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.SequenceFeature;
   6 import jalview.datamodel.SequenceI;
   7 import jalview.gui.AlignFrame;
   8 import jalview.schemes.GraduatedColor;
   9 import jalview.ws.jws2.jabaws2.Jws2Instance;
  10 import jalview.ws.params.WsParamSetI;
  11
  12 import java.awt.Color;
  13 import java.util.Hashtable;
  14 import java.util.Iterator;
  15 import java.util.List;
  16 import java.util.Map;
  17
  18 import compbio.data.sequence.Range;
  19 import compbio.data.sequence.Score;
  20 import compbio.data.sequence.ScoreManager.ScoreHolder;
  21 import compbio.metadata.Argument;
  22
  23 public class AADisorderClient extends JabawsAlignCalcWorker implements
  24         AlignCalcWorkerI
  25 {
  26
  27   String typeName;
  28
  29   String methodName;
  30
  31   String groupName;
  32
  33   AlignFrame af;
  34
  35   public AADisorderClient(Jws2Instance sh, AlignFrame alignFrame,
  36           WsParamSetI preset, List<Argument> paramset)
  37   {
  38     super(sh, alignFrame, preset, paramset);
  39     af = alignFrame;
  40     typeName = sh.action;
  41     methodName = sh.serviceType;
  42
  43     submitGaps = false;
  44     alignedSeqs = false;
  45     nucleotidesAllowed = false;
  46     proteinAllowed = true;
  47     bySequence = true;
  48   }
  49
  50   @Override
  51   public String getServiceActionText()
  52   {
  53     return "Submitting amino acid sequences for disorder prediction.";
  54   }
  55
  56   @Override
  57   public void updateResultAnnotation(boolean immediate)
  58   {
  59
  60     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
  61     {
  62       boolean dispFeatures = false;
  63       Map<String,Object> fc=new Hashtable<String, Object>();
  64       for (String seqId : seqNames.keySet())
  65       {
  66         SequenceI dseq, seq = seqNames.get(seqId);
  67         int base = seq.getStart() - 1;
  68         while ((dseq = seq).getDatasetSequence() != null)
  69         {
  70           seq = seq.getDatasetSequence();
  71         }
  72         ;
  73         ScoreHolder scores = scoremanager.getAnnotationForSequence(seqId);
  74         float last=Float.NaN,val=Float.NaN;
  75         for (Score scr : scores.scores)
  76         {
  77
  78           if (scr.getRanges() != null && scr.getRanges().size() > 0)
  79           {
  80             Iterator<Float> vals = scr.getScores().iterator();
  81             // make features on sequence
  82             for (Range rn : scr.getRanges())
  83             {
  84
  85               SequenceFeature sf;
  86               if (vals.hasNext())
  87               {
  88                 sf = new SequenceFeature(typeName + "(" + scr.getMethod()
  89                         + ")", "Disordered Region", base + rn.from, base
  90                         + rn.to, val=vals.next().floatValue(), methodName);
  91               }
  92               else
  93               {
  94                 sf = new SequenceFeature(typeName + "(" + scr.getMethod()
  95                         + ")", "Disordered Region", null, base + rn.from,
  96                         base + rn.to, methodName);
  97               }
  98               dseq.addSequenceFeature(sf);
  99               if (last!=val && last!=Float.NaN)
 100               {
 101                 fc.put(sf.getType(),sf);
 102               }
 103               last=val;
 104               dispFeatures = true;
 105             }
 106           }
 107           else
 108           {
 109             Iterator<Float> vals = scr.getScores().iterator();
 110             for (int start = base + 1; vals.hasNext(); start++)
 111             {
 112               SequenceFeature sf = new SequenceFeature(typeName + "("
 113                       + scr.getMethod() + ")", "Disordered Region", start,
 114                       start, val=vals.next().floatValue(), methodName);
 115               if (last!=val && last!=Float.NaN)
 116               {
 117                 fc.put(sf.getType(),sf);
 118               }
 119               last=val;
 120               dseq.addSequenceFeature(sf);
 121               dispFeatures = true;
 122             }
 123           }
 124         }
 125       }
 126       {
 127         if (dispFeatures)
 128         {
 129           jalview.gui.FeatureRenderer fr = ((jalview.gui.AlignmentPanel) ap).cloneFeatureRenderer();
 130           // TODO: configure feature display settings for added types if they don't already exist
 131           for (String ft:fc.keySet())
 132           {
 133             Cache.log.debug("Set graduated feature for new type:"+ft);
 134             Object gc=fr.getFeatureStyle(ft);
 135             if (gc instanceof Color)
 136             {
 137               // set graduated color as fading to white for minimum, and autoscaling to values on alignment
 138               GraduatedColor ggc=new GraduatedColor(Color.white, (Color)gc,Float.MIN_VALUE, Float.MAX_VALUE);
 139               ggc.setAutoScaled(true);
 140               fr.setColour(ft, ggc);
 141             }
 142           }
 143           af.alignPanel.updateFeatureRendererFrom(fr);
 144           af.alignPanel.av.setShowSequenceFeatures(true);
 145           ap.paintAlignment(true);
 146         }
 147       }
 148     }
 149   }
 150
 151 }