src/jalview/ws/jws2/AADisorderClient.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
   3  * Copyright (C) 2015 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[] { "Globular Domain",
 108         "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[] { "REM465", "Missing density" });
 114     fmap.put("HOTLOOPS", new String[] { "HOTLOOPS", "Flexible loops" });
 115     fmap.put("COILS", new String[] { "COILS", "Random coil" });
 116     featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 117             fmap = new HashMap<String, String[]>());
 118     fmap.put("GlobDoms", new String[] { "Globular Domain",
 119         "Predicted globular domain" });
 120     fmap.put("Disorder", new String[] { "Protein Disorder",
 121         "Probable unstructured peptide region" });
 122     Map<String, Map<String, Object>> amap;
 123     annotMap = new HashMap<String, Map<String, Map<String, Object>>>();
 124     annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 125             amap = new HashMap<String, Map<String, Object>>());
 126     amap.put("Dydx", new HashMap<String, Object>());
 127     amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
 128     amap.get("Dydx").put(THRESHOLD, new double[] { 1, 0 });
 129     amap.get("Dydx").put(RANGE, new float[] { -1, +1 });
 130
 131     amap.put("SmoothedScore", new HashMap<String, Object>());
 132     amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
 133     amap.put("RawScore", new HashMap<String, Object>());
 134     amap.get("RawScore").put(INVISIBLE, INVISIBLE);
 135     annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 136             amap = new HashMap<String, Map<String, Object>>());
 137     amap.put("COILS", new HashMap<String, Object>());
 138     amap.put("HOTLOOPS", new HashMap<String, Object>());
 139     amap.put("REM465", new HashMap<String, Object>());
 140     amap.get("COILS").put(THRESHOLD, new double[] { 1, 0.516 });
 141     amap.get("COILS").put(RANGE, new float[] { 0, 1 });
 142
 143     amap.get("HOTLOOPS").put(THRESHOLD, new double[] { 1, 0.6 });
 144     amap.get("HOTLOOPS").put(RANGE, new float[] { 0, 1 });
 145     amap.get("REM465").put(THRESHOLD, new double[] { 1, 0.1204 });
 146     amap.get("REM465").put(RANGE, new float[] { 0, 1 });
 147
 148     annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
 149             amap = new HashMap<String, Map<String, Object>>());
 150     amap.put("Long", new HashMap<String, Object>());
 151     amap.put("Short", new HashMap<String, Object>());
 152     amap.get("Long").put(THRESHOLD, new double[] { 1, 0.5 });
 153     amap.get("Long").put(RANGE, new float[] { 0, 1 });
 154     amap.get("Short").put(THRESHOLD, new double[] { 1, 0.5 });
 155     amap.get("Short").put(RANGE, new float[] { 0, 1 });
 156     annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
 157             amap = new HashMap<String, Map<String, Object>>());
 158     amap.put("JRonn", new HashMap<String, Object>());
 159     amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5 });
 160     amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
 161   }
 162
 163   @Override
 164   public void updateResultAnnotation(boolean immediate)
 165   {
 166
 167     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
 168     {
 169       Map<String, String[]> featureTypeMap = featureMap
 170               .get(service.serviceType);
 171       Map<String, Map<String, Object>> annotTypeMap = annotMap
 172               .get(service.serviceType);
 173       boolean dispFeatures = false;
 174       Map<String, Object> fc = new Hashtable<String, Object>();
 175       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
 176       /**
 177        * grouping for any annotation rows created
 178        */
 179       int graphGroup = 1;
 180       if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
 181       {
 182         for (AlignmentAnnotation ala : alignViewport.getAlignment()
 183                 .getAlignmentAnnotation())
 184         {
 185           if (ala.graphGroup > graphGroup)
 186           {
 187             graphGroup = ala.graphGroup;
 188           }
 189         }
 190       }
 191
 192       for (String seqId : seqNames.keySet())
 193       {
 194         boolean sameGroup = false;
 195         SequenceI dseq, aseq, seq = seqNames.get(seqId);
 196         int base = seq.findPosition(start) - 1;
 197         aseq = seq;
 198         while ((dseq = seq).getDatasetSequence() != null)
 199         {
 200           seq = seq.getDatasetSequence();
 201         }
 202         ScoreHolder scores = null;
 203         try
 204         {
 205           scores = scoremanager.getAnnotationForSequence(seqId);
 206         } catch (Exception q)
 207         {
 208           Cache.log
 209                   .info("Couldn't recover disorder prediction for sequence "
 210                           + seq.getName()
 211                           + "(Prediction name was "
 212                           + seqId
 213                           + ")"
 214                           + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
 215         }
 216         float last = Float.NaN, val = Float.NaN;
 217         int lastAnnot = ourAnnot.size();
 218         if (scores != null && scores.scores != null)
 219         {
 220           for (Score scr : scores.scores)
 221           {
 222
 223             if (scr.getRanges() != null && scr.getRanges().size() > 0)
 224             {
 225               Iterator<Float> vals = scr.getScores().iterator();
 226               // make features on sequence
 227               for (Range rn : scr.getRanges())
 228               {
 229
 230                 SequenceFeature sf;
 231                 String[] type = featureTypeMap.get(scr.getMethod());
 232                 if (type == null)
 233                 {
 234                   // create a default type for this feature
 235                   type = new String[] {
 236                       typeName + " (" + scr.getMethod() + ")",
 237                       service.getActionText() };
 238                 }
 239                 if (vals.hasNext())
 240                 {
 241                   sf = new SequenceFeature(type[0], type[1],
 242                           base + rn.from, base + rn.to, val = vals.next()
 243                                   .floatValue(), methodName);
 244                 }
 245                 else
 246                 {
 247                   sf = new SequenceFeature(type[0], type[1], null, base
 248                           + rn.from, base + rn.to, methodName);
 249                 }
 250                 dseq.addSequenceFeature(sf);
 251                 if (last != val && !Float.isNaN(last))
 252                 {
 253                   fc.put(sf.getType(), sf);
 254                 }
 255                 last = val;
 256                 dispFeatures = true;
 257               }
 258             }
 259             else
 260             {
 261               if (scr.getScores().size() == 0)
 262               {
 263                 continue;
 264               }
 265               String typename, calcName;
 266               AlignmentAnnotation annot = createAnnotationRowsForScores(
 267                       ourAnnot,
 268                       typename = service.serviceType + " ("
 269                               + scr.getMethod() + ")",
 270                       calcName = service.getServiceTypeURI() + "/"
 271                               + scr.getMethod(), aseq, base + 1, scr);
 272               annot.graph = AlignmentAnnotation.LINE_GRAPH;
 273
 274               Map<String, Object> styleMap = (annotTypeMap == null) ? null
 275                       : annotTypeMap.get(scr.getMethod());
 276
 277               annot.visible = (styleMap == null || styleMap.get(INVISIBLE) == null);
 278               double[] thrsh = (styleMap == null) ? null
 279                       : (double[]) styleMap.get(THRESHOLD);
 280               float[] range = (styleMap == null) ? null
 281                       : (float[]) styleMap.get(RANGE);
 282               if (range != null)
 283               {
 284                 annot.graphMin = range[0];
 285                 annot.graphMax = range[1];
 286               }
 287               if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
 288               {
 289                 {
 290                   if (!sameGroup)
 291                   {
 292                     graphGroup++;
 293                     sameGroup = true;
 294                   }
 295
 296                   annot.graphGroup = graphGroup;
 297                 }
 298               }
 299
 300               annot.description = "<html>" + service.getActionText()
 301                       + " - raw scores";
 302               if (thrsh != null)
 303               {
 304                 String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
 305                         + thrsh[1] + " indicates disorder";
 306                 annot.threshold = new GraphLine((float) thrsh[1],
 307                         threshNote, Color.red);
 308                 annot.description += "<br/>" + threshNote;
 309               }
 310               annot.description += "</html>";
 311               Color col = new UserColourScheme(typeName)
 312                       .createColourFromName(typeName + scr.getMethod());
 313               for (int p = 0, ps = annot.annotations.length; p < ps; p++)
 314               {
 315                 if (annot.annotations[p] != null)
 316                 {
 317                   annot.annotations[p].colour = col;
 318                 }
 319               }
 320               annot._linecolour = col;
 321               // finally, update any dataset annotation
 322               replaceAnnotationOnAlignmentWith(annot, typename, calcName,
 323                       aseq);
 324             }
 325           }
 326         }
 327         if (lastAnnot + 1 == ourAnnot.size())
 328         {
 329           // remove singleton alignment annotation row
 330           ourAnnot.get(lastAnnot).graphGroup = -1;
 331         }
 332       }
 333       {
 334         if (dispFeatures)
 335         {
 336           jalview.api.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
 337                   .cloneFeatureRenderer();
 338           for (String ft : fc.keySet())
 339           {
 340             Object gc = fr.getFeatureStyle(ft);
 341             if (gc instanceof Color)
 342             {
 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);
 349             }
 350           }
 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)
 355           {
 356             // only do this if the alignFrame is currently showing this view.
 357             af.setShowSeqFeatures(true);
 358           }
 359           ap.paintAlignment(true);
 360         }
 361         if (ourAnnot.size() > 0)
 362         {
 363           // Modify the visible annotation on the alignment viewport with the
 364           // new alignment annotation rows created.
 365           updateOurAnnots(ourAnnot);
 366           ap.adjustAnnotationHeight();
 367         }
 368       }
 369     }
 370   }
 371
 372   @Override
 373   public String getCalcId()
 374   {
 375     // Disorder predictions are not dynamically updated so we return null
 376     return null;
 377   }
 378
 379 }