public static List < GeneName > getGeneNames ( InputStream inStream ) throws IOException { ArrayList < GeneName > geneNames = new ArrayList < GeneName > ( ) ; BufferedReader reader = new BufferedReader ( new InputStreamReader ( inStream ) ) ; // skip reading first line (it is the legend) String line = reader . readLine ( ) ; while ( ( line = reader . readLine ( ) ) != null ) { // process line... //System.out.println(Arrays.toString(line.split("\t"))); GeneName geneName = getGeneName ( line ) ; if ( geneName != null ) geneNames . add ( geneName ) ; //System.out.println(geneName); } // since this is a large list, let's free up unused space... geneNames . trimToSize ( ) ; return geneNames ; }
Get a list of GeneNames from an input stream .