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