[Biojava-l] add isTaxonHidden to NCBITaxon

[David Scott]

in the genbank ORGANISM line where the taxonomy hierarchy is shown, not 
all levels are show by genbank. whether a level is shown or not is 
controlled by the isTaxonHidden flag in the genbank taxonomy file: 
"nodes.dmp". biosql does not currently provide for a isTaxonHidden field 
in the sg_taxon table. the table can be modified and the field added 
locally. it would make to easier to make this modification to add 
NCBITaxon.isTaxonHidden to NCBITaxon and SimpleNCBITaxon - modeling the 
methods after a similar field: ComparableTerm.getObsolete:

NCBITaxon:
   public boolean isTaxonHidden();
   public void setTaxonHidden(final boolean isHidden) throws 
ChangeVetoException;

SimpleNCBITaxon:
   private boolean isTaxonHidden=false;
     // for user
   private boolean isTaxonHidden() {
   ... }
   public void setTaxonHidden(final boolean isHidden) throws 
ChangeVetoException {
   ... }

   // for hibernate
   private String getTaxonHiddenChar() {
   ... }
   private void setTaxonHiddenChar(final String isHiddenChar) throws 
ChangeVetoException {
   ... }

SimpleNCBITaxonomyLoader:
   public NCBITaxon readNode(...
       ...
      final String isTaxonHidden = parts[10].trim()// either "0" or "1"
      ....
      try {
         ...
         t.setTaxonHidden(Integer.parseInt(isTaxonHidden)==1);
         ...

the code would continue to operate as it has - until the database has 
the additional field added locally and the hibernate mapping file 
modified to map the new field into the Taxon object.