diff --git a/uk/ac/sanger/artemis/editor/DataCollectionPane.java b/uk/ac/sanger/artemis/editor/DataCollectionPane.java index 0a633e3b927773e0c4779ebbe42cdca081e63e88..8199d3c6fdc0243d01e71631ea81439b3da76be0 100644 --- a/uk/ac/sanger/artemis/editor/DataCollectionPane.java +++ b/uk/ac/sanger/artemis/editor/DataCollectionPane.java @@ -553,11 +553,10 @@ public class DataCollectionPane extends JScrollPane * @param ortholog true if ortholog is selected. * */ - protected static void getzCall(HitInfo hit, boolean ortholog) + private static void getzCall(HitInfo hit, boolean ortholog) { - String env[] = { "PATH=/usr/local/pubseq/bin/" }; + final String env[] = { "PATH=/usr/local/pubseq/bin/" }; - File fmfetch = new File("/nfs/disk100/pubseq/bin/mfetch"); if(hit.getOrganism() == null || hit.getDescription() == null) { @@ -566,13 +565,13 @@ public class DataCollectionPane extends JScrollPane if(FastaTextPane.isRemoteMfetch()) { String cmd = - "mfetch -f \"org des gen\" -d uniprot -i \"acc:"+hit.getID()+"\"" ; + "mfetch -p 22140 -f \"org des gen\" -d uniprot -i \"acc:"+hit.getID()+"\"" ; uk.ac.sanger.artemis.j2ssh.SshPSUClient ssh = new uk.ac.sanger.artemis.j2ssh.SshPSUClient(cmd); ssh.run(); res = ssh.getStdOut(); } - else if(!fmfetch.exists()) + else if(!FastaTextPane.getMfetchExecutable().exists()) { try { @@ -603,7 +602,7 @@ public class DataCollectionPane extends JScrollPane } else { - String cmd[] = { "mfetch", "-f", "org des gen", + String cmd[] = { "mfetch", "-p", "22140", "-f", "org des gen", "-d", "uniprot", "-i", "acc:"+hit.getID() }; ExternalApplication app = new ExternalApplication(cmd, @@ -642,7 +641,7 @@ public class DataCollectionPane extends JScrollPane { File fgetz = new File("/usr/local/pubseq/bin/getz"); String res = FastaTextPane.getUniprotLinkToDatabase(fgetz, - fmfetch, hit, env, "EMBL"); + FastaTextPane.getMfetchExecutable(), hit, env, "EMBL"); int ind1 = res.indexOf("ID "); if(ind1 > -1)