2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
3 * Copyright (C) 2014 The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ws.jws2;
23 import jalview.api.AlignCalcWorkerI;
24 import jalview.bin.Cache;
25 import jalview.datamodel.AlignmentAnnotation;
26 import jalview.datamodel.GraphLine;
27 import jalview.datamodel.SequenceFeature;
28 import jalview.datamodel.SequenceI;
29 import jalview.gui.AlignFrame;
30 import jalview.schemes.GraduatedColor;
31 import jalview.schemes.UserColourScheme;
32 import jalview.ws.jws2.jabaws2.Jws2Instance;
33 import jalview.ws.params.WsParamSetI;
35 import java.awt.Color;
36 import java.util.ArrayList;
37 import java.util.HashMap;
38 import java.util.Hashtable;
39 import java.util.Iterator;
40 import java.util.List;
43 import compbio.data.sequence.Range;
44 import compbio.data.sequence.Score;
45 import compbio.data.sequence.ScoreManager.ScoreHolder;
46 import compbio.metadata.Argument;
48 public class AADisorderClient extends JabawsCalcWorker implements
52 private static final String THRESHOLD = "THRESHOLD";
54 private static final String RANGE = "RANGE";
64 public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
65 WsParamSetI preset, List<Argument> paramset)
67 super(sh, alignFrame, preset, paramset);
70 methodName = sh.serviceType;
74 nucleotidesAllowed = false;
75 proteinAllowed = true;
80 public String getServiceActionText()
82 return "Submitting amino acid sequences for disorder prediction.";
85 private static Map<String, Map<String, String[]>> featureMap;
87 private static Map<String, Map<String, Map<String, Object>>> annotMap;
89 private static String DONTCOMBINE = "DONTCOMBINE";
91 private static String INVISIBLE = "INVISIBLE";
94 // TODO: turn this into some kind of configuration file that's a bit easier
96 featureMap = new HashMap<String, Map<String, String[]>>();
97 Map<String, String[]> fmap;
98 featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
99 fmap = new HashMap<String, String[]>());
100 fmap.put("Glob", new String[]
101 { "Globular Domain", "Predicted globular domain" });
102 featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
103 fmap = new HashMap<String, String[]>());
104 featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
105 fmap = new HashMap<String, String[]>());
106 fmap.put("REM465", new String[]
107 { "REM465", "Missing density" });
108 fmap.put("HOTLOOPS", new String[]
109 { "HOTLOOPS", "Flexible loops" });
110 fmap.put("COILS", new String[]
111 { "COILS", "Random coil" });
112 featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
113 fmap = new HashMap<String, String[]>());
114 fmap.put("GlobDoms", new String[]
115 { "Globular Domain", "Predicted globular domain" });
116 fmap.put("Disorder", new String[]
117 { "Protein Disorder", "Probable unstructured peptide region" });
118 Map<String, Map<String, Object>> amap;
119 annotMap = new HashMap<String, Map<String, Map<String, Object>>>();
120 annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
121 amap = new HashMap<String, Map<String, Object>>());
122 amap.put("Dydx", new HashMap<String, Object>());
123 amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
124 amap.get("Dydx").put(THRESHOLD, new double[]
126 amap.get("Dydx").put(RANGE, new float[]
129 amap.put("SmoothedScore", new HashMap<String, Object>());
130 amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
131 amap.put("RawScore", new HashMap<String, Object>());
132 amap.get("RawScore").put(INVISIBLE, INVISIBLE);
133 annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
134 amap = new HashMap<String, Map<String, Object>>());
135 amap.put("COILS", new HashMap<String, Object>());
136 amap.put("HOTLOOPS", new HashMap<String, Object>());
137 amap.put("REM465", new HashMap<String, Object>());
138 amap.get("COILS").put(THRESHOLD, new double[]
140 amap.get("COILS").put(RANGE, new float[]
143 amap.get("HOTLOOPS").put(THRESHOLD, new double[]
145 amap.get("HOTLOOPS").put(RANGE, new float[]
147 amap.get("REM465").put(THRESHOLD, new double[]
149 amap.get("REM465").put(RANGE, new float[]
152 annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
153 amap = new HashMap<String, Map<String, Object>>());
154 amap.put("Long", new HashMap<String, Object>());
155 amap.put("Short", new HashMap<String, Object>());
156 amap.get("Long").put(THRESHOLD, new double[]
158 amap.get("Long").put(RANGE, new float[]
160 amap.get("Short").put(THRESHOLD, new double[]
162 amap.get("Short").put(RANGE, new float[]
164 annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
165 amap = new HashMap<String, Map<String, Object>>());
166 amap.put("JRonn", new HashMap<String, Object>());
167 amap.get("JRonn").put(THRESHOLD, new double[]
169 amap.get("JRonn").put(RANGE, new float[]
174 public void updateResultAnnotation(boolean immediate)
177 if (immediate || !calcMan.isWorking(this) && scoremanager != null)
179 Map<String, String[]> featureTypeMap = featureMap
180 .get(service.serviceType);
181 Map<String, Map<String, Object>> annotTypeMap = annotMap
182 .get(service.serviceType);
183 boolean dispFeatures = false;
184 Map<String, Object> fc = new Hashtable<String, Object>();
185 List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
187 * grouping for any annotation rows created
190 if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
192 for (AlignmentAnnotation ala : alignViewport.getAlignment()
193 .getAlignmentAnnotation())
195 if (ala.graphGroup > graphGroup)
197 graphGroup = ala.graphGroup;
202 for (String seqId : seqNames.keySet())
204 boolean sameGroup = false;
205 SequenceI dseq, aseq, seq = seqNames.get(seqId);
206 int base = seq.findPosition(start) - 1;
208 while ((dseq = seq).getDatasetSequence() != null)
210 seq = seq.getDatasetSequence();
212 ScoreHolder scores = null;
215 scores = scoremanager.getAnnotationForSequence(seqId);
216 } catch (Exception q)
219 .info("Couldn't recover disorder prediction for sequence "
221 + "(Prediction name was "
224 + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
226 float last = Float.NaN, val = Float.NaN;
227 int lastAnnot = ourAnnot.size();
228 if (scores != null && scores.scores != null)
230 for (Score scr : scores.scores)
233 if (scr.getRanges() != null && scr.getRanges().size() > 0)
235 Iterator<Float> vals = scr.getScores().iterator();
236 // make features on sequence
237 for (Range rn : scr.getRanges())
241 String[] type = featureTypeMap.get(scr.getMethod());
244 // create a default type for this feature
246 { typeName + " (" + scr.getMethod() + ")",
247 service.getActionText() };
251 sf = new SequenceFeature(type[0], type[1],
252 base + rn.from, base + rn.to, val = vals.next()
253 .floatValue(), methodName);
257 sf = new SequenceFeature(type[0], type[1], null, base
258 + rn.from, base + rn.to, methodName);
260 dseq.addSequenceFeature(sf);
261 if (last != val && last != Float.NaN)
263 fc.put(sf.getType(), sf);
271 if (scr.getScores().size() == 0)
275 AlignmentAnnotation annot = createAnnotationRowsForScores(
277 service.serviceType + " (" + scr.getMethod() + ")",
278 service.getServiceTypeURI() + "/" + scr.getMethod(),
279 aseq, base + 1, scr);
280 annot.graph = AlignmentAnnotation.LINE_GRAPH;
282 Map<String, Object> styleMap = (annotTypeMap == null) ? null
283 : annotTypeMap.get(scr.getMethod());
285 annot.visible = (styleMap == null || styleMap.get(INVISIBLE) == null);
286 double[] thrsh = (styleMap == null) ? null
287 : (double[]) styleMap.get(THRESHOLD);
288 float[] range = (styleMap == null) ? null
289 : (float[]) styleMap.get(RANGE);
292 annot.graphMin = range[0];
293 annot.graphMax = range[1];
295 if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
304 annot.graphGroup = graphGroup;
308 annot.description = "<html>" + service.getActionText()
312 String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
313 + thrsh[1] + " indicates disorder";
314 annot.threshold = new GraphLine((float) thrsh[1],
315 threshNote, Color.red);
316 annot.description += "<br/>" + threshNote;
318 annot.description += "</html>";
319 Color col = new UserColourScheme(typeName)
320 .createColourFromName(typeName + scr.getMethod());
321 for (int p = 0, ps = annot.annotations.length; p < ps; p++)
323 if (annot.annotations[p] != null)
325 annot.annotations[p].colour = col;
328 annot._linecolour = col;
332 if (lastAnnot + 1 == ourAnnot.size())
334 // remove singleton alignment annotation row
335 ourAnnot.get(lastAnnot).graphGroup = -1;
341 jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
342 .cloneFeatureRenderer();
343 for (String ft : fc.keySet())
345 Object gc = fr.getFeatureStyle(ft);
346 if (gc instanceof Color)
348 // set graduated color as fading to white for minimum, and
349 // autoscaling to values on alignment
350 GraduatedColor ggc = new GraduatedColor(Color.white,
351 (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE);
352 ggc.setAutoScaled(true);
353 fr.setColour(ft, ggc);
356 // TODO: JAL-1150 - create sequence feature settings API for defining
357 // styles and enabling/disabling feature overlay on alignment panel
358 ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
359 if (af.alignPanel == ap)
361 // only do this if the alignFrame is currently showing this view.
362 af.setShowSeqFeatures(true);
364 ap.paintAlignment(true);
366 if (ourAnnot.size() > 0)
368 // Modify the visible annotation on the alignment viewport with the
369 // new alignment annotation rows created.
370 updateOurAnnots(ourAnnot);
371 ap.adjustAnnotationHeight();