src/jalview/ws/jws2/AADisorderClient.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
   3  * Copyright (C) 2014 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.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 implements
  49         AlignCalcWorkerI
  50 {
  51
  52   private static final String THRESHOLD = "THRESHOLD";
  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   private static Map<String, Map<String, String[]>> featureMap;
  85
  86   private static Map<String, Map<String, Map<String, Object>>> annotMap;
  87
  88   private static String DONTCOMBINE = "DONTCOMBINE";
  89
  90   private static String INVISIBLE = "INVISIBLE";
  91   static
  92   {
  93     // TODO: turn this into some kind of configuration file that's a bit easier
  94     // to edit
  95     featureMap = new HashMap<String, Map<String, String[]>>();
  96     Map<String, String[]> fmap;
  97     featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
  98             fmap = new HashMap<String, String[]>());
  99     fmap.put("Glob", new String[]
 100     { "Globular Domain", "Predicted globular domain" });
 101     featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
 102             fmap = new HashMap<String, String[]>());
 103     featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 104             fmap = new HashMap<String, String[]>());
 105     fmap.put("REM465", new String[]
 106     { "REM465", "Missing density" });
 107     fmap.put("HOTLOOPS", new String[]
 108     { "HOTLOOPS", "Flexible loops" });
 109     fmap.put("COILS", new String[]
 110     { "COILS", "Random coil" });
 111     featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 112             fmap = new HashMap<String, String[]>());
 113     fmap.put("GlobDoms", new String[]
 114     { "Globular Domain", "Predicted globular domain" });
 115     fmap.put("Disorder", new String[]
 116     { "Protein Disorder", "Probable unstructured peptide region" });
 117     Map<String, Map<String, Object>> amap;
 118     annotMap = new HashMap<String, Map<String, Map<String, Object>>>();
 119     annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 120             amap = new HashMap<String, Map<String, Object>>());
 121     amap.put("Dydx", new HashMap<String, Object>());
 122     amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
 123     amap.get("Dydx").put(THRESHOLD, new double[]
 124     { 1, 0 });
 125     amap.get("Dydx").put(RANGE, new float[]
 126             { -1, +1 });
 127
 128     amap.put("SmoothedScore", new HashMap<String, Object>());
 129     amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
 130     amap.put("RawScore", new HashMap<String, Object>());
 131     amap.get("RawScore").put(INVISIBLE, INVISIBLE);
 132     annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 133             amap = new HashMap<String, Map<String, Object>>());
 134     amap.put("COILS", new HashMap<String, Object>());
 135     amap.put("HOTLOOPS", new HashMap<String, Object>());
 136     amap.put("REM465", new HashMap<String, Object>());
 137     amap.get("COILS").put(THRESHOLD, new double[]
 138     { 1, 0.516 });
 139     amap.get("COILS").put(RANGE, new float[]
 140             { 0, 1 });
 141
 142     amap.get("HOTLOOPS").put(THRESHOLD, new double[]
 143     { 1, 0.6 });
 144     amap.get("HOTLOOPS").put(RANGE, new float[]
 145             { 0, 1 });
 146     amap.get("REM465").put(THRESHOLD, new double[]
 147     { 1, 0.1204 });
 148     amap.get("REM465").put(RANGE, new float[]
 149             { 0, 1 });
 150
 151
 152     annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
 153             amap = new HashMap<String, Map<String, Object>>());
 154     amap.put("Long", new HashMap<String, Object>());
 155     amap.put("Short", new HashMap<String, Object>());
 156     amap.get("Long").put(THRESHOLD, new double[]
 157     { 1, 0.5 });
 158     amap.get("Long").put(RANGE, new float[]
 159             { 0, 1 });
 160     amap.get("Short").put(THRESHOLD, new double[]
 161     { 1, 0.5 });
 162     amap.get("Short").put(RANGE, new float[]
 163             { 0, 1 });
 164     annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
 165             amap = new HashMap<String, Map<String, Object>>());
 166     amap.put("JRonn", new HashMap<String, Object>());
 167     amap.get("JRonn").put(THRESHOLD, new double[]
 168     { 1, 0.5 });
 169     amap.get("JRonn").put(RANGE, new float[]
 170             { 0, 1 });
 171   }
 172
 173   @Override
 174   public void updateResultAnnotation(boolean immediate)
 175   {
 176
 177     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
 178     {
 179       Map<String, String[]> featureTypeMap = featureMap
 180               .get(service.serviceType);
 181       Map<String, Map<String, Object>> annotTypeMap = annotMap
 182               .get(service.serviceType);
 183       boolean dispFeatures = false;
 184       Map<String, Object> fc = new Hashtable<String, Object>();
 185       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
 186       /**
 187        * grouping for any annotation rows created
 188        */
 189       int graphGroup = 1;
 190       if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
 191       {
 192         for (AlignmentAnnotation ala : alignViewport.getAlignment()
 193                 .getAlignmentAnnotation())
 194         {
 195           if (ala.graphGroup > graphGroup)
 196           {
 197             graphGroup = ala.graphGroup;
 198           }
 199         }
 200       }
 201
 202       for (String seqId : seqNames.keySet())
 203       {
 204         boolean sameGroup = false;
 205         SequenceI dseq, aseq, seq = seqNames.get(seqId);
 206         int base = seq.findPosition(start)-1;
 207         aseq = seq;
 208         while ((dseq = seq).getDatasetSequence() != null)
 209         {
 210           seq = seq.getDatasetSequence();
 211         }
 212         ScoreHolder scores = null;
 213         try {
 214           scores = scoremanager.getAnnotationForSequence(seqId);
 215         } catch (Exception q)
 216         {
 217           Cache.log
 218                   .info("Couldn't recover disorder prediction for sequence "
 219                           + seq.getName()
 220                           + "(Prediction name was "
 221                           + seqId+")"
 222                           + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
 223         }
 224         float last = Float.NaN, val = Float.NaN;
 225         int lastAnnot = ourAnnot.size();
 226         if (scores!=null && scores.scores!=null) {
 227           for (Score scr : scores.scores)
 228           {
 229
 230             if (scr.getRanges() != null && scr.getRanges().size() > 0)
 231             {
 232               Iterator<Float> vals = scr.getScores().iterator();
 233               // make features on sequence
 234               for (Range rn : scr.getRanges())
 235               {
 236
 237                 SequenceFeature sf;
 238                 String[] type = featureTypeMap.get(scr.getMethod());
 239                 if (type == null)
 240                 {
 241                   // create a default type for this feature
 242                   type = new String[]
 243                   { typeName + " (" + scr.getMethod() + ")",
 244                       service.getActionText() };
 245                 }
 246                 if (vals.hasNext())
 247                 {
 248                   sf = new SequenceFeature(type[0], type[1],
 249                           base + rn.from, base + rn.to, val = vals.next()
 250                                   .floatValue(), methodName);
 251                 }
 252                 else
 253                 {
 254                   sf = new SequenceFeature(type[0], type[1], null, base
 255                           + rn.from, base + rn.to, methodName);
 256                 }
 257                 dseq.addSequenceFeature(sf);
 258                 if (last != val && last != Float.NaN)
 259                 {
 260                   fc.put(sf.getType(), sf);
 261                 }
 262                 last = val;
 263                 dispFeatures = true;
 264               }
 265             }
 266             else
 267             {
 268               if (scr.getScores().size() == 0)
 269               {
 270                 continue;
 271               }
 272               AlignmentAnnotation annot = createAnnotationRowsForScores(
 273                       ourAnnot,
 274                       service.serviceType + " (" + scr.getMethod() + ")",
 275                       service.getServiceTypeURI() + "/" + scr.getMethod(),
 276                       aseq, base + 1, scr);
 277               annot.graph = AlignmentAnnotation.LINE_GRAPH;
 278
 279               Map<String,Object> styleMap = (annotTypeMap == null) ? null : annotTypeMap.get(scr.getMethod());
 280
 281               annot.visible = (styleMap == null || styleMap.get(INVISIBLE) == null);
 282               double[] thrsh = (styleMap==null) ? null
 283                       : (double[]) styleMap.get(
 284                               THRESHOLD);
 285               float[] range = (styleMap==null) ? null : (float[]) styleMap.get(
 286                       RANGE);
 287               if (range!=null)
 288               {
 289                 annot.graphMin = range[0];
 290                 annot.graphMax = range[1];
 291               }
 292               if (styleMap==null || styleMap.get(DONTCOMBINE) == null)
 293               {
 294                 {
 295                   if (!sameGroup)
 296                   {
 297                     graphGroup++;
 298                     sameGroup = true;
 299                   }
 300
 301                   annot.graphGroup = graphGroup;
 302                 }
 303               }
 304
 305               annot.description = "<html>" + service.getActionText()
 306                       + " - raw scores";
 307               if (thrsh != null)
 308               {
 309                 String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
 310                         + thrsh[1] + " indicates disorder";
 311                 annot.threshold = new GraphLine((float) thrsh[1],
 312                         threshNote, Color.red);
 313                 annot.description += "<br/>" + threshNote;
 314               }
 315               annot.description += "</html>";
 316               Color col = new UserColourScheme(typeName)
 317                       .createColourFromName(typeName + scr.getMethod());
 318               for (int p = 0, ps = annot.annotations.length; p < ps; p++)
 319               {
 320                 if (annot.annotations[p] != null)
 321                 {
 322                   annot.annotations[p].colour = col;
 323                 }
 324               }
 325               annot._linecolour = col;
 326             }
 327           }
 328         }
 329         if (lastAnnot + 1 == ourAnnot.size())
 330         {
 331           // remove singleton alignment annotation row
 332           ourAnnot.get(lastAnnot).graphGroup = -1;
 333         }
 334       }
 335       {
 336         if (dispFeatures)
 337         {
 338           jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
 339                   .cloneFeatureRenderer();
 340           for (String ft : fc.keySet())
 341           {
 342             Object gc = fr.getFeatureStyle(ft);
 343             if (gc instanceof Color)
 344             {
 345               // set graduated color as fading to white for minimum, and
 346               // autoscaling to values on alignment
 347               GraduatedColor ggc = new GraduatedColor(Color.white,
 348                       (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE);
 349               ggc.setAutoScaled(true);
 350               fr.setColour(ft, ggc);
 351             }
 352           }
 353           // TODO: JAL-1150 - create sequence feature settings API for defining
 354           // styles and enabling/disabling feature overlay on alignment panel
 355           ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
 356           if (af.alignPanel == ap)
 357           {
 358             // only do this if the alignFrame is currently showing this view.
 359             af.setShowSeqFeatures(true);
 360           }
 361           ap.paintAlignment(true);
 362         }
 363         if (ourAnnot.size() > 0)
 364         {
 365           // Modify the visible annotation on the alignment viewport with the
 366           // new alignment annotation rows created.
 367           updateOurAnnots(ourAnnot);
 368           ap.adjustAnnotationHeight();
 369         }
 370       }
 371     }
 372   }
 373
 374 }