/*
- * 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.
*
*/
package jalview.ws.jws2;
-import jalview.api.AlignCalcWorkerI;
+import jalview.api.FeatureColourI;
import jalview.bin.Cache;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.GraphLine;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
-import jalview.schemes.GraduatedColor;
-import jalview.schemes.UserColourScheme;
+import jalview.schemes.FeatureColour;
+import jalview.util.ColorUtils;
import jalview.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
import compbio.data.sequence.ScoreManager.ScoreHolder;
import compbio.metadata.Argument;
-public class AADisorderClient extends JabawsCalcWorker implements
- AlignCalcWorkerI
+public class AADisorderClient extends JabawsCalcWorker
{
private static final String THRESHOLD = "THRESHOLD";
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;
{
// TODO: turn this into some kind of configuration file that's a bit easier
// to edit
- featureMap = new HashMap<String, Map<String, String[]>>();
+ featureMap = new HashMap<>();
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 = new HashMap<>());
+ fmap.put("Glob",
+ new String[]
+ { "Globular Domain", "Predicted globular domain" });
featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
- fmap = new HashMap<String, String[]>());
+ fmap = new HashMap<>());
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 = new HashMap<>());
+ 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 = new HashMap<>());
+ 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 = new HashMap<>();
annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
- amap = new HashMap<String, Map<String, Object>>());
+ amap = new HashMap<>());
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("RawScore", new HashMap<String, Object>());
amap.get("RawScore").put(INVISIBLE, INVISIBLE);
annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
- amap = new HashMap<String, Map<String, Object>>());
+ amap = new HashMap<>());
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 = new HashMap<>());
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 = new HashMap<>());
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
Map<String, Map<String, Object>> annotTypeMap = annotMap
.get(service.serviceType);
boolean dispFeatures = false;
- Map<String, Object> fc = new Hashtable<String, Object>();
- List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
+ Map<String, Object> fc = new Hashtable<>();
+ List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
/**
* grouping for any annotation rows created
*/
scores = scoremanager.getAnnotationForSequence(seqId);
} catch (Exception q)
{
- Cache.log
- .info("Couldn't recover disorder prediction for sequence "
- + seq.getName()
- + "(Prediction name was "
- + seqId
+ Cache.info("Couldn't recover disorder prediction for sequence "
+ + seq.getName() + "(Prediction name was " + seqId
+ ")"
+ "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
}
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())
{
+ 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 && last != Float.NaN)
+ if (last != val && !Float.isNaN(last))
{
fc.put(sf.getType(), sf);
}
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 = new UserColourScheme(typeName)
+ Color col = ColorUtils
.createColourFromName(typeName + scr.getMethod());
for (int p = 0, ps = annot.annotations.length; p < ps; p++)
{
.cloneFeatureRenderer();
for (String ft : fc.keySet())
{
- Object gc = fr.getFeatureStyle(ft);
- if (gc instanceof Color)
+ FeatureColourI gc = fr.getFeatureStyle(ft);
+ if (gc.isSimpleColour())
{
// set graduated color as fading to white for minimum, and
// autoscaling to values on alignment
- GraduatedColor ggc = new GraduatedColor(Color.white,
- (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE);
+ FeatureColourI ggc = new FeatureColour(gc.getColour(),
+ Color.white, gc.getColour(), Color.white,
+ Float.MIN_VALUE, Float.MAX_VALUE);
ggc.setAutoScaled(true);
fr.setColour(ft, ggc);
}
// only do this if the alignFrame is currently showing this view.
af.setShowSeqFeatures(true);
}
- ap.paintAlignment(true);
}
if (ourAnnot.size() > 0)
{
// new alignment annotation rows created.
updateOurAnnots(ourAnnot);
ap.adjustAnnotationHeight();
+ ap.paintAlignment(true, true);
}
}
}
git://source.jalview.org / jalview.git / blobdiff