private static final String RANGE = "RANGE";
- String typeName;
+ private String typeName;
- String methodName;
+ private String methodName;
- String groupName;
+ // private String groupName;
AlignFrame af;
- public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
- WsParamSetI thePreset, List<Argument> paramset)
- {
- super(sh, alignFrame, thePreset, paramset);
- af = alignFrame;
- typeName = sh.action;
- methodName = sh.serviceType;
+ private final static Map<String, Map<String, String[]>> featureMap;
- submitGaps = false;
- alignedSeqs = false;
- nucleotidesAllowed = false;
- proteinAllowed = true;
- bySequence = true;
- }
+ private final static Map<String, Map<String, Map<String, Object>>> annotMap;
- @Override
- public String getServiceActionText()
- {
- return "Submitting amino acid sequences for disorder prediction.";
- }
+ private final static String DONTCOMBINE = "DONTCOMBINE";
- @Override
- boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
- {
- return (seqs.size() > 0);
- }
-
- private static Map<String, Map<String, String[]>> featureMap;
+ private final static String INVISIBLE = "INVISIBLE";
- private static Map<String, Map<String, Map<String, Object>>> annotMap;
-
- private static String DONTCOMBINE = "DONTCOMBINE";
-
- private static String INVISIBLE = "INVISIBLE";
static
{
// TODO: turn this into some kind of configuration file that's a bit easier
amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
}
+ public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
+ WsParamSetI thePreset, List<Argument> paramset)
+ {
+ super(sh, alignFrame, thePreset, paramset);
+ af = alignFrame;
+ typeName = sh.action;
+ methodName = sh.serviceType;
+
+ submitGaps = false;
+ alignedSeqs = false;
+ nucleotidesAllowed = false;
+ proteinAllowed = true;
+ bySequence = true;
+ }
+
+ @Override
+ public String getServiceActionText()
+ {
+ return "Submitting amino acid sequences for disorder prediction.";
+ }
+
+ @Override
+ boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
+ {
+ return (seqs.size() > 0);
+ }
+
@Override
public void updateResultAnnotation(boolean immediate)
{
if (vals.hasNext())
{
val = vals.next().floatValue();
- sf = new SequenceFeature(type[0], type[1],
- base + rn.from, base + rn.to, val, methodName);
+ sf = new SequenceFeature(type[0], type[1], base + rn.from,
+ base + rn.to, val, methodName);
}
else
{
- sf = new SequenceFeature(type[0], type[1],
- base + rn.from, base + rn.to, methodName);
+ sf = new SequenceFeature(type[0], type[1], base + rn.from,
+ base + rn.to, methodName);
}
dseq.addSequenceFeature(sf);
if (last != val && !Float.isNaN(last))