+ * The format of each command is + * + *
+ *+ * + * @param featureMap + * @return + */ + @Override + public Listsetattr r+ *" " #modelnumber:range.chain + * e.g. setattr r jv_chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,... + *
+ * setatr res jv_chain 'primary' #1:12-34,48-55.B + ** + * @param attributeName + * @param attributeValue + * @param atomSpecModel + * @return */ - public static StructureMappingcommandSet[] getColourBySequenceCommand( - StructureSelectionManager ssm, String[] files, - SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, - AlignmentI alignment) + protected StructureCommandI 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, AtomSpecType.RESIDUE_ONLY)); + return new StructureCommand(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 + */ + @Override + protected String makeAttributeName(String featureType) + { + String attName = super.makeAttributeName(featureType); + + /* + * Chimera treats an attribute name ending in 'color' as colour-valued; + * Jalview doesn't, so prevent this by appending an underscore + */ + if (attName.toUpperCase(Locale.ROOT).endsWith("COLOR")) + { + attName += "_"; + } + + return attName; + } + + @Override + public StructureCommandI colourByChain() + { + return COLOUR_BY_CHAIN; + } + + @Override + public List
+ * #0:15.A,28.A,54.A,70-72.A|#1:2.A,6.A,11.A,13-14.A + *+ * + * where + *
+ *
+ * @param model
+ * @param specType
+ * @return
+ * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
+ */
+ @Override
+ public String getAtomSpec(AtomSpecModel atomSpec, AtomSpecType specType)
+ {
+ StringBuilder sb = new StringBuilder(128);
+ boolean firstModel = true;
+ for (String model : atomSpec.getModels())
+ {
+ if (!firstModel)
{
- coms.append("color #"+cr+" "+colranges.get(cr)+";");
+ sb.append("|");
}
- cset.add(new StructureMappingcommandSet(ChimeraCommands.class,
- files[pdbfnum], new String[] { coms.toString() }));
+ firstModel = false;
+ appendModel(sb, model, atomSpec, specType);
}
- return cset.toArray(new StructureMappingcommandSet[cset.size()]);
+ return sb.toString();
}
- private static void addColourRange(Hashtable colranges, Color lastCol, int startModel,
- int startPos, int lastPos, String lastChain)
+ /**
+ * 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, String model,
+ AtomSpecModel atomSpec, AtomSpecType specType)
{
-
- String colstring = ((lastCol.getRed()< 16) ? "0":"")+Integer.toHexString(lastCol.getRed())
- + ((lastCol.getGreen()< 16) ? "0":"")+Integer.toHexString(lastCol.getGreen())
- + ((lastCol.getBlue()< 16) ? "0":"")+Integer.toHexString(lastCol.getBlue());
- StringBuffer currange = colranges.get(colstring);
- if (currange==null)
+ sb.append("#").append(model).append(":");
+
+ boolean firstPositionForModel = true;
+
+ for (String chain : atomSpec.getChains(model))
+ {
+ chain = " ".equals(chain) ? chain : chain.trim();
+
+ List rangeList = atomSpec.getRanges(model, chain);
+ for (int[] range : rangeList)
+ {
+ appendRange(sb, range[0], range[1], chain, firstPositionForModel,
+ false);
+ firstPositionForModel = false;
+ }
+ }
+ if (specType == AtomSpecType.ALPHA)
{
- colranges.put(colstring,currange = new StringBuffer());
+ /*
+ * restrict to alpha carbon, no alternative locations
+ * (needed to ensuring matching atom counts for superposition)
+ */
+ sb.append("@CA").append(NO_ALTLOCS);
}
- if (currange.length()>0)
+ if (specType == AtomSpecType.PHOSPHATE)
{
- currange.append("|");
+ sb.append("@P").append(NO_ALTLOCS);
}
- currange.append("#" + startModel + ":" + ((startPos==lastPos) ? startPos : startPos + "-"
- + lastPos) + "." + lastChain);
+ }
+
+ @Override
+ public List showBackbone()
+ {
+ return Arrays.asList(SHOW_BACKBONE);
+ }
+
+ @Override
+ public StructureCommandI loadFile(String file)
+ {
+ return new StructureCommand("open " + file);
+ }
+
+ @Override
+ public StructureCommandI openSession(String filepath)
+ {
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
+ // this version of the command has no dependency on file extension
+ return new StructureCommand("open chimera:" + filepath);
+ }
+
+ @Override
+ public StructureCommandI closeViewer()
+ {
+ return CLOSE_CHIMERA;
+ }
+
+ @Override
+ public List startNotifications(String uri)
+ {
+ // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
+ List cmds = new ArrayList<>();
+ cmds.add(new StructureCommand("listen start models url " + uri));
+ cmds.add(new StructureCommand("listen start select prefix SelectionChanged url " + uri));
+ return cmds;
+ }
+
+ @Override
+ public List stopNotifications()
+ {
+ List cmds = new ArrayList<>();
+ cmds.add(STOP_NOTIFY_MODELS);
+ cmds.add(STOP_NOTIFY_SELECTION);
+ return cmds;
+ }
+
+ @Override
+ public StructureCommandI getSelectedResidues()
+ {
+ return GET_SELECTION;
+ }
+
+ @Override
+ public StructureCommandI listResidueAttributes()
+ {
+ return LIST_RESIDUE_ATTRIBUTES;
+ }
+
+ @Override
+ public StructureCommandI getResidueAttributes(String attName)
+ {
+ // this alternative command
+ // list residues spec ':*/attName' attr attName
+ // doesn't report 'None' values (which is good), but
+ // fails for 'average.bfactor' (which is bad):
+ return new StructureCommand("list residues attr '" + attName + "'");
}
}