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
  47     if (immediate || !calcMan.isWorking(this) && scoremanager != null)
  48     {
  49       AlignmentAnnotation annotation;
  50       ;
  51       Map<String, TreeSet<Score>> scoremap = scoremanager.asMap();
  52       int alWidth = alignViewport.getAlignment().getWidth();
  53       AlignmentI alignment;
  54       int ann = (alignment = alignViewport.getAlignment())
  55               .getAlignmentAnnotation().length;
  56       ArrayList<AlignmentAnnotation> ourAnnot = new ArrayList<AlignmentAnnotation>();
  57       for (String score : scoremap.keySet())
  58       {
  59         TreeSet<Score> scores = scoremap.get(score);
  60         for (Score scr : scores)
  61         {
  62           if (scr.getRanges() != null && scr.getRanges().size() > 0)
  63           {
  64             /**
  65              * annotation in range annotation = findOrCreate(scr.getMethod(),
  66              * true, null, null); Annotation[] elm = new Annotation[alWidth];
  67              * Iterator<Float> vals = scr.getScores().iterator(); for (Range rng
  68              * : scr.getRanges()) { float val = vals.next().floatValue(); for
  69              * (int i = rng.from; i <= rng.to; i++) { elm[i] = new
  70              * Annotation("", "", ' ', val); } } annotation.annotations = elm;
  71              * annotation.validateRangeAndDisplay();
  72              */
  73           }
  74           else
  75           {
  76             // simple annotation row
  77             annotation = alignViewport.getAlignment().findOrCreateAnnotation(scr.getMethod(), true, null, null);
  78             Annotation[] elm = new Annotation[alWidth];
  79             if (alWidth == gapMap.length) // scr.getScores().size())
  80             {
  81               Iterator<Float> vals = scr.getScores().iterator();
  82               float m = 0f, x = 0f;
  83               for (int i = 0; vals.hasNext(); i++)
  84               {
  85                 float val = vals.next().floatValue();
  86                 if (i == 0)
  87                 {
  88                   m = val;
  89                   x = val;
  90                 }
  91                 else
  92                 {
  93                   if (m > val)
  94                   {
  95                     m = val;
  96                   }
  97                   ;
  98                   if (x < val)
  99                   {
 100                     x = val;
 101                   }
 102                 }
 103                 // if we're at a gapped column then skip to next ungapped position
 104                 if (gapMap != null && gapMap.length > 0)
 105                 {
 106                   while (!gapMap[i])
 107                   {
 108                     elm[i++]=new Annotation("", "" , ' ', Float.NaN);
 109                   }
 110                 }
 111                 elm[i] = new Annotation("", "" + val, ' ', val);
 112               }
 113
 114               annotation.annotations = elm;
 115               annotation.belowAlignment = true;
 116               if (x < 0)
 117               {
 118                 x = 0;
 119               }
 120               x += (x - m) * 0.1;
 121               annotation.graphMax = x;
 122               annotation.graphMin = m;
 123               annotation.validateRangeAndDisplay();
 124               ourAnnot.add(annotation);
 125             }
 126           }
 127         }
 128       }
 129       if (ourAnnot.size() > 0)
 130       {
 131         List<AlignmentAnnotation> our = ourAnnots;
 132         ourAnnots = ourAnnot;
 133         if (our != null)
 134         {
 135           if (our.size() > 0)
 136           {
 137             for (AlignmentAnnotation an : our)
 138             {
 139               if (!ourAnnots.contains(an))
 140               {
 141                 // remove the old annotation
 142                 alignment.deleteAnnotation(an);
 143               }
 144             }
 145           }
 146           our.clear();
 147         }
 148       }
 149       // if (ann !=
 150       // alignViewport.getAlignment().getAlignmentAnnotation().length)
 151       {
 152         ap.adjustAnnotationHeight();
 153       }
 154       /*
 155        * else { ap.paintAlignment(true); }
 156        */
 157     }
 158   }
 159
 160   public static void removeAAConsAnnotation(AlignmentPanel alignPanel)
 161   {
 162     // List<AlignmentAnnotation>
 163     // ourannots=alignPanel.getAlignment().findAnnotation(Screen3D.)
 164     // TODO Auto-generated method stub
 165
 166   }
 167 }