394 SequenceFeature[] sfs = seq.getSequenceFeatures();
400 for (SequenceFeature sf : sfs)
402 String type = sf.getType();
403 if (!visibleFeatures.contains(type) || suppressFeature(type))
407 List<int[]> mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(),
410 if (!mappedRanges.isEmpty())
412 String value = sf.getDescription();
413 if (value == null || value.length() == 0)
417 float score = sf.getScore();
418 if (score != 0f && !Float.isNaN(score))
420 value = Float.toString(score);
422 Map<Object, AtomSpecModel> featureValues = theMap.get(type);
423 if (featureValues == null)
425 featureValues = new HashMap<Object, AtomSpecModel>();
426 theMap.put(type, featureValues);
428 for (int[] range : mappedRanges)
430 addRange(featureValues, value, modelNumber, range[0], range[1],
438 * Answers true if the feature type is one we don't wish to propagate to
439 * Chimera - for now, RESNUM
444 static boolean suppressFeature(String type)
446 return PDBChain.RESNUM_FEATURE.equals(type);
450 * Traverse the map of features/values/models/chains/positions to construct a
451 * list of 'setattr' commands (one per distinct feature type and value).
453 * The format of each command is
456 * <blockquote> setattr r <featureName> " " #modelnumber:range.chain
457 * e.g. setattr r jv:chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
464 protected static List<String> buildSetAttributeCommands(
465 Map<String, Map<Object, AtomSpecModel>> featureMap)
467 List<String> commands = new ArrayList<String>();
468 for (String featureType : featureMap.keySet())
470 String attributeName = makeAttributeName(featureType);
473 * clear down existing attributes for this feature
475 // 'problem' - sets attribute to None on all residues - overkill?
476 // commands.add("~setattr r " + attributeName + " :*");
478 Map<Object, AtomSpecModel> values = featureMap.get(featureType);
479 for (Object value : values.keySet())
482 * for each distinct value recorded for this feature type,
483 * add a command to set the attribute on the mapped residues
485 StringBuilder sb = new StringBuilder(128);
486 sb.append("setattr r ").append(attributeName).append(" \"")
487 .append(value.toString()).append("\" ");
488 sb.append(values.get(value).getAtomSpec());
489 commands.add(sb.toString());
497 * Makes a prefixed and valid Chimera attribute name. A jv_ prefix is applied
498 * for a 'Jalview' namespace, and any non-alphanumeric character is converted
503 * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
506 protected static String makeAttributeName(String featureType)
508 StringBuilder sb = new StringBuilder();
509 if (featureType != null)
511 for (char c : featureType.toCharArray())
513 sb.append(Character.isLetterOrDigit(c) ? c : '_');
516 String attName = NAMESPACE_PREFIX + sb.toString();
519 * Chimera treats an attribute name ending in 'color' as colour-valued;
520 * Jalview doesn't, so prevent this by appending an underscore
522 if (attName.toUpperCase().endsWith("COLOR"))