*/
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.util.Locale;
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
*
*/
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");
- 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#listresattr
+ private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand("list resattr");
- private static final String CMD_COLOUR_BY_CHAIN = "rainbow chain";
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html
+ private static final StructureCommand CLOSE_CHIMERA = new StructureCommand("stop really");
- // Chimera clause to exclude alternate locations in atom selection
- private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
+ private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("listen stop selection");
- @Override
- public String[] colourBySequence(Map<Object, AtomSpecModel> colourMap)
- {
- List<String> colourCommands = buildColourCommands(colourMap);
+ private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("listen stop models");
- return colourCommands.toArray(new String[colourCommands.size()]);
- }
+ // 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);
}
/**
* @param colour
* @return
*/
- @Override
protected String getColourString(Color colour)
{
return ColorUtils.toTkCode(colour);
}
/**
- * 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<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
- ssm, files, seqs, viewPanel);
-
- List<String> commands = buildSetAttributeCommands(featureMap);
-
- return commands.toArray(new String[commands.size()]);
- }
-
- /**
- * <pre>
- * Helper method to build a map of
- * { featureType, { feature value, AtomSpecModel } }
- * </pre>
- *
- * @param ssm
- * @param files
- * @param seqs
- * @param viewPanel
- * @return
- */
- protected Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
- StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
- AlignmentViewPanel viewPanel)
- {
- Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<>();
-
- FeatureRenderer fr = viewPanel.getFeatureRenderer();
- if (fr == null)
- {
- return theMap;
- }
-
- AlignViewportI viewport = viewPanel.getAlignViewport();
- List<String> 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<String> 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<String, Map<Object, AtomSpecModel>> 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<int[]> 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<Object, AtomSpecModel> 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<String> visibleFeatures,
- StructureMapping mapping, SequenceI seq,
- Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
- {
- List<SequenceFeature> 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<int[]> 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<Object, AtomSpecModel> 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).
* <p>
* @param featureMap
* @return
*/
- protected List<String> buildSetAttributeCommands(
+ @Override
+ public List<StructureCommandI> setAttributes(
Map<String, Map<Object, AtomSpecModel>> featureMap)
{
- List<String> commands = new ArrayList<>();
+ List<StructureCommandI> commands = new ArrayList<>();
for (String featureType : featureMap.keySet())
{
String attributeName = makeAttributeName(featureType);
AtomSpecModel atomSpecModel = values.get(value);
String featureValue = value.toString();
featureValue = featureValue.replaceAll("\\'", "'");
- String cmd = getSetAttributeCommand(attributeName, featureValue,
+ StructureCommandI cmd = setAttribute(attributeName, featureValue,
atomSpecModel);
commands.add(cmd);
}
* @param atomSpecModel
* @return
*/
- protected String getSetAttributeCommand(String attributeName,
+ protected StructureCommandI setAttribute(String attributeName,
String attributeValue,
AtomSpecModel atomSpecModel)
{
sb.append("setattr res ").append(attributeName).append(" '")
.append(attributeValue).append("' ");
sb.append(getAtomSpec(atomSpecModel, false));
- return sb.toString();
+ return new StructureCommand(sb.toString());
}
/**
* @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;
* Jalview doesn't, so prevent this by appending an underscore
*/
- if (attName.toUpperCase().endsWith("COLOR"))
+ if (attName.toUpperCase(Locale.ROOT).endsWith("COLOR"))
{
attName += "_";
}
}
@Override
- public String colourByChain()
+ public StructureCommandI colourByChain()
{
- return CMD_COLOUR_BY_CHAIN;
+ return COLOUR_BY_CHAIN;
}
@Override
- public String colourByCharge()
+ public List<StructureCommandI> colourByCharge()
{
- return CMD_COLOUR_BY_CHARGE;
+ return Arrays.asList(COLOUR_BY_CHARGE);
}
@Override
}
@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<String> toShow)
+ public List<StructureCommandI> showChains(List<String> toShow)
{
/*
* Construct a chimera command like
*/
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<StructureCommandI> superposeStructures(AtomSpecModel ref,
+ AtomSpecModel spec, boolean isNucleotide)
{
/*
* 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);
}
/**
{
StringBuilder sb = new StringBuilder(128);
boolean firstModel = true;
- for (Integer model : atomSpec.getModels())
+ for (String model : atomSpec.getModels())
{
if (!firstModel)
{
* @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(":");
chain = " ".equals(chain) ? chain : chain.trim();
List<int[]> 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<int[]> iterator = rangeList.iterator();
- while (iterator.hasNext())
- {
- 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())
+ for (int[] range : rangeList)
{
- appendRange(sb, start, end, chain, firstPositionForModel, false);
+ appendRange(sb, range[0], range[1], chain, firstPositionForModel,
+ false);
firstPositionForModel = false;
}
}
* 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<StructureCommandI> 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<StructureCommandI> startNotifications(String uri)
+ {
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
+ List<StructureCommandI> 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<StructureCommandI> stopNotifications()
+ {
+ List<StructureCommandI> 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 + "'");
}
}
git://source.jalview.org / jalview.git / blobdiff