ArgValuesMap avm = argParser.getLinkedArgs(id);
theseArgsWereParsed = true;
theseArgsWereParsed &= processLinked(id);
+ boolean processLinkedOkay = theseArgsWereParsed;
theseArgsWereParsed &= processImages(id);
+ if (processLinkedOkay)
+ theseArgsWereParsed &= processOutput(id);
// close ap
if (avm.getBoolean(Arg.CLOSE))
return true;
}
+ protected boolean processOutput(String id)
+ {
+ ArgValuesMap avm = argParser.getLinkedArgs(id);
+ AlignFrame af = afMap.get(id);
+
+ if (af == null)
+ {
+ Console.warn("Did not have an alignment window for id=" + id);
+ return false;
+ }
+
+ if (avm.containsArg(Arg.OUTPUT))
+ {
+ for (ArgValue av : avm.getArgValueList(Arg.OUTPUT))
+ {
+ String val = av.getValue();
+ SubVals subVal = av.getSubVals();
+ String type = null; // default
+ String fileName = subVal.getContent();
+ File file = new File(fileName);
+ }
+ }
+ return true;
+ }
+
private SequenceI getSpecifiedSequence(AlignFrame af, SubVals subId)
{
if (subId == null)