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.gui.AlignmentPanel;
   8 import jalview.ws.jws2.jabaws2.Jws2Instance;
   9 import jalview.ws.params.WsParamSetI;
  10
  11 import java.util.ArrayList;
  12 import java.util.Iterator;
  13 import java.util.List;
  14 import java.util.Map;
  15 import java.util.TreeSet;
  16
  17 import compbio.data.sequence.Score;
  18 import compbio.metadata.Argument;
  19
  20 public class AAConsClient extends JabawsAlignCalcWorker
  21 {
  22
  23   public AAConsClient(Jws2Instance service, AlignFrame alignFrame,
  24           WsParamSetI preset, List<Argument> paramset)
  25   {
  26     super(service, alignFrame, preset, paramset);
  27     submitGaps = true;
  28     alignedSeqs = true;
  29     nucleotidesAllowed = false;
  30     proteinAllowed = true;
  31     gapMap=new boolean[0];
  32   }
  33
  34   public String getServiceActionText()
  35   {
  36     return "calculating Amino acid consensus using AACons service";
  37   }
  38
  39   /**
  40    * update the consensus annotation from the sequence profile data using
  41    * current visualization settings.
  42    */
  43
  44   public void updateResultAnnotation(boolean immediate)
  45   {
  46     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
  47     {
  48       AlignmentAnnotation annotation;
  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 = alignViewport.getAlignment()
  76                     .findOrCreateAnnotation(scr.getMethod(), getCalcId(), true,
  77                             null, null);
  78
  79             Annotation[] elm = new Annotation[alWidth];
  80             if (alWidth == gapMap.length) // scr.getScores().size())
  81             {
  82               Iterator<Float> vals = scr.getScores().iterator();
  83               float m = 0f, x = 0f;
  84               for (int i = 0; vals.hasNext(); i++)
  85               {
  86                 float val = vals.next().floatValue();
  87                 if (i == 0)
  88                 {
  89                   m = val;
  90                   x = val;
  91                 }
  92                 else
  93                 {
  94                   if (m > val)
  95                   {
  96                     m = val;
  97                   }
  98                   ;
  99                   if (x < val)
 100                   {
 101                     x = val;
 102                   }
 103                 }
 104                 // if we're at a gapped column then skip to next ungapped position
 105                 if (gapMap != null && gapMap.length > 0)
 106                 {
 107                   while (!gapMap[i])
 108                   {
 109                     elm[i++]=new Annotation("", "" , ' ', Float.NaN);
 110                   }
 111                 }
 112                 elm[i] = new Annotation("", "" + val, ' ', val);
 113               }
 114
 115               annotation.annotations = elm;
 116               annotation.belowAlignment = true;
 117               if (x < 0)
 118               {
 119                 x = 0;
 120               }
 121               x += (x - m) * 0.1;
 122               annotation.graphMax = x;
 123               annotation.graphMin = m;
 124               annotation.validateRangeAndDisplay();
 125               ourAnnot.add(annotation);
 126             }
 127           }
 128         }
 129       }
 130       if (ourAnnot.size() > 0)
 131       {
 132         List<AlignmentAnnotation> our = ourAnnots;
 133         ourAnnots = ourAnnot;
 134         if (our != null)
 135         {
 136           if (our.size() > 0)
 137           {
 138             for (AlignmentAnnotation an : our)
 139             {
 140               if (!ourAnnots.contains(an))
 141               {
 142                 // remove the old annotation
 143                 alignment.deleteAnnotation(an);
 144               }
 145             }
 146           }
 147           our.clear();
 148         }
 149       }
 150       // if (ann !=
 151       // alignViewport.getAlignment().getAlignmentAnnotation().length)
 152       {
 153         ap.adjustAnnotationHeight();
 154       }
 155       /*
 156        * else { ap.paintAlignment(true); }
 157        */
 158     }
 159   }
 160
 161   public static void removeAAConsAnnotation(AlignmentPanel alignPanel)
 162   {
 163     // List<AlignmentAnnotation>
 164     // ourannots=alignPanel.getAlignment().findAnnotation(Screen3D.)
 165     // TODO Auto-generated method stub
 166
 167   }
 168 }