src/jalview/ws/jws2/AADisorderClient.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
   3  * Copyright (C) 2014 The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   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.
  11  *
  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.
  16  *
  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.
  20  */
  21 package jalview.ws.jws2;
  22
  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;
  34
  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;
  41 import java.util.Map;
  42
  43 import compbio.data.sequence.FastaSequence;
  44 import compbio.data.sequence.Range;
  45 import compbio.data.sequence.Score;
  46 import compbio.data.sequence.ScoreManager.ScoreHolder;
  47 import compbio.metadata.Argument;
  48
  49 public class AADisorderClient extends JabawsCalcWorker implements
  50         AlignCalcWorkerI
  51 {
  52
  53   private static final String THRESHOLD = "THRESHOLD";
  54
  55   private static final String RANGE = "RANGE";
  56
  57   String typeName;
  58
  59   String methodName;
  60
  61   String groupName;
  62
  63   AlignFrame af;
  64
  65   public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
  66           WsParamSetI preset, List<Argument> paramset)
  67   {
  68     super(sh, alignFrame, preset, paramset);
  69     af = alignFrame;
  70     typeName = sh.action;
  71     methodName = sh.serviceType;
  72
  73     submitGaps = false;
  74     alignedSeqs = false;
  75     nucleotidesAllowed = false;
  76     proteinAllowed = true;
  77     bySequence = true;
  78   }
  79
  80   @Override
  81   public String getServiceActionText()
  82   {
  83     return "Submitting amino acid sequences for disorder prediction.";
  84   }
  85
  86   @Override
  87   boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
  88   {
  89     return (seqs.size() > 0);
  90   }
  91
  92   private static Map<String, Map<String, String[]>> featureMap;
  93
  94   private static Map<String, Map<String, Map<String, Object>>> annotMap;
  95
  96   private static String DONTCOMBINE = "DONTCOMBINE";
  97
  98   private static String INVISIBLE = "INVISIBLE";
  99   static
 100   {
 101     // TODO: turn this into some kind of configuration file that's a bit easier
 102     // to edit
 103     featureMap = new HashMap<String, Map<String, String[]>>();
 104     Map<String, String[]> fmap;
 105     featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
 106             fmap = new HashMap<String, String[]>());
 107     fmap.put("Glob", new String[]
 108     { "Globular Domain", "Predicted globular domain" });
 109     featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
 110             fmap = new HashMap<String, String[]>());
 111     featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 112             fmap = new HashMap<String, String[]>());
 113     fmap.put("REM465", new String[]
 114     { "REM465", "Missing density" });
 115     fmap.put("HOTLOOPS", new String[]
 116     { "HOTLOOPS", "Flexible loops" });
 117     fmap.put("COILS", new String[]
 118     { "COILS", "Random coil" });
 119     featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 120             fmap = new HashMap<String, String[]>());
 121     fmap.put("GlobDoms", new String[]
 122     { "Globular Domain", "Predicted globular domain" });
 123     fmap.put("Disorder", new String[]
 124     { "Protein Disorder", "Probable unstructured peptide region" });
 125     Map<String, Map<String, Object>> amap;
 126     annotMap = new HashMap<String, Map<String, Map<String, Object>>>();
 127     annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 128             amap = new HashMap<String, Map<String, Object>>());
 129     amap.put("Dydx", new HashMap<String, Object>());
 130     amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
 131     amap.get("Dydx").put(THRESHOLD, new double[]
 132     { 1, 0 });
 133     amap.get("Dydx").put(RANGE, new float[]
 134     { -1, +1 });
 135
 136     amap.put("SmoothedScore", new HashMap<String, Object>());
 137     amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
 138     amap.put("RawScore", new HashMap<String, Object>());
 139     amap.get("RawScore").put(INVISIBLE, INVISIBLE);
 140     annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 141             amap = new HashMap<String, Map<String, Object>>());
 142     amap.put("COILS", new HashMap<String, Object>());
 143     amap.put("HOTLOOPS", new HashMap<String, Object>());
 144     amap.put("REM465", new HashMap<String, Object>());
 145     amap.get("COILS").put(THRESHOLD, new double[]
 146     { 1, 0.516 });
 147     amap.get("COILS").put(RANGE, new float[]
 148     { 0, 1 });
 149
 150     amap.get("HOTLOOPS").put(THRESHOLD, new double[]
 151     { 1, 0.6 });
 152     amap.get("HOTLOOPS").put(RANGE, new float[]
 153     { 0, 1 });
 154     amap.get("REM465").put(THRESHOLD, new double[]
 155     { 1, 0.1204 });
 156     amap.get("REM465").put(RANGE, new float[]
 157     { 0, 1 });
 158
 159     annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
 160             amap = new HashMap<String, Map<String, Object>>());
 161     amap.put("Long", new HashMap<String, Object>());
 162     amap.put("Short", new HashMap<String, Object>());
 163     amap.get("Long").put(THRESHOLD, new double[]
 164     { 1, 0.5 });
 165     amap.get("Long").put(RANGE, new float[]
 166     { 0, 1 });
 167     amap.get("Short").put(THRESHOLD, new double[]
 168     { 1, 0.5 });
 169     amap.get("Short").put(RANGE, new float[]
 170     { 0, 1 });
 171     annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
 172             amap = new HashMap<String, Map<String, Object>>());
 173     amap.put("JRonn", new HashMap<String, Object>());
 174     amap.get("JRonn").put(THRESHOLD, new double[]
 175     { 1, 0.5 });
 176     amap.get("JRonn").put(RANGE, new float[]
 177     { 0, 1 });
 178   }
 179
 180   @Override
 181   public void updateResultAnnotation(boolean immediate)
 182   {
 183
 184     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
 185     {
 186       Map<String, String[]> featureTypeMap = featureMap
 187               .get(service.serviceType);
 188       Map<String, Map<String, Object>> annotTypeMap = annotMap
 189               .get(service.serviceType);
 190       boolean dispFeatures = false;
 191       Map<String, Object> fc = new Hashtable<String, Object>();
 192       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
 193       /**
 194        * grouping for any annotation rows created
 195        */
 196       int graphGroup = 1;
 197       if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
 198       {
 199         for (AlignmentAnnotation ala : alignViewport.getAlignment()
 200                 .getAlignmentAnnotation())
 201         {
 202           if (ala.graphGroup > graphGroup)
 203           {
 204             graphGroup = ala.graphGroup;
 205           }
 206         }
 207       }
 208
 209       for (String seqId : seqNames.keySet())
 210       {
 211         boolean sameGroup = false;
 212         SequenceI dseq, aseq, seq = seqNames.get(seqId);
 213         int base = seq.findPosition(start) - 1;
 214         aseq = seq;
 215         while ((dseq = seq).getDatasetSequence() != null)
 216         {
 217           seq = seq.getDatasetSequence();
 218         }
 219         ScoreHolder scores = null;
 220         try
 221         {
 222           scores = scoremanager.getAnnotationForSequence(seqId);
 223         } catch (Exception q)
 224         {
 225           Cache.log
 226                   .info("Couldn't recover disorder prediction for sequence "
 227                           + seq.getName()
 228                           + "(Prediction name was "
 229                           + seqId
 230                           + ")"
 231                           + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
 232         }
 233         float last = Float.NaN, val = Float.NaN;
 234         int lastAnnot = ourAnnot.size();
 235         if (scores != null && scores.scores != null)
 236         {
 237           for (Score scr : scores.scores)
 238           {
 239
 240             if (scr.getRanges() != null && scr.getRanges().size() > 0)
 241             {
 242               Iterator<Float> vals = scr.getScores().iterator();
 243               // make features on sequence
 244               for (Range rn : scr.getRanges())
 245               {
 246
 247                 SequenceFeature sf;
 248                 String[] type = featureTypeMap.get(scr.getMethod());
 249                 if (type == null)
 250                 {
 251                   // create a default type for this feature
 252                   type = new String[]
 253                   { typeName + " (" + scr.getMethod() + ")",
 254                       service.getActionText() };
 255                 }
 256                 if (vals.hasNext())
 257                 {
 258                   sf = new SequenceFeature(type[0], type[1],
 259                           base + rn.from, base + rn.to, val = vals.next()
 260                                   .floatValue(), methodName);
 261                 }
 262                 else
 263                 {
 264                   sf = new SequenceFeature(type[0], type[1], null, base
 265                           + rn.from, base + rn.to, methodName);
 266                 }
 267                 dseq.addSequenceFeature(sf);
 268                 if (last != val && last != Float.NaN)
 269                 {
 270                   fc.put(sf.getType(), sf);
 271                 }
 272                 last = val;
 273                 dispFeatures = true;
 274               }
 275             }
 276             else
 277             {
 278               if (scr.getScores().size() == 0)
 279               {
 280                 continue;
 281               }
 282               String typename, calcName;
 283               AlignmentAnnotation annot = createAnnotationRowsForScores(
 284                       ourAnnot,
 285                       typename = service.serviceType + " ("
 286                               + scr.getMethod() + ")",
 287                       calcName = service.getServiceTypeURI() + "/"
 288                               + scr.getMethod(),
 289                       aseq, base + 1, scr);
 290               annot.graph = AlignmentAnnotation.LINE_GRAPH;
 291
 292               Map<String, Object> styleMap = (annotTypeMap == null) ? null
 293                       : annotTypeMap.get(scr.getMethod());
 294
 295               annot.visible = (styleMap == null || styleMap.get(INVISIBLE) == null);
 296               double[] thrsh = (styleMap == null) ? null
 297                       : (double[]) styleMap.get(THRESHOLD);
 298               float[] range = (styleMap == null) ? null
 299                       : (float[]) styleMap.get(RANGE);
 300               if (range != null)
 301               {
 302                 annot.graphMin = range[0];
 303                 annot.graphMax = range[1];
 304               }
 305               if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
 306               {
 307                 {
 308                   if (!sameGroup)
 309                   {
 310                     graphGroup++;
 311                     sameGroup = true;
 312                   }
 313
 314                   annot.graphGroup = graphGroup;
 315                 }
 316               }
 317
 318               annot.description = "<html>" + service.getActionText()
 319                       + " - raw scores";
 320               if (thrsh != null)
 321               {
 322                 String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
 323                         + thrsh[1] + " indicates disorder";
 324                 annot.threshold = new GraphLine((float) thrsh[1],
 325                         threshNote, Color.red);
 326                 annot.description += "<br/>" + threshNote;
 327               }
 328               annot.description += "</html>";
 329               Color col = new UserColourScheme(typeName)
 330                       .createColourFromName(typeName + scr.getMethod());
 331               for (int p = 0, ps = annot.annotations.length; p < ps; p++)
 332               {
 333                 if (annot.annotations[p] != null)
 334                 {
 335                   annot.annotations[p].colour = col;
 336                 }
 337               }
 338               annot._linecolour = col;
 339               // finally, update any dataset annotation
 340               replaceAnnotationOnAlignmentWith(annot, typename, calcName,
 341                       aseq);
 342             }
 343           }
 344         }
 345         if (lastAnnot + 1 == ourAnnot.size())
 346         {
 347           // remove singleton alignment annotation row
 348           ourAnnot.get(lastAnnot).graphGroup = -1;
 349         }
 350       }
 351       {
 352         if (dispFeatures)
 353         {
 354           jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
 355                   .cloneFeatureRenderer();
 356           for (String ft : fc.keySet())
 357           {
 358             Object gc = fr.getFeatureStyle(ft);
 359             if (gc instanceof Color)
 360             {
 361               // set graduated color as fading to white for minimum, and
 362               // autoscaling to values on alignment
 363               GraduatedColor ggc = new GraduatedColor(Color.white,
 364                       (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE);
 365               ggc.setAutoScaled(true);
 366               fr.setColour(ft, ggc);
 367             }
 368           }
 369           // TODO: JAL-1150 - create sequence feature settings API for defining
 370           // styles and enabling/disabling feature overlay on alignment panel
 371           ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
 372           if (af.alignPanel == ap)
 373           {
 374             // only do this if the alignFrame is currently showing this view.
 375             af.setShowSeqFeatures(true);
 376           }
 377           ap.paintAlignment(true);
 378         }
 379         if (ourAnnot.size() > 0)
 380         {
 381           // Modify the visible annotation on the alignment viewport with the
 382           // new alignment annotation rows created.
 383           updateOurAnnots(ourAnnot);
 384           ap.adjustAnnotationHeight();
 385         }
 386       }
 387     }
 388   }
 389
 390   @Override
 391   public String getCalcId()
 392   {
 393     // Disorder predictions are not dynamically updated so we return null
 394     return null;
 395   }
 396
 397 }