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
  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   private static Map<String, Map<String, String[]>> featureMap;
  86
  87   private static Map<String, Map<String, Map<String, Object>>> annotMap;
  88
  89   private static String DONTCOMBINE = "DONTCOMBINE";
  90
  91   private static String INVISIBLE = "INVISIBLE";
  92   static
  93   {
  94     // TODO: turn this into some kind of configuration file that's a bit easier
  95     // to edit
  96     featureMap = new HashMap<String, Map<String, String[]>>();
  97     Map<String, String[]> fmap;
  98     featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
  99             fmap = new HashMap<String, String[]>());
 100     fmap.put("Glob", new String[]
 101     { "Globular Domain", "Predicted globular domain" });
 102     featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
 103             fmap = new HashMap<String, String[]>());
 104     featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 105             fmap = new HashMap<String, String[]>());
 106     fmap.put("REM465", new String[]
 107     { "REM465", "Missing density" });
 108     fmap.put("HOTLOOPS", new String[]
 109     { "HOTLOOPS", "Flexible loops" });
 110     fmap.put("COILS", new String[]
 111     { "COILS", "Random coil" });
 112     featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 113             fmap = new HashMap<String, String[]>());
 114     fmap.put("GlobDoms", new String[]
 115     { "Globular Domain", "Predicted globular domain" });
 116     fmap.put("Disorder", new String[]
 117     { "Protein Disorder", "Probable unstructured peptide region" });
 118     Map<String, Map<String, Object>> amap;
 119     annotMap = new HashMap<String, Map<String, Map<String, Object>>>();
 120     annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 121             amap = new HashMap<String, Map<String, Object>>());
 122     amap.put("Dydx", new HashMap<String, Object>());
 123     amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
 124     amap.get("Dydx").put(THRESHOLD, new double[]
 125     { 1, 0 });
 126     amap.get("Dydx").put(RANGE, new float[]
 127     { -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[]
 139     { 1, 0.516 });
 140     amap.get("COILS").put(RANGE, new float[]
 141     { 0, 1 });
 142
 143     amap.get("HOTLOOPS").put(THRESHOLD, new double[]
 144     { 1, 0.6 });
 145     amap.get("HOTLOOPS").put(RANGE, new float[]
 146     { 0, 1 });
 147     amap.get("REM465").put(THRESHOLD, new double[]
 148     { 1, 0.1204 });
 149     amap.get("REM465").put(RANGE, new float[]
 150     { 0, 1 });
 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         {
 215           scores = scoremanager.getAnnotationForSequence(seqId);
 216         } catch (Exception q)
 217         {
 218           Cache.log
 219                   .info("Couldn't recover disorder prediction for sequence "
 220                           + seq.getName()
 221                           + "(Prediction name was "
 222                           + seqId
 223                           + ")"
 224                           + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
 225         }
 226         float last = Float.NaN, val = Float.NaN;
 227         int lastAnnot = ourAnnot.size();
 228         if (scores != null && scores.scores != null)
 229         {
 230           for (Score scr : scores.scores)
 231           {
 232
 233             if (scr.getRanges() != null && scr.getRanges().size() > 0)
 234             {
 235               Iterator<Float> vals = scr.getScores().iterator();
 236               // make features on sequence
 237               for (Range rn : scr.getRanges())
 238               {
 239
 240                 SequenceFeature sf;
 241                 String[] type = featureTypeMap.get(scr.getMethod());
 242                 if (type == null)
 243                 {
 244                   // create a default type for this feature
 245                   type = new String[]
 246                   { typeName + " (" + scr.getMethod() + ")",
 247                       service.getActionText() };
 248                 }
 249                 if (vals.hasNext())
 250                 {
 251                   sf = new SequenceFeature(type[0], type[1],
 252                           base + rn.from, base + rn.to, val = vals.next()
 253                                   .floatValue(), methodName);
 254                 }
 255                 else
 256                 {
 257                   sf = new SequenceFeature(type[0], type[1], null, base
 258                           + rn.from, base + rn.to, methodName);
 259                 }
 260                 dseq.addSequenceFeature(sf);
 261                 if (last != val && last != Float.NaN)
 262                 {
 263                   fc.put(sf.getType(), sf);
 264                 }
 265                 last = val;
 266                 dispFeatures = true;
 267               }
 268             }
 269             else
 270             {
 271               if (scr.getScores().size() == 0)
 272               {
 273                 continue;
 274               }
 275               AlignmentAnnotation annot = createAnnotationRowsForScores(
 276                       ourAnnot,
 277                       service.serviceType + " (" + scr.getMethod() + ")",
 278                       service.getServiceTypeURI() + "/" + scr.getMethod(),
 279                       aseq, base + 1, scr);
 280               annot.graph = AlignmentAnnotation.LINE_GRAPH;
 281
 282               Map<String, Object> styleMap = (annotTypeMap == null) ? null
 283                       : annotTypeMap.get(scr.getMethod());
 284
 285               annot.visible = (styleMap == null || styleMap.get(INVISIBLE) == null);
 286               double[] thrsh = (styleMap == null) ? null
 287                       : (double[]) styleMap.get(THRESHOLD);
 288               float[] range = (styleMap == null) ? null
 289                       : (float[]) styleMap.get(RANGE);
 290               if (range != null)
 291               {
 292                 annot.graphMin = range[0];
 293                 annot.graphMax = range[1];
 294               }
 295               if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
 296               {
 297                 {
 298                   if (!sameGroup)
 299                   {
 300                     graphGroup++;
 301                     sameGroup = true;
 302                   }
 303
 304                   annot.graphGroup = graphGroup;
 305                 }
 306               }
 307
 308               annot.description = "<html>" + service.getActionText()
 309                       + " - raw scores";
 310               if (thrsh != null)
 311               {
 312                 String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
 313                         + thrsh[1] + " indicates disorder";
 314                 annot.threshold = new GraphLine((float) thrsh[1],
 315                         threshNote, Color.red);
 316                 annot.description += "<br/>" + threshNote;
 317               }
 318               annot.description += "</html>";
 319               Color col = new UserColourScheme(typeName)
 320                       .createColourFromName(typeName + scr.getMethod());
 321               for (int p = 0, ps = annot.annotations.length; p < ps; p++)
 322               {
 323                 if (annot.annotations[p] != null)
 324                 {
 325                   annot.annotations[p].colour = col;
 326                 }
 327               }
 328               annot._linecolour = col;
 329             }
 330           }
 331         }
 332         if (lastAnnot + 1 == ourAnnot.size())
 333         {
 334           // remove singleton alignment annotation row
 335           ourAnnot.get(lastAnnot).graphGroup = -1;
 336         }
 337       }
 338       {
 339         if (dispFeatures)
 340         {
 341           jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
 342                   .cloneFeatureRenderer();
 343           for (String ft : fc.keySet())
 344           {
 345             Object gc = fr.getFeatureStyle(ft);
 346             if (gc instanceof Color)
 347             {
 348               // set graduated color as fading to white for minimum, and
 349               // autoscaling to values on alignment
 350               GraduatedColor ggc = new GraduatedColor(Color.white,
 351                       (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE);
 352               ggc.setAutoScaled(true);
 353               fr.setColour(ft, ggc);
 354             }
 355           }
 356           // TODO: JAL-1150 - create sequence feature settings API for defining
 357           // styles and enabling/disabling feature overlay on alignment panel
 358           ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
 359           if (af.alignPanel == ap)
 360           {
 361             // only do this if the alignFrame is currently showing this view.
 362             af.setShowSeqFeatures(true);
 363           }
 364           ap.paintAlignment(true);
 365         }
 366         if (ourAnnot.size() > 0)
 367         {
 368           // Modify the visible annotation on the alignment viewport with the
 369           // new alignment annotation rows created.
 370           updateOurAnnots(ourAnnot);
 371           ap.adjustAnnotationHeight();
 372         }
 373       }
 374     }
 375   }
 376
 377 }