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