X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAADisorderClient.java;h=a1b8e7ac32eb64b229724a37ba6437f6b642a5c3;hb=e42eed3a0089a8a064560df4cf17a5021fd1e16a;hp=7d1c5142e904a3dcf0adfb2a72d51551651b82a8;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java index 7d1c514..a1b8e7a 100644 --- a/src/jalview/ws/jws2/AADisorderClient.java +++ b/src/jalview/ws/jws2/AADisorderClient.java @@ -1,6 +1,6 @@ /* - * 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. * @@ -20,7 +20,6 @@ */ package jalview.ws.jws2; -import jalview.api.AlignCalcWorkerI; import jalview.api.FeatureColourI; import jalview.bin.Cache; import jalview.datamodel.AlignmentAnnotation; @@ -29,7 +28,7 @@ import jalview.datamodel.SequenceFeature; 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; @@ -63,9 +62,9 @@ public class AADisorderClient extends JabawsCalcWorker 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; @@ -100,29 +99,32 @@ public class AADisorderClient extends JabawsCalcWorker { // 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 = 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 }); @@ -133,7 +135,7 @@ public class AADisorderClient extends JabawsCalcWorker 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()); @@ -146,7 +148,7 @@ public class AADisorderClient extends JabawsCalcWorker 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 }); @@ -154,7 +156,7 @@ public class AADisorderClient extends JabawsCalcWorker 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 }); @@ -171,8 +173,8 @@ public class AADisorderClient extends JabawsCalcWorker 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 */ @@ -207,9 +209,7 @@ public class AADisorderClient extends JabawsCalcWorker { 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."); } @@ -238,14 +238,14 @@ public class AADisorderClient extends JabawsCalcWorker } 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)) @@ -268,13 +268,15 @@ public class AADisorderClient extends JabawsCalcWorker 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 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 @@ -308,8 +310,8 @@ public class AADisorderClient extends JabawsCalcWorker annot.description += "
" + threshNote; } annot.description += ""; - 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) @@ -342,8 +344,9 @@ public class AADisorderClient extends JabawsCalcWorker { // set graduated color as fading to white for minimum, and // autoscaling to values on alignment - FeatureColourI ggc = new FeatureColour(Color.white, - gc.getColour(), 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); } @@ -356,7 +359,6 @@ public class AADisorderClient extends JabawsCalcWorker // only do this if the alignFrame is currently showing this view. af.setShowSeqFeatures(true); } - ap.paintAlignment(true); } if (ourAnnot.size() > 0) { @@ -364,6 +366,7 @@ public class AADisorderClient extends JabawsCalcWorker // new alignment annotation rows created. updateOurAnnots(ourAnnot); ap.adjustAnnotationHeight(); + ap.paintAlignment(true, true); } } }