examples/groovy/stripUniprotPrefixes.groovy

   1 import jalview.analysis.*;
   2 import jalview.datamodel.*;
   3 import jalview.gui.AlignFrame;
   4 import jalview.gui.AlignViewport;
   5
   6 def af = Jalview.getAlignframes();
   7
   8 // walk through  all alignments, stripping off all text prior to and including last '|' symbol in sequence IDs
   9
  10 for (ala in af)
  11 {
  12         def al = ala.viewport.alignment;
  13         if (al!=null)
  14         {
  15                 SequenceI[] seqs = al.getSequencesArray();
  16                 for (sq in seqs)
  17                 {
  18                         if (sq!=null) {
  19                                 if (sq.getName().indexOf("|")>-1)
  20                                 {
  21                                         sq.setName(sq.getName().substring(sq.getName().lastIndexOf("|")+1));
  22                                         if (sq.getDatasetSequence()!=null)
  23                                         {
  24                                                 sq.getDatasetSequence().setName(sq.getName());
  25                                         }
  26                                 }
  27                         }
  28                 }
  29         }
  30 }
  31