src/jalview/ws/gui/AnnotationWsJob.java

   1 package jalview.ws.gui;
   2
   3 import jalview.api.FeatureRenderer;
   4 import jalview.datamodel.AlignmentAnnotation;
   5 import jalview.datamodel.SequenceI;
   6
   7 import java.util.List;
   8 import java.util.Map;
   9
  10 public class AnnotationWsJob extends WsJob
  11 {
  12   /**
  13    * sequences (anonymised)
  14    */
  15   List<SequenceI> seqs;
  16
  17   /**
  18    * mapping to original sequences
  19    */
  20   Map<String, SequenceI> seqNames;
  21
  22   /**
  23    * first column in the segment of the alignment view that was submitted
  24    */
  25   int startPos;
  26
  27   public int getStartPos()
  28   {
  29     return startPos;
  30   }
  31
  32   public void setStartPos(int startPos)
  33   {
  34     this.startPos = startPos;
  35   }
  36
  37   /**
  38    * outputs
  39    */
  40   List<AlignmentAnnotation> annotation = null;
  41
  42   boolean transferSequenceFeatures = false;
  43
  44   public boolean isTransferSequenceFeatures()
  45   {
  46     return transferSequenceFeatures;
  47   }
  48
  49   public void setTransferSequenceFeatures(boolean transferSequenceFeatures)
  50   {
  51     this.transferSequenceFeatures = transferSequenceFeatures;
  52   }
  53
  54   public List<AlignmentAnnotation> getAnnotation()
  55   {
  56     return annotation;
  57   }
  58
  59   public void setAnnotation(List<AlignmentAnnotation> annotation)
  60   {
  61     this.annotation = annotation;
  62   }
  63
  64   @Override
  65   public boolean hasResults()
  66   {
  67     return (isSubmitted() && isFinished()
  68             && (annotation != null || transferSequenceFeatures));
  69   }
  70
  71   public List<SequenceI> getSeqs()
  72   {
  73     return seqs;
  74   }
  75
  76   public void setSeqs(List<SequenceI> seqs)
  77   {
  78     this.seqs = seqs;
  79   }
  80
  81   public Map<String, SequenceI> getSeqNames()
  82   {
  83     return seqNames;
  84   }
  85
  86   public void setSeqNames(Map<String, SequenceI> seqNames)
  87   {
  88     this.seqNames = seqNames;
  89   }
  90
  91   /**
  92    * configured by the WS framework just before results are collected
  93    */
  94   FeatureRenderer featureRenderer;
  95
  96   public void setFeatureRenderer(FeatureRenderer fr)
  97   {
  98     this.featureRenderer = fr;
  99   }
 100   public FeatureRenderer getFeatureRenderer()
 101   {
 102     // TODO Auto-generated method stub
 103     return featureRenderer;
 104   }
 105
 106 }