X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAADisorderClient.java;h=ea225d42e8b2f4ec05e7ff3eb1b04a26142a85a5;hb=b57a02c25e335d033c97f8a6bacd6b54f62bd2b6;hp=baec45808176b807fa81b2e2042ce7bd09ff7b02;hpb=75b182d30793435148560fcdab3c6501bf7fd62a;p=jalview.git diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java index baec458..ea225d4 100644 --- a/src/jalview/ws/jws2/AADisorderClient.java +++ b/src/jalview/ws/jws2/AADisorderClient.java @@ -1,24 +1,37 @@ 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; @@ -48,24 +61,121 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements return "Submitting amino acid sequences for disorder prediction."; } + private static Map> featureMap; + + private static Map>> 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>(); + Map fmap; + featureMap.put(compbio.ws.client.Services.IUPredWS.toString(), + fmap = new HashMap()); + fmap.put("Glob", new String[] + { "Globular Domain", "Predicted globular domain" }); + featureMap.put(compbio.ws.client.Services.JronnWS.toString(), + fmap = new HashMap()); + featureMap.put(compbio.ws.client.Services.DisemblWS.toString(), + 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()); + fmap.put("GlobDoms", new String[] + { "Globular Domain", "Predicted globular domain" }); + fmap.put("Disorder", new String[] + { "Protein Disorder", "Probable unstructured peptide region" }); + Map> amap; + annotMap = new HashMap>>(); + annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(), + amap = new HashMap>()); + amap.put("Dydx", new HashMap()); + amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE); + amap.get("Dydx").put(THRESHOLD, new double[] + { 1, 0 }); + amap.put("SmoothedScore", new HashMap()); + amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE); + amap.put("RawScore", new HashMap()); + amap.get("RawScore").put(INVISIBLE, INVISIBLE); + annotMap.put(compbio.ws.client.Services.DisemblWS.toString(), + amap = new HashMap>()); + amap.put("COILS", new HashMap()); + amap.put("HOTLOOPS", new HashMap()); + amap.put("REM465", new HashMap()); + 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>()); + amap.put("Long", new HashMap()); + amap.put("Short", new HashMap()); + 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>()); + amap.put("JRonn", new HashMap()); + amap.get("JRonn").put(THRESHOLD, new double[] + { 1, 0.5 }); + } + @Override public void updateResultAnnotation(boolean immediate) { if (immediate || !calcMan.isWorking(this) && scoremanager != null) { + Map featureTypeMap = featureMap + .get(service.serviceType); + Map> annotTypeMap = annotMap + .get(service.serviceType); boolean dispFeatures = false; + Map fc = new Hashtable(); + List ourAnnot = new ArrayList(); + /** + * 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) { @@ -77,48 +187,132 @@ public class AADisorderClient extends JabawsAlignCalcWorker implements { 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 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 = "" + 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 += "
" + threshNote; + } + annot.description += ""; + 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); } - */ } }