2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
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 of the License, or (at your option) any later version.
11 * Jalview is distributed in the hope that it will be useful, but
12 * WITHOUT ANY WARRANTY; without even the implied warranty
13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
14 * PURPOSE. See the GNU General Public License for more details.
16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
17 * The Jalview Authors are detailed in the 'AUTHORS' file.
19 package jalview.ws.jws2;
21 import jalview.api.AlignCalcWorkerI;
22 import jalview.bin.Cache;
23 import jalview.datamodel.AlignmentAnnotation;
24 import jalview.datamodel.GraphLine;
25 import jalview.datamodel.SequenceFeature;
26 import jalview.datamodel.SequenceI;
27 import jalview.gui.AlignFrame;
28 import jalview.schemes.GraduatedColor;
29 import jalview.schemes.UserColourScheme;
30 import jalview.ws.jws2.jabaws2.Jws2Instance;
31 import jalview.ws.params.WsParamSetI;
33 import java.awt.Color;
34 import java.util.ArrayList;
35 import java.util.HashMap;
36 import java.util.Hashtable;
37 import java.util.Iterator;
38 import java.util.List;
41 import compbio.data.sequence.Range;
42 import compbio.data.sequence.Score;
43 import compbio.data.sequence.ScoreManager.ScoreHolder;
44 import compbio.metadata.Argument;
46 public class AADisorderClient extends JabawsCalcWorker implements
50 private static final String THRESHOLD = "THRESHOLD";
51 private static final String RANGE = "RANGE";
61 public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
62 WsParamSetI preset, List<Argument> paramset)
64 super(sh, alignFrame, preset, paramset);
67 methodName = sh.serviceType;
71 nucleotidesAllowed = false;
72 proteinAllowed = true;
77 public String getServiceActionText()
79 return "Submitting amino acid sequences for disorder prediction.";
82 private static Map<String, Map<String, String[]>> featureMap;
84 private static Map<String, Map<String, Map<String, Object>>> annotMap;
86 private static String DONTCOMBINE = "DONTCOMBINE";
88 private static String INVISIBLE = "INVISIBLE";
91 // TODO: turn this into some kind of configuration file that's a bit easier
93 featureMap = new HashMap<String, Map<String, String[]>>();
94 Map<String, String[]> fmap;
95 featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
96 fmap = new HashMap<String, String[]>());
97 fmap.put("Glob", new String[]
98 { "Globular Domain", "Predicted globular domain" });
99 featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
100 fmap = new HashMap<String, String[]>());
101 featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
102 fmap = new HashMap<String, String[]>());
103 fmap.put("REM465", new String[]
104 { "REM465", "Missing density" });
105 fmap.put("HOTLOOPS", new String[]
106 { "HOTLOOPS", "Flexible loops" });
107 fmap.put("COILS", new String[]
108 { "COILS", "Random coil" });
109 featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
110 fmap = new HashMap<String, String[]>());
111 fmap.put("GlobDoms", new String[]
112 { "Globular Domain", "Predicted globular domain" });
113 fmap.put("Disorder", new String[]
114 { "Protein Disorder", "Probable unstructured peptide region" });
115 Map<String, Map<String, Object>> amap;
116 annotMap = new HashMap<String, Map<String, Map<String, Object>>>();
117 annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
118 amap = new HashMap<String, Map<String, Object>>());
119 amap.put("Dydx", new HashMap<String, Object>());
120 amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
121 amap.get("Dydx").put(THRESHOLD, new double[]
123 amap.get("Dydx").put(RANGE, new float[]
126 amap.put("SmoothedScore", new HashMap<String, Object>());
127 amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
128 amap.put("RawScore", new HashMap<String, Object>());
129 amap.get("RawScore").put(INVISIBLE, INVISIBLE);
130 annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
131 amap = new HashMap<String, Map<String, Object>>());
132 amap.put("COILS", new HashMap<String, Object>());
133 amap.put("HOTLOOPS", new HashMap<String, Object>());
134 amap.put("REM465", new HashMap<String, Object>());
135 amap.get("COILS").put(THRESHOLD, new double[]
137 amap.get("COILS").put(RANGE, new float[]
140 amap.get("HOTLOOPS").put(THRESHOLD, new double[]
142 amap.get("HOTLOOPS").put(RANGE, new float[]
144 amap.get("REM465").put(THRESHOLD, new double[]
146 amap.get("REM465").put(RANGE, new float[]
150 annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
151 amap = new HashMap<String, Map<String, Object>>());
152 amap.put("Long", new HashMap<String, Object>());
153 amap.put("Short", new HashMap<String, Object>());
154 amap.get("Long").put(THRESHOLD, new double[]
156 amap.get("Long").put(RANGE, new float[]
158 amap.get("Short").put(THRESHOLD, new double[]
160 amap.get("Short").put(RANGE, new float[]
162 annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
163 amap = new HashMap<String, Map<String, Object>>());
164 amap.put("JRonn", new HashMap<String, Object>());
165 amap.get("JRonn").put(THRESHOLD, new double[]
167 amap.get("JRonn").put(RANGE, new float[]
172 public void updateResultAnnotation(boolean immediate)
175 if (immediate || !calcMan.isWorking(this) && scoremanager != null)
177 Map<String, String[]> featureTypeMap = featureMap
178 .get(service.serviceType);
179 Map<String, Map<String, Object>> annotTypeMap = annotMap
180 .get(service.serviceType);
181 boolean dispFeatures = false;
182 Map<String, Object> fc = new Hashtable<String, Object>();
183 List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
185 * grouping for any annotation rows created
188 if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
190 for (AlignmentAnnotation ala : alignViewport.getAlignment()
191 .getAlignmentAnnotation())
193 if (ala.graphGroup > graphGroup)
195 graphGroup = ala.graphGroup;
200 for (String seqId : seqNames.keySet())
202 boolean sameGroup = false;
203 SequenceI dseq, aseq, seq = seqNames.get(seqId);
204 int base = seq.findPosition(start)-1;
206 while ((dseq = seq).getDatasetSequence() != null)
208 seq = seq.getDatasetSequence();
210 ScoreHolder scores = null;
212 scores = scoremanager.getAnnotationForSequence(seqId);
213 } catch (Exception q)
216 .info("Couldn't recover disorder prediction for sequence "
218 + "(Prediction name was "
220 + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
222 float last = Float.NaN, val = Float.NaN;
223 int lastAnnot = ourAnnot.size();
224 if (scores!=null && scores.scores!=null) {
225 for (Score scr : scores.scores)
228 if (scr.getRanges() != null && scr.getRanges().size() > 0)
230 Iterator<Float> vals = scr.getScores().iterator();
231 // make features on sequence
232 for (Range rn : scr.getRanges())
236 String[] type = featureTypeMap.get(scr.getMethod());
239 // create a default type for this feature
241 { typeName + " (" + scr.getMethod() + ")",
242 service.getActionText() };
246 sf = new SequenceFeature(type[0], type[1],
247 base + rn.from, base + rn.to, val = vals.next()
248 .floatValue(), methodName);
252 sf = new SequenceFeature(type[0], type[1], null, base
253 + rn.from, base + rn.to, methodName);
255 dseq.addSequenceFeature(sf);
256 if (last != val && last != Float.NaN)
258 fc.put(sf.getType(), sf);
266 if (scr.getScores().size() == 0)
270 AlignmentAnnotation annot = createAnnotationRowsForScores(
272 service.serviceType + " (" + scr.getMethod() + ")",
273 service.getServiceTypeURI() + "/" + scr.getMethod(),
274 aseq, base + 1, scr);
275 annot.graph = AlignmentAnnotation.LINE_GRAPH;
277 Map<String,Object> styleMap = (annotTypeMap == null) ? null : annotTypeMap.get(scr.getMethod());
279 annot.visible = (styleMap == null || styleMap.get(INVISIBLE) == null);
280 double[] thrsh = (styleMap==null) ? null
281 : (double[]) styleMap.get(
283 float[] range = (styleMap==null) ? null : (float[]) styleMap.get(
287 annot.graphMin = range[0];
288 annot.graphMax = range[1];
290 if (styleMap==null || styleMap.get(DONTCOMBINE) == null)
299 annot.graphGroup = graphGroup;
303 annot.description = "<html>" + service.getActionText()
307 String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
308 + thrsh[1] + " indicates disorder";
309 annot.threshold = new GraphLine((float) thrsh[1],
310 threshNote, Color.red);
311 annot.description += "<br/>" + threshNote;
313 annot.description += "</html>";
314 Color col = new UserColourScheme(typeName)
315 .createColourFromName(typeName + scr.getMethod());
316 for (int p = 0, ps = annot.annotations.length; p < ps; p++)
318 if (annot.annotations[p] != null)
320 annot.annotations[p].colour = col;
323 annot._linecolour = col;
327 if (lastAnnot + 1 == ourAnnot.size())
329 // remove singleton alignment annotation row
330 ourAnnot.get(lastAnnot).graphGroup = -1;
336 jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
337 .cloneFeatureRenderer();
338 for (String ft : fc.keySet())
340 Object gc = fr.getFeatureStyle(ft);
341 if (gc instanceof Color)
343 // set graduated color as fading to white for minimum, and
344 // autoscaling to values on alignment
345 GraduatedColor ggc = new GraduatedColor(Color.white,
346 (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE);
347 ggc.setAutoScaled(true);
348 fr.setColour(ft, ggc);
351 // TODO: JAL-1150 - create sequence feature settings API for defining
352 // styles and enabling/disabling feature overlay on alignment panel
353 ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
354 if (af.alignPanel == ap)
356 // only do this if the alignFrame is currently showing this view.
357 af.setShowSeqFeatures(true);
359 ap.paintAlignment(true);
361 if (ourAnnot.size() > 0)
363 // Modify the visible annotation on the alignment viewport with the
364 // new alignment annotation rows created.
365 updateOurAnnots(ourAnnot);
366 ap.adjustAnnotationHeight();