src/jalview/ws/jws2/AADisorderClient.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
   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 of the License, or (at your option) any later version.
  10  *
  11  * Jalview is distributed in the hope that it will be useful, but
  12  * WITHOUT ANY WARRANTY; without even the implied warranty
  13  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  14  * PURPOSE.  See the GNU General Public License for more details.
  15  *
  16  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  17  * The Jalview Authors are detailed in the 'AUTHORS' file.
  18  */
  19 package jalview.ws.jws2;
  20
  21 import jalview.api.AlignCalcWorkerI;
  22 import jalview.bin.Cache;
  23 import jalview.datamodel.AlignmentAnnotation;
  24 import jalview.datamodel.GraphLine;
  25 import jalview.datamodel.SequenceFeature;
  26 import jalview.datamodel.SequenceI;
  27 import jalview.gui.AlignFrame;
  28 import jalview.schemes.GraduatedColor;
  29 import jalview.schemes.UserColourScheme;
  30 import jalview.ws.jws2.jabaws2.Jws2Instance;
  31 import jalview.ws.params.WsParamSetI;
  32
  33 import java.awt.Color;
  34 import java.util.ArrayList;
  35 import java.util.HashMap;
  36 import java.util.Hashtable;
  37 import java.util.Iterator;
  38 import java.util.List;
  39 import java.util.Map;
  40
  41 import compbio.data.sequence.Range;
  42 import compbio.data.sequence.Score;
  43 import compbio.data.sequence.ScoreManager.ScoreHolder;
  44 import compbio.metadata.Argument;
  45
  46 public class AADisorderClient extends JabawsCalcWorker implements
  47         AlignCalcWorkerI
  48 {
  49
  50   private static final String THRESHOLD = "THRESHOLD";
  51   private static final String RANGE = "RANGE";
  52
  53   String typeName;
  54
  55   String methodName;
  56
  57   String groupName;
  58
  59   AlignFrame af;
  60
  61   public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
  62           WsParamSetI preset, List<Argument> paramset)
  63   {
  64     super(sh, alignFrame, preset, paramset);
  65     af = alignFrame;
  66     typeName = sh.action;
  67     methodName = sh.serviceType;
  68
  69     submitGaps = false;
  70     alignedSeqs = false;
  71     nucleotidesAllowed = false;
  72     proteinAllowed = true;
  73     bySequence = true;
  74   }
  75
  76   @Override
  77   public String getServiceActionText()
  78   {
  79     return "Submitting amino acid sequences for disorder prediction.";
  80   }
  81
  82   private static Map<String, Map<String, String[]>> featureMap;
  83
  84   private static Map<String, Map<String, Map<String, Object>>> annotMap;
  85
  86   private static String DONTCOMBINE = "DONTCOMBINE";
  87
  88   private static String INVISIBLE = "INVISIBLE";
  89   static
  90   {
  91     // TODO: turn this into some kind of configuration file that's a bit easier
  92     // to edit
  93     featureMap = new HashMap<String, Map<String, String[]>>();
  94     Map<String, String[]> fmap;
  95     featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
  96             fmap = new HashMap<String, String[]>());
  97     fmap.put("Glob", new String[]
  98     { "Globular Domain", "Predicted globular domain" });
  99     featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
 100             fmap = new HashMap<String, String[]>());
 101     featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 102             fmap = new HashMap<String, String[]>());
 103     fmap.put("REM465", new String[]
 104     { "REM465", "Missing density" });
 105     fmap.put("HOTLOOPS", new String[]
 106     { "HOTLOOPS", "Flexible loops" });
 107     fmap.put("COILS", new String[]
 108     { "COILS", "Random coil" });
 109     featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 110             fmap = new HashMap<String, String[]>());
 111     fmap.put("GlobDoms", new String[]
 112     { "Globular Domain", "Predicted globular domain" });
 113     fmap.put("Disorder", new String[]
 114     { "Protein Disorder", "Probable unstructured peptide region" });
 115     Map<String, Map<String, Object>> amap;
 116     annotMap = new HashMap<String, Map<String, Map<String, Object>>>();
 117     annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 118             amap = new HashMap<String, Map<String, Object>>());
 119     amap.put("Dydx", new HashMap<String, Object>());
 120     amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
 121     amap.get("Dydx").put(THRESHOLD, new double[]
 122     { 1, 0 });
 123     amap.get("Dydx").put(RANGE, new float[]
 124             { -1, +1 });
 125
 126     amap.put("SmoothedScore", new HashMap<String, Object>());
 127     amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
 128     amap.put("RawScore", new HashMap<String, Object>());
 129     amap.get("RawScore").put(INVISIBLE, INVISIBLE);
 130     annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 131             amap = new HashMap<String, Map<String, Object>>());
 132     amap.put("COILS", new HashMap<String, Object>());
 133     amap.put("HOTLOOPS", new HashMap<String, Object>());
 134     amap.put("REM465", new HashMap<String, Object>());
 135     amap.get("COILS").put(THRESHOLD, new double[]
 136     { 1, 0.516 });
 137     amap.get("COILS").put(RANGE, new float[]
 138             { 0, 1 });
 139
 140     amap.get("HOTLOOPS").put(THRESHOLD, new double[]
 141     { 1, 0.6 });
 142     amap.get("HOTLOOPS").put(RANGE, new float[]
 143             { 0, 1 });
 144     amap.get("REM465").put(THRESHOLD, new double[]
 145     { 1, 0.1204 });
 146     amap.get("REM465").put(RANGE, new float[]
 147             { 0, 1 });
 148
 149
 150     annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
 151             amap = new HashMap<String, Map<String, Object>>());
 152     amap.put("Long", new HashMap<String, Object>());
 153     amap.put("Short", new HashMap<String, Object>());
 154     amap.get("Long").put(THRESHOLD, new double[]
 155     { 1, 0.5 });
 156     amap.get("Long").put(RANGE, new float[]
 157             { 0, 1 });
 158     amap.get("Short").put(THRESHOLD, new double[]
 159     { 1, 0.5 });
 160     amap.get("Short").put(RANGE, new float[]
 161             { 0, 1 });
 162     annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
 163             amap = new HashMap<String, Map<String, Object>>());
 164     amap.put("JRonn", new HashMap<String, Object>());
 165     amap.get("JRonn").put(THRESHOLD, new double[]
 166     { 1, 0.5 });
 167     amap.get("JRonn").put(RANGE, new float[]
 168             { 0, 1 });
 169   }
 170
 171   @Override
 172   public void updateResultAnnotation(boolean immediate)
 173   {
 174
 175     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
 176     {
 177       Map<String, String[]> featureTypeMap = featureMap
 178               .get(service.serviceType);
 179       Map<String, Map<String, Object>> annotTypeMap = annotMap
 180               .get(service.serviceType);
 181       boolean dispFeatures = false;
 182       Map<String, Object> fc = new Hashtable<String, Object>();
 183       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
 184       /**
 185        * grouping for any annotation rows created
 186        */
 187       int graphGroup = 1;
 188       if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
 189       {
 190         for (AlignmentAnnotation ala : alignViewport.getAlignment()
 191                 .getAlignmentAnnotation())
 192         {
 193           if (ala.graphGroup > graphGroup)
 194           {
 195             graphGroup = ala.graphGroup;
 196           }
 197         }
 198       }
 199
 200       for (String seqId : seqNames.keySet())
 201       {
 202         boolean sameGroup = false;
 203         SequenceI dseq, aseq, seq = seqNames.get(seqId);
 204         int base = seq.findPosition(start)-1;
 205         aseq = seq;
 206         while ((dseq = seq).getDatasetSequence() != null)
 207         {
 208           seq = seq.getDatasetSequence();
 209         }
 210         ScoreHolder scores = null;
 211         try {
 212           scores = scoremanager.getAnnotationForSequence(seqId);
 213         } catch (Exception q)
 214         {
 215           Cache.log
 216                   .info("Couldn't recover disorder prediction for sequence "
 217                           + seq.getName()
 218                           + "(Prediction name was "
 219                           + seqId+")"
 220                           + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
 221         }
 222         float last = Float.NaN, val = Float.NaN;
 223         int lastAnnot = ourAnnot.size();
 224         if (scores!=null && scores.scores!=null) {
 225           for (Score scr : scores.scores)
 226           {
 227
 228             if (scr.getRanges() != null && scr.getRanges().size() > 0)
 229             {
 230               Iterator<Float> vals = scr.getScores().iterator();
 231               // make features on sequence
 232               for (Range rn : scr.getRanges())
 233               {
 234
 235                 SequenceFeature sf;
 236                 String[] type = featureTypeMap.get(scr.getMethod());
 237                 if (type == null)
 238                 {
 239                   // create a default type for this feature
 240                   type = new String[]
 241                   { typeName + " (" + scr.getMethod() + ")",
 242                       service.getActionText() };
 243                 }
 244                 if (vals.hasNext())
 245                 {
 246                   sf = new SequenceFeature(type[0], type[1],
 247                           base + rn.from, base + rn.to, val = vals.next()
 248                                   .floatValue(), methodName);
 249                 }
 250                 else
 251                 {
 252                   sf = new SequenceFeature(type[0], type[1], null, base
 253                           + rn.from, base + rn.to, methodName);
 254                 }
 255                 dseq.addSequenceFeature(sf);
 256                 if (last != val && last != Float.NaN)
 257                 {
 258                   fc.put(sf.getType(), sf);
 259                 }
 260                 last = val;
 261                 dispFeatures = true;
 262               }
 263             }
 264             else
 265             {
 266               if (scr.getScores().size() == 0)
 267               {
 268                 continue;
 269               }
 270               AlignmentAnnotation annot = createAnnotationRowsForScores(
 271                       ourAnnot,
 272                       service.serviceType + " (" + scr.getMethod() + ")",
 273                       service.getServiceTypeURI() + "/" + scr.getMethod(),
 274                       aseq, base + 1, scr);
 275               annot.graph = AlignmentAnnotation.LINE_GRAPH;
 276
 277               Map<String,Object> styleMap = (annotTypeMap == null) ? null : annotTypeMap.get(scr.getMethod());
 278
 279               annot.visible = (styleMap == null || styleMap.get(INVISIBLE) == null);
 280               double[] thrsh = (styleMap==null) ? null
 281                       : (double[]) styleMap.get(
 282                               THRESHOLD);
 283               float[] range = (styleMap==null) ? null : (float[]) styleMap.get(
 284                       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 = new UserColourScheme(typeName)
 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             }
 325           }
 326         }
 327         if (lastAnnot + 1 == ourAnnot.size())
 328         {
 329           // remove singleton alignment annotation row
 330           ourAnnot.get(lastAnnot).graphGroup = -1;
 331         }
 332       }
 333       {
 334         if (dispFeatures)
 335         {
 336           jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
 337                   .cloneFeatureRenderer();
 338           for (String ft : fc.keySet())
 339           {
 340             Object gc = fr.getFeatureStyle(ft);
 341             if (gc instanceof Color)
 342             {
 343               // set graduated color as fading to white for minimum, and
 344               // autoscaling to values on alignment
 345               GraduatedColor ggc = new GraduatedColor(Color.white,
 346                       (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE);
 347               ggc.setAutoScaled(true);
 348               fr.setColour(ft, ggc);
 349             }
 350           }
 351           // TODO: JAL-1150 - create sequence feature settings API for defining
 352           // styles and enabling/disabling feature overlay on alignment panel
 353           ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
 354           if (af.alignPanel == ap)
 355           {
 356             // only do this if the alignFrame is currently showing this view.
 357             af.setShowSeqFeatures(true);
 358           }
 359           ap.paintAlignment(true);
 360         }
 361         if (ourAnnot.size() > 0)
 362         {
 363           // Modify the visible annotation on the alignment viewport with the
 364           // new alignment annotation rows created.
 365           updateOurAnnots(ourAnnot);
 366           ap.adjustAnnotationHeight();
 367         }
 368       }
 369     }
 370   }
 371
 372 }