[Biojava-dev] Issue with SimpleNCBITaxon class

[Deepak Sheoran]

Hi,

Their is very fundamental issue in SimpleNCBITaxon class becuase of 
which it is producing wrong taxonomy hierarchy. I am explaing what I 
have found let me what you guys think of it, and me suggest how to fix it.

1) Columns in taxon table are (taxon_id, ncbi_taxon_id, parent_taxon_id, 
nodeRank, geneticCode, mitoGeneticCode, leftValue, rightValue)
2) In the class SimpleNCBITaxon we are thinking "parent_taxon_id" to 
have parent ncbi_taxon_id for current ncbi_taxon_id value, but its not 
true. The value which "parent_taxon_id" have is "taxon_id" which have 
parent_ncbi_taxon_id of current ncbi_taxon_id.

<property name="NCBITaxID" column="ncbi_taxon_id" node="@NCBITaxId"/>
<property name="nodeRank" column="node_rank"/>
<property name="geneticCode" column="genetic_code"/>
<property name="mitoGeneticCode" column="mito_genetic_code"/>
<property name="leftValue" column="left_value"/>
<property name="rightValue" column="right_value"/>
<property name="parentNCBITaxID" column="parent_taxon_id"/>      ----- 
its not correct column parent_taxon_id stores the taxon_id which have 
parent_ncbi_taxon_id for current entry

Thanks
Deepak Sheoran