Test

From GMOD

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Above TOC

**An example table**

MediaWiki:Mainpage

1 Five
- 1.1 Three
  - 1.1.1 Four
- 1.2 Two
- 1.3 One
2 References

Five

#Three

#Four

 
sub check_names {
   my $self = shift;
 
   my $tree = $self->tree;
   my $aln  = $self->alignment;
   if( ! $aln ) {
       $self->warn("must have supplied a valid alignment file in order to run njtree_best");
       return 0;
   }
   if( ! $tree ) {
       $self->warn("must have supplied a valid species tree file in order to run njtree_best");
       return 0;
   }
   foreach my $leaf ($tree->get_leaf_nodes) {
       my $id = $leaf->id;
       $id =~ s/\-\*.+//; # njtree does not consider anything after a \-\*
       $self->{_treeids}{$id} = 1;
   }
   foreach my $seq ($aln->each_seq) {
       my $id = $seq->id;
       $id =~ s/.+\_//; # njtree only looks at the right side of the \_
       $self->{_alnids}{$id} = 1;
   }
   foreach my $alnid (keys %{$self->{_alnids}}) {
       $self->{_unmappedids}{$alnid} = 1 unless (defined($self->{_treeids}{$alnid}));
   }
   if (defined($self->{_unmappedids})) {
       my $count = scalar(keys%{$self->{_unmappedids}});
       my $unmapped = join(",",keys %{$self->{_unmappedids}});
       $self->warn("$count unmapped ids between the aln and the tree $unmapped");
   }
}

Text

Three

dfjlgh

Four

ldufg

Two

ldjfhg

One

 
try {
 sqlMap.startTransaction();
 pGene.id =featureDAO.insert(pGene.getFeatureWithBLOBs());
 featurepropDAO.insert(pGene.getPropertyDescription());
 pGene.featurelocId = featurelocDAO.insert(pGene
                                  .getFeaturelocWithBLOBS());
 pGene = insertExons(pGene);
 insertSynonyms(pGene);
 sqlMap.commitTransaction();
} catch (Exception e) {
       System.out.println(e);
       throw (e);
} finally {
      sqlMap.endTransaction();
}