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lib/InSilicoSpectro/InSilico/ModRes.pm  view on Meta::CPAN

    foreach (qw (aaCur aa aaBefore )) {
      $mr->set($_, $elres->atts->{$_});
    }
    my $str="(?<=[$mr->{aaBefore}]" if $mr->{aaBefore};
    $str.="[$mr->{aa}]";
    $str.="(?=[$mr->{aaAfter}])" if $mr->{aaAfter};
    $mr->regexp($str);
  } elsif (my $elSite=$el->first_child('site')) {
    my $elRes=$elSite->first_child('residue') or croak "no [residue] child";
    $mr->nTerm(defined $elSite->first_child('nterm'));
    $mr->cTerm(defined $elSite->first_child('cterm'));
    $mr->{site}{residue}=$elRes;
    my $re.=$mr->nTerm?'^':'';
    $re.="[".($elRes->text || '.')."]";
    $re.=$mr->cTerm?'$':'';
    $mr->regexp($re);
  } elsif (my $elSite=$el->first_child('siteRegexp')) {
    $mr->nTerm(defined $elSite->atts->{nterm});
    $mr->cTerm(defined $elSite->atts->{cterm});
    my $re.=$mr->nTerm?'^':'';
    $re.=$elSite->text;
    $re.=$mr->cTerm?'$':'';
    $mr->regexp($re);
  } else {
    croak "in oneModRes tag, could not find any of (residue|site|siteRegexp) child notations";
  }

  my @tmp=$el->get_xpath('delta') or  InSilicoSpectro::Utils::io::croakIt "cannot find <delta> tag";
  my $eldelta=$tmp[0];
  foreach (qw (monoisotopic average)) {
    $mr->set("delta_$_", $eldelta->atts->{$_});
  }
  if (@tmp=$el->get_xpath('sprotFT')) {
    $mr->set('sprotFT', $tmp[0]->text);
  }

#  $mr->add2Dico();
  if(registerModResHandler()){
    registerModResHandler()->($mr);
  }

}

sub getXMLTwigElt{
  my $this=shift;
  my $el=XML::Twig::Elt->new()->parse("<oneModRes type='".($this->{type}||'aaModif')."' name='$this->{name}'/>");
  XML::Twig::Elt->new()->parse("<description><![CDATA[$this->{description}]]></description>")->paste(last_child=>$el);
  if($this->{site}){
    my $termtag="";
    $termtag.='<nterm/>' if($this->nTerm);
    $termtag.='<cterm/>' if($this->cTerm);
    XML::Twig::Elt->new()->parse("<site><residue>$this->{site}{residue}</residue>$termtag</site>")->paste(last_child=>$el);
  }else{
    my $termatts="";
    $termatts=' nterm="yes"' if($this->nTerm);
    $termatts=' cterm="yes"' if($this->cTerm);
    XML::Twig::Elt->new()->parse("<siteRegexp$termatts>$this->{regexpStr}</siteRegexp>")->paste(last_child=>$el);
  }
  XML::Twig::Elt->new()->parse("<delta monoisotopic='$this->{delta_monoisotopic}' average='$this->{delta_average}'/>")->paste(last_child=>$el);

  XML::Twig::Elt->new()->parse("<formula>$this->{formula}</formula>")->paste(last_child=>$el);
  XML::Twig::Elt->new()->parse("<sprotFT><![CDATA[$this->{sprotFT}]]></sprotFT>")->paste(last_child=>$el) if $this->{sprotFT};
  return $el;
}

sub registerModResHandler{
  my $sub=shift;
  if($sub){
    $rsRegisterModResHandler=$sub;
  }
  return $rsRegisterModResHandler;
}
# -------------------------------   misc
return 1;