test/jalview/datamodel/xdb/embl/EmblTestHelper.java

   1 package jalview.datamodel.xdb.embl;
   2
   3 import java.io.StringReader;
   4
   5 public class EmblTestHelper
   6 {
   7   // adapted from http://www.ebi.ac.uk/ena/data/view/X07547&display=xml
   8   // dna and translations truncated for convenience
   9   private static final String TESTDATA = "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>"
  10           + "<ROOT>"
  11           + "<entry accession=\"X07547\" version=\"1\" entryVersion=\"8\""
  12           + " dataClass=\"STD\" taxonomicDivision=\"PRO\""
  13           + " moleculeType=\"genomic DNA\" sequenceLength=\"7499\" topology=\"linear\""
  14           + " firstPublic=\"1988-11-10\" firstPublicRelease=\"18\""
  15           + " lastUpdated=\"1999-02-10\" lastUpdatedRelease=\"58\">"
  16           + "<secondaryAccession>X07574</secondaryAccession>"
  17           + "<description>C. trachomatis plasmid</description>"
  18           + "<keyword>plasmid</keyword><keyword>unidentified reading frame</keyword>"
  19           + "<xref db=\"EuropePMC\" id=\"PMC107176\" secondaryId=\"9573186\" />"
  20           + "<xref db=\"MD5\" id=\"ac73317\" />"
  21           /*
  22            * first CDS (range and translation changed to keep test data manageable)
  23            */
  24           + "<feature name=\"CDS\" location=\"complement(46..57)\">"
  25           // test the case of >1 cross-ref to the same database (JAL-2029)
  26           + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"B0BCM4\" secondaryId=\"2.1\" />"
  27           + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"P0CE20\" />"
  28           + "<qualifier name=\"note\"><value>ORF 8 (AA 1-330)</value><value>pickle</value></qualifier>"
  29           + "<qualifier name=\"protein_id\"><value>CAA30420.1</value></qualifier>"
  30           + "<qualifier name=\"translation\"><value>MLCF</value><evidence>Keith</evidence></qualifier>"
  31           + "</feature>"
  32           /*
  33            * second CDS (range and translation changed to keep test data manageable)
  34            */
  35           + "<feature name=\"CDS\" location=\"4..15\">"
  36           + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"B0BCM3\" />"
  37           + "<qualifier name=\"protein_id\"><value>CAA30421.1</value></qualifier>"
  38           + "<qualifier name=\"translation\"><value>MSSS</value></qualifier>"
  39           + "</feature>"
  40           /*
  41            * third CDS is made up - has no xref - code should synthesize
  42            * one to an assumed EMBLCDSPROTEIN accession
  43            */
  44           + "<feature name=\"CDS\" location=\"join(4..6,10..15)\">"
  45           + "<qualifier name=\"protein_id\"><value>CAA12345.6</value></qualifier>"
  46           + "<qualifier name=\"translation\"><value>MSS</value></qualifier>"
  47           + "</feature>"
  48           /*
  49            * sequence (modified for test purposes)
  50            * emulates EMBL XML 1.2 which splits sequence data every 60 characters
  51            * see EmblSequence.setSequence
  52            */
  53           + "<sequence>GGTATGTCCTCTAGTACAAAC\n"
  54           + "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT"
  55           + "</sequence></entry></ROOT>";
  56
  57   static EmblFile getEmblFile()
  58   {
  59     return EmblFile.getEmblFile(new StringReader(TESTDATA));
  60   }
  61 }