X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAADisorderClient.java;h=b877d206a33eca95a5241e359f52cdd6861e98a5;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=dfb13a6ecd99a66bd96f91b9f54b3771ab4a4c77;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java index dfb13a6..b877d20 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"; @@ -104,34 +103,29 @@ public class AADisorderClient extends JabawsCalcWorker implements Map fmap; featureMap.put(compbio.ws.client.Services.IUPredWS.toString(), fmap = new HashMap()); - fmap.put("Glob", new String[] - { "Globular Domain", "Predicted globular domain" }); + 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" }); + 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.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.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); @@ -142,39 +136,27 @@ public class AADisorderClient extends JabawsCalcWorker implements 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.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.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 @@ -249,23 +231,23 @@ 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 && last != Float.NaN) + if (last != val && !Float.isNaN(last)) { fc.put(sf.getType(), sf); } @@ -285,8 +267,7 @@ public class AADisorderClient extends JabawsCalcWorker implements 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 @@ -326,8 +307,8 @@ public class AADisorderClient extends JabawsCalcWorker implements annot.description += "
" + threshNote; } annot.description += ""; - Color col = new UserColourScheme(typeName) - .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) @@ -355,13 +336,13 @@ 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); }