src/jalview/ws/jws2/AADisorderClient.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ 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.api.FeatureColourI;
  25 import jalview.bin.Cache;
  26 import jalview.datamodel.AlignmentAnnotation;
  27 import jalview.datamodel.GraphLine;
  28 import jalview.datamodel.SequenceFeature;
  29 import jalview.datamodel.SequenceI;
  30 import jalview.gui.AlignFrame;
  31 import jalview.schemes.FeatureColour;
  32 import jalview.schemes.UserColourScheme;
  33 import jalview.ws.jws2.jabaws2.Jws2Instance;
  34 import jalview.ws.params.WsParamSetI;
  35
  36 import java.awt.Color;
  37 import java.util.ArrayList;
  38 import java.util.HashMap;
  39 import java.util.Hashtable;
  40 import java.util.Iterator;
  41 import java.util.List;
  42 import java.util.Map;
  43
  44 import compbio.data.sequence.FastaSequence;
  45 import compbio.data.sequence.Range;
  46 import compbio.data.sequence.Score;
  47 import compbio.data.sequence.ScoreManager.ScoreHolder;
  48 import compbio.metadata.Argument;
  49
  50 public class AADisorderClient extends JabawsCalcWorker implements
  51         AlignCalcWorkerI
  52 {
  53
  54   private static final String THRESHOLD = "THRESHOLD";
  55
  56   private static final String RANGE = "RANGE";
  57
  58   String typeName;
  59
  60   String methodName;
  61
  62   String groupName;
  63
  64   AlignFrame af;
  65
  66   public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
  67           WsParamSetI preset, List<Argument> paramset)
  68   {
  69     super(sh, alignFrame, preset, paramset);
  70     af = alignFrame;
  71     typeName = sh.action;
  72     methodName = sh.serviceType;
  73
  74     submitGaps = false;
  75     alignedSeqs = false;
  76     nucleotidesAllowed = false;
  77     proteinAllowed = true;
  78     bySequence = true;
  79   }
  80
  81   @Override
  82   public String getServiceActionText()
  83   {
  84     return "Submitting amino acid sequences for disorder prediction.";
  85   }
  86
  87   @Override
  88   boolean checkValidInputSeqs(boolean dynamic, List<FastaSequence> seqs)
  89   {
  90     return (seqs.size() > 0);
  91   }
  92
  93   private static Map<String, Map<String, String[]>> featureMap;
  94
  95   private static Map<String, Map<String, Map<String, Object>>> annotMap;
  96
  97   private static String DONTCOMBINE = "DONTCOMBINE";
  98
  99   private static String INVISIBLE = "INVISIBLE";
 100   static
 101   {
 102     // TODO: turn this into some kind of configuration file that's a bit easier
 103     // to edit
 104     featureMap = new HashMap<String, Map<String, String[]>>();
 105     Map<String, String[]> fmap;
 106     featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
 107             fmap = new HashMap<String, String[]>());
 108     fmap.put("Glob", new String[] { "Globular Domain",
 109         "Predicted globular domain" });
 110     featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
 111             fmap = new HashMap<String, String[]>());
 112     featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 113             fmap = new HashMap<String, String[]>());
 114     fmap.put("REM465", new String[] { "REM465", "Missing density" });
 115     fmap.put("HOTLOOPS", new String[] { "HOTLOOPS", "Flexible loops" });
 116     fmap.put("COILS", new String[] { "COILS", "Random coil" });
 117     featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 118             fmap = new HashMap<String, String[]>());
 119     fmap.put("GlobDoms", new String[] { "Globular Domain",
 120         "Predicted globular domain" });
 121     fmap.put("Disorder", new String[] { "Protein Disorder",
 122         "Probable unstructured peptide region" });
 123     Map<String, Map<String, Object>> amap;
 124     annotMap = new HashMap<String, Map<String, Map<String, Object>>>();
 125     annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 126             amap = new HashMap<String, Map<String, Object>>());
 127     amap.put("Dydx", new HashMap<String, Object>());
 128     amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
 129     amap.get("Dydx").put(THRESHOLD, new double[] { 1, 0 });
 130     amap.get("Dydx").put(RANGE, new float[] { -1, +1 });
 131
 132     amap.put("SmoothedScore", new HashMap<String, Object>());
 133     amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
 134     amap.put("RawScore", new HashMap<String, Object>());
 135     amap.get("RawScore").put(INVISIBLE, INVISIBLE);
 136     annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 137             amap = new HashMap<String, Map<String, Object>>());
 138     amap.put("COILS", new HashMap<String, Object>());
 139     amap.put("HOTLOOPS", new HashMap<String, Object>());
 140     amap.put("REM465", new HashMap<String, Object>());
 141     amap.get("COILS").put(THRESHOLD, new double[] { 1, 0.516 });
 142     amap.get("COILS").put(RANGE, new float[] { 0, 1 });
 143
 144     amap.get("HOTLOOPS").put(THRESHOLD, new double[] { 1, 0.6 });
 145     amap.get("HOTLOOPS").put(RANGE, new float[] { 0, 1 });
 146     amap.get("REM465").put(THRESHOLD, new double[] { 1, 0.1204 });
 147     amap.get("REM465").put(RANGE, new float[] { 0, 1 });
 148
 149     annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
 150             amap = new HashMap<String, Map<String, Object>>());
 151     amap.put("Long", new HashMap<String, Object>());
 152     amap.put("Short", new HashMap<String, Object>());
 153     amap.get("Long").put(THRESHOLD, new double[] { 1, 0.5 });
 154     amap.get("Long").put(RANGE, new float[] { 0, 1 });
 155     amap.get("Short").put(THRESHOLD, new double[] { 1, 0.5 });
 156     amap.get("Short").put(RANGE, new float[] { 0, 1 });
 157     annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
 158             amap = new HashMap<String, Map<String, Object>>());
 159     amap.put("JRonn", new HashMap<String, Object>());
 160     amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5 });
 161     amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
 162   }
 163
 164   @Override
 165   public void updateResultAnnotation(boolean immediate)
 166   {
 167
 168     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
 169     {
 170       Map<String, String[]> featureTypeMap = featureMap
 171               .get(service.serviceType);
 172       Map<String, Map<String, Object>> annotTypeMap = annotMap
 173               .get(service.serviceType);
 174       boolean dispFeatures = false;
 175       Map<String, Object> fc = new Hashtable<String, Object>();
 176       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
 177       /**
 178        * grouping for any annotation rows created
 179        */
 180       int graphGroup = 1;
 181       if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
 182       {
 183         for (AlignmentAnnotation ala : alignViewport.getAlignment()
 184                 .getAlignmentAnnotation())
 185         {
 186           if (ala.graphGroup > graphGroup)
 187           {
 188             graphGroup = ala.graphGroup;
 189           }
 190         }
 191       }
 192
 193       for (String seqId : seqNames.keySet())
 194       {
 195         boolean sameGroup = false;
 196         SequenceI dseq, aseq, seq = seqNames.get(seqId);
 197         int base = seq.findPosition(start) - 1;
 198         aseq = seq;
 199         while ((dseq = seq).getDatasetSequence() != null)
 200         {
 201           seq = seq.getDatasetSequence();
 202         }
 203         ScoreHolder scores = null;
 204         try
 205         {
 206           scores = scoremanager.getAnnotationForSequence(seqId);
 207         } catch (Exception q)
 208         {
 209           Cache.log
 210                   .info("Couldn't recover disorder prediction for sequence "
 211                           + seq.getName()
 212                           + "(Prediction name was "
 213                           + seqId
 214                           + ")"
 215                           + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
 216         }
 217         float last = Float.NaN, val = Float.NaN;
 218         int lastAnnot = ourAnnot.size();
 219         if (scores != null && scores.scores != null)
 220         {
 221           for (Score scr : scores.scores)
 222           {
 223
 224             if (scr.getRanges() != null && scr.getRanges().size() > 0)
 225             {
 226               Iterator<Float> vals = scr.getScores().iterator();
 227               // make features on sequence
 228               for (Range rn : scr.getRanges())
 229               {
 230
 231                 SequenceFeature sf;
 232                 String[] type = featureTypeMap.get(scr.getMethod());
 233                 if (type == null)
 234                 {
 235                   // create a default type for this feature
 236                   type = new String[] {
 237                       typeName + " (" + scr.getMethod() + ")",
 238                       service.getActionText() };
 239                 }
 240                 if (vals.hasNext())
 241                 {
 242                   sf = new SequenceFeature(type[0], type[1],
 243                           base + rn.from, base + rn.to, val = vals.next()
 244                                   .floatValue(), methodName);
 245                 }
 246                 else
 247                 {
 248                   sf = new SequenceFeature(type[0], type[1], null, base
 249                           + rn.from, base + rn.to, methodName);
 250                 }
 251                 dseq.addSequenceFeature(sf);
 252                 if (last != val && !Float.isNaN(last))
 253                 {
 254                   fc.put(sf.getType(), sf);
 255                 }
 256                 last = val;
 257                 dispFeatures = true;
 258               }
 259             }
 260             else
 261             {
 262               if (scr.getScores().size() == 0)
 263               {
 264                 continue;
 265               }
 266               String typename, calcName;
 267               AlignmentAnnotation annot = createAnnotationRowsForScores(
 268                       ourAnnot,
 269                       typename = service.serviceType + " ("
 270                               + scr.getMethod() + ")",
 271                       calcName = service.getServiceTypeURI() + "/"
 272                               + scr.getMethod(), aseq, base + 1, scr);
 273               annot.graph = AlignmentAnnotation.LINE_GRAPH;
 274
 275               Map<String, Object> styleMap = (annotTypeMap == null) ? null
 276                       : annotTypeMap.get(scr.getMethod());
 277
 278               annot.visible = (styleMap == null || styleMap.get(INVISIBLE) == null);
 279               double[] thrsh = (styleMap == null) ? null
 280                       : (double[]) styleMap.get(THRESHOLD);
 281               float[] range = (styleMap == null) ? null
 282                       : (float[]) styleMap.get(RANGE);
 283               if (range != null)
 284               {
 285                 annot.graphMin = range[0];
 286                 annot.graphMax = range[1];
 287               }
 288               if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
 289               {
 290                 {
 291                   if (!sameGroup)
 292                   {
 293                     graphGroup++;
 294                     sameGroup = true;
 295                   }
 296
 297                   annot.graphGroup = graphGroup;
 298                 }
 299               }
 300
 301               annot.description = "<html>" + service.getActionText()
 302                       + " - raw scores";
 303               if (thrsh != null)
 304               {
 305                 String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
 306                         + thrsh[1] + " indicates disorder";
 307                 annot.threshold = new GraphLine((float) thrsh[1],
 308                         threshNote, Color.red);
 309                 annot.description += "<br/>" + threshNote;
 310               }
 311               annot.description += "</html>";
 312               Color col = UserColourScheme.createColourFromName(typeName
 313                       + scr.getMethod());
 314               for (int p = 0, ps = annot.annotations.length; p < ps; p++)
 315               {
 316                 if (annot.annotations[p] != null)
 317                 {
 318                   annot.annotations[p].colour = col;
 319                 }
 320               }
 321               annot._linecolour = col;
 322               // finally, update any dataset annotation
 323               replaceAnnotationOnAlignmentWith(annot, typename, calcName,
 324                       aseq);
 325             }
 326           }
 327         }
 328         if (lastAnnot + 1 == ourAnnot.size())
 329         {
 330           // remove singleton alignment annotation row
 331           ourAnnot.get(lastAnnot).graphGroup = -1;
 332         }
 333       }
 334       {
 335         if (dispFeatures)
 336         {
 337           jalview.api.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
 338                   .cloneFeatureRenderer();
 339           for (String ft : fc.keySet())
 340           {
 341             FeatureColourI gc = fr.getFeatureStyle(ft);
 342             if (gc.isSimpleColour())
 343             {
 344               // set graduated color as fading to white for minimum, and
 345               // autoscaling to values on alignment
 346               FeatureColourI ggc = new FeatureColour(Color.white,
 347                       gc.getColour(), Float.MIN_VALUE, Float.MAX_VALUE);
 348               ggc.setAutoScaled(true);
 349               fr.setColour(ft, ggc);
 350             }
 351           }
 352           // TODO: JAL-1150 - create sequence feature settings API for defining
 353           // styles and enabling/disabling feature overlay on alignment panel
 354           ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
 355           if (af.alignPanel == ap)
 356           {
 357             // only do this if the alignFrame is currently showing this view.
 358             af.setShowSeqFeatures(true);
 359           }
 360           ap.paintAlignment(true);
 361         }
 362         if (ourAnnot.size() > 0)
 363         {
 364           // Modify the visible annotation on the alignment viewport with the
 365           // new alignment annotation rows created.
 366           updateOurAnnots(ourAnnot);
 367           ap.adjustAnnotationHeight();
 368         }
 369       }
 370     }
 371   }
 372
 373   @Override
 374   public String getCalcId()
 375   {
 376     // Disorder predictions are not dynamically updated so we return null
 377     return null;
 378   }
 379
 380 }