JAL-2136 New Phyre2 branch + attempt to resynced with develop

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

diff --git a/test/jalview/io/AnnotationFileIOTest.java b/test/jalview/io/AnnotationFileIOTest.java
index e016f54..14b4747 100644 (file)
--- a/test/jalview/io/AnnotationFileIOTest.java
+++ b/test/jalview/io/AnnotationFileIOTest.java
@@ -24,8 +24,8 @@ import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.DynamicData;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
@@ -125,7 +125,7 @@ public class AnnotationFileIOTest
     try
     {
       AlignmentI al = readAlignmentFile(f);
-      ColumnSelection cs = new ColumnSelection();
+      HiddenColumns cs = new HiddenColumns();
       assertTrue(
               "Test "
                       + testname
@@ -134,6 +134,7 @@ public class AnnotationFileIOTest
                       DataSourceType.FILE));
 
       AnnotationFile aff = new AnnotationFile();
+      // ViewDef is not used by Jalview
       ViewDef v = aff.new ViewDef(null, al.getHiddenSequences(), cs,
               new Hashtable());
       String anfileout = new AnnotationFile().printAnnotations(
@@ -162,7 +163,8 @@ public class AnnotationFileIOTest
                       DataSourceType.PASTE));
 
       // test for consistency in io
-      StockholmFileTest.testAlignmentEquivalence(al, al_new, false);
+      StockholmFileTest.testAlignmentEquivalence(al, al_new, false, false,
+              false);
       return;
     } catch (Exception e)
     {
@@ -189,7 +191,7 @@ public class AnnotationFileIOTest
     File alignmentFile = new File(
             "examples/testdata/phyre2results/56da5616b4559c93/allhits.fasta");
     String annotationFile = "examples/testdata/phyre2results/56da5616b4559c93/allhits.ann";
-    ColumnSelection cs = new ColumnSelection();
+    HiddenColumns cs = new HiddenColumns();
     al = readAlignmentFile(alignmentFile);
     boolean annotationRead = new AnnotationFile().readAnnotationFile(al,
             cs, annotationFile, DataSourceType.FILE);