*/
package jalview.ext.rbvi.chimera;
+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.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
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 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.List;
-import java.util.Map;
/**
* Routines for generating Chimera commands for Jalview/Chimera binding
*/
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 String CMD_COLOUR_BY_CHARGE = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS";
+ private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
+ "color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS");
- private static final String CMD_COLOUR_BY_CHAIN = "rainbow chain";
+ 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 getColourCommand(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);
}
/**
* @return
*/
@Override
- public String[] setAttributesForFeatures(
+ public List<StructureCommandI> setAttributesForFeatures(
StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
AlignmentViewPanel viewPanel)
{
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)
if (!visibleFeatures.isEmpty())
{
scanSequenceFeatures(visibleFeatures, structureMapping, seq,
- theMap, modelNumber);
+ theMap, modelId);
}
if (showLinkedFeatures)
{
scanComplementFeatures(complementRenderer, structureMapping,
- seq, theMap, modelNumber);
+ seq, theMap, modelId);
}
}
}
protected static void scanComplementFeatures(
FeatureRenderer complementRenderer,
StructureMapping structureMapping, SequenceI seq,
- Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
+ Map<String, Map<Object, AtomSpecModel>> theMap,
+ String modelNumber)
{
/*
* for each sequence residue mapped to a structure position...
}
/**
- * 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.
+ * 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
+ * @param modelId
*/
protected static void scanSequenceFeatures(List<String> visibleFeatures,
StructureMapping mapping, SequenceI seq,
- Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
+ Map<String, Map<Object, AtomSpecModel>> theMap, String modelId)
{
List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures(
visibleFeatures.toArray(new String[visibleFeatures.size()]));
}
for (int[] range : mappedRanges)
{
- addAtomSpecRange(featureValues, value, modelNumber, range[0],
+ addAtomSpecRange(featureValues, value, modelId, range[0],
range[1], mapping.getChain());
}
}
* @param featureMap
* @return
*/
- protected String[] setAttributes(
+ protected 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 = setAttribute(attributeName, featureValue,
+ StructureCommandI cmd = setAttribute(attributeName, featureValue,
atomSpecModel);
commands.add(cmd);
}
}
- return commands.toArray(new String[commands.size()]);
+ return commands;
}
/**
* @param atomSpecModel
* @return
*/
- protected String setAttribute(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());
}
/**
}
@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 new StructureCommand("focus");
}
@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)
{
/*
* 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())
+ 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;
}
}
* 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 "~display all;chain @CA|P";
+ return new StructureCommand("open " + file);
+ }
+
+ /**
+ * Overrides the default method to concatenate colour commands into one
+ */
+ @Override
+ public List<StructureCommandI> colourBySequence(
+ Map<Object, AtomSpecModel> colourMap)
+ {
+ List<StructureCommandI> 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;
}
}
git://source.jalview.org / jalview.git / blobdiff