Merge branch 'bug/JAL-2507_rnasecstrstockholm' into develop

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

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 1a18fb9..228c935 100644 (file)
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -60,7 +60,7 @@ public class StockholmFileTest
   public void pfamFileIO() throws Exception
   {
     testFileIOwithFormat(new File(PfamFile), FileFormat.Stockholm, -1, 0,
-            false);
+            false, false, false);
   }
 
   @Test(groups = { "Functional" })
@@ -86,7 +86,7 @@ public class StockholmFileTest
   public void rfamFileIO() throws Exception
   {
     testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1,
-            false);
+            false, false, false);
   }
 
   /**
@@ -98,11 +98,14 @@ public class StockholmFileTest
    * @param ioformat
    *          - label for IO class used to write and read back in the data from
    *          f
+   * @param ignoreFeatures
    * @param ignoreRowVisibility
+   * @param allowNullAnnotations
    */
 
   public static void testFileIOwithFormat(File f, FileFormatI ioformat,
-          int naliannot, int nminseqann, boolean ignoreRowVisibility)
+          int naliannot, int nminseqann, boolean ignoreFeatures,
+          boolean ignoreRowVisibility, boolean allowNullAnnotations)
   {
     System.out.println("Reading file: " + f);
     String ff = f.getPath();
@@ -136,7 +139,8 @@ public class StockholmFileTest
               "Identify routine could not recognise output generated by '"
                       + ioformat + "' writer",
               ioformat.equals(identifyoutput));
-      testAlignmentEquivalence(al, al_input, false);
+      testAlignmentEquivalence(al, al_input, ignoreFeatures,
+              ignoreRowVisibility, allowNullAnnotations);
       int numaliannot = 0, numsqswithali = 0;
       for (AlignmentAnnotation ala : al_input.getAlignmentAnnotation())
       {