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
 122   }
 123
 124   @Override
 125   public void updateResultAnnotation(boolean immediate)
 126   {
 127
 128     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
 129     {
 130       Map<String, String[]> featureTypeMap = featureMap
 131               .get(service.serviceType);
 132       Map<String, Map<String, Object>> annotTypeMap = annotMap
 133               .get(service.serviceType);
 134       boolean dispFeatures = false;
 135       Map<String, Object> fc = new Hashtable<String, Object>();
 136       List<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
 137       /**
 138        * grouping for any annotation rows created
 139        */
 140       int graphGroup = 1, iGraphGroup = 1;
 141       if (alignViewport.getAlignment().getAlignmentAnnotation() != null)
 142       {
 143         for (AlignmentAnnotation ala : alignViewport.getAlignment()
 144                 .getAlignmentAnnotation())
 145         {
 146           if (ala.graphGroup > graphGroup)
 147           {
 148             graphGroup = ala.graphGroup;
 149           }
 150         }
 151       }
 152
 153       for (String seqId : seqNames.keySet())
 154       {
 155         boolean sameGroup = false;
 156         SequenceI dseq, aseq, seq = seqNames.get(seqId);
 157         int base = seq.getStart() - 1;
 158         aseq = seq;
 159         while ((dseq = seq).getDatasetSequence() != null)
 160         {
 161           seq = seq.getDatasetSequence();
 162         }
 163         ;
 164         ScoreHolder scores = scoremanager.getAnnotationForSequence(seqId);
 165         float last = Float.NaN, val = Float.NaN;
 166         int lastAnnot = ourAnnot.size();
 167         for (Score scr : scores.scores)
 168         {
 169
 170           if (scr.getRanges() != null && scr.getRanges().size() > 0)
 171           {
 172             Iterator<Float> vals = scr.getScores().iterator();
 173             // make features on sequence
 174             for (Range rn : scr.getRanges())
 175             {
 176
 177               SequenceFeature sf;
 178               String[] type = featureTypeMap.get(scr.getMethod());
 179               if (type == null)
 180               {
 181                 // create a default type for this feature
 182                 type = new String[]
 183                 { typeName + " (" + scr.getMethod() + ")",
 184                     service.getActionText() };
 185               }
 186               if (vals.hasNext())
 187               {
 188                 sf = new SequenceFeature(type[0], type[1], base + rn.from,
 189                         base + rn.to, val = vals.next().floatValue(),
 190                         methodName);
 191               }
 192               else
 193               {
 194                 sf = new SequenceFeature(type[0], type[1], null, base
 195                         + rn.from, base + rn.to, methodName);
 196               }
 197               dseq.addSequenceFeature(sf);
 198               if (last != val && last != Float.NaN)
 199               {
 200                 fc.put(sf.getType(), sf);
 201               }
 202               last = val;
 203               dispFeatures = true;
 204             }
 205           }
 206           else
 207           {
 208             if (scr.getScores().size()==0)
 209             {
 210               continue;
 211             }
 212             AlignmentAnnotation annot = createAnnotationRowsForScores(
 213                     ourAnnot, service.serviceType + " (" + scr.getMethod()
 214                             + ")", service.getServiceTypeURI()+"/"+ scr.getMethod(), aseq,
 215                     base, scr);
 216             annot.graph = AlignmentAnnotation.LINE_GRAPH;
 217             annot.visible = (annotTypeMap==null || annotTypeMap.get(scr.getMethod())==null || annotTypeMap.get(scr.getMethod()).get(INVISIBLE) == null);
 218             double[] thrsh=(annotTypeMap==null || annotTypeMap.get(scr.getMethod())==null) ? null : (double[]) annotTypeMap.get(scr.getMethod()).get(THRESHOLD);
 219             if (annotTypeMap==null || annotTypeMap.get(scr.getMethod())==null || annotTypeMap.get(scr.getMethod()).get(DONTCOMBINE) == null)
 220             {
 221               {
 222                 if (!sameGroup)
 223                 {
 224                   graphGroup++;
 225                   sameGroup = true;
 226                 }
 227
 228                 annot.graphGroup = graphGroup;
 229               }
 230             }
 231
 232             annot.description = "<html>"+service.getActionText() + " - raw scores";
 233             if (thrsh!=null)
 234             {
 235               String threshNote=(thrsh[0]>0 ? "Above " : "Below ")+thrsh[1]+" indicates disorder";
 236               annot.threshold=new GraphLine((float) thrsh[1], threshNote, Color.red);
 237               annot.description+="<br/>"+threshNote;
 238             }
 239             annot.description+="</html>";
 240             Color col = new UserColourScheme(typeName)
 241                     .createColourFromName(typeName + scr.getMethod());
 242             for (int p = 0, ps = annot.annotations.length; p < ps; p++)
 243             {
 244               if (annot.annotations[p] != null)
 245               {
 246                 annot.annotations[p].colour = col;
 247               }
 248             }
 249             annot._linecolour=col;
 250           }
 251         }
 252         if (lastAnnot + 1 == ourAnnot.size())
 253         {
 254           // remove singleton alignment annotation row
 255           ourAnnot.get(lastAnnot).graphGroup = -1;
 256         }
 257       }
 258       {
 259         if (dispFeatures)
 260         {
 261           jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap)
 262                   .cloneFeatureRenderer();
 263           for (String ft : fc.keySet())
 264           {
 265             Object gc = fr.getFeatureStyle(ft);
 266             if (gc instanceof Color)
 267             {
 268               // set graduated color as fading to white for minimum, and
 269               // autoscaling to values on alignment
 270               GraduatedColor ggc = new GraduatedColor(Color.white,
 271                       (Color) gc, Float.MIN_VALUE, Float.MAX_VALUE);
 272               ggc.setAutoScaled(true);
 273               fr.setColour(ft, ggc);
 274             }
 275           }
 276           // TODO: JAL-1150 - create sequence feature settings API for defining styles and enabling/disabling feature overlay on alignment panel
 277           ((jalview.gui.AlignmentPanel) ap).updateFeatureRendererFrom(fr);
 278           if (af.alignPanel==ap)
 279           {
 280             // only do this if the alignFrame is currently showing this view.
 281             af.setShowSeqFeatures(true);
 282           }
 283           ap.paintAlignment(true);
 284         }
 285         if (ourAnnot.size() > 0)
 286         {
 287           // Modify the visible annotation on the alignment viewport with the
 288           // new alignment annotation rows created.
 289           updateOurAnnots(ourAnnot);
 290           ap.adjustAnnotationHeight();
 291         }
 292       }
 293     }
 294   }
 295
 296 }