package jalview.ws.jws2;
import jalview.api.AlignCalcWorkerI;
+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.ws.jws2.jabaws2.Jws2Instance;
import jalview.ws.params.WsParamSetI;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Hashtable;
import java.util.Iterator;
import java.util.List;
-
+import java.util.Map;
import compbio.data.sequence.Range;
import compbio.data.sequence.Score;
import compbio.data.sequence.ScoreManager.ScoreHolder;
import compbio.metadata.Argument;
+import compbio.ws.client.Services;
public class AADisorderClient extends JabawsAlignCalcWorker implements
AlignCalcWorkerI
{
+ private static final String THRESHOLD = "THRESHOLD";
+
String typeName;
String methodName;
return "Submitting amino acid sequences for disorder prediction.";
}
+ private static Map<String, Map<String, String[]>> featureMap;
+
+ 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
+ // to edit
+ featureMap = new HashMap<String, Map<String, String[]>>();
+ 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" });
+ 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" });
+ 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" });
+ 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.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.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("HOTLOOPS").put(THRESHOLD, new double[]
+ { 1, 0.6 });
+ amap.get("REM465").put(THRESHOLD, new double[]
+ { 1, 0.1204 });
+
+ 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("Short").put(THRESHOLD, new double[]
+ { 1, 0.5 });
+ 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 });
+ }
+
@Override
public void updateResultAnnotation(boolean immediate)
{
if (immediate || !calcMan.isWorking(this) && scoremanager != null)
{
+ Map<String, String[]> featureTypeMap = featureMap
+ .get(service.serviceType);
+ 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>();
+ /**
+ * grouping for any annotation rows created
+ */
+ int graphGroup = 1;
+ if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
+ {
+ for (AlignmentAnnotation ala : alignViewport.getAlignment()
+ .getAlignmentAnnotation())
+ {
+ if (ala.graphGroup > graphGroup)
+ {
+ graphGroup = ala.graphGroup;
+ }
+ }
+ }
+
for (String seqId : seqNames.keySet())
{
- SequenceI dseq, seq = seqNames.get(seqId);
+ boolean sameGroup = false;
+ SequenceI dseq, aseq, seq = seqNames.get(seqId);
int base = seq.getStart() - 1;
+ aseq = seq;
while ((dseq = seq).getDatasetSequence() != null)
{
seq = seq.getDatasetSequence();
}
;
ScoreHolder scores = scoremanager.getAnnotationForSequence(seqId);
-
+ float last = Float.NaN, val = Float.NaN;
+ int lastAnnot = ourAnnot.size();
for (Score scr : scores.scores)
{
{
SequenceFeature sf;
+ String[] type = featureTypeMap.get(scr.getMethod());
+ if (type == null)
+ {
+ // create a default type for this feature
+ type = new String[]
+ { typeName + " (" + scr.getMethod() + ")",
+ service.getActionText() };
+ }
if (vals.hasNext())
{
- sf = new SequenceFeature(typeName + "(" + scr.getMethod()
- + ")", "Disordered Region", base + rn.from, base
- + rn.to, vals.next().floatValue(), methodName);
+ sf = new SequenceFeature(type[0], type[1], base + rn.from,
+ base + rn.to, val = vals.next().floatValue(),
+ methodName);
}
else
{
- sf = new SequenceFeature(typeName + "(" + scr.getMethod()
- + ")", "Disordered Region", null, base + rn.from,
- base + rn.to, methodName);
+ sf = new SequenceFeature(type[0], type[1], null, base
+ + rn.from, base + rn.to, methodName);
}
dseq.addSequenceFeature(sf);
+ if (last != val && last != Float.NaN)
+ {
+ fc.put(sf.getType(), sf);
+ }
+ last = val;
dispFeatures = true;
}
}
else
{
- Iterator<Float> vals = scr.getScores().iterator();
- for (int start = base + 1; vals.hasNext(); start++)
+ if (scr.getScores().size() == 0)
{
- SequenceFeature sf = new SequenceFeature(typeName + "("
- + scr.getMethod() + ")", "Disordered Region", start,
- start, vals.next().floatValue(), methodName);
- dseq.addSequenceFeature(sf);
- dispFeatures = true;
+ continue;
+ }
+ AlignmentAnnotation annot = createAnnotationRowsForScores(
+ ourAnnot, service.serviceType + " (" + scr.getMethod()
+ + ")",
+ service.getServiceTypeURI() + "/" + scr.getMethod(),
+ aseq, base + 1, scr);
+ annot.graph = AlignmentAnnotation.LINE_GRAPH;
+ annot.visible = (annotTypeMap == null
+ || annotTypeMap.get(scr.getMethod()) == null || annotTypeMap
+ .get(scr.getMethod()).get(INVISIBLE) == null);
+ double[] thrsh = (annotTypeMap == null || annotTypeMap.get(scr
+ .getMethod()) == null) ? null : (double[]) annotTypeMap
+ .get(scr.getMethod()).get(THRESHOLD);
+ if (annotTypeMap == null
+ || annotTypeMap.get(scr.getMethod()) == null
+ || annotTypeMap.get(scr.getMethod()).get(DONTCOMBINE) == null)
+ {
+ {
+ if (!sameGroup)
+ {
+ graphGroup++;
+ sameGroup = true;
+ }
+
+ annot.graphGroup = graphGroup;
+ }
+ }
+
+ annot.description = "<html>" + service.getActionText()
+ + " - raw scores";
+ if (thrsh != null)
+ {
+ String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
+ + thrsh[1] + " indicates disorder";
+ annot.threshold = new GraphLine((float) thrsh[1], threshNote,
+ Color.red);
+ annot.description += "<br/>" + threshNote;
+ }
+ annot.description += "</html>";
+ Color col = new UserColourScheme(typeName)
+ .createColourFromName(typeName + scr.getMethod());
+ for (int p = 0, ps = annot.annotations.length; p < ps; p++)
+ {
+ if (annot.annotations[p] != null)
+ {
+ annot.annotations[p].colour = col;
+ }
}
+ annot._linecolour = col;
}
}
+ if (lastAnnot + 1 == ourAnnot.size())
+ {
+ // remove singleton alignment annotation row
+ ourAnnot.get(lastAnnot).graphGroup = -1;
+ }
}
{
if (dispFeatures)
{
- // TODO: configure feature display settings for added types if they don't already exist
-
- af.alignPanel.av.setShowSequenceFeatures(true);
+ jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
+ .cloneFeatureRenderer();
+ for (String ft : fc.keySet())
+ {
+ Object gc = fr.getFeatureStyle(ft);
+ if (gc instanceof Color)
+ {
+ // 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);
+ ggc.setAutoScaled(true);
+ fr.setColour(ft, ggc);
+ }
+ }
+ // TODO: JAL-1150 - create sequence feature settings API for defining
+ // styles and enabling/disabling feature overlay on alignment panel
+ ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
+ if (af.alignPanel == ap)
+ {
+ // only do this if the alignFrame is currently showing this view.
+ af.setShowSeqFeatures(true);
+ }
ap.paintAlignment(true);
}
+ if (ourAnnot.size() > 0)
+ {
+ // Modify the visible annotation on the alignment viewport with the
+ // new alignment annotation rows created.
+ updateOurAnnots(ourAnnot);
+ ap.adjustAnnotationHeight();
+ }
}
- /*
- * else { ap.paintAlignment(true); }
- */
}
}
git://source.jalview.org / jalview.git / blobdiff