X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAADisorderClient.java;h=9a2316c47b8d479e78dee9a43e2c9de1a79c8162;hb=a57976ba40e1abe6d7c1940386e1a25419ef9c9d;hp=91be2e62969e0256a484d57f9de73bed104e6769;hpb=0873fd1ab406be7ef121f466c7b53e4b6315bbca;p=jalview.git diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java index 91be2e6..9a2316c 100644 --- a/src/jalview/ws/jws2/AADisorderClient.java +++ b/src/jalview/ws/jws2/AADisorderClient.java @@ -20,15 +20,15 @@ */ 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; @@ -46,8 +46,7 @@ import compbio.data.sequence.Score; 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"; @@ -63,9 +62,9 @@ public class AADisorderClient extends JabawsCalcWorker implements AlignFrame af; public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame, - WsParamSetI preset, List paramset) + WsParamSetI thePreset, List paramset) { - super(sh, alignFrame, preset, paramset); + super(sh, alignFrame, thePreset, paramset); af = alignFrame; typeName = sh.action; methodName = sh.serviceType; @@ -100,81 +99,67 @@ public class AADisorderClient extends JabawsCalcWorker implements { // TODO: turn this into some kind of configuration file that's a bit easier // to edit - featureMap = new HashMap>(); + 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" }); + fmap = new HashMap<>()); + fmap.put("Glob", + new String[] + { "Globular Domain", "Predicted globular domain" }); featureMap.put(compbio.ws.client.Services.JronnWS.toString(), - fmap = new HashMap()); + 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" }); + 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" }); + 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 = new HashMap<>(); annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(), - amap = new HashMap>()); + amap = new HashMap<>()); amap.put("Dydx", new HashMap()); 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()); 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 = 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("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>()); + 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("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>()); + amap = new HashMap<>()); amap.put("JRonn", new HashMap()); - 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 @@ -188,8 +173,8 @@ public class AADisorderClient extends JabawsCalcWorker implements Map> annotTypeMap = annotMap .get(service.serviceType); boolean dispFeatures = false; - Map fc = new Hashtable(); - List ourAnnot = new ArrayList(); + Map fc = new Hashtable<>(); + List ourAnnot = new ArrayList<>(); /** * grouping for any annotation rows created */ @@ -224,9 +209,7 @@ public class AADisorderClient extends JabawsCalcWorker implements { 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."); } @@ -249,20 +232,20 @@ public class AADisorderClient extends JabawsCalcWorker implements 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 && !Float.isNaN(last)) @@ -292,7 +275,8 @@ public class AADisorderClient extends JabawsCalcWorker implements Map 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 @@ -326,7 +310,7 @@ public class AADisorderClient extends JabawsCalcWorker implements annot.description += "
" + threshNote; } annot.description += ""; - Color col = new UserColourScheme(typeName) + Color col = ColorUtils .createColourFromName(typeName + scr.getMethod()); for (int p = 0, ps = annot.annotations.length; p < ps; p++) { @@ -355,13 +339,13 @@ public class AADisorderClient extends JabawsCalcWorker implements .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(Color.white, + gc.getColour(), Float.MIN_VALUE, Float.MAX_VALUE); ggc.setAutoScaled(true); fr.setColour(ft, ggc); } @@ -374,7 +358,6 @@ public class AADisorderClient extends JabawsCalcWorker implements // only do this if the alignFrame is currently showing this view. af.setShowSeqFeatures(true); } - ap.paintAlignment(true); } if (ourAnnot.size() > 0) { @@ -382,6 +365,7 @@ public class AADisorderClient extends JabawsCalcWorker implements // new alignment annotation rows created. updateOurAnnots(ourAnnot); ap.adjustAnnotationHeight(); + ap.paintAlignment(true, true); } } }