+
+ // load a pAE file if given
+ if (avm.containsArg(Arg.PAEMATRIX))
+ {
+ AlignFrame af = afMap.get(id);
+ if (af != null)
+ {
+ for (ArgValue av : avm.getArgValueList(Arg.PAEMATRIX))
+ {
+ String val = av.getValue();
+ SubVals subVals = ArgParser.getSubVals(val);
+ String paeLabel = subVals.get("label");
+ File paeFile = new File(subVals.getContent());
+ String paePath = null;
+ try
+ {
+ paePath = paeFile.getCanonicalPath();
+ } catch (IOException e)
+ {
+ paePath = paeFile.getAbsolutePath();
+ Console.warn(
+ "Problem with the PAE file path: '" + paePath + "'");
+ }
+ String structid = null;
+ String structfile = null;
+ String seqid = null;
+ if (subVals.notSet())
+ {
+ ArgValue likelyStructure = avm
+ .getClosestPreviousArgValueOfArg(av, Arg.STRUCTURE);
+ if (likelyStructure != null)
+ {
+ SubVals sv = likelyStructure.getSubVals();
+ if (sv != null && sv.has(ArgValues.ID))
+ {
+ structid = sv.get(ArgValues.ID);
+ }
+ else
+ {
+ structfile = likelyStructure.getValue();
+ }
+ }
+ }
+ else if (subVals.has("structfile"))
+ {
+ structfile = subVals.get("structfile");
+ }
+ else if (subVals.has("structid"))
+ {
+ structid = subVals.get("structid");
+ }
+ if (structfile != null)
+ {
+ Console.info("***** Attaching paeFile '" + paePath + "' to "
+ + "structfile=" + subVals.get("structfile"));
+ EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+ paeFile, subVals.getIndex(), subVals.get("structfile"),
+ true, false, paeLabel);
+ }
+ else if (structid != null)
+ {
+ Console.info("***** Attaching paeFile '" + paePath + "' to "
+ + "structid=" + subVals.get("structid"));
+ EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+ paeFile, subVals.getIndex(), subVals.get("structid"),
+ true, true, paeLabel);
+ }
+ else
+ {
+ Console.debug("***** Attaching paeFile '" + paePath
+ + "' to sequence index " + subVals.getIndex());
+ EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
+ paeFile, subVals.getIndex(), null, false, false,
+ paeLabel);
+ // required to readjust the height and position of the pAE
+ // annotation
+ }
+ for (AlignmentViewPanel ap : af.getAlignPanels())
+ {
+ ap.adjustAnnotationHeight();
+ }
+ }
+ }
+ }
+
+ boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
+ if (doShading)
+ {
+ AlignFrame af = afMap.get(id);
+ for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
+ .findAnnotation(PDBChain.class.getName().toString()))
+ {
+ AnnotationColourGradient acg = new AnnotationColourGradient(aa,
+ af.alignPanel.av.getGlobalColourScheme(), 0);
+ acg.setSeqAssociated(true);
+ af.changeColour(acg);
+ Console.info("Changed colour " + acg.toString());
+ }
+ }
+
+ return theseArgsWereParsed;