private String extractGeneSymbol ( Xref xref ) { if ( xref . getDb ( ) != null && ( xref . getDb ( ) . equalsIgnoreCase ( "HGNC Symbol" ) || xref . getDb ( ) . equalsIgnoreCase ( "Gene Symbol" ) || xref . getDb ( ) . equalsIgnoreCase ( "HGNC" ) ) ) { String ref = xref . getId ( ) ; if ( ref != null ) { ref = ref . trim ( ) ; if ( ref . contains ( ":" ) ) ref = ref . substring ( ref . indexOf ( ":" ) + 1 ) ; if ( ref . contains ( "_" ) ) ref = ref . substring ( ref . indexOf ( "_" ) + 1 ) ; // if the reference is an HGNC ID, then convert it to a symbol if ( ! HGNC . containsSymbol ( ref ) && Character . isDigit ( ref . charAt ( 0 ) ) ) { ref = HGNC . getSymbol ( ref ) ; } } return ref ; } return null ; }
Searches for gene symbol in Xref .