{
public AnnotationFile()
{
- super(new Class[]
- { AlignmentI.class });
+ super(new Class[] { AlignmentI.class });
}
/**
AlignmentI al = rj.getAlignmentForInput(token, molType.MIX);
if (format.equals(JVANNOT))
{
- return new StringBody(
- new jalview.io.AnnotationFile()
- .printAnnotationsForAlignment(al));
+ return new StringBody(new jalview.io.AnnotationFile()
+ .printAnnotationsForAlignment(al));
}
else
{
"Unrecognised format for exporting Annotation (" + format
+ ")");
}
- return new StringBody(
- new jalview.io.AnnotationFile().printCSVAnnotations(al
- .getAlignmentAnnotation()));
+ return new StringBody(new jalview.io.AnnotationFile()
+ .printCSVAnnotations(al.getAlignmentAnnotation()));
}
}
if (tok.startsWith("format"))
{
- for (String fmt : new String[]
- { CSVANNOT, JVANNOT })
+ for (String fmt : new String[] { CSVANNOT, JVANNOT })
{
if (val.equalsIgnoreCase(fmt))
{
}
warnings.append("Invalid annotation file format '" + val
+ "'. Must be one of (");
- for (String fmt : new String[]
- { CSVANNOT, JVANNOT })
+ for (String fmt : new String[] { CSVANNOT, JVANNOT })
{
warnings.append(" " + fmt);
}
{
// TODO - consider disregarding base options here.
List<OptionI> lst = getBaseOptions();
- lst.add(new Option("format", "Alignment annotation upload format",
- true, JVANNOT, format, Arrays.asList(new String[]
+ lst.add(new Option("format", "Alignment annotation upload format", true,
+ JVANNOT, format, Arrays.asList(new String[]
{ JVANNOT, CSVANNOT }), null));
return lst;
}