+ // load a pAE file if given
+ if (avm.hasValue(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);
+ 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 = subVals.get("structid");
+ if (subVals.notSet())
+ {
+ // take structid from pdbfilename
+ }
+ if (subVals.has("structfile"))
+ {
+ Console.info("***** Attaching paeFile '" + paePath + "' to "
+ + "structfile=" + subVals.get("structfile"));
+ EBIAlfaFold.addAlphaFoldPAEToStructure(
+ af.getCurrentView().getAlignment(), paeFile,
+ subVals.getIndex(), subVals.get("structfile"), false);
+ }
+ else if (subVals.has("structid"))
+ {
+ Console.info("***** Attaching paeFile '" + paePath + "' to "
+ + "structid=" + subVals.get("structid"));
+ EBIAlfaFold.addAlphaFoldPAEToStructure(
+ af.getCurrentView().getAlignment(), paeFile,
+ subVals.getIndex(), subVals.get("structid"), true);
+ }
+ else
+ {
+ Console.debug("***** Attaching paeFile '" + paePath
+ + "' to sequence index " + subVals.getIndex());
+ EBIAlfaFold.addAlphaFoldPAEToSequence(
+ af.getCurrentView().getAlignment(), paeFile,
+ subVals.getIndex(), null);
+ // 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());
+ }