examples/groovy/selectColumnsByFeatureAndGroup.groovy

   1 import jalview.analysis.*;
   2 import jalview.datamodel.*;
   3 import jalview.gui.AlignFrame;
   4 import jalview.gui.AlignViewport;
   5 import java.util.BitSet;
   6 import javax.swing.JOptionPane;
   7 import groovy.swing.SwingBuilder;
   8 def toselect = getFeatureInput(); // change this to select the desired feature type
   9
  10 def nal=0;
  11 def nfeat=0;
  12 def nseq=0;
  13
  14 for (ala in Jalview.getAlignFrames()) {
  15   def al = ala.viewport.alignment;
  16     if (al!=null)
  17     {
  18       BitSet bs = new BitSet();
  19       SequenceI[] seqs = al.getSequencesArray();
  20       for (sq in seqs)
  21       {
  22           def tfeat=0;
  23         if (sq!=null) {
  24           SequenceFeature[] sf = sq.getSequenceFeatures();
  25           for (sfpos in sf)
  26           {
  27             if (sfpos!=null && sfpos.getType().equals(toselect))
  28             {
  29               tfeat++;
  30               int i=sq.findIndex(sfpos.getBegin());
  31               int ist=sq.findIndex(sq.getStart());
  32               if (i<ist)
  33               {
  34                 i=ist;
  35               }
  36               int j=sq.findIndex(sfpos.getEnd());
  37               if (j>al.getWidth())
  38               {
  39                 j = al.getWidth();
  40               }
  41               for (; i<=j; i++)
  42               {
  43                 bs.set(i-1);
  44               }
  45             }
  46           }
  47         }
  48         if (tfeat>0) {
  49             nseq++;
  50             nfeat+=tfeat;
  51         }
  52       }
  53       if (bs.cardinality()>0)
  54       {
  55         nal ++;
  56         ColumnSelection cs = ala.viewport.getColumnSelection();
  57         if (cs == null) {
  58           cs = new ColumnSelection();
  59         }
  60     for (int i = bs.nextSetBit(0); i >= 0; i = bs.nextSetBit(i+1)) {
  61         cs.addElement(i);
  62         }
  63       ala.viewport.setColumnSelection(cs);
  64       ala.alignPanel.paintAlignment(true);
  65       ala.statusBar.setText("Marked "+bs.cardinality()+" columns containing features of type "+toselect)
  66       } else {
  67         ala.statusBar.setText("No features of type "+toselect+" found.");
  68       }
  69     }
  70 }
  71 return "Found a total of ${nfeat} features across ${nseq} sequences in ${nal} alignments.";
  72
  73 String getFeatureInput(){
  74         def swingBuilder = new SwingBuilder();
  75         def response = JOptionPane.showInputDialog(
  76                    null, 'Select columns by feature by type','Enter type of feature', JOptionPane.OK_OPTION)
  77
  78         return response
  79     }