src/jalview/ws/jws2/AADisorderClient.java

   1 package jalview.ws.jws2;
   2
   3 import jalview.api.AlignCalcWorkerI;
   4 import jalview.datamodel.SequenceFeature;
   5 import jalview.datamodel.SequenceI;
   6 import jalview.gui.AlignFrame;
   7 import jalview.ws.jws2.jabaws2.Jws2Instance;
   8 import jalview.ws.params.WsParamSetI;
   9
  10 import java.util.Iterator;
  11 import java.util.List;
  12
  13 import compbio.data.sequence.Range;
  14 import compbio.data.sequence.Score;
  15 import compbio.data.sequence.ScoreManager.ScoreHolder;
  16 import compbio.metadata.Argument;
  17
  18 public class AADisorderClient extends JabawsAlignCalcWorker implements
  19         AlignCalcWorkerI
  20 {
  21
  22   String typeName;
  23
  24   String methodName;
  25
  26   String groupName;
  27
  28   AlignFrame af;
  29
  30   public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
  31           WsParamSetI preset, List<Argument> paramset)
  32   {
  33     super(sh, alignFrame, preset, paramset);
  34     af = alignFrame;
  35     typeName = sh.action;
  36     methodName = sh.serviceType;
  37
  38     submitGaps = false;
  39     alignedSeqs = false;
  40     nucleotidesAllowed = false;
  41     proteinAllowed = true;
  42     bySequence = true;
  43   }
  44
  45   @Override
  46   public String getServiceActionText()
  47   {
  48     return "Submitting amino acid sequences for disorder prediction.";
  49   }
  50
  51   @Override
  52   public void updateResultAnnotation(boolean immediate)
  53   {
  54
  55     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
  56     {
  57       boolean dispFeatures = false;
  58       for (String seqId : seqNames.keySet())
  59       {
  60         SequenceI dseq, seq = seqNames.get(seqId);
  61         int base = seq.getStart() - 1;
  62         while ((dseq = seq).getDatasetSequence() != null)
  63         {
  64           seq = seq.getDatasetSequence();
  65         }
  66         ;
  67         ScoreHolder scores = scoremanager.getAnnotationForSequence(seqId);
  68
  69         for (Score scr : scores.scores)
  70         {
  71
  72           if (scr.getRanges() != null && scr.getRanges().size() > 0)
  73           {
  74             Iterator<Float> vals = scr.getScores().iterator();
  75             // make features on sequence
  76             for (Range rn : scr.getRanges())
  77             {
  78
  79               SequenceFeature sf;
  80               if (vals.hasNext())
  81               {
  82                 sf = new SequenceFeature(typeName + "(" + scr.getMethod()
  83                         + ")", "Disordered Region", base + rn.from, base
  84                         + rn.to, vals.next().floatValue(), methodName);
  85               }
  86               else
  87               {
  88                 sf = new SequenceFeature(typeName + "(" + scr.getMethod()
  89                         + ")", "Disordered Region", null, base + rn.from,
  90                         base + rn.to, methodName);
  91               }
  92               dseq.addSequenceFeature(sf);
  93               dispFeatures = true;
  94             }
  95           }
  96           else
  97           {
  98             Iterator<Float> vals = scr.getScores().iterator();
  99             for (int start = base + 1; vals.hasNext(); start++)
 100             {
 101               SequenceFeature sf = new SequenceFeature(typeName + "("
 102                       + scr.getMethod() + ")", "Disordered Region", start,
 103                       start, vals.next().floatValue(), methodName);
 104               dseq.addSequenceFeature(sf);
 105               dispFeatures = true;
 106             }
 107           }
 108         }
 109       }
 110       {
 111         if (dispFeatures)
 112         {
 113           // TODO: configure feature display settings for added types if they don't already exist
 114
 115           af.alignPanel.av.setShowSequenceFeatures(true);
 116           ap.paintAlignment(true);
 117         }
 118       }
 119       /*
 120        * else { ap.paintAlignment(true); }
 121        */
 122     }
 123   }
 124
 125 }