X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommands.java;h=ced22faa58f7b20b7822ef3725a726bba9605270;hb=490bea038483dcc853766de08a8971668930f43a;hp=1b1dd35dd071fce529275ed8e55778a46ff370d5;hpb=fea6f8ed76719fd78b600adfea8891dafb8c9d12;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java index 1b1dd35..ced22fa 100644 --- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java +++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java @@ -20,30 +20,18 @@ */ 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.AtomSpecModel; -import jalview.structure.StructureCommandsBase; -import jalview.structure.StructureMapping; -import jalview.structure.StructureSelectionManager; -import jalview.util.ColorUtils; -import jalview.util.IntRangeComparator; - import java.awt.Color; import java.util.ArrayList; -import java.util.Collections; -import java.util.HashMap; -import java.util.Iterator; -import java.util.LinkedHashMap; +import java.util.Arrays; import java.util.List; import java.util.Map; +import jalview.structure.AtomSpecModel; +import jalview.structure.StructureCommand; +import jalview.structure.StructureCommandI; +import jalview.structure.StructureCommandsBase; +import jalview.util.ColorUtils; + /** * Routines for generating Chimera commands for Jalview/Chimera binding * @@ -52,21 +40,42 @@ import java.util.Map; */ public class ChimeraCommands extends StructureCommandsBase { - public static final String NAMESPACE_PREFIX = "jv_"; + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html + private static final StructureCommand FOCUS_VIEW = new StructureCommand("focus"); + + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listresattr + private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand("list resattr"); + + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html + private static final StructureCommand CLOSE_CHIMERA = new StructureCommand("stop really"); - private static final String CMD_COLOUR_BY_CHARGE = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS"; + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html + private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("listen stop selection"); - private static final String CMD_COLOUR_BY_CHAIN = "rainbow chain"; + private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("listen stop models"); + + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listselection + private static final StructureCommand GET_SELECTION = new StructureCommand("list selection level residue"); + + private static final StructureCommand SHOW_BACKBONE = new StructureCommand( + "~display all;~ribbon;chain @CA|P"); + + private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand( + "color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS"); + + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/rainbow.html + private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand( + "rainbow chain"); // Chimera clause to exclude alternate locations in atom selection private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9"; @Override - public String getColourCommand(String atomSpec, Color colour) + public StructureCommandI colourResidues(String atomSpec, Color colour) { // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/color.html String colourCode = getColourString(colour); - return "color " + colourCode + " " + atomSpec; + return new StructureCommand("color " + colourCode + " " + atomSpec); } /** @@ -81,254 +90,6 @@ public class ChimeraCommands extends StructureCommandsBase } /** - * Constructs and returns Chimera commands to set attributes on residues - * corresponding to features in Jalview. Attribute names are the Jalview feature - * type, with a "jv_" prefix. - * - * @param ssm - * @param files - * @param seqs - * @param viewPanel - * @return - */ - @Override - public String[] setAttributesForFeatures( - StructureSelectionManager ssm, String[] files, SequenceI[][] seqs, - AlignmentViewPanel viewPanel) - { - Map> featureMap = buildFeaturesMap( - ssm, files, seqs, viewPanel); - - return setAttributes(featureMap); - } - - /** - * 
-   * Helper method to build a map of 
-   *   { featureType, { feature value, AtomSpecModel } }
-   *
- * - * @param ssm - * @param files - * @param seqs - * @param viewPanel - * @return - */ - protected Map> buildFeaturesMap( - StructureSelectionManager ssm, String[] files, SequenceI[][] seqs, - AlignmentViewPanel viewPanel) - { - Map> theMap = new LinkedHashMap<>(); - - FeatureRenderer fr = viewPanel.getFeatureRenderer(); - if (fr == null) - { - return theMap; - } - - AlignViewportI viewport = viewPanel.getAlignViewport(); - List visibleFeatures = fr.getDisplayedFeatureTypes(); - - /* - * if alignment is showing features from complement, we also transfer - * these features to the corresponding mapped structure residues - */ - boolean showLinkedFeatures = viewport.isShowComplementFeatures(); - List complementFeatures = new ArrayList<>(); - FeatureRenderer complementRenderer = null; - if (showLinkedFeatures) - { - AlignViewportI comp = fr.getViewport().getCodingComplement(); - if (comp != null) - { - complementRenderer = Desktop.getAlignFrameFor(comp) - .getFeatureRenderer(); - complementFeatures = complementRenderer.getDisplayedFeatureTypes(); - } - } - if (visibleFeatures.isEmpty() && complementFeatures.isEmpty()) - { - return theMap; - } - - AlignmentI alignment = viewPanel.getAlignment(); - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - final int modelNumber = pdbfnum + getModelStartNo(); - StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); - - if (mapping == null || mapping.length < 1) - { - continue; - } - - for (int seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++) - { - for (int m = 0; m < mapping.length; m++) - { - final SequenceI seq = seqs[pdbfnum][seqNo]; - int sp = alignment.findIndex(seq); - StructureMapping structureMapping = mapping[m]; - if (structureMapping.getSequence() == seq && sp > -1) - { - /* - * found a sequence with a mapping to a structure; - * now scan its features - */ - if (!visibleFeatures.isEmpty()) - { - scanSequenceFeatures(visibleFeatures, structureMapping, seq, - theMap, modelNumber); - } - if (showLinkedFeatures) - { - scanComplementFeatures(complementRenderer, structureMapping, - seq, theMap, modelNumber); - } - } - } - } - } - return theMap; - } - - /** - * Scans visible features in mapped positions of the CDS/peptide complement, and - * adds any found to the map of attribute values/structure positions - * - * @param complementRenderer - * @param structureMapping - * @param seq - * @param theMap - * @param modelNumber - */ - protected static void scanComplementFeatures( - FeatureRenderer complementRenderer, - StructureMapping structureMapping, SequenceI seq, - Map> theMap, int modelNumber) - { - /* - * for each sequence residue mapped to a structure position... - */ - for (int seqPos : structureMapping.getMapping().keySet()) - { - /* - * find visible complementary features at mapped position(s) - */ - MappedFeatures mf = complementRenderer - .findComplementFeaturesAtResidue(seq, seqPos); - if (mf != null) - { - for (SequenceFeature sf : mf.features) - { - String type = sf.getType(); - - /* - * Don't copy features which originated from Chimera - */ - if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP - .equals(sf.getFeatureGroup())) - { - continue; - } - - /* - * record feature 'value' (score/description/type) as at the - * corresponding structure position - */ - List mappedRanges = structureMapping - .getPDBResNumRanges(seqPos, seqPos); - - if (!mappedRanges.isEmpty()) - { - String value = sf.getDescription(); - if (value == null || value.length() == 0) - { - value = type; - } - float score = sf.getScore(); - if (score != 0f && !Float.isNaN(score)) - { - value = Float.toString(score); - } - Map featureValues = theMap.get(type); - if (featureValues == null) - { - featureValues = new HashMap<>(); - theMap.put(type, featureValues); - } - for (int[] range : mappedRanges) - { - addAtomSpecRange(featureValues, value, modelNumber, range[0], - range[1], structureMapping.getChain()); - } - } - } - } - } - } - - /** - * Inspect features on the sequence; for each feature that is visible, determine - * its mapped ranges in the structure (if any) according to the given mapping, - * and add them to the map. - * - * @param visibleFeatures - * @param mapping - * @param seq - * @param theMap - * @param modelNumber - */ - protected static void scanSequenceFeatures(List visibleFeatures, - StructureMapping mapping, SequenceI seq, - Map> theMap, int modelNumber) - { - List sfs = seq.getFeatures().getPositionalFeatures( - visibleFeatures.toArray(new String[visibleFeatures.size()])); - for (SequenceFeature sf : sfs) - { - String type = sf.getType(); - - /* - * Don't copy features which originated from Chimera - */ - if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP - .equals(sf.getFeatureGroup())) - { - continue; - } - - List mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(), - sf.getEnd()); - - if (!mappedRanges.isEmpty()) - { - String value = sf.getDescription(); - if (value == null || value.length() == 0) - { - value = type; - } - float score = sf.getScore(); - if (score != 0f && !Float.isNaN(score)) - { - value = Float.toString(score); - } - Map featureValues = theMap.get(type); - if (featureValues == null) - { - featureValues = new HashMap<>(); - theMap.put(type, featureValues); - } - for (int[] range : mappedRanges) - { - addAtomSpecRange(featureValues, value, modelNumber, range[0], - range[1], mapping.getChain()); - } - } - } - } - - /** * Traverse the map of features/values/models/chains/positions to construct a * list of 'setattr' commands (one per distinct feature type and value). *

@@ -343,10 +104,11 @@ public class ChimeraCommands extends StructureCommandsBase * @param featureMap * @return */ - protected String[] setAttributes( + @Override + public List setAttributes( Map> featureMap) { - List commands = new ArrayList<>(); + List commands = new ArrayList<>(); for (String featureType : featureMap.keySet()) { String attributeName = makeAttributeName(featureType); @@ -368,13 +130,13 @@ public class ChimeraCommands extends StructureCommandsBase AtomSpecModel atomSpecModel = values.get(value); String featureValue = value.toString(); featureValue = featureValue.replaceAll("\\'", "'"); - String cmd = setAttribute(attributeName, featureValue, + StructureCommandI cmd = setAttribute(attributeName, featureValue, atomSpecModel); commands.add(cmd); } } - return commands.toArray(new String[commands.size()]); + return commands; } /** @@ -390,7 +152,7 @@ public class ChimeraCommands extends StructureCommandsBase * @param atomSpecModel * @return */ - protected String setAttribute(String attributeName, + protected StructureCommandI setAttribute(String attributeName, String attributeValue, AtomSpecModel atomSpecModel) { @@ -398,7 +160,7 @@ public class ChimeraCommands extends StructureCommandsBase sb.append("setattr res ").append(attributeName).append(" '") .append(attributeValue).append("' "); sb.append(getAtomSpec(atomSpecModel, false)); - return sb.toString(); + return new StructureCommand(sb.toString()); } /** @@ -410,17 +172,10 @@ public class ChimeraCommands extends StructureCommandsBase * @return * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html */ - protected static String makeAttributeName(String featureType) + @Override + protected String makeAttributeName(String featureType) { - StringBuilder sb = new StringBuilder(); - if (featureType != null) - { - for (char c : featureType.toCharArray()) - { - sb.append(Character.isLetterOrDigit(c) ? c : '_'); - } - } - String attName = NAMESPACE_PREFIX + sb.toString(); + String attName = super.makeAttributeName(featureType); /* * Chimera treats an attribute name ending in 'color' as colour-valued; @@ -435,15 +190,15 @@ public class ChimeraCommands extends StructureCommandsBase } @Override - public String colourByChain() + public StructureCommandI colourByChain() { - return CMD_COLOUR_BY_CHAIN; + return COLOUR_BY_CHAIN; } @Override - public String colourByCharge() + public List colourByCharge() { - return CMD_COLOUR_BY_CHARGE; + return Arrays.asList(COLOUR_BY_CHARGE); } @Override @@ -453,21 +208,20 @@ public class ChimeraCommands extends StructureCommandsBase } @Override - public String setBackgroundColour(Color col) + public StructureCommandI setBackgroundColour(Color col) { // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/set.html#bgcolor - return "set bgColor " + ColorUtils.toTkCode(col); + return new StructureCommand("set bgColor " + ColorUtils.toTkCode(col)); } @Override - public String focusView() + public StructureCommandI focusView() { - // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html - return "focus"; + return FOCUS_VIEW; } @Override - public String showChains(List toShow) + public List showChains(List toShow) { /* * Construct a chimera command like @@ -498,48 +252,49 @@ public class ChimeraCommands extends StructureCommandsBase */ final String command = "~display #*; ~ribbon #*; ribbon :" + cmd.toString(); - return command; + return Arrays.asList(new StructureCommand(command)); } @Override - public String superposeStructures(AtomSpecModel spec, AtomSpecModel ref) + public List superposeStructures(AtomSpecModel ref, + AtomSpecModel spec) { /* * Form Chimera match command to match spec to ref + * (the first set of atoms are moved on to the second) * * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA * - * @see - * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html + * @see https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html */ StringBuilder cmd = new StringBuilder(); - String atomSpec = getAtomSpec(spec, true); - String refSpec = getAtomSpec(ref, true); - cmd.append("match ").append(atomSpec).append(" ").append(refSpec); + String atomSpecAlphaOnly = getAtomSpec(spec, true); + String refSpecAlphaOnly = getAtomSpec(ref, true); + cmd.append("match ").append(atomSpecAlphaOnly).append(" ").append(refSpecAlphaOnly); /* - * show superposed residues as ribbon, others as chain + * show superposed residues as ribbon */ - // fixme this should precede the loop over all alignments/structures - cmd.append(";~display all; chain @CA|P"); + String atomSpec = getAtomSpec(spec, false); + String refSpec = getAtomSpec(ref, false); cmd.append("; ribbon "); cmd.append(atomSpec).append("|").append(refSpec).append("; focus"); - return cmd.toString(); + return Arrays.asList(new StructureCommand(cmd.toString())); } @Override - public String openCommandFile(String path) + public StructureCommandI openCommandFile(String path) { // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html - return "open cmd:" + path; + return new StructureCommand("open cmd:" + path); } @Override - public String saveSession(String filepath) + public StructureCommandI saveSession(String filepath) { // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/save.html - return "save " + filepath; + return new StructureCommand("save " + filepath); } /** @@ -571,7 +326,7 @@ public class ChimeraCommands extends StructureCommandsBase { StringBuilder sb = new StringBuilder(128); boolean firstModel = true; - for (Integer model : atomSpec.getModels()) + for (String model : atomSpec.getModels()) { if (!firstModel) { @@ -591,7 +346,7 @@ public class ChimeraCommands extends StructureCommandsBase * @param atomSpec * @param alphaOnly */ - protected void appendModel(StringBuilder sb, Integer model, + protected void appendModel(StringBuilder sb, String model, AtomSpecModel atomSpec, boolean alphaOnly) { sb.append("#").append(model).append(":"); @@ -603,46 +358,10 @@ public class ChimeraCommands extends StructureCommandsBase chain = " ".equals(chain) ? chain : chain.trim(); List rangeList = atomSpec.getRanges(model, chain); - - /* - * sort ranges into ascending start position order - */ - Collections.sort(rangeList, IntRangeComparator.ASCENDING); - - int start = rangeList.isEmpty() ? 0 : rangeList.get(0)[0]; - int end = rangeList.isEmpty() ? 0 : rangeList.get(0)[1]; - - Iterator iterator = rangeList.iterator(); - while (iterator.hasNext()) + for (int[] range : rangeList) { - int[] range = iterator.next(); - if (range[0] <= end + 1) - { - /* - * range overlaps or is contiguous with the last one - * - so just extend the end position, and carry on - * (unless this is the last in the list) - */ - end = Math.max(end, range[1]); - } - else - { - /* - * we have a break so append the last range - */ - appendRange(sb, start, end, chain, firstPositionForModel, false); - firstPositionForModel = false; - start = range[0]; - end = range[1]; - } - } - - /* - * and append the last range - */ - if (!rangeList.isEmpty()) - { - appendRange(sb, start, end, chain, firstPositionForModel, false); + appendRange(sb, range[0], range[1], chain, firstPositionForModel, + false); firstPositionForModel = false; } } @@ -652,14 +371,76 @@ public class ChimeraCommands extends StructureCommandsBase * restrict to alpha carbon, no alternative locations * (needed to ensuring matching atom counts for superposition) */ - sb.append("@CA|P").append(NO_ALTLOCS); + // TODO @P instead if RNA - add nucleotide flag to AtomSpecModel? + sb.append("@CA").append(NO_ALTLOCS); } } @Override - public String showBackbone() + public List showBackbone() + { + return Arrays.asList(SHOW_BACKBONE); + } + + @Override + public StructureCommandI loadFile(String file) + { + return new StructureCommand("open " + file); + } + + @Override + public StructureCommandI openSession(String filepath) + { + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html + // this version of the command has no dependency on file extension + return new StructureCommand("open chimera:" + filepath); + } + + @Override + public StructureCommandI closeViewer() + { + return CLOSE_CHIMERA; + } + + @Override + public List startNotifications(String uri) + { + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html + List cmds = new ArrayList<>(); + cmds.add(new StructureCommand("listen start models url " + uri)); + cmds.add(new StructureCommand("listen start select prefix SelectionChanged url " + uri)); + return cmds; + } + + @Override + public List stopNotifications() + { + List cmds = new ArrayList<>(); + cmds.add(STOP_NOTIFY_MODELS); + cmds.add(STOP_NOTIFY_SELECTION); + return cmds; + } + + @Override + public StructureCommandI getSelectedResidues() + { + return GET_SELECTION; + } + + @Override + public StructureCommandI listResidueAttributes() + { + return LIST_RESIDUE_ATTRIBUTES; + } + + @Override + public StructureCommandI getResidueAttributes(String attName) { - return "~display all;chain @CA|P"; + // this alternative command + // list residues spec ':*/attName' attr attName + // doesn't report 'None' values (which is good), but + // fails for 'average.bfactor' (which is bad): + return new StructureCommand("list residues attr '" + attName + "'"); } }