/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
Map<String, String[]> fmap;
featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
fmap = new HashMap<String, String[]>());
- fmap.put("Glob", new String[]
- { "Globular Domain", "Predicted globular domain" });
+ fmap.put("Glob", new String[] { "Globular Domain",
+ "Predicted globular domain" });
featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
fmap = new HashMap<String, String[]>());
featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
fmap = new HashMap<String, String[]>());
- fmap.put("REM465", new String[]
- { "REM465", "Missing density" });
- fmap.put("HOTLOOPS", new String[]
- { "HOTLOOPS", "Flexible loops" });
- fmap.put("COILS", new String[]
- { "COILS", "Random coil" });
+ fmap.put("REM465", new String[] { "REM465", "Missing density" });
+ fmap.put("HOTLOOPS", new String[] { "HOTLOOPS", "Flexible loops" });
+ fmap.put("COILS", new String[] { "COILS", "Random coil" });
featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
fmap = new HashMap<String, String[]>());
- fmap.put("GlobDoms", new String[]
- { "Globular Domain", "Predicted globular domain" });
- fmap.put("Disorder", new String[]
- { "Protein Disorder", "Probable unstructured peptide region" });
+ fmap.put("GlobDoms", new String[] { "Globular Domain",
+ "Predicted globular domain" });
+ fmap.put("Disorder", new String[] { "Protein Disorder",
+ "Probable unstructured peptide region" });
Map<String, Map<String, Object>> amap;
annotMap = new HashMap<String, Map<String, Map<String, Object>>>();
annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
amap = new HashMap<String, Map<String, Object>>());
amap.put("Dydx", new HashMap<String, Object>());
amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
- amap.get("Dydx").put(THRESHOLD, new double[]
- { 1, 0 });
- amap.get("Dydx").put(RANGE, new float[]
- { -1, +1 });
+ amap.get("Dydx").put(THRESHOLD, new double[] { 1, 0 });
+ amap.get("Dydx").put(RANGE, new float[] { -1, +1 });
amap.put("SmoothedScore", new HashMap<String, Object>());
amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
amap.put("COILS", new HashMap<String, Object>());
amap.put("HOTLOOPS", new HashMap<String, Object>());
amap.put("REM465", new HashMap<String, Object>());
- amap.get("COILS").put(THRESHOLD, new double[]
- { 1, 0.516 });
- amap.get("COILS").put(RANGE, new float[]
- { 0, 1 });
-
- amap.get("HOTLOOPS").put(THRESHOLD, new double[]
- { 1, 0.6 });
- amap.get("HOTLOOPS").put(RANGE, new float[]
- { 0, 1 });
- amap.get("REM465").put(THRESHOLD, new double[]
- { 1, 0.1204 });
- amap.get("REM465").put(RANGE, new float[]
- { 0, 1 });
+ amap.get("COILS").put(THRESHOLD, new double[] { 1, 0.516 });
+ amap.get("COILS").put(RANGE, new float[] { 0, 1 });
+
+ amap.get("HOTLOOPS").put(THRESHOLD, new double[] { 1, 0.6 });
+ amap.get("HOTLOOPS").put(RANGE, new float[] { 0, 1 });
+ amap.get("REM465").put(THRESHOLD, new double[] { 1, 0.1204 });
+ amap.get("REM465").put(RANGE, new float[] { 0, 1 });
annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
amap = new HashMap<String, Map<String, Object>>());
amap.put("Long", new HashMap<String, Object>());
amap.put("Short", new HashMap<String, Object>());
- amap.get("Long").put(THRESHOLD, new double[]
- { 1, 0.5 });
- amap.get("Long").put(RANGE, new float[]
- { 0, 1 });
- amap.get("Short").put(THRESHOLD, new double[]
- { 1, 0.5 });
- amap.get("Short").put(RANGE, new float[]
- { 0, 1 });
+ amap.get("Long").put(THRESHOLD, new double[] { 1, 0.5 });
+ amap.get("Long").put(RANGE, new float[] { 0, 1 });
+ amap.get("Short").put(THRESHOLD, new double[] { 1, 0.5 });
+ amap.get("Short").put(RANGE, new float[] { 0, 1 });
annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
amap = new HashMap<String, Map<String, Object>>());
amap.put("JRonn", new HashMap<String, Object>());
- amap.get("JRonn").put(THRESHOLD, new double[]
- { 1, 0.5 });
- amap.get("JRonn").put(RANGE, new float[]
- { 0, 1 });
+ amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5 });
+ amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
}
@Override
if (type == null)
{
// create a default type for this feature
- type = new String[]
- { typeName + " (" + scr.getMethod() + ")",
+ type = new String[] {
+ typeName + " (" + scr.getMethod() + ")",
service.getActionText() };
}
if (vals.hasNext())
+ rn.from, base + rn.to, methodName);
}
dseq.addSequenceFeature(sf);
- if (last != val && last != Float.NaN)
+ if (last != val && !Float.isNaN(last))
{
fc.put(sf.getType(), sf);
}
typename = service.serviceType + " ("
+ scr.getMethod() + ")",
calcName = service.getServiceTypeURI() + "/"
- + scr.getMethod(),
- aseq, base + 1, scr);
+ + scr.getMethod(), aseq, base + 1, scr);
annot.graph = AlignmentAnnotation.LINE_GRAPH;
Map<String, Object> styleMap = (annotTypeMap == null) ? null