swiss org.embl.ebi.escience.scuflworkers.java.SplitByRegex String[] split = input.split("\n"); Vector nonEmpty = new Vector(); for (int i = 0; i < split.length; i++) { String trimmed = split[i].trim(); String[] trimmedSplit = trimmed.split(":"); System.out.println(trimmedSplit.length); if (trimmedSplit.length == 2){ nonEmpty.add(trimmedSplit[1].trim()); } } String output = ""; for (int i = 0; i < nonEmpty.size(); i++) { output = output + (String) (nonEmpty.elementAt(i) + "\n"); } input output \n extract information from geneGeneInfo processor at http://xml.nig.ac.jp/wsdl/Ensembl.wsdl http://phoebus.cs.man.ac.uk:1977/axis/services/seq_analysis.parse_ddbj_gene_info Gets ENSEMBL gene IDS that are based on the probeset names passed to it http://phoebus.cs.man.ac.uk:1977/axis/services/qtl_analysis.probeset_to_gene get gene information http://xml.nig.ac.jp/wsdl/Ensembl.wsdl getGeneInfo 17 mus_musculus_core_37_34e Mouse430A_2:1454738_x_at,Mouse430_2:1443660_at,Mouse430_2:1453598_at,Mouse430_2:1458299_s_at,Mouse430A_2:1425346_at,Mouse430A_2:1418255_s_at,Mouse430A_2:1427620_at,Mouse430_2:1460036_at,Mouse430_2:1458623_at,Mouse430_2:1440225_at,Mouse430A_2:1426479_a_at,Mouse430A_2:1425347_a_at,Mouse430_2:1460140_at,Mouse430_2:1431494_at,Mouse430_2:1443710_s_at,Mouse430_2:1434580_at 19592504 44592504