JAL-2245 Castor mapping and code changes for change to ENA XML format

[jalview.git] / test / jalview / datamodel / xdb / embl / EmblTestHelper.java

diff --git a/test/jalview/datamodel/xdb/embl/EmblTestHelper.java b/test/jalview/datamodel/xdb/embl/EmblTestHelper.java
index 9957c72..a79bdb8 100644 (file)
--- a/test/jalview/datamodel/xdb/embl/EmblTestHelper.java
+++ b/test/jalview/datamodel/xdb/embl/EmblTestHelper.java
@@ -7,7 +7,7 @@ public class EmblTestHelper
   // adapted from http://www.ebi.ac.uk/ena/data/view/X07547&display=xml
   // dna and translations truncated for convenience
   private static final String TESTDATA = "<?xml version=\"1.0\" encoding=\"UTF-8\" ?>"
-          + "<ROOT>"
+          // + "<ROOT>"
           + "<entry accession=\"X07547\" version=\"1\" entryVersion=\"8\""
           + " dataClass=\"STD\" taxonomicDivision=\"PRO\""
           + " moleculeType=\"genomic DNA\" sequenceLength=\"7499\" topology=\"linear\""
@@ -38,16 +38,24 @@ public class EmblTestHelper
           + "<qualifier name=\"translation\"><value>MSSS</value></qualifier>"
           + "</feature>"
           /*
+           * third CDS is made up - has no xref - code should synthesize 
+           * one to an assumed EMBLCDSPROTEIN accession
+           */
+          + "<feature name=\"CDS\" location=\"join(4..6,10..15)\">"
+          + "<qualifier name=\"protein_id\"><value>CAA12345.6</value></qualifier>"
+          + "<qualifier name=\"translation\"><value>MSS</value></qualifier>"
+          + "</feature>"
+          /*
            * sequence (modified for test purposes)
            * emulates EMBL XML 1.2 which splits sequence data every 60 characters
            * see EmblSequence.setSequence
            */
           + "<sequence>GGTATGTCCTCTAGTACAAAC\n"
           + "ACCCCCAATATTGTGATATAATTAAAAACATAGCAT"
-          + "</sequence></entry></ROOT>";
+ + "</sequence></entry>";
 
-  static EmblFile getEmblFile()
+  static EmblEntry getEmblFile()
   {
-    return EmblFile.getEmblFile(new StringReader(TESTDATA));
+    return EmblFile.getEntry(new StringReader(TESTDATA));
   }
 }