/*
- * 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.api.structures.JalviewStructureDisplayI;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
-import jalview.util.Format;
+import jalview.structures.models.AAStructureBindingModel;
+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;
/**
* Routines for generating Chimera commands for Jalview/Chimera binding
*/
public class ChimeraCommands
{
+ public static final String NAMESPACE_PREFIX = "jv_";
+
+ /*
+ * colour for residues shown in structure but hidden in alignment
+ */
+ private static final String COLOR_GRAY_HEX = "color "
+ + ColorUtils.toTkCode(Color.GRAY);
+
+ /**
+ * Constructs Chimera commands to colour residues as per the Jalview alignment
+ *
+ * @param colourMap
+ * @param binding
+ * @return
+ */
+ public static String[] getColourBySequenceCommand(
+ Map<Object, AtomSpecModel> colourMap,
+ AAStructureBindingModel binding)
+ {
+ List<String> colourCommands = buildColourCommands(colourMap, binding);
+
+ return colourCommands.toArray(new String[colourCommands.size()]);
+ }
/**
- * utility to construct the commands to colour chains by the given alignment
- * for passing to Chimera
+ * 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
*
- * @returns Object[] { Object[] { <model being coloured>,
+ * <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
+ * @param binding
+ * @return
*/
- public static StructureMappingcommandSet[] getColourBySequenceCommand(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
- AlignmentI alignment)
+ protected static List<String> buildColourCommands(
+ Map<Object, AtomSpecModel> colourMap,
+ AAStructureBindingModel binding)
{
+ /*
+ * 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);
+ sb.append(COLOR_GRAY_HEX);
- ArrayList<StructureMappingcommandSet> cset = new ArrayList<StructureMappingcommandSet>();
+ for (Object key : colourMap.keySet())
+ {
+ Color colour = (Color) key;
+ String colourCode = ColorUtils.toTkCode(colour);
+ sb.append("; ");
+ sb.append("color ").append(colourCode).append(" ");
+ final AtomSpecModel colourData = colourMap.get(colour);
+ sb.append(getAtomSpec(colourData, binding));
+ }
+ commands.add(sb.toString());
+ return commands;
+ }
+
+ /**
+ * Build a data structure which records contiguous subsequences for each colour.
+ * From this we can easily generate the Chimera command for colour by sequence.
+ *
+ * <pre>
+ * Color
+ * Model number
+ * Chain
+ * list of start/end ranges
+ * </pre>
+ *
+ * Ordering is by order of addition (for colours and positions), natural
+ * ordering (for models and chains)
+ *
+ * @param ssm
+ * @param files
+ * @param sequence
+ * @param sr
+ * @param hideHiddenRegions
+ * @param viewPanel
+ * @return
+ */
+ protected static Map<Object, AtomSpecModel> buildColoursMap(
+ StructureSelectionManager ssm, String[] files,
+ SequenceI[][] sequence, SequenceRenderer sr,
+ boolean hideHiddenRegions, AlignmentViewPanel viewPanel)
+ {
+ 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++)
{
- float cols[] = new float[4];
StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
- StringBuffer command = new StringBuffer();
- StructureMappingcommandSet smc;
- ArrayList<String> str = new ArrayList<String>();
if (mapping == null || mapping.length < 1)
+ {
continue;
+ }
- int startPos = -1, lastPos = -1, startModel = -1, lastModel = -1;
- String startChain = "", lastChain = "";
- Color lastCol = null;
+ 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++)
{
- if (mapping[m].getSequence() == sequence[pdbfnum][s]
- && (sp = alignment.findIndex(sequence[pdbfnum][s])) > -1)
+ final SequenceI seq = sequence[pdbfnum][s];
+ if (mapping[m].getSequence() == seq
+ && (sp = al.findIndex(seq)) > -1)
{
- SequenceI asp = alignment.getSequenceAt(sp);
+ SequenceI asp = al.getSequenceAt(sp);
for (int r = 0; r < asp.getLength(); r++)
{
// no mapping to gaps in sequence
- if (jalview.util.Comparison.isGap(asp.getCharAt(r)))
+ if (Comparison.isGap(asp.getCharAt(r)))
{
continue;
}
int pos = mapping[m].getPDBResNum(asp.findPosition(r));
if (pos < 1 || pos == lastPos)
+ {
continue;
+ }
- Color col = sr.getResidueBoxColour(sequence[pdbfnum][s], r);
+ Color colour = sr.getResidueColour(seq, r, finder);
- if (fr != null)
- col = fr.findFeatureColour(col, sequence[pdbfnum][s], r);
- if (lastCol != col || lastPos + 1 != pos
- || pdbfnum != lastModel
- || !mapping[m].getChain().equals(lastChain))
+ /*
+ * hidden regions are shown gray or, optionally, ignored
+ */
+ if (!cs.isVisible(r))
{
- if (lastCol != null)
+ if (hideHiddenRegions)
{
+ continue;
+ }
+ else
+ {
+ colour = Color.GRAY;
+ }
+ }
+
+ final String chain = mapping[m].getChain();
- lastCol.getRGBComponents(cols);
- String newSelcom = "color " + cols[0] + "," + cols[1]
- + "," + cols[2] + " #" + startModel + ":"
- + startPos + "-" + lastPos + "." + lastChain;
- if (str.size() > 0
- && (str.get(str.size() - 1).length() + newSelcom
- .length()) < 4096)
- {
- str.set(str.size() - 1, str.get(str.size() - 1) + ";"
- + newSelcom);
- }
- else
- {
- str.add(newSelcom);
- }
+ /*
+ * 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)
+ {
+ addMapRange(colourMap, lastColour, pdbfnum, startPos,
+ lastPos, lastChain);
}
- lastCol = null;
startPos = pos;
- startModel = pdbfnum;
- startChain = mapping[m].getChain();
}
- lastCol = col;
+ lastColour = colour;
lastPos = pos;
- lastModel = pdbfnum;
- lastChain = mapping[m].getChain();
+ lastChain = chain;
}
// final colour range
- if (lastCol != null)
+ if (lastColour != null)
{
-
- lastCol.getRGBComponents(cols);
- String newSelcom = "color " + cols[0] + "," + cols[1] + ","
- + cols[2] + " #" + startModel + ":" + startPos + "-"
- + lastPos + "." + lastChain;
- if (str.size() > 0
- && (str.get(str.size() - 1).length() + newSelcom
- .length()) < 4096)
- {
- str.set(str.size() - 1, str.get(str.size() - 1) + ";"
- + newSelcom);
- }
- else
- {
- str.add(newSelcom);
- }
+ addMapRange(colourMap, lastColour, pdbfnum, startPos,
+ lastPos, lastChain);
}
- break;
+ // break;
+ }
+ }
+ }
+ }
+ return colourMap;
+ }
+
+ /**
+ * Helper method to add one contiguous range to the map, for a given value key
+ * (e.g. colour or feature type), structure model number, and chain
+ *
+ * @param map
+ * @param key
+ * @param model
+ * @param startPos
+ * @param endPos
+ * @param chain
+ */
+ public static void addMapRange(Map<Object, AtomSpecModel> map,
+ Object key, int model, int startPos, int endPos, String chain)
+ {
+ /*
+ * Get/initialize map of data for the colour
+ */
+ AtomSpecModel atomSpec = map.get(key);
+ if (atomSpec == null)
+ {
+ atomSpec = new AtomSpecModel();
+ map.put(key, atomSpec);
+ }
+
+ atomSpec.addRange(model, startPos, endPos, chain);
+ }
+
+ /**
+ * 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
+ * @param binding
+ * @return
+ */
+ public static StructureMappingcommandSet getSetAttributeCommandsForFeatures(
+ AlignmentViewPanel viewPanel, AAStructureBindingModel binding)
+ {
+ StructureSelectionManager ssm = binding.getSsm();
+ String[] files = binding.getStructureFiles();
+ SequenceI[][] seqs = binding.getSequence();
+
+ Map<String, Map<Object, AtomSpecModel>> featureMap = buildFeaturesMap(
+ ssm, files, seqs, viewPanel);
+
+ List<String> commands = buildSetAttributeCommands(featureMap, binding);
+
+ StructureMappingcommandSet cs = new StructureMappingcommandSet(
+ ChimeraCommands.class, null,
+ commands.toArray(new String[commands.size()]));
+
+ return cs;
+ }
+
+ /**
+ * <pre>
+ * Helper method to build a map of
+ * { featureType, { feature value, AtomSpecModel } }
+ * </pre>
+ *
+ * @param ssm
+ * @param files
+ * @param seqs
+ * @param viewPanel
+ * @return
+ */
+ protected static 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;
+ }
+
+ List<String> visibleFeatures = fr.getDisplayedFeatureTypes();
+ if (visibleFeatures.isEmpty())
+ {
+ return theMap;
+ }
+
+ AlignmentI alignment = viewPanel.getAlignment();
+ for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+ {
+ 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);
+ if (mapping[m].getSequence() == seq && sp > -1)
+ {
+ /*
+ * found a sequence with a mapping to a structure;
+ * now scan its features
+ */
+ SequenceI asp = alignment.getSequenceAt(sp);
+
+ scanSequenceFeatures(visibleFeatures, mapping[m], asp, theMap,
+ pdbfnum);
+ }
+ }
+ }
+ }
+ return theMap;
+ }
+
+ /**
+ * 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();
+
+ /*
+ * Only copy visible features, don't copy any which originated
+ * from Chimera, and suppress uninteresting ones (e.g. RESNUM)
+ */
+ boolean isFromViewer = JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
+ .equals(sf.getFeatureGroup());
+ if (isFromViewer)
+ {
+ 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)
+ {
+ addMapRange(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>
+ * 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 featureMap
+ * @param binding
+ * @return
+ */
+ protected static List<String> buildSetAttributeCommands(
+ Map<String, Map<Object, AtomSpecModel>> featureMap,
+ AAStructureBindingModel binding)
+ {
+ List<String> commands = new ArrayList<>();
+ for (String featureType : featureMap.keySet())
+ {
+ String attributeName = makeAttributeName(featureType);
+
+ /*
+ * clear down existing attributes for this feature
+ */
+ // '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
+ */
+ StringBuilder sb = new StringBuilder(128);
+ String featureValue = value.toString();
+ featureValue = featureValue.replaceAll("\\'", "'");
+ sb.append("setattr r ").append(attributeName).append(" '")
+ .append(featureValue).append("' ");
+ sb.append(getAtomSpec(values.get(value), binding));
+ commands.add(sb.toString());
+ }
+ }
+
+ return commands;
+ }
+
+ /**
+ * 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
+ *
+ * <pre>
+ * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
+ * </pre>
+ */
+ protected static 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();
+
+ /*
+ * 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;
+ }
+
+ /**
+ * Returns the range(s) formatted as a Chimera atomspec
+ *
+ * @return
+ */
+ public static String getAtomSpec(AtomSpecModel atomSpec,
+ AAStructureBindingModel binding)
+ {
+ StringBuilder sb = new StringBuilder(128);
+ boolean firstModel = true;
+ for (Integer model : atomSpec.getModels())
+ {
+ if (!firstModel)
+ {
+ sb.append("|");
+ }
+ firstModel = false;
+ // todo use JalviewChimeraBinding.getModelSpec(model)
+ // which means this cannot be static
+ sb.append(binding.getModelSpec(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);
+ firstPositionForModel = false;
+ start = range[0];
+ end = range[1];
}
}
+
+ /*
+ * and append the last range
+ */
+ if (!rangeList.isEmpty())
+ {
+ appendRange(sb, start, end, chain, firstPositionForModel);
+ firstPositionForModel = false;
+ }
}
- // Finally, add the command set ready to be returned.
- cset.add(new StructureMappingcommandSet(ChimeraCommands.class,
- files[pdbfnum], str.toArray(new String[str.size()])));
}
- return cset.toArray(new StructureMappingcommandSet[cset.size()]);
+ return sb.toString();
+ }
+
+ /**
+ * A helper method that appends one start-end range to a Chimera atomspec
+ *
+ * @param sb
+ * @param start
+ * @param end
+ * @param chain
+ * @param firstPositionForModel
+ */
+ static void appendRange(StringBuilder sb, int start, int end,
+ String chain, boolean firstPositionForModel)
+ {
+ if (!firstPositionForModel)
+ {
+ sb.append(",");
+ }
+ if (end == start)
+ {
+ sb.append(start);
+ }
+ else
+ {
+ sb.append(start).append("-").append(end);
+ }
+
+ sb.append(".");
+ if (!" ".equals(chain))
+ {
+ sb.append(chain);
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff