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.util.ColorUtils;
  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
  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",
 108             new String[]
 109             { "Globular Domain", "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",
 120             new String[]
 121             { "Globular Domain", "Predicted globular domain" });
 122     fmap.put("Disorder",
 123             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[] { 1, 0 });
 132     amap.get("Dydx").put(RANGE, new float[] { -1, +1 });
 133
 134     amap.put("SmoothedScore", new HashMap<String, Object>());
 135     amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
 136     amap.put("RawScore", new HashMap<String, Object>());
 137     amap.get("RawScore").put(INVISIBLE, INVISIBLE);
 138     annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 139             amap = new HashMap<String, Map<String, Object>>());
 140     amap.put("COILS", new HashMap<String, Object>());
 141     amap.put("HOTLOOPS", new HashMap<String, Object>());
 142     amap.put("REM465", new HashMap<String, Object>());
 143     amap.get("COILS").put(THRESHOLD, new double[] { 1, 0.516 });
 144     amap.get("COILS").put(RANGE, new float[] { 0, 1 });
 145
 146     amap.get("HOTLOOPS").put(THRESHOLD, new double[] { 1, 0.6 });
 147     amap.get("HOTLOOPS").put(RANGE, new float[] { 0, 1 });
 148     amap.get("REM465").put(THRESHOLD, new double[] { 1, 0.1204 });
 149     amap.get("REM465").put(RANGE, new float[] { 0, 1 });
 150
 151     annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
 152             amap = new HashMap<String, Map<String, Object>>());
 153     amap.put("Long", new HashMap<String, Object>());
 154     amap.put("Short", new HashMap<String, Object>());
 155     amap.get("Long").put(THRESHOLD, new double[] { 1, 0.5 });
 156     amap.get("Long").put(RANGE, new float[] { 0, 1 });
 157     amap.get("Short").put(THRESHOLD, new double[] { 1, 0.5 });
 158     amap.get("Short").put(RANGE, new float[] { 0, 1 });
 159     annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
 160             amap = new HashMap<String, Map<String, Object>>());
 161     amap.put("JRonn", new HashMap<String, Object>());
 162     amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5 });
 163     amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
 164   }
 165
 166   @Override
 167   public void updateResultAnnotation(boolean immediate)
 168   {
 169
 170     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
 171     {
 172       Map<String, String[]> featureTypeMap = featureMap
 173               .get(service.serviceType);
 174       Map<String, Map<String, Object>> annotTypeMap = annotMap
 175               .get(service.serviceType);
 176       boolean dispFeatures = false;
 177       Map<String, Object> fc = new Hashtable<String, Object>();
 178       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
 179       /**
 180        * grouping for any annotation rows created
 181        */
 182       int graphGroup = 1;
 183       if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
 184       {
 185         for (AlignmentAnnotation ala : alignViewport.getAlignment()
 186                 .getAlignmentAnnotation())
 187         {
 188           if (ala.graphGroup > graphGroup)
 189           {
 190             graphGroup = ala.graphGroup;
 191           }
 192         }
 193       }
 194
 195       for (String seqId : seqNames.keySet())
 196       {
 197         boolean sameGroup = false;
 198         SequenceI dseq, aseq, seq = seqNames.get(seqId);
 199         int base = seq.findPosition(start) - 1;
 200         aseq = seq;
 201         while ((dseq = seq).getDatasetSequence() != null)
 202         {
 203           seq = seq.getDatasetSequence();
 204         }
 205         ScoreHolder scores = null;
 206         try
 207         {
 208           scores = scoremanager.getAnnotationForSequence(seqId);
 209         } catch (Exception q)
 210         {
 211           Cache.log
 212                   .info("Couldn't recover disorder prediction for sequence "
 213                           + seq.getName() + "(Prediction name was " + 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], base + rn.from,
 243                           base + rn.to, val = vals.next().floatValue(),
 244                           methodName);
 245                 }
 246                 else
 247                 {
 248                   sf = new SequenceFeature(type[0], type[1], null,
 249                           base + 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(),
 273                       aseq, base + 1, scr);
 274               annot.graph = AlignmentAnnotation.LINE_GRAPH;
 275
 276               Map<String, Object> styleMap = (annotTypeMap == null) ? null
 277                       : annotTypeMap.get(scr.getMethod());
 278
 279               annot.visible = (styleMap == null
 280                       || styleMap.get(INVISIBLE) == null);
 281               double[] thrsh = (styleMap == null) ? null
 282                       : (double[]) styleMap.get(THRESHOLD);
 283               float[] range = (styleMap == null) ? null
 284                       : (float[]) styleMap.get(RANGE);
 285               if (range != null)
 286               {
 287                 annot.graphMin = range[0];
 288                 annot.graphMax = range[1];
 289               }
 290               if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
 291               {
 292                 {
 293                   if (!sameGroup)
 294                   {
 295                     graphGroup++;
 296                     sameGroup = true;
 297                   }
 298
 299                   annot.graphGroup = graphGroup;
 300                 }
 301               }
 302
 303               annot.description = "<html>" + service.getActionText()
 304                       + " - raw scores";
 305               if (thrsh != null)
 306               {
 307                 String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
 308                         + thrsh[1] + " indicates disorder";
 309                 annot.threshold = new GraphLine((float) thrsh[1],
 310                         threshNote, Color.red);
 311                 annot.description += "<br/>" + threshNote;
 312               }
 313               annot.description += "</html>";
 314               Color col = ColorUtils
 315                       .createColourFromName(typeName + scr.getMethod());
 316               for (int p = 0, ps = annot.annotations.length; p < ps; p++)
 317               {
 318                 if (annot.annotations[p] != null)
 319                 {
 320                   annot.annotations[p].colour = col;
 321                 }
 322               }
 323               annot._linecolour = col;
 324               // finally, update any dataset annotation
 325               replaceAnnotationOnAlignmentWith(annot, typename, calcName,
 326                       aseq);
 327             }
 328           }
 329         }
 330         if (lastAnnot + 1 == ourAnnot.size())
 331         {
 332           // remove singleton alignment annotation row
 333           ourAnnot.get(lastAnnot).graphGroup = -1;
 334         }
 335       }
 336       {
 337         if (dispFeatures)
 338         {
 339           jalview.api.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
 340                   .cloneFeatureRenderer();
 341           for (String ft : fc.keySet())
 342           {
 343             FeatureColourI gc = fr.getFeatureStyle(ft);
 344             if (gc.isSimpleColour())
 345             {
 346               // set graduated color as fading to white for minimum, and
 347               // autoscaling to values on alignment
 348               FeatureColourI ggc = new FeatureColour(Color.white,
 349                       gc.getColour(), Float.MIN_VALUE, Float.MAX_VALUE);
 350               ggc.setAutoScaled(true);
 351               fr.setColour(ft, ggc);
 352             }
 353           }
 354           // TODO: JAL-1150 - create sequence feature settings API for defining
 355           // styles and enabling/disabling feature overlay on alignment panel
 356           ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
 357           if (af.alignPanel == ap)
 358           {
 359             // only do this if the alignFrame is currently showing this view.
 360             af.setShowSeqFeatures(true);
 361           }
 362           ap.paintAlignment(true);
 363         }
 364         if (ourAnnot.size() > 0)
 365         {
 366           // Modify the visible annotation on the alignment viewport with the
 367           // new alignment annotation rows created.
 368           updateOurAnnots(ourAnnot);
 369           ap.adjustAnnotationHeight();
 370         }
 371       }
 372     }
 373   }
 374
 375   @Override
 376   public String getCalcId()
 377   {
 378     // Disorder predictions are not dynamically updated so we return null
 379     return null;
 380   }
 381
 382 }