44592504 Mouse430_2 \n 17 mus_musculus 19592504 \n org.embl.ebi.escience.scuflworkers.java.SplitByRegex , org.embl.ebi.escience.scuflworkers.java.SplitByRegex org.embl.ebi.escience.scuflworkers.java.StringListMerge org.embl.ebi.escience.scuflworkers.java.StringListMerge get gene information http://xml.nig.ac.jp/wsdl/Ensembl.wsdl getGeneInfo \n org.embl.ebi.escience.scuflworkers.java.SplitByRegex Retrieves a list of Ensembl genes for a given species, chromosome and position http://phoebus.cs.man.ac.uk:1977/axis/services/qtl_analysis.getgenesbyspecies Retrieves the current databases from ENSEMBL for a species http://phoebus.cs.man.ac.uk:1977/axis/services/qtl_analysis.getcurrentdatabase Gets the probesets that are in a region of a chromosome e.g. in a QTL or based on 2 marker names http://phoebus.cs.man.ac.uk:1977/axis/services/qtl_analysis.probeset_in_qtl gene_name 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("\t"); System.out.println(trimmedSplit.length); if (trimmedSplit.length == 4){ nonEmpty.add(trimmedSplit[3].trim()); } } String output = ""; for (int i = 0; i < nonEmpty.size(); i++) { output = output + (String) (nonEmpty.elementAt(i) + "\n"); } input output 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 Alltext To be added http://phoebus.cs.man.ac.uk:1977/axis/services/uniprotsequence.uniprot swiss 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"); } //String[] split2 = intermediate.split(":"); //Vector nonEmpty2 = new Vector(); //for (int i = 0; i < split2.length; i++) //{ // String trimmed2 = split2[i].trim(); // String[] trimmedSplit2 = trimmed2.split(":"); // nonEmpty2.add(trimmedSplit2[1].trim()); //} //String output = ""; //for (int i = 0; i < nonEmpty2.size(); i++) //{ // output = output + (String) (nonEmpty2.elementAt(i) + "\n"); //} input output 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 org.embl.ebi.escience.scuflworkers.java.StringStripDuplicates org.embl.ebi.escience.scuflworkers.java.StringConcat