/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.ext.rbvi.chimera;
+import jalview.api.AlignViewportI;
+import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
-import jalview.api.SequenceRenderer;
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.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
-import jalview.util.Comparison;
+import jalview.util.ColorUtils;
+import jalview.util.IntRangeComparator;
import java.awt.Color;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
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;
* @author JimP
*
*/
-public class ChimeraCommands
+public class ChimeraCommands extends StructureCommandsBase
{
+ 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 String CMD_COLOUR_BY_CHAIN = "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)
+ {
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/color.html
+ String colourCode = getColourString(colour);
+ return "color " + colourCode + " " + atomSpec;
+ }
+
+ /**
+ * Returns a colour formatted suitable for use in viewer command syntax
+ *
+ * @param colour
+ * @return
+ */
+ protected String getColourString(Color colour)
+ {
+ return ColorUtils.toTkCode(colour);
+ }
/**
- * utility to construct the commands to colour chains by the given alignment
- * for passing to Chimera
+ * 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.
*
- * @returns Object[] { Object[] { <model being coloured>,
+ * @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);
+
+ return setAttributes(featureMap);
+ }
+
+ /**
+ * <pre>
+ * Helper method to build a map of
+ * { featureType, { feature value, AtomSpecModel } }
+ * </pre>
*
+ * @param ssm
+ * @param files
+ * @param seqs
+ * @param viewPanel
+ * @return
*/
- public static StructureMappingcommandSet[] getColourBySequenceCommand(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
+ protected Map<String, Map<Object, AtomSpecModel>> buildFeaturesMap(
+ StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
+ AlignmentViewPanel viewPanel)
{
- String defAttrPath = null;
- FileOutputStream fos = null;
- try
- {
- File outFile = File.createTempFile("jalviewdefattr", ".xml");
- outFile.deleteOnExit();
- defAttrPath = outFile.getPath();
- fos = new FileOutputStream(outFile);
- fos.write("attribute: jalviewclr\n".getBytes());
- } catch (IOException e1)
+ Map<String, Map<Object, AtomSpecModel>> theMap = new LinkedHashMap<>();
+
+ FeatureRenderer fr = viewPanel.getFeatureRenderer();
+ if (fr == null)
{
- e1.printStackTrace();
+ return theMap;
}
- List<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
+
+ AlignViewportI viewport = viewPanel.getAlignViewport();
+ List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
/*
- * Map of { colour, positionSpecs}
+ * if alignment is showing features from complement, we also transfer
+ * these features to the corresponding mapped structure residues
*/
- Map<String, StringBuilder> colranges = new LinkedHashMap<String, StringBuilder>();
- StringBuilder setAttributes = new StringBuilder(256);
- String lastColour = "none";
- Color lastCol = null;
+ 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++)
{
- boolean startModel = true;
+ 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 seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++)
{
- for (int sp, m = 0; m < mapping.length; m++)
+ for (int m = 0; m < mapping.length; m++)
{
- final SequenceI seq = sequence[pdbfnum][s];
- if (mapping[m].getSequence() == seq
- && (sp = alignment.findIndex(seq)) > -1)
+ final SequenceI seq = seqs[pdbfnum][seqNo];
+ int sp = alignment.findIndex(seq);
+ StructureMapping structureMapping = mapping[m];
+ if (structureMapping.getSequence() == seq && sp > -1)
{
- SequenceI asp = alignment.getSequenceAt(sp);
- for (int r = 0; r < asp.getLength(); r++)
+ /*
+ * found a sequence with a mapping to a structure;
+ * now scan its features
+ */
+ if (!visibleFeatures.isEmpty())
{
- // 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 col = getResidueColour(seq, r, sr, fr);
- /*
- * 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 = !col.equals(lastCol);
- final boolean nonContig = lastPos + 1 != pos;
- final boolean newChain = !mapping[m].getChain().equals(lastChain);
- if (newColour || nonContig || startModel || newChain)
- {
- if (/* lastCol != null */startPos != -1)
- {
- addColourRange(colranges, lastCol, pdbfnum, startPos,
- lastPos, lastChain, startModel);
- startModel = false;
- }
- // lastCol = null;
- startPos = pos;
- }
- lastCol = col;
- lastPos = pos;
- // lastModel = pdbfnum;
- lastChain = mapping[m].getChain();
+ scanSequenceFeatures(visibleFeatures, structureMapping, seq,
+ theMap, modelNumber);
}
- // final colour range
- if (lastCol != null)
+ if (showLinkedFeatures)
{
- addColourRange(colranges, lastCol, pdbfnum, startPos,
- lastPos, lastChain, false);
+ scanComplementFeatures(complementRenderer, structureMapping,
+ seq, theMap, modelNumber);
}
- break;
}
}
}
}
- try
- {
- lastColour = buildColourCommands(cset, colranges,
- fos, setAttributes);
- } catch (IOException e)
- {
- e.printStackTrace();
- }
-
- try
- {
- fos.close();
- } catch (IOException e)
- {
- e.printStackTrace();
- }
+ 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)
+ {
/*
- * Send a rangeColor command, preceded by either defattr or setattr,
- * whichever we end up preferring!
- *
- * rangecolor requires a minimum of two attribute values to operate on
+ * for each sequence residue mapped to a structure position...
*/
- StringBuilder rangeColor = new StringBuilder(256);
- rangeColor.append("rangecolor jalviewclr");
- int colourId = 0;
- for (String colour : colranges.keySet())
- {
- colourId++;
- rangeColor.append(" " + colourId + " " + colour);
- }
- String rangeColorCommand = rangeColor.toString();
- if (rangeColorCommand.split(" ").length < 5)
+ for (int seqPos : structureMapping.getMapping().keySet())
{
- rangeColorCommand += " max " + lastColour;
+ /*
+ * 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());
+ }
+ }
+ }
+ }
}
- final String defAttrCommand = "defattr " + defAttrPath
- + " raiseTool false";
- final String setAttrCommand = setAttributes.toString();
- final String attrCommand = false ? defAttrCommand : setAttrCommand;
- cset.add(new StructureMappingcommandSet(ChimeraCommands.class, null,
- new String[]
- { attrCommand /* , rangeColorCommand */}));
-
- return cset.toArray(new StructureMappingcommandSet[cset.size()]);
}
/**
- * Get the residue colour at the given sequence position - as determined by
- * the sequence group colour (if any), else the colour scheme, possibly
- * overridden by a feature colour.
+ * 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 position
- * @param sr
- * @param fr
- * @return
+ * @param theMap
+ * @param modelNumber
*/
- protected static Color getResidueColour(final SequenceI seq,
- int position, SequenceRenderer sr, FeatureRenderer fr)
+ protected static void scanSequenceFeatures(List<String> visibleFeatures,
+ StructureMapping mapping, SequenceI seq,
+ Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
{
- Color col = sr.getResidueBoxColour(seq, position);
-
- if (fr != null)
+ List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures(
+ visibleFeatures.toArray(new String[visibleFeatures.size()]));
+ for (SequenceFeature sf : sfs)
{
- col = fr.findFeatureColour(col, seq, position);
+ 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());
+ }
+ }
}
- return col;
}
/**
- * Helper method to build the colour commands for one PDBfile.
+ * Traverse the map of features/values/models/chains/positions to construct a
+ * list of 'setattr' commands (one per distinct feature type and value).
+ * <p>
+ * The format of each command is
+ *
+ * <pre>
+ * <blockquote> setattr r <featureName> " " #modelnumber:range.chain
+ * e.g. setattr r jv_chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
+ * </blockquote>
+ * </pre>
*
- * @param cset
- * the list of commands to be added to
- * @param colranges
- * the map of colours to residue positions already determined
- * @param fos
- * file to write 'defattr' commands to
- * @param setAttributes
- * @throws IOException
+ * @param featureMap
+ * @return
*/
- protected static String buildColourCommands(
- List<StructureMappingcommandSet> cset,
- Map<String, StringBuilder> colranges,
- FileOutputStream fos, StringBuilder setAttributes)
- throws IOException
+ protected String[] setAttributes(
+ Map<String, Map<Object, AtomSpecModel>> featureMap)
{
- int colourId = 0;
- String lastColour = null;
- for (String colour : colranges.keySet())
+ List<String> commands = new ArrayList<>();
+ for (String featureType : featureMap.keySet())
{
- lastColour = colour;
- colourId++;
+ String attributeName = makeAttributeName(featureType);
+
/*
- * Using color command directly is slow for larger structures.
- * setAttributes.append("color #" + colour + " " + colranges.get(colour)+
- * ";");
+ * clear down existing attributes for this feature
*/
- setAttributes.append("color " + colour + " " + colranges.get(colour)
- + ";");
- final String atomSpec = new String(colranges.get(colour));
- // setAttributes.append("setattr r jalviewclr " + colourId + " "
- // + atomSpec + ";");
- fos.write(("\t" + atomSpec + "\t" + colourId + "\n").getBytes());
+ // 'problem' - sets attribute to None on all residues - overkill?
+ // commands.add("~setattr r " + attributeName + " :*");
+
+ Map<Object, AtomSpecModel> values = featureMap.get(featureType);
+ for (Object value : values.keySet())
+ {
+ /*
+ * for each distinct value recorded for this feature type,
+ * add a command to set the attribute on the mapped residues
+ * Put values in single quotes, encoding any embedded single quotes
+ */
+ AtomSpecModel atomSpecModel = values.get(value);
+ String featureValue = value.toString();
+ featureValue = featureValue.replaceAll("\\'", "'");
+ String cmd = setAttribute(attributeName, featureValue,
+ atomSpecModel);
+ commands.add(cmd);
+ }
}
- return lastColour;
+
+ return commands.toArray(new String[commands.size()]);
}
/**
- * Helper method to record a range of positions of the same colour.
+ * Returns a viewer command to set the given residue attribute value on
+ * residues specified by the AtomSpecModel, for example
*
- * @param colranges
- * @param colour
- * @param model
- * @param startPos
- * @param endPos
- * @param chain
- * @param changeModel
+ * <pre>
+ * setatr res jv_chain 'primary' #1:12-34,48-55.B
+ * </pre>
+ *
+ * @param attributeName
+ * @param attributeValue
+ * @param atomSpecModel
+ * @return
+ */
+ 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(getAtomSpec(atomSpecModel, false));
+ return sb.toString();
+ }
+
+ /**
+ * Makes a prefixed and valid Chimera attribute name. A jv_ prefix is applied
+ * for a 'Jalview' namespace, and any non-alphanumeric character is converted
+ * to an underscore.
+ *
+ * @param featureType
+ * @return
+ * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
*/
- private static void addColourRange(Map<String, StringBuilder> colranges,
- Color colour, int model, int startPos, int endPos, String chain,
- boolean startModel)
+ protected static String makeAttributeName(String featureType)
{
- String colstring = "#" + ((colour.getRed() < 16) ? "0" : "")
- + Integer.toHexString(colour.getRed())
- + ((colour.getGreen()< 16) ? "0":"")+Integer.toHexString(colour.getGreen())
- + ((colour.getBlue()< 16) ? "0":"")+Integer.toHexString(colour.getBlue());
- StringBuilder currange = colranges.get(colstring);
- if (currange == null)
+ StringBuilder sb = new StringBuilder();
+ if (featureType != null)
{
- colranges.put(colstring, currange = new StringBuilder(256));
+ for (char c : featureType.toCharArray())
+ {
+ sb.append(Character.isLetterOrDigit(c) ? c : '_');
+ }
}
+ String attName = NAMESPACE_PREFIX + sb.toString();
+
+ /*
+ * 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"))
+ {
+ attName += "_";
+ }
+
+ return attName;
+ }
+
+ @Override
+ public String colourByChain()
+ {
+ return CMD_COLOUR_BY_CHAIN;
+ }
+
+ @Override
+ public String colourByCharge()
+ {
+ return CMD_COLOUR_BY_CHARGE;
+ }
+
+ @Override
+ public String getResidueSpec(String residue)
+ {
+ 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";
+ }
+
+ @Override
+ public String showChains(List<String> toShow)
+ {
+ /*
+ * Construct a chimera command like
+ *
+ * ~display #*;~ribbon #*;ribbon :.A,:.B
+ */
+ StringBuilder cmd = new StringBuilder(64);
+ boolean first = true;
+ for (String chain : toShow)
+ {
+ String[] tokens = chain.split(":");
+ if (tokens.length == 2)
+ {
+ String showChainCmd = tokens[0] + ":." + tokens[1];
+ if (!first)
+ {
+ cmd.append(",");
+ }
+ cmd.append(showChainCmd);
+ first = false;
+ }
+ }
+
+ /*
+ * could append ";focus" to this command to resize the display to fill the
+ * window, but it looks more helpful not to (easier to relate chains to the
+ * whole)
+ */
+ final String command = "~display #*; ~ribbon #*; ribbon :"
+ + cmd.toString();
+ 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);
+
/*
- * Format as (e.g.) #0:1-3.A,5.A,7-10.A,...#1:1-4.B,..etc
+ * show superposed residues as ribbon, others as chain
*/
- // if (currange.length() > 0)
- // {
- // currange.append("|");
- // }
- // currange.append("#" + model + ":" + ((startPos==endPos) ? startPos :
- // startPos + "-"
- // + endPos) + "." + chain);
- if (currange.length() == 0)
+ // 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())
{
- currange.append("#" + model + ":");
+ if (!firstModel)
+ {
+ sb.append("|");
+ }
+ firstModel = false;
+ appendModel(sb, model, atomSpec, alphaOnly);
}
- else if (startModel)
+ 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))
{
- currange.append(",#" + 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;
+ }
}
- else
+ if (alphaOnly)
{
- currange.append(",");
+ /*
+ * restrict to alpha carbon, no alternative locations
+ * (needed to ensuring matching atom counts for superposition)
+ */
+ sb.append("@CA|P").append(NO_ALTLOCS);
}
- final String rangeSpec = (startPos == endPos) ? Integer
- .toString(startPos) : (startPos + "-" + endPos);
- currange.append(rangeSpec + "." + chain);
+ }
+
+ @Override
+ public String showBackbone()
+ {
+ return "~display all;chain @CA|P";
}
}
git://source.jalview.org / jalview.git / blobdiff