import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.HiddenColumns;
import jalview.datamodel.MappedFeatures;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.Desktop;
-import jalview.renderer.seqfeatures.FeatureColourFinder;
+import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandsBase;
import jalview.structure.StructureMapping;
import jalview.structure.StructureSelectionManager;
import jalview.util.ColorUtils;
-import jalview.util.Comparison;
+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;
-import java.util.Map.Entry;
/**
* Routines for generating Chimera commands for Jalview/Chimera binding
{
public static final String NAMESPACE_PREFIX = "jv_";
- protected static final String CMD_SEPARATOR = ";";
-
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 String CMD_COLOUR_BY_CHAIN = "rainbow chain";
- @Override
- public String[] colourBySequence(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr,
- AlignmentViewPanel viewPanel)
- {
- Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
- sequence, sr, viewPanel);
-
- List<String> colourCommands = buildColourCommands(colourMap);
-
- return colourCommands.toArray(new String[colourCommands.size()]);
- }
-
- /**
- * Traverse the map of colours/models/chains/positions to construct a list of
- * 'color' commands (one per distinct colour used). The format of each command
- * is
- *
- * <pre>
- * <blockquote>
- * color colorname #modelnumber:range.chain
- * e.g. color #00ff00 #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
- * </blockquote>
- * </pre>
- *
- * @param colourMap
- * @return
- */
- protected List<String> buildColourCommands(
- Map<Object, AtomSpecModel> colourMap)
- {
- /*
- * This version concatenates all commands into a single String (semi-colon
- * delimited). If length limit issues arise, refactor to return one color
- * command per colour.
- */
- List<String> commands = new ArrayList<>();
- StringBuilder sb = new StringBuilder(256);
- boolean firstColour = true;
- for (Object key : colourMap.keySet())
- {
- Color colour = (Color) key;
- String colourCode = ColorUtils.toTkCode(colour);
- if (!firstColour)
- {
- sb.append("; ");
- }
- firstColour = false;
- final AtomSpecModel colourData = colourMap.get(colour);
- sb.append(getColourCommand(colourData, colourCode));
- }
- commands.add(sb.toString());
- return commands;
- }
-
- protected String getColourCommand(AtomSpecModel colourData,
- String colourCode)
- {
- return "color " + colourCode + " " + colourData.getAtomSpec();
- }
-
- /**
- * Traverses a map of { modelNumber, {chain, {list of from-to ranges} } } and
- * builds a Chimera format atom spec
- *
- * @param modelAndChainRanges
- */
- protected static String getAtomSpec(
- Map<Integer, Map<String, List<int[]>>> modelAndChainRanges)
- {
- StringBuilder sb = new StringBuilder(128);
- boolean firstModelForColour = true;
- for (Integer model : modelAndChainRanges.keySet())
- {
- boolean firstPositionForModel = true;
- if (!firstModelForColour)
- {
- sb.append("|");
- }
- firstModelForColour = false;
- sb.append("#").append(model).append(":");
-
- final Map<String, List<int[]>> modelData = modelAndChainRanges
- .get(model);
- for (String chain : modelData.keySet())
- {
- boolean hasChain = !"".equals(chain.trim());
- for (int[] range : modelData.get(chain))
- {
- if (!firstPositionForModel)
- {
- sb.append(",");
- }
- if (range[0] == range[1])
- {
- sb.append(range[0]);
- }
- else
- {
- sb.append(range[0]).append("-").append(range[1]);
- }
- if (hasChain)
- {
- sb.append(".").append(chain);
- }
- firstPositionForModel = false;
- }
- }
- }
- return sb.toString();
- }
+ // Chimera clause to exclude alternate locations in atom selection
+ private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
- /**
- * <pre>
- * Build a data structure which records contiguous subsequences for each colour.
- * From this we can easily generate the Chimera command for colour by sequence.
- * Color
- * Model number
- * Chain
- * list of start/end ranges
- * Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
- * </pre>
- *
- * @param ssm
- * @param files
- * @param sequence
- * @param sr
- * @param viewPanel
- * @return
- */
- protected static Map<Object, AtomSpecModel> buildColoursMap(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr,
- AlignmentViewPanel viewPanel)
+ @Override
+ public String getColourCommand(String atomSpec, Color colour)
{
- FeatureRenderer fr = viewPanel.getFeatureRenderer();
- FeatureColourFinder finder = new FeatureColourFinder(fr);
- AlignViewportI viewport = viewPanel.getAlignViewport();
- HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
- AlignmentI al = viewport.getAlignment();
- Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<>();
- Color lastColour = null;
-
- 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;
- }
-
- int startPos = -1, lastPos = -1;
- String lastChain = "";
- for (int s = 0; s < sequence[pdbfnum].length; s++)
- {
- for (int sp, m = 0; m < mapping.length; m++)
- {
- final SequenceI seq = sequence[pdbfnum][s];
- if (mapping[m].getSequence() == seq
- && (sp = al.findIndex(seq)) > -1)
- {
- SequenceI asp = al.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
- {
- // no mapping to gaps in sequence
- if (Comparison.isGap(asp.getCharAt(r)))
- {
- continue;
- }
- int pos = mapping[m].getPDBResNum(asp.findPosition(r));
-
- if (pos < 1 || pos == lastPos)
- {
- continue;
- }
-
- Color colour = sr.getResidueColour(seq, r, finder);
-
- /*
- * darker colour for hidden regions
- */
- if (!cs.isVisible(r))
- {
- colour = Color.GRAY;
- }
-
- final String chain = mapping[m].getChain();
-
- /*
- * Just keep incrementing the end position for this colour range
- * _unless_ colour, PDB model or chain has changed, or there is a
- * gap in the mapped residue sequence
- */
- final boolean newColour = !colour.equals(lastColour);
- final boolean nonContig = lastPos + 1 != pos;
- final boolean newChain = !chain.equals(lastChain);
- if (newColour || nonContig || newChain)
- {
- if (startPos != -1)
- {
- addAtomSpecRange(colourMap, lastColour, modelNumber,
- startPos, lastPos, lastChain);
- }
- startPos = pos;
- }
- lastColour = colour;
- lastPos = pos;
- lastChain = chain;
- }
- // final colour range
- if (lastColour != null)
- {
- addAtomSpecRange(colourMap, lastColour, modelNumber, startPos,
- lastPos, lastChain);
- }
- // break;
- }
- }
- }
- }
- return colourMap;
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/color.html
+ String colourCode = getColourString(colour);
+ return "color " + colourCode + " " + atomSpec;
}
/**
- * Returns the lowest model number used by the structure viewer
+ * Returns a colour formatted suitable for use in viewer command syntax
*
+ * @param colour
* @return
*/
- protected static int getModelStartNo()
+ protected String getColourString(Color colour)
{
- return 0;
- }
-
- /**
- * Helper method to add one contiguous range to the AtomSpec model for the given
- * value (creating the model if necessary). As used by Jalview, {@code value} is
- * <ul>
- * <li>a colour, when building a 'colour structure by sequence' command</li>
- * <li>a feature value, when building a 'set Chimera attributes from features'
- * command</li>
- * </ul>
- *
- * @param map
- * @param value
- * @param model
- * @param startPos
- * @param endPos
- * @param chain
- */
- protected static final void addAtomSpecRange(
- Map<Object, AtomSpecModel> map,
- Object value, int model, int startPos, int endPos, String chain)
- {
- /*
- * Get/initialize map of data for the colour
- */
- AtomSpecModel atomSpec = map.get(value);
- if (atomSpec == null)
- {
- atomSpec = new AtomSpecModel();
- map.put(value, atomSpec);
- }
-
- atomSpec.addRange(model, startPos, endPos, chain);
+ return ColorUtils.toTkCode(colour);
}
/**
Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
ssm, files, seqs, viewPanel);
- List<String> commands = buildSetAttributeCommands(featureMap);
-
- return commands.toArray(new String[commands.size()]);
+ return setAttributes(featureMap);
}
/**
* @param viewPanel
* @return
*/
- protected static Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
+ protected Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
AlignmentViewPanel viewPanel)
{
* @param featureMap
* @return
*/
- protected List<String> buildSetAttributeCommands(
+ protected String[] setAttributes(
Map<String, Map<Object, AtomSpecModel>> featureMap)
{
List<String> commands = new ArrayList<>();
AtomSpecModel atomSpecModel = values.get(value);
String featureValue = value.toString();
featureValue = featureValue.replaceAll("\\'", "'");
- String cmd = getSetAttributeCommand(attributeName, featureValue,
+ String cmd = setAttribute(attributeName, featureValue,
atomSpecModel);
commands.add(cmd);
}
}
- return commands;
+ return commands.toArray(new String[commands.size()]);
}
/**
* @param atomSpecModel
* @return
*/
- protected String getSetAttributeCommand(String attributeName,
+ protected String setAttribute(String attributeName,
String attributeValue,
AtomSpecModel atomSpecModel)
{
StringBuilder sb = new StringBuilder(128);
sb.append("setattr res ").append(attributeName).append(" '")
.append(attributeValue).append("' ");
- sb.append(atomSpecModel.getAtomSpec());
+ sb.append(getAtomSpec(atomSpecModel, false));
return sb.toString();
}
}
@Override
- public String colourByResidues(Map<String, Color> colours)
+ public String getResidueSpec(String residue)
{
- StringBuilder cmd = new StringBuilder(12 * colours.size());
-
- /*
- * concatenate commands like
- * color #4949b6 ::VAL
- */
- for (Entry<String, Color> entry : colours.entrySet())
- {
- String colorSpec = ColorUtils.toTkCode(entry.getValue());
- String resCode = entry.getKey();
- cmd.append("color ").append(colorSpec).append(" ::").append(resCode)
- .append(CMD_SEPARATOR);
- }
- return cmd.toString();
+ return "::" + residue;
}
@Override
public String setBackgroundColour(Color col)
{
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/set.html#bgcolor
return "set bgColor " + ColorUtils.toTkCode(col);
}
@Override
public String focusView()
{
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html
return "focus";
}
return command;
}
+ @Override
+ public String superposeStructures(AtomSpecModel spec, AtomSpecModel ref)
+ {
+ /*
+ * Form Chimera match command to match spec to ref
+ *
+ * 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
+ */
+ StringBuilder cmd = new StringBuilder();
+ String atomSpec = getAtomSpec(spec, true);
+ String refSpec = getAtomSpec(ref, true);
+ cmd.append("match ").append(atomSpec).append(" ").append(refSpec);
+
+ /*
+ * show superposed residues as ribbon, others as chain
+ */
+ // fixme this should precede the loop over all alignments/structures
+ cmd.append(";~display all; chain @CA|P");
+ cmd.append("; ribbon ");
+ cmd.append(atomSpec).append("|").append(refSpec).append("; focus");
+
+ return cmd.toString();
+ }
+
+ @Override
+ public String openCommandFile(String path)
+ {
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
+ return "open cmd:" + path;
+ }
+
+ @Override
+ public String saveSession(String filepath)
+ {
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/save.html
+ return "save " + filepath;
+ }
+
+ /**
+ * Returns the range(s) modelled by {@code atomSpec} formatted as a Chimera
+ * atomspec string, e.g.
+ *
+ * <pre>
+ * #0:15.A,28.A,54.A,70-72.A|#1:2.A,6.A,11.A,13-14.A
+ * </pre>
+ *
+ * where
+ * <ul>
+ * <li>#0 is a model number</li>
+ * <li>15 or 70-72 is a residue number, or range of residue numbers</li>
+ * <li>.A is a chain identifier</li>
+ * <li>residue ranges are separated by comma</li>
+ * <li>atomspecs for distinct models are separated by | (or)</li>
+ * </ul>
+ *
+ * <pre>
+ *
+ * @param model
+ * @param alphaOnly
+ * @return
+ * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
+ */
+ @Override
+ public String getAtomSpec(AtomSpecModel atomSpec, boolean alphaOnly)
+ {
+ StringBuilder sb = new StringBuilder(128);
+ boolean firstModel = true;
+ for (Integer model : atomSpec.getModels())
+ {
+ if (!firstModel)
+ {
+ sb.append("|");
+ }
+ firstModel = false;
+ appendModel(sb, model, atomSpec, alphaOnly);
+ }
+ return sb.toString();
+ }
+
+ /**
+ * A helper method to append an atomSpec string for atoms in the given model
+ *
+ * @param sb
+ * @param model
+ * @param atomSpec
+ * @param alphaOnly
+ */
+ protected void appendModel(StringBuilder sb, Integer model,
+ AtomSpecModel atomSpec, boolean alphaOnly)
+ {
+ sb.append("#").append(model).append(":");
+
+ boolean firstPositionForModel = true;
+
+ for (String chain : atomSpec.getChains(model))
+ {
+ 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())
+ {
+ appendRange(sb, start, end, chain, firstPositionForModel, false);
+ firstPositionForModel = false;
+ }
+ }
+ if (alphaOnly)
+ {
+ /*
+ * restrict to alpha carbon, no alternative locations
+ * (needed to ensuring matching atom counts for superposition)
+ */
+ sb.append("@CA|P").append(NO_ALTLOCS);
+ }
+ }
+
+ @Override
+ public String showBackbone()
+ {
+ return "~display all;chain @CA|P";
+ }
+
}