X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommands.java;h=5beee568eb8397fb3fea1121c9d9d8e5407bcaaa;hb=c38d37887ae51d63942ac4321f6769308188ed6b;hp=c355abed0db9cc01e6478e948aebfdd28075e9cb;hpb=28f21e26830c0df0529e74f8de1019476eaca7bf;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java index c355abe..5beee56 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.StructureCommand; -import jalview.structure.StructureCommandI; -import jalview.structure.StructureCommandsBase; -import jalview.structure.StructureMapping; -import jalview.structure.StructureSelectionManager; -import jalview.util.ColorUtils; - import java.awt.Color; import java.util.ArrayList; import java.util.Arrays; -import java.util.HashMap; -import java.util.LinkedHashMap; 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 * @@ -55,8 +43,6 @@ public class ChimeraCommands extends StructureCommandsBase private static final StructureCommand SHOW_BACKBONE = new StructureCommand( "~display all;~ribbon;chain @CA|P"); - public static final String NAMESPACE_PREFIX = "jv_"; - private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand( "color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS"); @@ -67,7 +53,7 @@ public class ChimeraCommands extends StructureCommandsBase private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9"; @Override - public StructureCommandI 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); @@ -86,256 +72,6 @@ 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 List 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(); - String modelId = String.valueOf(modelNumber); - 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, modelId); - } - if (showLinkedFeatures) - { - scanComplementFeatures(complementRenderer, structureMapping, - seq, theMap, modelId); - } - } - } - } - } - 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, - String 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 modelId - */ - protected static void scanSequenceFeatures(List visibleFeatures, - StructureMapping mapping, SequenceI seq, - Map> theMap, String modelId) - { - 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, modelId, 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). *

@@ -350,7 +86,8 @@ public class ChimeraCommands extends StructureCommandsBase * @param featureMap * @return */ - protected List setAttributes( + @Override + public List setAttributes( Map> featureMap) { List commands = new ArrayList<>(); @@ -417,17 +154,10 @@ 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; @@ -641,4 +371,39 @@ public class ChimeraCommands extends StructureCommandsBase return new StructureCommand("open " + file); } + /** + * Overrides the default method to concatenate colour commands into one + */ + @Override + public List colourBySequence( + Map colourMap) + { + List commands = new ArrayList<>(); + StringBuilder sb = new StringBuilder(colourMap.size() * 20); + boolean first = true; + for (Object key : colourMap.keySet()) + { + Color colour = (Color) key; + final AtomSpecModel colourData = colourMap.get(colour); + StructureCommandI command = getColourCommand(colourData, colour); + if (!first) + { + sb.append(getCommandSeparator()); + } + first = false; + sb.append(command.getCommand()); + } + + commands.add(new StructureCommand(sb.toString())); + return commands; + } + + @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); + } + }