src/jalview/ws/jws2/jabaws2/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.jabaws2;
  22
  23 import jalview.api.AlignViewportI;
  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.schemes.FeatureColour;
  31 import jalview.util.ColorUtils;
  32 import jalview.ws.gui.AnnotationWsJob;
  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.Range;
  43 import compbio.data.sequence.Score;
  44 import compbio.data.sequence.ScoreManager.ScoreHolder;
  45
  46 public class AADisorderClient extends JabawsAnnotationInstance
  47 {
  48   // static configuration
  49   public static String getServiceActionText()
  50   {
  51     return "Submitting amino acid sequences for disorder prediction.";
  52   }
  53
  54   // minSeq = 1; protein only, no gaps
  55
  56   // instance
  57   public AADisorderClient(Jws2Instance handle)
  58   {
  59     super(handle);
  60
  61   }
  62
  63   @Override
  64   List<AlignmentAnnotation> annotationFromScoreManager(
  65           AnnotationWsJob running, AlignViewportI alignViewport,
  66           boolean[] gapMap)
  67   {
  68
  69     Map<String, String[]> featureTypeMap = featureMap.get(our.getName());
  70     Map<String, Map<String, Object>> annotTypeMap = annotMap
  71             .get(our.getName());
  72     boolean dispFeatures = false;
  73     Map<String, Object> fc = new Hashtable<>();
  74     List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
  75     /**
  76      * grouping for any annotation rows created
  77      */
  78     int graphGroup = 1;
  79     if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
  80     {
  81       for (AlignmentAnnotation ala : alignViewport.getAlignment()
  82               .getAlignmentAnnotation())
  83       {
  84         if (ala.graphGroup > graphGroup)
  85         {
  86           graphGroup = ala.graphGroup;
  87         }
  88       }
  89     }
  90
  91     // TODO: downgrade code below so we don't annotate sequences directly
  92     Map<String, SequenceI> seqNames = running.getSeqNames();
  93     int start = running.getStartPos();
  94     for (String seqId : seqNames.keySet())
  95     {
  96       boolean sameGroup = false;
  97       SequenceI dseq, aseq, seq = seqNames.get(seqId);
  98       int base = seq.findPosition(start) - 1;
  99       aseq = seq;
 100       while ((dseq = seq).getDatasetSequence() != null)
 101       {
 102         seq = seq.getDatasetSequence();
 103       }
 104       ScoreHolder scores = null;
 105       try
 106       {
 107         scores = scoremanager.getAnnotationForSequence(seqId);
 108       } catch (Exception q)
 109       {
 110         Cache.log.info("Couldn't recover disorder prediction for sequence "
 111                 + seq.getName() + "(Prediction name was " + seqId + ")"
 112                 + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.");
 113       }
 114       float last = Float.NaN, val = Float.NaN;
 115       int lastAnnot = ourAnnot.size();
 116       if (scores != null && scores.scores != null)
 117       {
 118         for (Score scr : scores.scores)
 119         {
 120
 121           if (scr.getRanges() != null && scr.getRanges().size() > 0)
 122           {
 123             Iterator<Float> vals = scr.getScores().iterator();
 124             // make features on sequence
 125             for (Range rn : scr.getRanges())
 126             {
 127
 128               SequenceFeature sf;
 129               String[] type = featureTypeMap.get(scr.getMethod());
 130               if (type == null)
 131               {
 132                 // create a default type for this feature
 133                 type = new String[] {
 134                     typeName + " (" + scr.getMethod() + ")",
 135                     our.getActionText() };
 136               }
 137               if (vals.hasNext())
 138               {
 139                 val = vals.next().floatValue();
 140                 sf = new SequenceFeature(type[0], type[1], base + rn.from,
 141                         base + rn.to, val, methodName);
 142               }
 143               else
 144               {
 145                 sf = new SequenceFeature(type[0], type[1], base + rn.from,
 146                         base + rn.to, methodName);
 147               }
 148               dseq.addSequenceFeature(sf);
 149               if (last != val && !Float.isNaN(last))
 150               {
 151                 fc.put(sf.getType(), sf);
 152               }
 153               last = val;
 154               running.setTransferSequenceFeatures(true);
 155               dispFeatures = true;
 156             }
 157           }
 158           else
 159           {
 160             if (scr.getScores().size() == 0)
 161             {
 162               continue;
 163             }
 164             String typename, calcName;
 165             AlignmentAnnotation annot = createAnnotationRowsForScores(
 166                     alignViewport, gapMap, ourAnnot,
 167                     typename = our.getName() + " (" + scr.getMethod() + ")",
 168                     calcName = our.getNameURI() + "/" + scr.getMethod(),
 169                     aseq, base + 1, scr);
 170             annot.graph = AlignmentAnnotation.LINE_GRAPH;
 171
 172             Map<String, Object> styleMap = (annotTypeMap == null) ? null
 173                     : annotTypeMap.get(scr.getMethod());
 174
 175             annot.visible = (styleMap == null
 176                     || styleMap.get(INVISIBLE) == null);
 177             double[] thrsh = (styleMap == null) ? null
 178                     : (double[]) styleMap.get(THRESHOLD);
 179             float[] range = (styleMap == null) ? null
 180                     : (float[]) styleMap.get(RANGE);
 181             if (range != null)
 182             {
 183               annot.graphMin = range[0];
 184               annot.graphMax = range[1];
 185             }
 186             if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
 187             {
 188               {
 189                 if (!sameGroup)
 190                 {
 191                   graphGroup++;
 192                   sameGroup = true;
 193                 }
 194
 195                 annot.graphGroup = graphGroup;
 196               }
 197             }
 198
 199             annot.description = "<html>" + our.getActionText()
 200                     + " - raw scores";
 201             if (thrsh != null)
 202             {
 203               String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
 204                       + thrsh[1] + " indicates disorder";
 205               annot.threshold = new GraphLine((float) thrsh[1], threshNote,
 206                       Color.red);
 207               annot.description += "<br/>" + threshNote;
 208             }
 209             annot.description += "</html>";
 210             Color col = ColorUtils
 211                     .createColourFromName(typeName + scr.getMethod());
 212             for (int p = 0, ps = annot.annotations.length; p < ps; p++)
 213             {
 214               if (annot.annotations[p] != null)
 215               {
 216                 annot.annotations[p].colour = col;
 217               }
 218             }
 219             annot._linecolour = col;
 220             // finally, update any dataset annotation
 221             replaceAnnotationOnAlignmentWith(annot, typename, calcName,
 222                     aseq);
 223           }
 224         }
 225       }
 226       if (lastAnnot + 1 == ourAnnot.size())
 227       {
 228         // remove singleton alignment annotation row
 229         ourAnnot.get(lastAnnot).graphGroup = -1;
 230       }
 231     }
 232     {
 233       if (dispFeatures)
 234       {
 235         jalview.api.FeatureRenderer fr = running.getFeatureRenderer();
 236         for (String ft : fc.keySet())
 237         {
 238           FeatureColourI gc = fr.getFeatureStyle(ft);
 239           if (gc.isSimpleColour())
 240           {
 241             // set graduated color as fading to white for minimum, and
 242             // autoscaling to values on alignment
 243             FeatureColourI ggc = new FeatureColour(gc.getColour(),
 244                     Color.white, gc.getColour(), Color.white,
 245                     Float.MIN_VALUE, Float.MAX_VALUE);
 246             ggc.setAutoScaled(true);
 247             fr.setColour(ft, ggc);
 248           }
 249         }
 250
 251       }
 252       return ourAnnot;
 253     }
 254   }
 255
 256   private static final String THRESHOLD = "THRESHOLD";
 257
 258   private static final String RANGE = "RANGE";
 259
 260   String typeName;
 261
 262   String methodName;
 263
 264   String groupName;
 265
 266   private static Map<String, Map<String, String[]>> featureMap;
 267
 268   private static Map<String, Map<String, Map<String, Object>>> annotMap;
 269
 270   private static String DONTCOMBINE = "DONTCOMBINE";
 271
 272   private static String INVISIBLE = "INVISIBLE";
 273   static
 274   {
 275     // TODO: turn this into some kind of configuration file that's a bit easier
 276     // to edit
 277     featureMap = new HashMap<>();
 278     Map<String, String[]> fmap;
 279     featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
 280             fmap = new HashMap<>());
 281     fmap.put("Glob",
 282             new String[]
 283             { "Globular Domain", "Predicted globular domain" });
 284     featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
 285             fmap = new HashMap<>());
 286     featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 287             fmap = new HashMap<>());
 288     fmap.put("REM465", new String[] { "REM465", "Missing density" });
 289     fmap.put("HOTLOOPS", new String[] { "HOTLOOPS", "Flexible loops" });
 290     fmap.put("COILS", new String[] { "COILS", "Random coil" });
 291     featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 292             fmap = new HashMap<>());
 293     fmap.put("GlobDoms",
 294             new String[]
 295             { "Globular Domain", "Predicted globular domain" });
 296     fmap.put("Disorder",
 297             new String[]
 298             { "Protein Disorder", "Probable unstructured peptide region" });
 299     Map<String, Map<String, Object>> amap;
 300     annotMap = new HashMap<>();
 301     annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 302             amap = new HashMap<>());
 303     amap.put("Dydx", new HashMap<String, Object>());
 304     amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
 305     amap.get("Dydx").put(THRESHOLD, new double[] { 1, 0 });
 306     amap.get("Dydx").put(RANGE, new float[] { -1, +1 });
 307
 308     amap.put("SmoothedScore", new HashMap<String, Object>());
 309     amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
 310     amap.put("RawScore", new HashMap<String, Object>());
 311     amap.get("RawScore").put(INVISIBLE, INVISIBLE);
 312     annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 313             amap = new HashMap<>());
 314     amap.put("COILS", new HashMap<String, Object>());
 315     amap.put("HOTLOOPS", new HashMap<String, Object>());
 316     amap.put("REM465", new HashMap<String, Object>());
 317     amap.get("COILS").put(THRESHOLD, new double[] { 1, 0.516 });
 318     amap.get("COILS").put(RANGE, new float[] { 0, 1 });
 319
 320     amap.get("HOTLOOPS").put(THRESHOLD, new double[] { 1, 0.6 });
 321     amap.get("HOTLOOPS").put(RANGE, new float[] { 0, 1 });
 322     amap.get("REM465").put(THRESHOLD, new double[] { 1, 0.1204 });
 323     amap.get("REM465").put(RANGE, new float[] { 0, 1 });
 324
 325     annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
 326             amap = new HashMap<>());
 327     amap.put("Long", new HashMap<String, Object>());
 328     amap.put("Short", new HashMap<String, Object>());
 329     amap.get("Long").put(THRESHOLD, new double[] { 1, 0.5 });
 330     amap.get("Long").put(RANGE, new float[] { 0, 1 });
 331     amap.get("Short").put(THRESHOLD, new double[] { 1, 0.5 });
 332     amap.get("Short").put(RANGE, new float[] { 0, 1 });
 333     annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
 334             amap = new HashMap<>());
 335     amap.put("JRonn", new HashMap<String, Object>());
 336     amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5 });
 337     amap.get("JRonn").put(RANGE, new float[] { 0, 1 });
 338   }
 339
 340 }