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.AlignViewportI;
24 import jalview.api.FeatureRenderer;
25 import jalview.api.SequenceRenderer;
26 import jalview.datamodel.AlignmentI;
27 import jalview.datamodel.ColumnSelection;
28 import jalview.datamodel.SequenceFeature;
29 import jalview.datamodel.SequenceI;
30 import jalview.structure.StructureMapping;
31 import jalview.structure.StructureMappingcommandSet;
32 import jalview.structure.StructureSelectionManager;
33 import jalview.util.ColorUtils;
34 import jalview.util.Comparison;
36 import java.awt.Color;
37 import java.util.ArrayList;
38 import java.util.HashMap;
39 import java.util.LinkedHashMap;
40 import java.util.List;
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,
68 AlignViewportI viewport)
70 Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
71 sequence, sr, fr, viewport);
73 List<String> colourCommands = buildColourCommands(colourMap);
75 StructureMappingcommandSet cs = new StructureMappingcommandSet(
76 ChimeraCommands.class, null,
77 colourCommands.toArray(new String[colourCommands.size()]));
79 return new StructureMappingcommandSet[] { cs };
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.get(colour);
119 sb.append(colourData.getAtomSpec());
121 commands.add(sb.toString());
126 * Traverses a map of { modelNumber, {chain, {list of from-to ranges} } } and
127 * builds a Chimera format atom spec
129 * @param modelAndChainRanges
131 protected static String getAtomSpec(
132 Map<Integer, Map<String, List<int[]>>> modelAndChainRanges)
134 StringBuilder sb = new StringBuilder(128);
135 boolean firstModelForColour = true;
136 for (Integer model : modelAndChainRanges.keySet())
138 boolean firstPositionForModel = true;
139 if (!firstModelForColour)
143 firstModelForColour = false;
144 sb.append("#").append(model).append(":");
146 final Map<String, List<int[]>> modelData = modelAndChainRanges
148 for (String chain : modelData.keySet())
150 boolean hasChain = !"".equals(chain.trim());
151 for (int[] range : modelData.get(chain))
153 if (!firstPositionForModel)
157 if (range[0] == range[1])
163 sb.append(range[0]).append("-").append(range[1]);
167 sb.append(".").append(chain);
169 firstPositionForModel = false;
173 return sb.toString();
178 * Build a data structure which records contiguous subsequences for each colour.
179 * From this we can easily generate the Chimera command for colour by sequence.
183 * list of start/end ranges
184 * Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
187 protected static Map<Object, AtomSpecModel> buildColoursMap(
188 StructureSelectionManager ssm, String[] files,
189 SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
190 AlignViewportI viewport)
192 ColumnSelection cs = viewport.getColumnSelection();
193 AlignmentI al = viewport.getAlignment();
194 Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<Object, AtomSpecModel>();
195 Color lastColour = null;
197 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
199 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
201 if (mapping == null || mapping.length < 1)
206 int startPos = -1, lastPos = -1;
207 String lastChain = "";
208 for (int s = 0; s < sequence[pdbfnum].length; s++)
210 for (int sp, m = 0; m < mapping.length; m++)
212 final SequenceI seq = sequence[pdbfnum][s];
213 if (mapping[m].getSequence() == seq
214 && (sp = al.findIndex(seq)) > -1)
216 SequenceI asp = al.getSequenceAt(sp);
217 for (int r = 0; r < asp.getLength(); r++)
219 // no mapping to gaps in sequence
220 if (Comparison.isGap(asp.getCharAt(r)))
224 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
226 if (pos < 1 || pos == lastPos)
231 Color colour = sr.getResidueColour(seq, r, fr);
234 * darker colour for hidden regions
236 if (!cs.isVisible(r))
238 // colour = ColorUtils.darkerThan(colour);
242 final String chain = mapping[m].getChain();
245 * Just keep incrementing the end position for this colour range
246 * _unless_ colour, PDB model or chain has changed, or there is a
247 * gap in the mapped residue sequence
249 final boolean newColour = !colour.equals(lastColour);
250 final boolean nonContig = lastPos + 1 != pos;
251 final boolean newChain = !chain.equals(lastChain);
252 if (newColour || nonContig || newChain)
256 addColourRange(colourMap, lastColour, pdbfnum, startPos,
265 // final colour range
266 if (lastColour != null)
268 addColourRange(colourMap, lastColour, pdbfnum, startPos, lastPos,
280 * Helper method to add one contiguous colour range to the colour map.
289 protected static void addColourRange(Map<Object, AtomSpecModel> map,
290 Object key, int model, int startPos, int endPos, String chain)
293 * Get/initialize map of data for the colour
295 AtomSpecModel atomSpec = map.get(key);
296 if (atomSpec == null)
298 atomSpec = new AtomSpecModel();
299 map.put(key, atomSpec);
302 atomSpec.addRange(model, startPos, endPos, chain);
306 * Constructs and returns Chimera commands to set attributes on residues
307 * corresponding to features in Jalview. Attribute names are the Jalview
308 * feature type, with a "jv_" prefix.
317 public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
318 StructureSelectionManager ssm, String[] files,
319 SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
321 Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
322 ssm, files, seqs, fr, alignment);
324 List<String> commands = buildSetAttributeCommands(featureMap);
326 StructureMappingcommandSet cs = new StructureMappingcommandSet(
327 ChimeraCommands.class, null,
328 commands.toArray(new String[commands.size()]));
335 * Helper method to build a map of
336 * { featureType, { feature value, AtomSpecModel } }
346 protected static Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
347 StructureSelectionManager ssm, String[] files,
348 SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
350 Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<String, Map<Object, AtomSpecModel>>();
352 List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
353 if (visibleFeatures.isEmpty())
358 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
360 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
362 if (mapping == null || mapping.length < 1)
367 for (int seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++)
369 for (int m = 0; m < mapping.length; m++)
371 final SequenceI seq = seqs[pdbfnum][seqNo];
372 int sp = alignment.findIndex(seq);
373 if (mapping[m].getSequence() == seq && sp > -1)
376 * found a sequence with a mapping to a structure;
377 * now scan its features
379 SequenceI asp = alignment.getSequenceAt(sp);
381 scanSequenceFeatures(visibleFeatures, mapping[m], asp, theMap,
391 * Inspect features on the sequence; for each feature that is visible,
392 * determine its mapped ranges in the structure (if any) according to the
393 * given mapping, and add them to the map
395 * @param visibleFeatures
401 protected static void scanSequenceFeatures(List<String> visibleFeatures,
402 StructureMapping mapping, SequenceI seq,
403 Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
405 SequenceFeature[] sfs = seq.getSequenceFeatures();
411 for (SequenceFeature sf : sfs)
413 String type = sf.getType();
416 * Only copy visible features, don't copy any which originated
417 * from Chimera, and suppress uninteresting ones (e.g. RESNUM)
419 boolean isFromViewer = JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
420 .equals(sf.getFeatureGroup());
421 if (isFromViewer || !visibleFeatures.contains(type))
425 List<int[]> mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(),
428 if (!mappedRanges.isEmpty())
430 String value = sf.getDescription();
431 if (value == null || value.length() == 0)
435 float score = sf.getScore();
436 if (score != 0f && !Float.isNaN(score))
438 value = Float.toString(score);
440 Map<Object, AtomSpecModel> featureValues = theMap.get(type);
441 if (featureValues == null)
443 featureValues = new HashMap<Object, AtomSpecModel>();
444 theMap.put(type, featureValues);
446 for (int[] range : mappedRanges)
448 addColourRange(featureValues, value, modelNumber, range[0], range[1],
456 * Traverse the map of features/values/models/chains/positions to construct a
457 * list of 'setattr' commands (one per distinct feature type and value).
459 * The format of each command is
462 * <blockquote> setattr r <featureName> " " #modelnumber:range.chain
463 * e.g. setattr r jv:chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
470 protected static List<String> buildSetAttributeCommands(
471 Map<String, Map<Object, AtomSpecModel>> featureMap)
473 List<String> commands = new ArrayList<String>();
474 for (String featureType : featureMap.keySet())
476 String attributeName = makeAttributeName(featureType);
479 * clear down existing attributes for this feature
481 // 'problem' - sets attribute to None on all residues - overkill?
482 // commands.add("~setattr r " + attributeName + " :*");
484 Map<Object, AtomSpecModel> values = featureMap.get(featureType);
485 for (Object value : values.keySet())
488 * for each distinct value recorded for this feature type,
489 * add a command to set the attribute on the mapped residues
490 * Put values in single quotes, encoding any embedded single quotes
492 StringBuilder sb = new StringBuilder(128);
493 String featureValue = value.toString();
494 featureValue = featureValue.replaceAll("\\'", "'");
495 sb.append("setattr r ").append(attributeName).append(" '")
496 .append(featureValue).append("' ");
497 sb.append(values.get(value).getAtomSpec());
498 commands.add(sb.toString());
506 * Makes a prefixed and valid Chimera attribute name. A jv_ prefix is applied
507 * for a 'Jalview' namespace, and any non-alphanumeric character is converted
512 * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
515 protected static String makeAttributeName(String featureType)
517 StringBuilder sb = new StringBuilder();
518 if (featureType != null)
520 for (char c : featureType.toCharArray())
522 sb.append(Character.isLetterOrDigit(c) ? c : '_');
525 String attName = NAMESPACE_PREFIX + sb.toString();
528 * Chimera treats an attribute name ending in 'color' as colour-valued;
529 * Jalview doesn't, so prevent this by appending an underscore
531 if (attName.toUpperCase().endsWith("COLOR"))