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public String getBiggIdFromSynonym(String data_source_biggId, String synonym, String type){ | |
String biggId = new String(); | |
String query; | |
switch (type){ | |
case TYPE_SPECIES: | |
query = SELECT + "c." + COLUMN_BIGG_ID + FROM + COMPONENT + " c, " + DATA_SOURCE + " d, " + SYNONYM + " s" | |
+ WHERE + "d." + COLUMN_BIGG_ID + " = '%s' AND d." + COLUMN_ID + " = s." + | |
COLUMN_DATA_SOURCE_ID + " AND s." + COLUMN_SYNONYM + " = '%s' AND s." + COLUMN_OME_ID + " = c." | |
+ COLUMN_ID; | |
break; | |
case TYPE_REACTION: | |
query = SELECT + "r." + COLUMN_BIGG_ID + FROM + REACTION + " r, " + DATA_SOURCE + " d, " + SYNONYM + " s" | |
+ WHERE + "d." + COLUMN_BIGG_ID + " = '%s' AND d." + COLUMN_ID + " = s." + | |
COLUMN_DATA_SOURCE_ID + " AND s." + COLUMN_SYNONYM + " = '%s' AND s." + COLUMN_OME_ID + " = r." | |
+ COLUMN_ID; | |
break; | |
case TYPE_GENE_PRODUCT: | |
query = SELECT + "g." + COLUMN_LOCUS_TAG + FROM + GENE + " g, " + DATA_SOURCE + " d, " + SYNONYM + " s" | |
+ WHERE + "d." + COLUMN_BIGG_ID + " = '%s' AND d." + COLUMN_ID + " = s." + | |
COLUMN_DATA_SOURCE_ID + " AND s." + COLUMN_SYNONYM + " = '%s' AND s." + COLUMN_OME_ID + " = g." | |
+ COLUMN_ID; | |
break; | |
default: return null; | |
} | |
try { | |
ResultSet rst = connector.query(query, data_source_biggId, synonym); | |
if(rst.next()){ | |
biggId = rst.getString(1); | |
} | |
else{ | |
return null; | |
} | |
//return null if more than one BiGG Id is obtained | |
if(rst.next()){ | |
return null; | |
} | |
} | |
catch (SQLException exc) { | |
logger.warning(Utils.getMessage(exc)); | |
} | |
return biggId; | |
} |
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