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.bin.Console;
  27 import jalview.datamodel.AlignmentAnnotation;
  28 import jalview.datamodel.AlignmentI;
  29 import jalview.datamodel.GraphLine;
  30 import jalview.datamodel.SequenceFeature;
  31 import jalview.datamodel.SequenceI;
  32 import jalview.datamodel.features.FeatureMatcherSetI;
  33 import jalview.schemes.FeatureColour;
  34 import jalview.util.ColorUtils;
  35
  36 import java.awt.Color;
  37 import java.util.ArrayList;
  38 import java.util.HashMap;
  39 import java.util.Hashtable;
  40 import java.util.Iterator;
  41 import java.util.List;
  42 import java.util.Map;
  43
  44 import compbio.data.sequence.Range;
  45 import compbio.data.sequence.Score;
  46 import compbio.data.sequence.ScoreManager.ScoreHolder;
  47
  48 public class AADisorderClient extends JabawsAnnotationInstance
  49 {
  50   // static configuration
  51   public static String getServiceActionText()
  52   {
  53     return "Submitting amino acid sequences for disorder prediction.";
  54   }
  55
  56   // minSeq = 1; protein only, no gaps
  57
  58   // instance
  59   public AADisorderClient(Jws2Instance handle)
  60   {
  61     super(handle);
  62
  63   }
  64
  65   @Override
  66   List<AlignmentAnnotation> annotationFromScoreManager(AlignmentI seqs,
  67           Map<String, FeatureColourI> featureColours,
  68           Map<String, FeatureMatcherSetI> featureFilters)
  69   {
  70
  71     Map<String, String[]> featureTypeMap = featureMap.get(our.getName());
  72     Map<String, Map<String, Object>> annotTypeMap = annotMap
  73             .get(our.getName());
  74     boolean dispFeatures = false;
  75     Map<String, SequenceFeature> fc = new Hashtable<>(),
  76             fex = new Hashtable();
  77     List<AlignmentAnnotation> ourAnnot = new ArrayList<>();
  78     int graphGroup = 1, lastAnnot = 0;
  79
  80     for (SequenceI seq : seqs.getSequences())
  81     {
  82       String seqId = seq.getName();
  83       boolean sameGroup = false;
  84       SequenceI dseq, aseq;
  85       int base = seq.findPosition(0) - 1;
  86       aseq = seq;
  87       while ((dseq = seq).getDatasetSequence() != null)
  88       {
  89         seq = seq.getDatasetSequence();
  90       }
  91       ScoreHolder scores = null;
  92       try
  93       {
  94         scores = scoremanager.getAnnotationForSequence(seqId);
  95       } catch (Exception q)
  96       {
  97         Console.info("Couldn't recover disorder prediction for sequence "
  98                 + seq.getName() + "(Prediction name was " + seqId + ")"
  99                 + "\nSee http://issues.jalview.org/browse/JAL-1319 for one possible reason why disorder predictions might fail.",
 100                 q);
 101       }
 102       float last = Float.NaN, val = Float.NaN;
 103       if (scores != null && scores.scores != null)
 104       {
 105         for (Score scr : scores.scores)
 106         {
 107
 108           if (scr.getRanges() != null && scr.getRanges().size() > 0)
 109           {
 110             Iterator<Float> vals = scr.getScores().iterator();
 111             // make features on sequence
 112             for (Range rn : scr.getRanges())
 113             {
 114               // TODO: Create virtual feature settings
 115               SequenceFeature sf;
 116               String[] type = featureTypeMap.get(scr.getMethod());
 117               if (type == null)
 118               {
 119                 // create a default type for this feature
 120                 type = new String[] {
 121                     typeName + " (" + scr.getMethod() + ")",
 122                     our.getActionText() };
 123               }
 124               if (vals.hasNext())
 125               {
 126                 val = vals.next().floatValue();
 127                 sf = new SequenceFeature(type[0], type[1], base + rn.from,
 128                         base + rn.to, val, methodName);
 129               }
 130               else
 131               {
 132                 sf = new SequenceFeature(type[0], type[1], base + rn.from,
 133                         base + rn.to, methodName);
 134               }
 135               dseq.addSequenceFeature(sf);
 136               // mark feature as requiring a graduated colourscheme if has
 137               // variable scores
 138               if (!Float.isNaN(last) && !Float.isNaN(val) && last != val)
 139               {
 140                 fc.put(sf.getType(), sf);
 141               } else
 142               {
 143                 fex.put(sf.getType(), sf);
 144               }
 145               last = val;
 146               dispFeatures = true;
 147             }
 148           }
 149           else
 150           {
 151             if (scr.getScores().size() == 0)
 152             {
 153               continue;
 154             }
 155             String typename, calcName;
 156             AlignmentAnnotation annot = createAnnotationRowsForScores(
 157                     seqs, null, ourAnnot,
 158                     typename = our.getName() + " (" + scr.getMethod() + ")",
 159                     calcName = our.getNameURI() + "/" + scr.getMethod(),
 160                     aseq, base + 1, scr);
 161             annot.graph = AlignmentAnnotation.LINE_GRAPH;
 162
 163             Map<String, Object> styleMap = (annotTypeMap == null) ? null
 164                     : annotTypeMap.get(scr.getMethod());
 165
 166             annot.visible = (styleMap == null
 167                     || styleMap.get(INVISIBLE) == null);
 168             double[] thrsh = (styleMap == null) ? null
 169                     : (double[]) styleMap.get(THRESHOLD);
 170             float[] range = (styleMap == null) ? null
 171                     : (float[]) styleMap.get(RANGE);
 172             if (range != null)
 173             {
 174               annot.graphMin = range[0];
 175               annot.graphMax = range[1];
 176             }
 177             if (styleMap == null || styleMap.get(DONTCOMBINE) == null)
 178             {
 179               {
 180                 if (!sameGroup)
 181                 {
 182                   graphGroup++;
 183                   sameGroup = true;
 184                 }
 185
 186                 annot.graphGroup = graphGroup;
 187               }
 188             }
 189
 190             annot.description = "<html>" + our.getActionText()
 191                     + " - raw scores";
 192             if (thrsh != null)
 193             {
 194               String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
 195                       + thrsh[1] + " indicates disorder";
 196               annot.threshold = new GraphLine((float) thrsh[1], threshNote,
 197                       Color.red);
 198               annot.description += "<br/>" + threshNote;
 199             }
 200             annot.description += "</html>";
 201             Color col = ColorUtils
 202                     .createColourFromName(typeName + scr.getMethod());
 203             for (int p = 0, ps = annot.annotations.length; p < ps; p++)
 204             {
 205               if (annot.annotations[p] != null)
 206               {
 207                 annot.annotations[p].colour = col;
 208               }
 209             }
 210             annot._linecolour = col;
 211             // finally, update any dataset annotation
 212             AlignmentAnnotationUtils.replaceAnnotationOnAlignmentWith(annot,
 213                     typename, calcName);
 214           }
 215         }
 216       }
 217       if (lastAnnot + 1 == ourAnnot.size())
 218       {
 219         // remove singleton alignment annotation row
 220         ourAnnot.get(lastAnnot).graphGroup = -1;
 221       }
 222     }
 223     {
 224       if (dispFeatures)
 225       {
 226         // TODO: virtual feature settings
 227         // feature colours need to merged with current viewport's colours
 228         // simple feature colours promoted to colour-by-score ranges using
 229         // currently assigned or created feature colour
 230         for (String ft : fex.keySet())
 231         {
 232           Color col = ColorUtils.createColourFromName(ft);
 233           // set graduated color as fading to white for minimum, and
 234           // autoscaling to values on alignment
 235
 236           FeatureColourI ggc;
 237           if (fc.get(ft) != null)
 238           {
 239             ggc = new FeatureColour(col, Color.white, col,
 240
 241                   Color.white, Float.MIN_VALUE, Float.MAX_VALUE);
 242             ggc.setAutoScaled(true);
 243           }
 244           else
 245           {
 246             ggc = new FeatureColour(col);
 247           }
 248           featureColours.put(ft, ggc);
 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 }