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JAL-3692 fix up test for 2.11.1 series datamodel API
[jalview.git]
/
test
/
jalview
/
io
/
EmblFlatFileTest.java
diff --git
a/test/jalview/io/EmblFlatFileTest.java
b/test/jalview/io/EmblFlatFileTest.java
index
4ca826c
..
35b378b
100644
(file)
--- a/
test/jalview/io/EmblFlatFileTest.java
+++ b/
test/jalview/io/EmblFlatFileTest.java
@@
-18,7
+18,6
@@
import org.testng.annotations.Test;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
-import jalview.datamodel.Sequence.DBModList;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.SequenceFeatures;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.SequenceFeatures;
@@
-37,7
+36,7
@@
public class EmblFlatFileTest
public void testParse() throws MalformedURLException, IOException
{
File dataFile = new File("test/jalview/io/J03321.embl.txt");
public void testParse() throws MalformedURLException, IOException
{
File dataFile = new File("test/jalview/io/J03321.embl.txt");
- FileParse fp = new FileParse(dataFile, DataSourceType.FILE);
+ FileParse fp = new FileParse(dataFile.getAbsolutePath(), DataSourceType.FILE);
EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
parser.parse();
List<SequenceI> seqs = parser.getSeqs();
EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
parser.parse();
List<SequenceI> seqs = parser.getSeqs();
@@
-127,7
+126,8
@@
public class EmblFlatFileTest
* (some e.g. INTERPRO are duplicates). Jalview adds a dbref to 'self'.
* Sample a few here. Note DBRefEntry constructor capitalises source.
*/
* (some e.g. INTERPRO are duplicates). Jalview adds a dbref to 'self'.
* Sample a few here. Note DBRefEntry constructor capitalises source.
*/
- List<DBRefEntry> dbrefs = seq.getDBRefs();
+ List<DBRefEntry> dbrefs = Arrays.asList(seq.getDBRefs());
+
assertEquals(dbrefs.size(), 32);
// xref to 'self':
DBRefEntry selfRef = new DBRefEntry("EMBLTEST", "1", "J03321");
assertEquals(dbrefs.size(), 32);
// xref to 'self':
DBRefEntry selfRef = new DBRefEntry("EMBLTEST", "1", "J03321");
@@
-256,7
+256,7
@@
public class EmblFlatFileTest
List<SequenceI> seqs = parser.getSeqs();
assertEquals(seqs.size(), 1);
SequenceI seq = seqs.get(0);
List<SequenceI> seqs = parser.getSeqs();
assertEquals(seqs.size(), 1);
SequenceI seq = seqs.get(0);
- DBModList<DBRefEntry> dbrefs = seq.getDBRefs();
+ List<DBRefEntry> dbrefs = Arrays.asList(seq.getDBRefs());
/*
* dna should have dbref to itself, and to inferred EMBLCDSPROTEIN:QHD43415.1
/*
* dna should have dbref to itself, and to inferred EMBLCDSPROTEIN:QHD43415.1