Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

[jalview.git] / test / jalview / io / FormatAdapterTest.java

diff --git a/test/jalview/io/FormatAdapterTest.java b/test/jalview/io/FormatAdapterTest.java
index 8f3ad2f..d63fb70 100644 (file)
--- a/test/jalview/io/FormatAdapterTest.java
+++ b/test/jalview/io/FormatAdapterTest.java
@@ -56,8 +56,17 @@ public class FormatAdapterTest
   {
     try
     {
-      AlignmentI al = new FormatAdapter().readFile("examples/uniref50.fa",
+      AlignmentI al;
+      if (format == FileFormat.HMMER3)
+      {
+        al = new FormatAdapter().readFile("examples/uniref50.hmm",
+                DataSourceType.FILE, FileFormat.HMMER3);
+      }
+      else
+      {
+        al = new FormatAdapter().readFile("examples/uniref50.fa",
               DataSourceType.FILE, FileFormat.Fasta);
+      }
 
       /*
        * 'gap' is the gap character used in the alignment data file here,
@@ -73,8 +82,9 @@ public class FormatAdapterTest
       AlignmentI reloaded = new FormatAdapter().readFile(formatted,
               DataSourceType.PASTE, format);
       List<SequenceI> reread = reloaded.getSequences();
-      assertEquals("Wrong number of reloaded sequences", seqs.length,
-              reread.size());
+        assertEquals("Wrong number of reloaded sequences", seqs.length,
+                reread.size());
+
 
       int i = 0;
       for (SequenceI seq : reread)
@@ -130,7 +140,7 @@ public class FormatAdapterTest
   @DataProvider(name = "formats")
   static Object[][] getFormats()
   {
-    List<FileFormatI> both = new ArrayList<FileFormatI>();
+    List<FileFormatI> both = new ArrayList<>();
     for (FileFormatI format : FileFormats.getInstance().getFormats())
     {
       if (format.isReadable() && format.isWritable()