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

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.datamodel.xdb.embl;
  22
  23 import java.io.StringReader;
  24
  25 public class EmblTestHelper
  26 {
  27   // adapted from http://www.ebi.ac.uk/ena/data/view/X07547&display=xml
  28   // dna and translations truncated for convenience
  29   private static final String TESTDATA = "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>"
  30           + "<ROOT>"
  31           + "<entry accession=\"X07547\" version=\"1\" entryVersion=\"8\""
  32           + " dataClass=\"STD\" taxonomicDivision=\"PRO\""
  33           + " moleculeType=\"genomic DNA\" sequenceLength=\"7499\" topology=\"linear\""
  34           + " firstPublic=\"1988-11-10\" firstPublicRelease=\"18\""
  35           + " lastUpdated=\"1999-02-10\" lastUpdatedRelease=\"58\">"
  36           + "<secondaryAccession>X07574</secondaryAccession>"
  37           + "<description>C. trachomatis plasmid</description>"
  38           + "<keyword>plasmid</keyword><keyword>unidentified reading frame</keyword>"
  39           + "<xref db=\"EuropePMC\" id=\"PMC107176\" secondaryId=\"9573186\" />"
  40           + "<xref db=\"MD5\" id=\"ac73317\" />"
  41           /*
  42            * first CDS (range and translation changed to keep test data manageable)
  43            */
  44           + "<feature name=\"CDS\" location=\"complement(46..57)\">"
  45           // test the case of >1 cross-ref to the same database (JAL-2029)
  46           + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"B0BCM4\" secondaryId=\"2.1\" />"
  47           + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"P0CE20\" />"
  48           + "<qualifier name=\"note\"><value>ORF 8 (AA 1-330)</value><value>pickle</value></qualifier>"
  49           + "<qualifier name=\"protein_id\"><value>CAA30420.1</value></qualifier>"
  50           + "<qualifier name=\"translation\"><value>MLCF</value><evidence>Keith</evidence></qualifier>"
  51           + "</feature>"
  52           /*
  53            * second CDS (range and translation changed to keep test data manageable)
  54            */
  55           + "<feature name=\"CDS\" location=\"4..15\">"
  56           + "<xref db=\"UniProtKB/Swiss-Prot\" id=\"B0BCM3\" />"
  57           + "<qualifier name=\"protein_id\"><value>CAA30421.1</value></qualifier>"
  58           + "<qualifier name=\"translation\"><value>MSSS</value></qualifier>"
  59           + "</feature>"
  60           /*
  61            * third CDS is made up - has no xref - code should synthesize
  62            * one to an assumed EMBLCDSPROTEIN accession
  63            */
  64           + "<feature name=\"CDS\" location=\"join(4..6,10..15)\">"
  65           + "<qualifier name=\"protein_id\"><value>CAA12345.6</value></qualifier>"
  66           + "<qualifier name=\"translation\"><value>MSS</value></qualifier>"
  67           + "</feature>"
  68           /*
  69            * sequence (modified for test purposes)
  70            * emulates EMBL XML 1.2 which splits sequence data every 60 characters
  71            * see EmblSequence.setSequence
  72            */
  73           + "<sequence>GGTATGTCCTCTAGTACAAAC\n"
  74           + "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT"
  75           + "</sequence></entry></ROOT>";
  76
  77   static EmblFile getEmblFile()
  78   {
  79     return EmblFile.getEmblFile(new StringReader(TESTDATA));
  80   }
  81 }