// Show secondary structure annotations?
boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
- Arg.SSANNOTATIONS, av.getSubVals(), null,
+ Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
"STRUCT_FROM_PDB", true);
af.setAnnotationsVisibility(showSSAnnotations, true, false);
af.getCurrentView().getAlignment(), hideThese, null,
false, false);
}
- else
- /*
- * comment out hacky approach up to here and add this line: if
- * (showTemperatureFactor)
- */
- {
- /*
- if (avm.containsArg(Arg.TEMPFAC_LABEL))
- {
- AlignmentAnnotation aa = AlignmentUtils
- .getFirstSequenceAnnotationOfType(
- af.getCurrentView().getAlignment(),
- AlignmentAnnotation.LINE_GRAPH);
- String label = avm.getValue(Arg.TEMPFAC_LABEL);
- if (aa != null)
- {
- aa.label = label;
- }
- else
- {
- Console.info(
- "Could not find annotation to apply tempfac_label '"
- + label);
- }
- }
- */
- }
// store the AlignFrame for this id
afMap.put(id, af);
String structureFilepath = structureFile.getAbsolutePath();
// get PAEMATRIX file and label from subvals or Arg.PAEMATRIX
- String paeFilepath = subVals.getWithSubstitutions(argParser, id,
- "paematrix");
- ArgValue paeAv = getArgAssociatedWithStructure(Arg.PAEMATRIX, avm,
- af, structureFilepath);
- if (paeFilepath == null && paeAv != null)
+ String paeFilepath = ArgParser
+ .getFromSubValArgOrPrefWithSubstitutions(argParser, avm,
+ Arg.PAEMATRIX, Position.AFTER, av, subVals, null,
+ null, null);
+ if (paeFilepath != null)
{
- SubVals sv = paeAv.getSubVals();
- File paeFile = new File(sv.getContent());
+ File paeFile = new File(paeFilepath);
try
{
// showing annotations from structure file or not
boolean ssFromStructure = ArgParser.getFromSubValArgOrPref(avm,
- Arg.SSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
+ Arg.SHOWSSANNOTATIONS, subVals, null, "STRUCT_FROM_PDB",
true);
// get TEMPFAC type from subvals or Arg.TEMPFAC in case user Adds
return null;
if (subVals != null)
{
- if (subVals.has("seqid"))
+ if (subVals.has(Arg.SEQID.getName()))
{
- seq = al.findName(subVals.get("seqid"));
+ seq = al.findName(subVals.get(Arg.SEQID.getName()));
}
else if (-1 < subVals.getIndex()
&& subVals.getIndex() < al.getSequences().size())