/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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.
*
*/
package jalview.ws.jws2;
-import jalview.api.AlignCalcWorkerI;
import jalview.api.FeatureColourI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.schemes.FeatureColour;
-import jalview.schemes.UserColourScheme;
+import jalview.util.ColorUtils;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
AlignFrame af;
public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
- WsParamSetI preset, List<Argument> paramset)
+ WsParamSetI thePreset, List<Argument> paramset)
{
- super(sh, alignFrame, preset, paramset);
+ super(sh, alignFrame, thePreset, paramset);
af = alignFrame;
typeName = sh.action;
methodName = sh.serviceType;
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.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(),
{
Cache.log
.info("Couldn't recover disorder prediction for sequence "
- + seq.getName()
- + "(Prediction name was "
- + seqId
+ + seq.getName() + "(Prediction name was " + seqId
+ ")"
+ "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
}
}
if (vals.hasNext())
{
+ val = vals.next().floatValue();
sf = new SequenceFeature(type[0], type[1],
- base + rn.from, base + rn.to, val = vals.next()
- .floatValue(), methodName);
+ base + rn.from, base + rn.to, val, methodName);
}
else
{
- sf = new SequenceFeature(type[0], type[1], null, 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))
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
: annotTypeMap.get(scr.getMethod());
- annot.visible = (styleMap == null || styleMap.get(INVISIBLE) == null);
+ annot.visible = (styleMap == null
+ || styleMap.get(INVISIBLE) == null);
double[] thrsh = (styleMap == null) ? null
: (double[]) styleMap.get(THRESHOLD);
float[] range = (styleMap == null) ? null
annot.description += "<br/>" + threshNote;
}
annot.description += "</html>";
- Color col = UserColourScheme.createColourFromName(typeName
- + scr.getMethod());
+ Color col = ColorUtils
+ .createColourFromName(typeName + scr.getMethod());
for (int p = 0, ps = annot.annotations.length; p < ps; p++)
{
if (annot.annotations[p] != null)