git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
Merge branch 'develop' into features/JAL-845splitPaneMergeDevelop
[jalview.git]
/
test
/
jalview
/
io
/
AnnotationFileIOTest.java
diff --git
a/test/jalview/io/AnnotationFileIOTest.java
b/test/jalview/io/AnnotationFileIOTest.java
index
18e008e
..
0962452
100644
(file)
--- a/
test/jalview/io/AnnotationFileIOTest.java
+++ b/
test/jalview/io/AnnotationFileIOTest.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-24,8
+24,11
@@
import static org.junit.Assert.assertNotNull;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import jalview.datamodel.AlignmentI;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.fail;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.io.AnnotationFile.ViewDef;
import java.io.File;
import java.io.File;
+import java.util.Hashtable;
import org.junit.Test;
import org.junit.Test;
@@
-44,7
+47,9
@@
public class AnnotationFileIOTest
"examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
{
"Test group only annotation file parsing results in parser indicating annotation was parsed",
"examples/uniref50.fa", "examples/testdata/uniref50_iupred.jva" },
{
"Test group only annotation file parsing results in parser indicating annotation was parsed",
- "examples/uniref50.fa", "examples/testdata/test_grpannot.jva" } };
+ "examples/uniref50.fa", "examples/testdata/test_grpannot.jva" },
+ { "Test hiding/showing of insertions on sequence_ref",
+ "examples/uniref50.fa", "examples/testdata/uniref50_seqref.jva" } };
@Test
public void exampleAnnotationFileIO() throws Exception
@Test
public void exampleAnnotationFileIO() throws Exception
@@
-102,17
+107,20
@@
public class AnnotationFileIOTest
try
{
AlignmentI al = readAlignmentFile(f);
try
{
AlignmentI al = readAlignmentFile(f);
-
+ ColumnSelection cs = new ColumnSelection();
assertTrue(
"Test "
+ testname
+ "\nAlignment was not annotated - annotation file not imported.",
assertTrue(
"Test "
+ testname
+ "\nAlignment was not annotated - annotation file not imported.",
- new AnnotationFile().readAnnotationFile(al, af,
+ new AnnotationFile().readAnnotationFile(al, cs, af,
FormatAdapter.FILE));
FormatAdapter.FILE));
+ AnnotationFile aff = new AnnotationFile();
+ ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
+ new Hashtable());
String anfileout = new AnnotationFile().printAnnotations(
al.getAlignmentAnnotation(), al.getGroups(),
String anfileout = new AnnotationFile().printAnnotations(
al.getAlignmentAnnotation(), al.getGroups(),
- al.getProperties());
+ al.getProperties(), null, al, v);
assertTrue(
"Test "
+ testname
assertTrue(
"Test "
+ testname