src/jalview/ws/jws2/AADisorderClient.java

   1 package jalview.ws.jws2;
   2
   3 import jalview.api.AlignCalcWorkerI;
   4 import jalview.bin.Cache;
   5 import jalview.datamodel.AlignmentAnnotation;
   6
   7 import jalview.datamodel.GraphLine;
   8 import jalview.datamodel.SequenceFeature;
   9 import jalview.datamodel.SequenceI;
  10 import jalview.gui.AlignFrame;
  11 import jalview.schemes.GraduatedColor;
  12 import jalview.schemes.UserColourScheme;
  13 import jalview.ws.jws2.jabaws2.Jws2Instance;
  14 import jalview.ws.params.WsParamSetI;
  15
  16 import java.awt.Color;
  17 import java.util.ArrayList;
  18 import java.util.HashMap;
  19 import java.util.Hashtable;
  20 import java.util.Iterator;
  21 import java.util.List;
  22 import java.util.Map;
  23 import compbio.data.sequence.Range;
  24 import compbio.data.sequence.Score;
  25 import compbio.data.sequence.ScoreManager.ScoreHolder;
  26 import compbio.metadata.Argument;
  27 import compbio.ws.client.Services;
  28
  29 public class AADisorderClient extends JabawsAlignCalcWorker implements
  30         AlignCalcWorkerI
  31 {
  32
  33   private static final String THRESHOLD = "THRESHOLD";
  34
  35   String typeName;
  36
  37   String methodName;
  38
  39   String groupName;
  40
  41   AlignFrame af;
  42
  43   public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
  44           WsParamSetI preset, List<Argument> paramset)
  45   {
  46     super(sh, alignFrame, preset, paramset);
  47     af = alignFrame;
  48     typeName = sh.action;
  49     methodName = sh.serviceType;
  50
  51     submitGaps = false;
  52     alignedSeqs = false;
  53     nucleotidesAllowed = false;
  54     proteinAllowed = true;
  55     bySequence = true;
  56   }
  57
  58   @Override
  59   public String getServiceActionText()
  60   {
  61     return "Submitting amino acid sequences for disorder prediction.";
  62   }
  63
  64   private static Map<String, Map<String, String[]>> featureMap;
  65
  66   private static Map<String, Map<String, Map<String, Object>>> annotMap;
  67
  68   private static String DONTCOMBINE = "DONTCOMBINE";
  69
  70   private static String INVISIBLE = "INVISIBLE";
  71   static
  72   {
  73     // TODO: turn this into some kind of configuration file that's a bit easier
  74     // to edit
  75     featureMap = new HashMap<String, Map<String, String[]>>();
  76     Map<String, String[]> fmap;
  77     featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
  78             fmap = new HashMap<String, String[]>());
  79     fmap.put("Glob", new String[]
  80     { "Globular Domain", "Predicted globular domain" });
  81     featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
  82             fmap = new HashMap<String, String[]>());
  83     featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
  84             fmap = new HashMap<String, String[]>());
  85     fmap.put("REM465", new String[]
  86     { "REM465", "Missing density" });
  87     fmap.put("HOTLOOPS", new String[]
  88     { "HOTLOOPS", "Flexible loops" });
  89     fmap.put("COILS", new String[]
  90     { "COILS", "Random coil" });
  91     featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
  92             fmap = new HashMap<String, String[]>());
  93     fmap.put("GlobDoms", new String[]
  94     { "Globular Domain", "Predicted globular domain" });
  95     fmap.put("Disorder", new String[]
  96     { "Protein Disorder", "Probable unstructured peptide region" });
  97     Map<String, Map<String, Object>> amap;
  98     annotMap = new HashMap<String, Map<String, Map<String, Object>>>();
  99     annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
 100             amap = new HashMap<String, Map<String, Object>>());
 101     amap.put("Dydx", new HashMap<String, Object>());
 102     amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
 103     amap.get("Dydx").put(THRESHOLD, new double[]
 104     { 1, 0 });
 105     amap.put("SmoothedScore", new HashMap<String, Object>());
 106     amap.get("SmoothedScore").put(INVISIBLE, INVISIBLE);
 107     amap.put("RawScore", new HashMap<String, Object>());
 108     amap.get("RawScore").put(INVISIBLE, INVISIBLE);
 109     annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 110             amap = new HashMap<String, Map<String, Object>>());
 111     amap.put("COILS", new HashMap<String, Object>());
 112     amap.put("HOTLOOPS", new HashMap<String, Object>());
 113     amap.put("REM465", new HashMap<String, Object>());
 114     amap.get("COILS").put(THRESHOLD, new double[]
 115     { 1, 0.516 });
 116     amap.get("HOTLOOPS").put(THRESHOLD, new double[]
 117     { 1, 0.6 });
 118     amap.get("REM465").put(THRESHOLD, new double[]
 119     { 1, 0.1204 });
 120
 121     annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
 122             amap = new HashMap<String, Map<String, Object>>());
 123     amap.put("Long", new HashMap<String, Object>());
 124     amap.put("Short", new HashMap<String, Object>());
 125     amap.get("Long").put(THRESHOLD, new double[]
 126     { 1, 0.5 });
 127     amap.get("Short").put(THRESHOLD, new double[]
 128     { 1, 0.5 });
 129     annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
 130             amap = new HashMap<String, Map<String, Object>>());
 131     amap.put("JRonn", new HashMap<String, Object>());
 132     amap.get("JRonn").put(THRESHOLD, new double[]
 133     { 1, 0.5 });
 134   }
 135
 136   @Override
 137   public void updateResultAnnotation(boolean immediate)
 138   {
 139
 140     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
 141     {
 142       Map<String, String[]> featureTypeMap = featureMap
 143               .get(service.serviceType);
 144       Map<String, Map<String, Object>> annotTypeMap = annotMap
 145               .get(service.serviceType);
 146       boolean dispFeatures = false;
 147       Map<String, Object> fc = new Hashtable<String, Object>();
 148       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
 149       /**
 150        * grouping for any annotation rows created
 151        */
 152       int graphGroup = 1;
 153       if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
 154       {
 155         for (AlignmentAnnotation ala : alignViewport.getAlignment()
 156                 .getAlignmentAnnotation())
 157         {
 158           if (ala.graphGroup > graphGroup)
 159           {
 160             graphGroup = ala.graphGroup;
 161           }
 162         }
 163       }
 164
 165       for (String seqId : seqNames.keySet())
 166       {
 167         boolean sameGroup = false;
 168         SequenceI dseq, aseq, seq = seqNames.get(seqId);
 169         int base = seq.getStart() - 1;
 170         aseq = seq;
 171         while ((dseq = seq).getDatasetSequence() != null)
 172         {
 173           seq = seq.getDatasetSequence();
 174         }
 175         ;
 176         ScoreHolder scores = scoremanager.getAnnotationForSequence(seqId);
 177         float last = Float.NaN, val = Float.NaN;
 178         int lastAnnot = ourAnnot.size();
 179         for (Score scr : scores.scores)
 180         {
 181
 182           if (scr.getRanges() != null && scr.getRanges().size() > 0)
 183           {
 184             Iterator<Float> vals = scr.getScores().iterator();
 185             // make features on sequence
 186             for (Range rn : scr.getRanges())
 187             {
 188
 189               SequenceFeature sf;
 190               String[] type = featureTypeMap.get(scr.getMethod());
 191               if (type == null)
 192               {
 193                 // create a default type for this feature
 194                 type = new String[]
 195                 { typeName + " (" + scr.getMethod() + ")",
 196                     service.getActionText() };
 197               }
 198               if (vals.hasNext())
 199               {
 200                 sf = new SequenceFeature(type[0], type[1], base + rn.from,
 201                         base + rn.to, val = vals.next().floatValue(),
 202                         methodName);
 203               }
 204               else
 205               {
 206                 sf = new SequenceFeature(type[0], type[1], null, base
 207                         + rn.from, base + rn.to, methodName);
 208               }
 209               dseq.addSequenceFeature(sf);
 210               if (last != val && last != Float.NaN)
 211               {
 212                 fc.put(sf.getType(), sf);
 213               }
 214               last = val;
 215               dispFeatures = true;
 216             }
 217           }
 218           else
 219           {
 220             if (scr.getScores().size() == 0)
 221             {
 222               continue;
 223             }
 224             AlignmentAnnotation annot = createAnnotationRowsForScores(
 225                     ourAnnot, service.serviceType + " (" + scr.getMethod()
 226                             + ")",
 227                     service.getServiceTypeURI() + "/" + scr.getMethod(),
 228                     aseq, base + 1, scr);
 229             annot.graph = AlignmentAnnotation.LINE_GRAPH;
 230             annot.visible = (annotTypeMap == null
 231                     || annotTypeMap.get(scr.getMethod()) == null || annotTypeMap
 232                     .get(scr.getMethod()).get(INVISIBLE) == null);
 233             double[] thrsh = (annotTypeMap == null || annotTypeMap.get(scr
 234                     .getMethod()) == null) ? null : (double[]) annotTypeMap
 235                     .get(scr.getMethod()).get(THRESHOLD);
 236             if (annotTypeMap == null
 237                     || annotTypeMap.get(scr.getMethod()) == null
 238                     || annotTypeMap.get(scr.getMethod()).get(DONTCOMBINE) == null)
 239             {
 240               {
 241                 if (!sameGroup)
 242                 {
 243                   graphGroup++;
 244                   sameGroup = true;
 245                 }
 246
 247                 annot.graphGroup = graphGroup;
 248               }
 249             }
 250
 251             annot.description = "<html>" + service.getActionText()
 252                     + " - raw scores";
 253             if (thrsh != null)
 254             {
 255               String threshNote = (thrsh[0] > 0 ? "Above " : "Below ")
 256                       + thrsh[1] + " indicates disorder";
 257               annot.threshold = new GraphLine((float) thrsh[1], threshNote,
 258                       Color.red);
 259               annot.description += "<br/>" + threshNote;
 260             }
 261             annot.description += "</html>";
 262             Color col = new UserColourScheme(typeName)
 263                     .createColourFromName(typeName + scr.getMethod());
 264             for (int p = 0, ps = annot.annotations.length; p < ps; p++)
 265             {
 266               if (annot.annotations[p] != null)
 267               {
 268                 annot.annotations[p].colour = col;
 269               }
 270             }
 271             annot._linecolour = col;
 272           }
 273         }
 274         if (lastAnnot + 1 == ourAnnot.size())
 275         {
 276           // remove singleton alignment annotation row
 277           ourAnnot.get(lastAnnot).graphGroup = -1;
 278         }
 279       }
 280       {
 281         if (dispFeatures)
 282         {
 283           jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
 284                   .cloneFeatureRenderer();
 285           for (String ft : fc.keySet())
 286           {
 287             Object gc = fr.getFeatureStyle(ft);
 288             if (gc instanceof Color)
 289             {
 290               // set graduated color as fading to white for minimum, and
 291               // autoscaling to values on alignment
 292               GraduatedColor ggc = new GraduatedColor(Color.white,
 293                       (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE);
 294               ggc.setAutoScaled(true);
 295               fr.setColour(ft, ggc);
 296             }
 297           }
 298           // TODO: JAL-1150 - create sequence feature settings API for defining
 299           // styles and enabling/disabling feature overlay on alignment panel
 300           ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
 301           if (af.alignPanel == ap)
 302           {
 303             // only do this if the alignFrame is currently showing this view.
 304             af.setShowSeqFeatures(true);
 305           }
 306           ap.paintAlignment(true);
 307         }
 308         if (ourAnnot.size() > 0)
 309         {
 310           // Modify the visible annotation on the alignment viewport with the
 311           // new alignment annotation rows created.
 312           updateOurAnnots(ourAnnot);
 313           ap.adjustAnnotationHeight();
 314         }
 315       }
 316     }
 317   }
 318
 319 }