groovy/sdppred_testing.groovy

   1
   2 import jalview.bin.Jalview
   3 import jalview.io.gff.GffConstants;
   4 import jalview.workers.AnnotationProviderI
   5 import jalview.workers.AlignmentAnnotationFactory
   6 import jalview.datamodel.*;
   7
   8 /*
   9  * Define something that counts each visible feature type
  10  */
  11 def sdppredCounter =
  12     [
  13      getNames: { visibleFeatures as String[] },
  14      getDescriptions:  { visibleFeatures as String[] },
  15      getMinColour: { [0, 255, 255] as int[] }, // cyan
  16      getMaxColour: { [0, 0, 255] as int[] }, // blue
  17      count:
  18          { res, feats ->
  19              getCounts.call(feats)
  20          },
  21      calculateAnnotation:
  22          { al, feat_rend ->
  23          ProfilesI a_prof=al.getSequenceConsensusHash();
  24          al_width = a_prof.getEndColumn();
  25 //         jalview.datamodel.Annotation ai[] = new jalview.datamodel.Annotation[al_width];
  26          def sg_profs = [];
  27          al.getGroups().each({group -> sg_profs << group.getSequenceConsensusHash() });
  28          if (sg_profs==null) {
  29            return null;
  30          }
  31          annot = new Annotation[al_width];
  32          for (int c=0;c<al_width;c++) {
  33            def al_p=a_prof.get(c);
  34            if (al_p!=null) {
  35            def al_ng = al_p.getNonGapped()
  36            if (al_p.getCounts()!=null) {
  37            al_p = al_p.getCounts().getSymbolCounts();
  38            def tot_count=[foo:0];
  39            for (int a=al_p.values.length-1;a>-1;a--) {
  40              tot_count << [(al_p.symbols[a]):(al_p.values[a])]
  41            }
  42            Ip=0.0;
  43            if (al_ng>0) {
  44              sg_profs.each({sg_prof ->
  45                if (sg_prof!=null) {count = sg_prof.get(c);
  46                if ((count!=null) && (count.getCounts()!=null)) {
  47                  g_size = count.getHeight();
  48                  count = count.getCounts().getSymbolCounts();
  49                  for (int a=count.values.length-1;a>-1; a--) {
  50                    Ip+= (count.values[a]/al_ng) * Math.log((count.values[a]*al_ng)/(g_size*tot_count[(count.symbols[a])]));
  51                  }
  52                }
  53                }
  54              });
  55            annot[c]=new Annotation((float) Ip);
  56
  57            }
  58          }
  59          }
  60          }
  61          AlignmentAnnotation annotrow = new AlignmentAnnotation("SDPpred","SDP calculation results",annot);
  62          annotrow.setCalcId("SDPPRED");
  63          return [annotrow];
  64      }
  65      ] as AnnotationProviderI
  66
  67 /*
  68  * and register the counter
  69  */
  70 AlignmentAnnotationFactory.newCalculator(sdppredCounter)