How to use

FilterGraph_GAF2

in

slib.graph.io.loader.utils.filter.graph.gaf2

/**
 *
 * @param conf
 * @throws SLIB_Ex_Critic
 */
public FilterGraph_GAF2(Conf conf) throws SLIB_Ex_Critic {
  super(conf);
  String taxids = (String) conf.getParam(FilterGraph_GAF2_cst.TAXONS_IDS);
  String ecids = (String) conf.getParam(FilterGraph_GAF2_cst.REMOVE_EC);
  if (taxids != null) {
    addTaxons(Arrays.asList(taxids.split(",")));
  }
  if (ecids != null) {
    addECtoExclude(Arrays.asList(ecids.split(",")));
  }
}

logger.info("Filtering according to filter " + filter.getId() + "\ttype" + filter.getType());
taxons = filter.getTaxons();
excludedEC = filter.getExcludedEC();

/**
 *
 * @param gconf
 * @return a filter
 * @throws SLIB_Ex_Critic
 */
public static Filter buildFilter(Conf gconf) throws SLIB_Ex_Critic {
  Filter f = null;
  String id = (String) gconf.getParam(XmlTags.ID_ATTR);
  String type = (String) gconf.getParam(XmlTags.TYPE_ATTR);
  if (id == null) {
    Util.error("Missing " + XmlTags.ID_ATTR + " in a filter specification");
  }
  if (type == null) {
    Util.error("Missing " + XmlTags.TYPE_ATTR + " in a filter specification");
  }
  if (!supportType(type)) {
    Util.error("Unsupported Filter type " + type + " found in filter '" + id + "' specification");
  }
  if (type.equals(FilterGraph_GAF2_cst.TYPE)) {
    f = new FilterGraph_GAF2(gconf);
  } else if (type.equals(FilterGraph_Metrics_cst.TYPE)) {
    f = new FilterGraph_Metrics(gconf);
  } else // do not pass 
  {
    throw new UnsupportedOperationException("Sorry, filter is not taking into account, please repor the issue");
  }
  return f;
}

logger.info("Filtering according to filter " + filter.getId() + "\ttype" + filter.getType());
taxons = filter.getTaxons();
excludedEC = filter.getExcludedEC();

/**
 *
 * @param gconf
 * @return a filter
 * @throws SLIB_Ex_Critic
 */
public static Filter buildFilter(Conf gconf) throws SLIB_Ex_Critic {
  Filter f = null;
  String id = (String) gconf.getParam(XmlTags.ID_ATTR);
  String type = (String) gconf.getParam(XmlTags.TYPE_ATTR);
  if (id == null) {
    Util.error("Missing " + XmlTags.ID_ATTR + " in a filter specification");
  }
  if (type == null) {
    Util.error("Missing " + XmlTags.TYPE_ATTR + " in a filter specification");
  }
  if (!supportType(type)) {
    Util.error("Unsupported Filter type " + type + " found in filter '" + id + "' specification");
  }
  if (type.equals(FilterGraph_GAF2_cst.TYPE)) {
    f = new FilterGraph_GAF2(gconf);
  } else if (type.equals(FilterGraph_Metrics_cst.TYPE)) {
    f = new FilterGraph_Metrics(gconf);
  } else // do not pass 
  {
    throw new UnsupportedOperationException("Sorry, filter is not taking into account, please repor the issue");
  }
  return f;
}

/**
 *
 * @param conf
 * @throws SLIB_Ex_Critic
 */
public FilterGraph_GAF2(Conf conf) throws SLIB_Ex_Critic {
  super(conf);
  String taxids = (String) conf.getParam(FilterGraph_GAF2_cst.TAXONS_IDS);
  String ecids = (String) conf.getParam(FilterGraph_GAF2_cst.REMOVE_EC);
  if (taxids != null) {
    addTaxons(Arrays.asList(taxids.split(",")));
  }
  if (ecids != null) {
    addECtoExclude(Arrays.asList(ecids.split(",")));
  }
}