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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
{
{
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);
DataSourceType.FILE, FileFormat.Fasta);
+ }
/*
* 'gap' is the gap character used in the alignment data file here,
/*
* '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();
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)
int i = 0;
for (SequenceI seq : reread)
@@
-130,7
+140,7
@@
public class FormatAdapterTest
@DataProvider(name = "formats")
static Object[][] getFormats()
{
@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()
for (FileFormatI format : FileFormats.getInstance().getFormats())
{
if (format.isReadable() && format.isWritable()