src/jalview/ws/jws2/AAConsClient.java

   1 package jalview.ws.jws2;
   2
   3 import jalview.datamodel.AlignmentAnnotation;
   4 import jalview.datamodel.AlignmentI;
   5 import jalview.datamodel.Annotation;
   6 import jalview.gui.AlignFrame;
   7 import jalview.ws.jws2.jabaws2.Jws2Instance;
   8 import jalview.ws.params.WsParamSetI;
   9
  10 import java.util.ArrayList;
  11 import java.util.Iterator;
  12 import java.util.List;
  13 import java.util.Map;
  14 import java.util.TreeSet;
  15
  16 import compbio.data.sequence.Score;
  17 import compbio.metadata.Argument;
  18
  19 public class AAConsClient extends JabawsAlignCalcWorker
  20 {
  21
  22   public AAConsClient(Jws2Instance service, AlignFrame alignFrame,
  23           WsParamSetI preset, List<Argument> paramset)
  24   {
  25     super(service, alignFrame, preset, paramset);
  26     submitGaps=true;
  27     alignedSeqs=true;
  28     nucleotidesAllowed=false;
  29     proteinAllowed=true;
  30   }
  31
  32   public String getServiceActionText()
  33   {
  34     return "calculating Amino acid consensus using AACons service";
  35   }
  36
  37   /**
  38    * update the consensus annotation from the sequence profile data using
  39    * current visualization settings.
  40    */
  41
  42   public void updateResultAnnotation(boolean immediate)
  43   {
  44
  45     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
  46     {
  47       AlignmentAnnotation annotation;
  48       ;
  49       Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
  50       int alWidth = alignViewport.getAlignment().getWidth();
  51       AlignmentI alignment;
  52       int ann = (alignment = alignViewport.getAlignment())
  53               .getAlignmentAnnotation().length;
  54       ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
  55       for (String score : scoremap.keySet())
  56       {
  57         TreeSet<Score> scores = scoremap.get(score);
  58         for (Score scr : scores)
  59         {
  60           if (scr.getRanges() != null && scr.getRanges().size() > 0)
  61           {
  62             /**
  63              * annotation in range annotation = findOrCreate(scr.getMethod(),
  64              * true, null, null); Annotation[] elm = new Annotation[alWidth];
  65              * Iterator<Float> vals = scr.getScores().iterator(); for (Range rng
  66              * : scr.getRanges()) { float val = vals.next().floatValue(); for
  67              * (int i = rng.from; i <= rng.to; i++) { elm[i] = new
  68              * Annotation("", "", ' ', val); } } annotation.annotations = elm;
  69              * annotation.validateRangeAndDisplay();
  70              */
  71           }
  72           else
  73           {
  74             // simple annotation row
  75             annotation = findOrCreate(scr.getMethod(), true, null, null);
  76             Annotation[] elm = new Annotation[alWidth];
  77             if (alWidth == scr.getScores().size())
  78             {
  79               Iterator<Float> vals = scr.getScores().iterator();
  80               float m = 0f, x = 0f;
  81               for (int i = 0; vals.hasNext(); i++)
  82               {
  83                 float val = vals.next().floatValue();
  84                 if (i == 0)
  85                 {
  86                   m = val;
  87                   x = val;
  88                 }
  89                 else
  90                 {
  91                   if (m > val)
  92                   {
  93                     m = val;
  94                   }
  95                   ;
  96                   if (x < val)
  97                   {
  98                     x = val;
  99                   }
 100                 }
 101                 elm[i] = new Annotation("", "" + val, ' ', val);
 102               }
 103
 104               annotation.annotations = elm;
 105               annotation.belowAlignment = true;
 106               if (x < 0)
 107               {
 108                 x = 0;
 109               }
 110               x += (x - m) * 0.1;
 111               annotation.graphMax = x;
 112               annotation.graphMin = m;
 113               annotation.validateRangeAndDisplay();
 114               ourAnnot.add(annotation);
 115             }
 116           }
 117         }
 118       }
 119       if (ourAnnot.size() > 0)
 120       {
 121         List<AlignmentAnnotation> our = ourAnnots;
 122         ourAnnots = ourAnnot;
 123         if (our != null)
 124         {
 125           if (our.size() > 0)
 126           {
 127             for (AlignmentAnnotation an : our)
 128             {
 129               if (!ourAnnots.contains(an))
 130               {
 131                 // remove the old annotation
 132                 alignment.deleteAnnotation(an);
 133               }
 134             }
 135           }
 136           our.clear();
 137         }
 138       }
 139       // if (ann !=
 140       // alignViewport.getAlignment().getAlignmentAnnotation().length)
 141       {
 142         ap.adjustAnnotationHeight();
 143       }
 144       /*
 145        * else { ap.paintAlignment(true); }
 146        */
 147     }
 148   }
 149
 150 }