JAL-2507 simplify round trip test via AppletFormatAdapter

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

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index e9edd1b..185eedf 100644 (file)
--- 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);
 
@@ -207,8 +231,12 @@ public class StockholmFileTest
           // 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
@@ -408,4 +436,33 @@ public class StockholmFileTest
       }
     }
   }
+
+  String aliFile = ">Dm\nAAACCCUUUUACACACGGGAAAGGG";
+  String annFile = "JALVIEW_ANNOTATION\n# Created: Thu May 04 11:16:52 BST 2017\n\n"
+          + "SEQUENCE_REF\tDm\nNO_GRAPH\tsecondary structure\tsecondary structure\t"
+          + "(|(|(|(|, .|, .|, .|, .|)|)|)|)|\t0.0\nROWPROPERTIES\t"
+          + "secondary structure\tscaletofit=true\tshowalllabs=true\tcentrelabs=false";
+
+  @Test(groups = { "Functional" })
+  public void secondaryStructureForRNASequence() throws Exception
+  {
+    AlignmentI al = new AppletFormatAdapter().readFile(aliFile,
+            DataSourceType.PASTE, jalview.io.FileFormat.Fasta);
+    AnnotationFile aaf = new AnnotationFile();
+    aaf.readAnnotationFile(al, annFile, DataSourceType.PASTE);
+    al.getAlignmentAnnotation()[0].visible = true;
+
+    // TODO: create a better 'save as <format>' pattern
+    StockholmFile sf = new StockholmFile(al);
+
+    String stockholmFile = sf.print(al.getSequencesArray(), true);
+
+    AlignmentI newAl = new AppletFormatAdapter().readFile(stockholmFile,
+            DataSourceType.PASTE, jalview.io.FileFormat.Stockholm);
+    // AlignmentUtils.showOrHideSequenceAnnotations(newAl.getViewport()
+    // .getAlignment(), Arrays.asList("Secondary Structure"), newAl
+    // .getViewport().getAlignment().getSequences(), true, true);
+    testAlignmentEquivalence(al, newAl, true, true);
+
+  }
 }