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   private static String INVISIBLE = "INVISIBLE";
  70   static
  71   {
  72     // TODO: turn this into some kind of configuration file that's a bit easier to edit
  73     featureMap = new HashMap<String, Map<String, String[]>>();
  74     Map<String, String[]> fmap;
  75     featureMap.put(compbio.ws.client.Services.IUPredWS.toString(),
  76             fmap = new HashMap<String, String[]>());
  77     fmap.put("Glob", new String[]
  78     { "Globular Domain", "Predicted globular domain" });
  79     featureMap.put(compbio.ws.client.Services.JronnWS.toString(),
  80             fmap = new HashMap<String, String[]>());
  81     featureMap.put(compbio.ws.client.Services.DisemblWS.toString(),
  82             fmap = new HashMap<String, String[]>());
  83     fmap.put("REM465", new String[]
  84     { "REM465", "Missing density" });
  85     fmap.put("HOTLOOPS", new String[]
  86     { "HOTLOOPS", "Flexible loops" });
  87     fmap.put("COILS", new String[]
  88     { "COILS", "Random coil" });
  89     featureMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
  90             fmap = new HashMap<String, String[]>());
  91     fmap.put("GlobDoms", new String[]
  92     { "Globular Domain", "Predicted globular domain" });
  93     fmap.put("Disorder", new String[]
  94     { "Protein Disorder", "Probable unstructured peptide region" });
  95     Map<String, Map<String, Object>> amap;
  96     annotMap = new HashMap<String, Map<String, Map<String, Object>>>();
  97     annotMap.put(compbio.ws.client.Services.GlobPlotWS.toString(),
  98             amap = new HashMap<String, Map<String, Object>>());
  99     amap.put("Dydx", new HashMap<String, Object>());
 100     amap.get("Dydx").put(DONTCOMBINE, DONTCOMBINE);
 101     amap.get("Dydx").put(THRESHOLD, new double[] {1, 0});
 102     amap.put("SmoothedScore", new HashMap<String, Object>());
 103     amap.get("SmoothedScore").put(INVISIBLE,INVISIBLE);
 104     amap.put("RawScore", new HashMap<String, Object>());
 105     amap.get("RawScore").put(INVISIBLE,INVISIBLE);
 106     annotMap.put(compbio.ws.client.Services.DisemblWS.toString(),
 107             amap = new HashMap<String, Map<String, Object>>());
 108     amap.put("COILS", new HashMap<String, Object>());
 109     amap.put("HOTLOOPS", new HashMap<String, Object>());
 110     amap.put("REM465", new HashMap<String, Object>());
 111     amap.get("COILS").put(THRESHOLD, new double[] { 1, 0.516});
 112     amap.get("HOTLOOPS").put(THRESHOLD, new double[] { 1, 0.6});
 113     amap.get("REM465").put(THRESHOLD, new double[] { 1, 0.1204});
 114
 115     annotMap.put(compbio.ws.client.Services.IUPredWS.toString(),
 116             amap = new HashMap<String, Map<String, Object>>());
 117     amap.put("Long", new HashMap<String, Object>());
 118     amap.put("Short", new HashMap<String, Object>());
 119     amap.get("Long").put(THRESHOLD, new double[] { 1, 0.5});
 120     amap.get("Short").put(THRESHOLD, new double[] { 1, 0.5});
 121     annotMap.put(compbio.ws.client.Services.JronnWS.toString(),
 122             amap = new HashMap<String, Map<String, Object>>());
 123     amap.put("JRonn", new HashMap<String, Object>());
 124     amap.get("JRonn").put(THRESHOLD, new double[] { 1, 0.5});
 125   }
 126
 127   @Override
 128   public void updateResultAnnotation(boolean immediate)
 129   {
 130
 131     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
 132     {
 133       Map<String, String[]> featureTypeMap = featureMap
 134               .get(service.serviceType);
 135       Map<String, Map<String, Object>> annotTypeMap = annotMap
 136               .get(service.serviceType);
 137       boolean dispFeatures = false;
 138       Map<String, Object> fc = new Hashtable<String, Object>();
 139       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
 140       /**
 141        * grouping for any annotation rows created
 142        */
 143       int graphGroup = 1;
 144       if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
 145       {
 146         for (AlignmentAnnotation ala : alignViewport.getAlignment()
 147                 .getAlignmentAnnotation())
 148         {
 149           if (ala.graphGroup > graphGroup)
 150           {
 151             graphGroup = ala.graphGroup;
 152           }
 153         }
 154       }
 155
 156       for (String seqId : seqNames.keySet())
 157       {
 158         boolean sameGroup = false;
 159         SequenceI dseq, aseq, seq = seqNames.get(seqId);
 160         int base = seq.getStart() - 1;
 161         aseq = seq;
 162         while ((dseq = seq).getDatasetSequence() != null)
 163         {
 164           seq = seq.getDatasetSequence();
 165         }
 166         ;
 167         ScoreHolder scores = scoremanager.getAnnotationForSequence(seqId);
 168         float last = Float.NaN, val = Float.NaN;
 169         int lastAnnot = ourAnnot.size();
 170         for (Score scr : scores.scores)
 171         {
 172
 173           if (scr.getRanges() != null && scr.getRanges().size() > 0)
 174           {
 175             Iterator<Float> vals = scr.getScores().iterator();
 176             // make features on sequence
 177             for (Range rn : scr.getRanges())
 178             {
 179
 180               SequenceFeature sf;
 181               String[] type = featureTypeMap.get(scr.getMethod());
 182               if (type == null)
 183               {
 184                 // create a default type for this feature
 185                 type = new String[]
 186                 { typeName + " (" + scr.getMethod() + ")",
 187                     service.getActionText() };
 188               }
 189               if (vals.hasNext())
 190               {
 191                 sf = new SequenceFeature(type[0], type[1], base + rn.from,
 192                         base + rn.to, val = vals.next().floatValue(),
 193                         methodName);
 194               }
 195               else
 196               {
 197                 sf = new SequenceFeature(type[0], type[1], null, base
 198                         + rn.from, base + rn.to, methodName);
 199               }
 200               dseq.addSequenceFeature(sf);
 201               if (last != val && last != Float.NaN)
 202               {
 203                 fc.put(sf.getType(), sf);
 204               }
 205               last = val;
 206               dispFeatures = true;
 207             }
 208           }
 209           else
 210           {
 211             if (scr.getScores().size()==0)
 212             {
 213               continue;
 214             }
 215             AlignmentAnnotation annot = createAnnotationRowsForScores(
 216                     ourAnnot, service.serviceType + " (" + scr.getMethod()
 217                             + ")", service.getServiceTypeURI()+"/"+ scr.getMethod(), aseq,
 218                     base+1, scr);
 219             annot.graph = AlignmentAnnotation.LINE_GRAPH;
 220             annot.visible = (annotTypeMap==null || annotTypeMap.get(scr.getMethod())==null || annotTypeMap.get(scr.getMethod()).get(INVISIBLE) == null);
 221             double[] thrsh=(annotTypeMap==null || annotTypeMap.get(scr.getMethod())==null) ? null : (double[]) annotTypeMap.get(scr.getMethod()).get(THRESHOLD);
 222             if (annotTypeMap==null || annotTypeMap.get(scr.getMethod())==null || annotTypeMap.get(scr.getMethod()).get(DONTCOMBINE) == null)
 223             {
 224               {
 225                 if (!sameGroup)
 226                 {
 227                   graphGroup++;
 228                   sameGroup = true;
 229                 }
 230
 231                 annot.graphGroup = graphGroup;
 232               }
 233             }
 234
 235             annot.description = "<html>"+service.getActionText() + " - raw scores";
 236             if (thrsh!=null)
 237             {
 238               String threshNote=(thrsh[0]>0 ? "Above " : "Below ")+thrsh[1]+" indicates disorder";
 239               annot.threshold=new GraphLine((float) thrsh[1], threshNote, Color.red);
 240               annot.description+="<br/>"+threshNote;
 241             }
 242             annot.description+="</html>";
 243             Color col = new UserColourScheme(typeName)
 244                     .createColourFromName(typeName + scr.getMethod());
 245             for (int p = 0, ps = annot.annotations.length; p < ps; p++)
 246             {
 247               if (annot.annotations[p] != null)
 248               {
 249                 annot.annotations[p].colour = col;
 250               }
 251             }
 252             annot._linecolour=col;
 253           }
 254         }
 255         if (lastAnnot + 1 == ourAnnot.size())
 256         {
 257           // remove singleton alignment annotation row
 258           ourAnnot.get(lastAnnot).graphGroup = -1;
 259         }
 260       }
 261       {
 262         if (dispFeatures)
 263         {
 264           jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
 265                   .cloneFeatureRenderer();
 266           for (String ft : fc.keySet())
 267           {
 268             Object gc = fr.getFeatureStyle(ft);
 269             if (gc instanceof Color)
 270             {
 271               // set graduated color as fading to white for minimum, and
 272               // autoscaling to values on alignment
 273               GraduatedColor ggc = new GraduatedColor(Color.white,
 274                       (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE);
 275               ggc.setAutoScaled(true);
 276               fr.setColour(ft, ggc);
 277             }
 278           }
 279           // TODO: JAL-1150 - create sequence feature settings API for defining styles and enabling/disabling feature overlay on alignment panel
 280           ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
 281           if (af.alignPanel==ap)
 282           {
 283             // only do this if the alignFrame is currently showing this view.
 284             af.setShowSeqFeatures(true);
 285           }
 286           ap.paintAlignment(true);
 287         }
 288         if (ourAnnot.size() > 0)
 289         {
 290           // Modify the visible annotation on the alignment viewport with the
 291           // new alignment annotation rows created.
 292           updateOurAnnots(ourAnnot);
 293           ap.adjustAnnotationHeight();
 294         }
 295       }
 296     }
 297   }
 298
 299 }