This is revised from the old wbsa workflow. String[] split = old_report.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[1].trim().split("\.").length); //System.out.println(trimmedSplit[1].trim().split("\.")[0].trim()); nonEmpty.add(trimmedSplit[1].trim()); } String old_gi_list = ""; for (int i = 0; i < nonEmpty.size(); i++){ old_gi_list = old_gi_list + (String) (nonEmpty.elementAt(i) + "\n"); } old_report old_gi_list String [] split = embl_list.split("(accession)"); Vector nonEmpty = new Vector(); for(int i = 0 ; i < split.length ; i++){ String trimmed = split[i].trim(); if(trimmed.length() > 0){ nonEmpty.add(trimmed); } } embl = new String [nonEmpty.size()]; //String gi = ""; for(int i = 0 ;i < nonEmpty.size() ; i++){ embl[i] = (String)(nonEmpty.elementAt(i)); } embl_list embl http://www.cs.man.ac.uk/~zhaoj/data/xsl/wrdfblast.xsl emnew uk.ac.man.cs.img.metadata.taverna.processor.NCBIRDFProcessor uk.ac.man.cs.img.metadata.taverna.processor.ReadRDFBlastReport <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about=" "><contains rdf:resource=" "/></rdf:Description> <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about=" "><contains rdf:resource=" "/></rdf:Description> String[] split = old_gi_list.split("(\n)"); //String[] splitNew = gi_list.split("(\n)"); boolean notHasIt = true; Vector nonEmpty = new Vector(); //for (int i = 0; i < splitNew.length; i++){ //notHasIt = true; for (int j = 0; j < split.length; j ++){ if (gi.equals(split[j])){ notHasIt = false; // break; } } if (notHasIt){ nonEmpty.add(gi); } if (nonEmpty.size()>0){ new_gi = (String) ("urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:genbank_gb:"+nonEmpty.elementAt(0)); } //} //String[] new_gi = new String[nonEmpty.size()]; //for (int i = 0; i < nonEmpty.size(); i ++){ // new_gi[i] = (String) ("urn:lsid:ncbi.nlm.nih.gov.lsid.biopathways.org:genbank_gb:"+nonEmpty.elementAt(i)); //} old_gi_list gi new_gi http://www.cs.man.ac.uk/~zhaoj/data/xsl/wublast.xsl uk.ac.man.cs.img.metadata.taverna.processor.WUBLASTRDFProcessor <rdf:Description xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" rdf:about=" "><sameAs rdf:resource=" "/></rdf:Description> WU-BLAST with output in XML format, for DNA/RNA http://www.ebi.ac.uk/soaplab/services/alignment.wu_blastn_xml