+ else if ( line.startsWith( "SQ" ) ) {
+ saw_sq = true;
+ if ( line.contains( "AA;" ) ) {
+ is_aa = true;
+ }
+ }
+ else if ( saw_sq && line.startsWith( " " ) ) {
+ sq_buffer.append( line.replaceAll( "\\s+", "" ) );
+ }
+ }
+ if ( ( sq_buffer.length() > 0 ) && is_aa ) {
+ e.setMolecularSequence( BasicSequence.createAaSequence( e.getAccession(), sq_buffer.toString() ) );