import jalview.analysis.AlignmentUtils;
import jalview.api.AlignmentViewPanel;
import jalview.bin.ArgParser.Arg;
import jalview.analysis.AlignmentUtils;
import jalview.api.AlignmentViewPanel;
import jalview.bin.ArgParser.Arg;
-import jalview.bin.ArgParser.ArgValues;
-import jalview.bin.ArgParser.SubVal;
+import jalview.bin.ArgParser.ArgValue;
+import jalview.bin.ArgParser.ArgValuesMap;
+import jalview.bin.ArgParser.SubVals;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
// get kind of temperature factor annotation
StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
// get kind of temperature factor annotation
StructureImportSettings.TFType tempfacType = TFType.DEFAULT;
- tempfacType = StructureImportSettings.TFType.valueOf(ArgParser
- .getValue(m, Arg.TEMPFAC).toUpperCase(Locale.ROOT));
+ tempfacType = StructureImportSettings.TFType
+ .valueOf(avm.getArgValue(Arg.TEMPFAC).getValue()
+ .toUpperCase(Locale.ROOT));
- if (ArgParser.getValue(m, Arg.TITLE) != null)
- af.setTitle(ArgParser.getValue(m, Arg.TITLE));
+ if (avm.hasValue(Arg.TITLE))
+ af.setTitle(avm.getValue(Arg.TITLE));
{
AlignmentAnnotation aa = AlignmentUtils
.getFirstSequenceAnnotationOfType(
af.getCurrentView().getAlignment(),
AlignmentAnnotation.LINE_GRAPH);
{
AlignmentAnnotation aa = AlignmentUtils
.getFirstSequenceAnnotationOfType(
af.getCurrentView().getAlignment(),
AlignmentAnnotation.LINE_GRAPH);
- SubVal subVal = ArgParser.getSubVal(val);
- File paeFile = new File(subVal.content);
+ String val = av.getValue();
+ SubVals subVals = ArgParser.getSubVals(val);
+ File paeFile = new File(subVals.getContent());
EBIAlfaFold.addAlphaFoldPAEToStructure(
af.getCurrentView().getAlignment(), paeFile,
EBIAlfaFold.addAlphaFoldPAEToStructure(
af.getCurrentView().getAlignment(), paeFile,
EBIAlfaFold.addAlphaFoldPAEToStructure(
af.getCurrentView().getAlignment(), paeFile,
EBIAlfaFold.addAlphaFoldPAEToStructure(
af.getCurrentView().getAlignment(), paeFile,
EBIAlfaFold.addAlphaFoldPAEToSequence(
af.getCurrentView().getAlignment(), paeFile,
EBIAlfaFold.addAlphaFoldPAEToSequence(
af.getCurrentView().getAlignment(), paeFile,