- SubId subId = ArgParser.getSubId(val);
- File paeFile = new File(subId.content);
- EBIAlfaFold.addAlphaFoldPAE(af.getCurrentView().getAlignment(),
- paeFile, subId.index,
- "id".equals(subId.keyName) ? subId.keyValue : null);
- // required to readjust the height and position of the pAE
- // annotation
+ SubVal subVal = ArgParser.getSubVal(val);
+ File paeFile = new File(subVal.content);
+ String structId = "structid".equals(subVal.keyName)
+ ? subVal.keyValue
+ : null;
+ if (subVal.notSet())
+ {
+ // take structid from pdbfilename
+ }
+ if ("structfile".equals(subVal.keyName))
+ {
+ EBIAlfaFold.addAlphaFoldPAEToStructure(
+ af.getCurrentView().getAlignment(), paeFile,
+ subVal.index, subVal.keyValue, false);
+ }
+ else if ("structid".equals(subVal.keyName))
+ {
+ EBIAlfaFold.addAlphaFoldPAEToStructure(
+ af.getCurrentView().getAlignment(), paeFile,
+ subVal.index, subVal.keyValue, true);
+ }
+ else
+ {
+ EBIAlfaFold.addAlphaFoldPAEToSequence(
+ af.getCurrentView().getAlignment(), paeFile,
+ subVal.index,
+ "seqid".equals(subVal.keyName) ? subVal.keyValue
+ : null);
+ // required to readjust the height and position of the pAE
+ // annotation
+ }