From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 18 Aug 2020 13:39:25 +0000 (+0100)
Subject: JAL-1260 unit test for FileFormats updated for GenBank/ENA
X-Git-Tag: Release_2_11_2_0~34^2~8^2~2
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=41e20dff103d6d1995b2ed3b6d6479f359025531;p=jalview.git

JAL-1260 unit test for FileFormats updated for GenBank/ENA
---

diff --git a/test/jalview/io/FileFormatsTest.java b/test/jalview/io/FileFormatsTest.java
index 53f18bf..bf01fb7 100644
--- a/test/jalview/io/FileFormatsTest.java
+++ b/test/jalview/io/FileFormatsTest.java
@@ -31,14 +31,15 @@ public class FileFormatsTest
   public void testIsIdentifiable()
   {
     FileFormats formats = FileFormats.getInstance();
-    assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Fasta
-            .getName())));
-    assertTrue(formats.isIdentifiable(formats.forName(FileFormat.MMCif
-            .getName())));
-    assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Jnet
-            .getName())));
-    assertTrue(formats.isIdentifiable(formats.forName(FileFormat.Jalview
-            .getName())));
+    assertTrue(formats
+            .isIdentifiable(formats.forName(FileFormat.Fasta.getName())));
+    assertTrue(formats
+            .isIdentifiable(formats.forName(FileFormat.MMCif.getName())));
+    assertTrue(formats
+            .isIdentifiable(formats.forName(FileFormat.Jnet.getName())));
+    assertTrue(formats
+            .isIdentifiable(formats.forName(FileFormat.Jalview.getName())));
+    // GenBank/ENA
     assertFalse(formats.isIdentifiable(null));
 
     /*
@@ -55,7 +56,7 @@ public class FileFormatsTest
   @Test(groups = "Functional")
   public void testGetReadableFormats()
   {
-    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+    String expected = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
     FileFormats formats = FileFormats.getInstance();
     assertEquals(formats.getReadableFormats().toString(), expected);
   }
@@ -74,14 +75,14 @@ public class FileFormatsTest
   public void testDeregisterFileFormat()
   {
     String writable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
-    String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+    String readable = "[Fasta, PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
     FileFormats formats = FileFormats.getInstance();
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
 
     formats.deregisterFileFormat(FileFormat.Fasta.getName());
     writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP]";
-    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview]";
+    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview]";
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
 
@@ -90,7 +91,7 @@ public class FileFormatsTest
      */
     formats.registerFileFormat(FileFormat.Fasta);
     writable = "[PFAM, Stockholm, PIR, BLC, AMSA, JSON, PileUp, MSF, Clustal, PHYLIP, Fasta]";
-    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GFF or Jalview features, PDB, mmCIF, Jalview, Fasta]";
+    readable = "[PFAM, Stockholm, PIR, BLC, AMSA, HTML, RNAML, JSON, PileUp, MSF, Clustal, PHYLIP, GenBank Flatfile, ENA Flatfile, GFF or Jalview features, PDB, mmCIF, Jalview, Fasta]";
     assertEquals(formats.getWritableFormats(true).toString(), writable);
     assertEquals(formats.getReadableFormats().toString(), readable);
   }
@@ -144,8 +145,7 @@ public class FileFormatsTest
      * verify the list of file formats registered matches the enum values
      */
     FileFormats instance = FileFormats.getInstance();
-    Iterator<FileFormatI> formats = instance.getFormats()
-            .iterator();
+    Iterator<FileFormatI> formats = instance.getFormats().iterator();
     FileFormatI[] builtIn = FileFormat.values();
 
     for (FileFormatI ff : builtIn)
diff --git a/test/jalview/io/GenBankFileTest.java b/test/jalview/io/GenBankFileTest.java
index 25ad601..89f0d0e 100644
--- a/test/jalview/io/GenBankFileTest.java
+++ b/test/jalview/io/GenBankFileTest.java
@@ -7,7 +7,6 @@ import static org.testng.AssertJUnit.assertNull;
 import java.io.File;
 import java.io.IOException;
 import java.net.MalformedURLException;
-import java.util.Arrays;
 import java.util.List;
 import java.util.Set;
 
@@ -131,7 +130,7 @@ public class GenBankFileTest
      * xref to self : 1
      * protein products: 8
      */
-    List<DBRefEntry> dbrefs = Arrays.asList(seq.getDBRefs());
+    List<DBRefEntry> dbrefs = seq.getDBRefs();
 
     assertEquals(dbrefs.size(), 9);
     // xref to 'self':
@@ -184,7 +183,7 @@ public class GenBankFileTest
     assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
     assertEquals(dbref.getAccessionId(), "AAA91574.1");
     mapping = dbref.getMap();
-     mapTo = mapping.getTo();
+    mapTo = mapping.getTo();
     assertEquals(mapTo.getName(), "AAA91574.1");
     // the /product qualifier transfers to protein product description
     assertEquals(mapTo.getDescription(), "hypothetical protein");