JAL-2360 JAL-2371 updates from review CR-JAL-1

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

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index d09eb2a..885c673 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 2.8.2b1)
- * 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.
  * 
@@ -20,20 +20,32 @@
  */
 package jalview.io;
 
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.gui.JvOptionPane;
+import jalview.io.AnnotationFile.ViewDef;
 
 import java.io.File;
+import java.util.Hashtable;
 
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
 public class AnnotationFileIOTest
 {
 
-  static String TestFiles[][] =
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
   {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  static String TestFiles[][] = {
       { "Test example annotation import/export", "examples/uniref50.fa",
           "examples/testdata/example_annot_file.jva" },
       { "Test multiple combine annotation statements import/export",
@@ -44,9 +56,11 @@ 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/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
+  @Test(groups = { "Functional" })
   public void exampleAnnotationFileIO() throws Exception
   {
     for (String[] testPair : TestFiles)
@@ -56,7 +70,7 @@ public class AnnotationFileIOTest
     }
   }
 
-  public static AlignmentI readAlignmentFile(File f)
+  AlignmentI readAlignmentFile(File f)
   {
     System.out.println("Reading file: " + f);
     String ff = f.getPath();
@@ -64,14 +78,13 @@ public class AnnotationFileIOTest
     {
       FormatAdapter rf = new FormatAdapter();
 
-      AlignmentI al = rf.readFile(ff, AppletFormatAdapter.FILE,
-              new IdentifyFile().Identify(ff, AppletFormatAdapter.FILE));
+      AlignmentI al = rf.readFile(ff, DataSourceType.FILE,
+              new IdentifyFile().identify(ff, DataSourceType.FILE));
 
       // make sure dataset is initialised ? not sure about this
       for (int i = 0; i < al.getSequencesArray().length; ++i)
       {
-        al.getSequenceAt(i).setDatasetSequence(
-                al.getSequenceAt(i).createDatasetSequence());
+        al.getSequenceAt(i).createDatasetSequence();
       }
       assertNotNull("Couldn't read supplied alignment data.", al);
       return al;
@@ -79,7 +92,7 @@ public class AnnotationFileIOTest
     {
       e.printStackTrace();
     }
-    fail("Couln't read the alignment in file '" + f.toString() + "'");
+    Assert.fail("Couln't read the alignment in file '" + f.toString() + "'");
     return null;
   }
 
@@ -93,7 +106,7 @@ public class AnnotationFileIOTest
    *          - label for IO class used to write and read back in the data from
    *          f
    */
-  public static void testAnnotationFileIO(String testname, File f,
+  void testAnnotationFileIO(String testname, File f,
           File annotFile)
   {
     System.out.println("Test: " + testname + "\nReading annotation file '"
@@ -102,17 +115,20 @@ public class AnnotationFileIOTest
     try
     {
       AlignmentI al = readAlignmentFile(f);
-
+      ColumnSelection cs = new ColumnSelection();
       assertTrue(
               "Test "
                       + testname
                       + "\nAlignment was not annotated - annotation file not imported.",
-              new AnnotationFile().readAnnotationFile(al, af,
-                      FormatAdapter.FILE));
+              new AnnotationFile().readAnnotationFile(al, cs, af,
+                      DataSourceType.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(),
-              al.getProperties());
+              al.getProperties(), null, al, v);
       assertTrue(
               "Test "
                       + testname
@@ -133,16 +149,16 @@ public class AnnotationFileIOTest
                       + testname
                       + "\nregenerated annotation file did not annotate alignment.",
               new AnnotationFile().readAnnotationFile(al_new, anfileout,
-                      FormatAdapter.PASTE));
+                      DataSourceType.PASTE));
 
       // test for consistency in io
-      StockholmFileTest.testAlignmentEquivalence(al, al_new);
+      StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
       return;
     } catch (Exception e)
     {
       e.printStackTrace();
     }
-    fail("Test "
+    Assert.fail("Test "
             + testname
             + "\nCouldn't complete Annotation file roundtrip input/output/input test for '"
             + annotFile + "'.");