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.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
import jalview.util.ColorUtils;
-import jalview.util.Comparison;
+import jalview.util.StructureCommands;
import java.awt.Color;
import java.util.ArrayList;
* @author JimP
*
*/
-public class ChimeraCommands
+public class ChimeraCommands extends StructureCommands
{
-
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 ssm
- * @param files
- * @param sequence
- * @param sr
- * @param fr
- * @param viewPanel
+ * @param colourMap
+ * @param binding
* @return
*/
- public static StructureMappingcommandSet[] getColourBySequenceCommand(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr,
- AlignmentViewPanel viewPanel)
+ public static String[] getColourBySequenceCommand(
+ Map<Object, AtomSpecModel> colourMap,
+ AAStructureBindingModel binding)
{
- Map<Object, AtomSpecModel> colourMap = buildColoursMap(ssm, files,
- sequence, sr, viewPanel);
+ List<String> colourCommands = buildColourCommands(colourMap, binding);
- List<String> colourCommands = buildColourCommands(colourMap);
-
- StructureMappingcommandSet cs = new StructureMappingcommandSet(
- ChimeraCommands.class, null,
- colourCommands.toArray(new String[colourCommands.size()]));
-
- return new StructureMappingcommandSet[] { cs };
+ return colourCommands.toArray(new String[colourCommands.size()]);
}
/**
* </pre>
*
* @param colourMap
+ * @param binding
* @return
*/
protected static List<String> buildColourCommands(
- Map<Object, AtomSpecModel> colourMap)
+ Map<Object, AtomSpecModel> colourMap,
+ AAStructureBindingModel binding)
{
/*
* This version concatenates all commands into a single String (semi-colon
*/
List<String> commands = new ArrayList<>();
StringBuilder sb = new StringBuilder(256);
- boolean firstColour = true;
+ sb.append(COLOR_GRAY_HEX);
+
for (Object key : colourMap.keySet())
{
Color colour = (Color) key;
String colourCode = ColorUtils.toTkCode(colour);
- if (!firstColour)
- {
- sb.append("; ");
- }
+ sb.append("; ");
sb.append("color ").append(colourCode).append(" ");
- firstColour = false;
final AtomSpecModel colourData = colourMap.get(colour);
- sb.append(colourData.getAtomSpec());
+ sb.append(getAtomSpec(colourData, binding));
}
commands.add(sb.toString());
return commands;
}
/**
- * 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();
- }
-
- /**
- * <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>
- */
- protected static Map<Object, AtomSpecModel> buildColoursMap(
- StructureSelectionManager ssm, String[] files,
- SequenceI[][] sequence, SequenceRenderer sr,
- 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++)
- {
- 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, pdbfnum, startPos,
- lastPos, lastChain);
- }
- startPos = pos;
- }
- lastColour = colour;
- lastPos = pos;
- lastChain = chain;
- }
- // final colour range
- if (lastColour != null)
- {
- addAtomSpecRange(colourMap, lastColour, pdbfnum, startPos,
- lastPos, lastChain);
- }
- // break;
- }
- }
- }
- }
- return colourMap;
- }
-
- /**
- * 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 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);
- }
-
- /**
* 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.
+ * 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(
- StructureSelectionManager ssm, String[] files, SequenceI[][] seqs,
- AlignmentViewPanel viewPanel)
+ 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);
+ List<String> commands = buildSetAttributeCommands(featureMap, binding);
StructureMappingcommandSet cs = new StructureMappingcommandSet(
ChimeraCommands.class, null,
* </pre>
*
* @param featureMap
+ * @param binding
* @return
*/
protected static List<String> buildSetAttributeCommands(
- Map<String, Map<Object, AtomSpecModel>> featureMap)
+ Map<String, Map<Object, AtomSpecModel>> featureMap,
+ AAStructureBindingModel binding)
{
List<String> commands = new ArrayList<>();
for (String featureType : featureMap.keySet())
featureValue = featureValue.replaceAll("\\'", "'");
sb.append("setattr r ").append(attributeName).append(" '")
.append(featureValue).append("' ");
- sb.append(values.get(value).getAtomSpec());
+ sb.append(getAtomSpec(values.get(value), binding));
commands.add(sb.toString());
}
}
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;
+ 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);
+
+ String chainToken = " ".equals(chain) ? "." : "." + chain;
+ appendResidueRange(sb, rangeList, chainToken,
+ firstPositionForModel);
+ firstPositionForModel = false;
+ }
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Chimera atomspec requires chain to be specified for each start-end residue
+ * range, otherwise it will apply to all chains
+ *
+ * @param sb
+ * @param chain
+ */
+ protected static void appendChainToRange(StringBuilder sb, String chain)
+ {
+ sb.append(".");
+ if (!" ".equals(chain))
+ {
+ sb.append(chain);
+ }
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff