X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fjws2%2FAADisorderClient.java;h=887a5d93e20f049a5177edf76e4be5da74b79f1b;hb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;hp=630c974989abc87ca726ac363ca3ab2468dfad16;hpb=2f4f1d8fb6878271b64f327bc58c895f458137af;p=jalview.git diff --git a/src/jalview/ws/jws2/AADisorderClient.java b/src/jalview/ws/jws2/AADisorderClient.java index 630c974..887a5d9 100644 --- a/src/jalview/ws/jws2/AADisorderClient.java +++ b/src/jalview/ws/jws2/AADisorderClient.java @@ -1,32 +1,34 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1) - * Copyright (C) 2014 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. * * Jalview is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. * * Jalview is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty * of MERCHANTABILITY or FITNESS FOR A PARTICULAR * PURPOSE. See the GNU General Public License for more details. * - * You should have received a copy of the GNU General Public License along with Jalview. If not, see . + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . * The Jalview Authors are detailed in the 'AUTHORS' file. */ 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; @@ -37,17 +39,20 @@ import java.util.Hashtable; import java.util.Iterator; import java.util.List; import java.util.Map; + +import compbio.data.sequence.FastaSequence; import compbio.data.sequence.Range; 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"; + private static final String RANGE = "RANGE"; + String typeName; String methodName; @@ -57,9 +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; @@ -77,6 +82,12 @@ public class AADisorderClient extends JabawsCalcWorker implements return "Submitting amino acid sequences for disorder prediction."; } + @Override + boolean checkValidInputSeqs(boolean dynamic, List seqs) + { + return (seqs.size() > 0); + } + private static Map> featureMap; private static Map>> annotMap; @@ -88,65 +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(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("HOTLOOPS").put(THRESHOLD, new double[] - { 1, 0.6 }); - amap.get("REM465").put(THRESHOLD, new double[] - { 1, 0.1204 }); + 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("Short").put(THRESHOLD, new double[] - { 1, 0.5 }); + 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(THRESHOLD, new double[] { 1, 0.5 }); + amap.get("JRonn").put(RANGE, new float[] { 0, 1 }); } @Override @@ -160,8 +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 */ @@ -182,17 +195,27 @@ public class AADisorderClient extends JabawsCalcWorker implements { boolean sameGroup = false; SequenceI dseq, aseq, seq = seqNames.get(seqId); - int base = seq.findPosition(start)-1; + int base = seq.findPosition(start) - 1; aseq = seq; while ((dseq = seq).getDatasetSequence() != null) { seq = seq.getDatasetSequence(); } - ; - ScoreHolder scores = scoremanager.getAnnotationForSequence(seqId); + ScoreHolder scores = null; + try + { + scores = scoremanager.getAnnotationForSequence(seqId); + } catch (Exception q) + { + Cache.info("Couldn't recover disorder prediction for sequence " + + seq.getName() + "(Prediction name was " + seqId + + ")" + + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail."); + } float last = Float.NaN, val = Float.NaN; int lastAnnot = ourAnnot.size(); - if (scores!=null && scores.scores!=null) { + if (scores != null && scores.scores != null) + { for (Score scr : scores.scores) { @@ -208,23 +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); } @@ -238,22 +261,31 @@ public class AADisorderClient extends JabawsCalcWorker implements { continue; } + String typename, calcName; AlignmentAnnotation annot = createAnnotationRowsForScores( ourAnnot, - service.serviceType + " (" + scr.getMethod() + ")", - service.getServiceTypeURI() + "/" + scr.getMethod(), + typename = service.serviceType + " (" + + scr.getMethod() + ")", + calcName = 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) + + Map styleMap = (annotTypeMap == null) ? null + : annotTypeMap.get(scr.getMethod()); + + annot.visible = (styleMap == null + || styleMap.get(INVISIBLE) == null); + double[] thrsh = (styleMap == null) ? null + : (double[]) styleMap.get(THRESHOLD); + float[] range = (styleMap == null) ? null + : (float[]) styleMap.get(RANGE); + if (range != null) + { + annot.graphMin = range[0]; + annot.graphMax = range[1]; + } + if (styleMap == null || styleMap.get(DONTCOMBINE) == null) { { if (!sameGroup) @@ -277,7 +309,7 @@ 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++) { @@ -287,6 +319,9 @@ public class AADisorderClient extends JabawsCalcWorker implements } } annot._linecolour = col; + // finally, update any dataset annotation + replaceAnnotationOnAlignmentWith(annot, typename, calcName, + aseq); } } } @@ -299,17 +334,18 @@ public class AADisorderClient extends JabawsCalcWorker implements { if (dispFeatures) { - jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap) + jalview.api.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap) .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(gc.getColour(), + Color.white, gc.getColour(), Color.white, + Float.MIN_VALUE, Float.MAX_VALUE); ggc.setAutoScaled(true); fr.setColour(ft, ggc); } @@ -322,7 +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) { @@ -330,9 +365,17 @@ public class AADisorderClient extends JabawsCalcWorker implements // new alignment annotation rows created. updateOurAnnots(ourAnnot); ap.adjustAnnotationHeight(); + ap.paintAlignment(true, true); } } } } + @Override + public String getCalcId() + { + // Disorder predictions are not dynamically updated so we return null + return null; + } + }