X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=blobdiff_plain;f=test%2Fjalview%2Fio%2FStockholmFileTest.java;fp=test%2Fjalview%2Fio%2FStockholmFileTest.java;h=e7f1435ec4073ad65b3fd691532701181d0d6632;hp=4028913c7a30763d38a6e41adba6264e0884cb06;hb=3c75c089a56859ec8e7f674d7054e82af41e4b77;hpb=e5b2edf3955c50cfd61799ad12cdc9016603ee1c

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 4028913..e7f1435 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -56,7 +56,8 @@ public class StockholmFileTest
   @Test(groups = { "Functional" })
   public void pfamFileIO() throws Exception
   {
-    testFileIOwithFormat(new File(PfamFile), FileFormat.Stockholm, -1, 0);
+    testFileIOwithFormat(new File(PfamFile), FileFormat.Stockholm, -1, 0,
+            false);
   }
 
   @Test(groups = { "Functional" })
@@ -81,7 +82,8 @@ public class StockholmFileTest
   @Test(groups = { "Functional" })
   public void rfamFileIO() throws Exception
   {
-    testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1);
+    testFileIOwithFormat(new File(RfamFile), FileFormat.Stockholm, 2, 1,
+            false);
   }
 
   /**
@@ -93,10 +95,11 @@ public class StockholmFileTest
    * @param ioformat
    *          - label for IO class used to write and read back in the data from
    *          f
+   * @param ignoreRowVisibility
    */
 
   public static void testFileIOwithFormat(File f, FileFormatI ioformat,
-          int naliannot, int nminseqann)
+          int naliannot, int nminseqann, boolean ignoreRowVisibility)
   {
     System.out.println("Reading file: " + f);
     String ff = f.getPath();
@@ -174,6 +177,27 @@ public class StockholmFileTest
   public static void testAlignmentEquivalence(AlignmentI al,
           AlignmentI al_input, boolean ignoreFeatures)
   {
+  }
+
+  /**
+   * assert alignment equivalence
+   * 
+   * @param al
+   *          'original'
+   * @param al_input
+   *          'secondary' or generated alignment from some datapreserving
+   *          transformation
+   * @param ignoreFeatures
+   *          when true, differences in sequence feature annotation are ignored
+   * 
+   * @param ignoreRowVisibility
+   *          when true, do not fail if there are differences in the visibility
+   *          of annotation rows
+   */
+  public static void testAlignmentEquivalence(AlignmentI al,
+          AlignmentI al_input, boolean ignoreFeatures,
+          boolean ignoreRowVisibility)
+  {
     assertNotNull("Original alignment was null", al);
     assertNotNull("Generated alignment was null", al_input);
 
@@ -201,13 +225,18 @@ public class StockholmFileTest
       {
         if (aa_new.length > i)
         {
-          assertTrue("Different alignment annotation at position " + i,
-                  equalss(aa_original[i], aa_new[i]));
+          assertEqualSecondaryStructure(
+                  "Different alignment annotation at position " + i,
+                  aa_original[i], aa_new[i]);
           // compare graphGroup or graph properties - needed to verify JAL-1299
           assertEquals("Graph type not identical.", aa_original[i].graph,
                   aa_new[i].graph);
-          assertEquals("Visibility not identical.", aa_original[i].visible,
+          if (!ignoreRowVisibility)
+          {
+            assertEquals("Visibility not identical.",
+                    aa_original[i].visible,
                   aa_new[i].visible);
+          }
           assertEquals("Threshold line not identical.",
                   aa_original[i].threshold, aa_new[i].threshold);
           // graphGroup may differ, but pattern should be the same
@@ -310,8 +339,9 @@ public class StockholmFileTest
               {
                 annot_original = al.getSequenceAt(i).getAnnotation()[j];
                 annot_new = al_input.getSequenceAt(in).getAnnotation()[j];
-                assertTrue("Different annotation elements",
-                        equalss(annot_original, annot_new));
+                assertEqualSecondaryStructure(
+                        "Different annotation elements", annot_original,
+                        annot_new);
               }
             }
           }
@@ -333,39 +363,57 @@ public class StockholmFileTest
     }
   }
 
-  /*
-   * compare annotations
-   */
-  private static boolean equalss(AlignmentAnnotation annot_or,
+  private static void assertEqualSecondaryStructure(String message,
+          AlignmentAnnotation annot_or,
           AlignmentAnnotation annot_new)
   {
+    // TODO: test to cover this assert behaves correctly for all allowed
+    // variations of secondary structure annotation row equivalence
     if (annot_or.annotations.length != annot_new.annotations.length)
     {
-      System.err.println("Different lengths for annotation row elements: "
+      fail("Different lengths for annotation row elements: "
               + annot_or.annotations.length + "!="
               + annot_new.annotations.length);
-      return false;
     }
+    boolean isRna = annot_or.isRNA();
+    assertTrue("Expected " + (isRna ? " valid RNA " : " no RNA ")
+            + " secondary structure in the row.",
+            isRna == annot_new.isRNA());
     for (int i = 0; i < annot_or.annotations.length; i++)
     {
       Annotation an_or = annot_or.annotations[i], an_new = annot_new.annotations[i];
       if (an_or != null && an_new != null)
       {
-        if (!an_or.displayCharacter.trim().equals(
-                an_new.displayCharacter.trim())
-                || !("" + an_or.secondaryStructure).trim().equals(
-                        ("" + an_new.secondaryStructure).trim())
-                || (an_or.description != an_new.description && !((an_or.description == null && an_new.description
-                        .trim().length() == 0)
-                        || (an_new.description == null && an_or.description
-                                .trim().length() == 0) || an_or.description
-                        .trim().equals(an_new.description.trim()))))
+
+        if (isRna)
         {
-          System.err.println("Annotation Element Mismatch\nElement " + i
-                  + " in original: " + annot_or.annotations[i].toString()
-                  + "\nElement " + i + " in new: "
-                  + annot_new.annotations[i].toString());
-          return false;
+          if (an_or.secondaryStructure != an_new.secondaryStructure
+                  || an_or.value != an_new.value)
+          {
+            fail("Different RNA secondary structure at column " + i
+                    + " expected: [" + annot_or.annotations[i].toString()
+                    + "] but got: [" + annot_new.annotations[i].toString()
+                    + "]");
+          }
+        }
+        else
+        {
+          // not RNA secondary structure, so expect all elements to match...
+          if (!an_or.displayCharacter.trim().equals(
+                  an_new.displayCharacter.trim())
+                  || !("" + an_or.secondaryStructure).trim().equals(
+                          ("" + an_new.secondaryStructure).trim())
+                  || (an_or.description != an_new.description && !((an_or.description == null && an_new.description
+                          .trim().length() == 0)
+                          || (an_new.description == null && an_or.description
+                                  .trim().length() == 0) || an_or.description
+                          .trim().equals(an_new.description.trim()))))
+          {
+            fail("Annotation Element Mismatch\nElement " + i
+                    + " in original: " + annot_or.annotations[i].toString()
+                    + "\nElement " + i + " in new: "
+                    + annot_new.annotations[i].toString());
+          }
         }
       }
       else if (annot_or.annotations[i] == null
@@ -375,7 +423,7 @@ public class StockholmFileTest
       }
       else
       {
-        System.err.println("Annotation Element Mismatch\nElement "
+        fail("Annotation Element Mismatch\nElement "
                 + i
                 + " in original: "
                 + (annot_or.annotations[i] == null ? "is null"
@@ -385,9 +433,7 @@ public class StockholmFileTest
                 + " in new: "
                 + (annot_new.annotations[i] == null ? "is null"
                         : annot_new.annotations[i].toString()));
-        return false;
       }
     }
-    return true;
   }
 }