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