Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index e4f2abc..10f368a 100644 (file)
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -137,6 +137,31 @@ public class StockholmFileTest
 
   }
 
+  @Test(groups = { "Functional" })
+  public void descriptionLineOutput() throws Exception
+  {
+    // quick test that sequence description is exported & reimported
+
+    SequenceI sq = new Sequence("FER2_SPIOL", "AASSDDDFFF");
+    String expected_descr = "This is a description !@&^%@£@";
+    sq.setDescription(expected_descr);
+    AppletFormatAdapter af = new AppletFormatAdapter();
+    String toStockholm = af.formatSequences(FileFormat.Stockholm,
+            new Alignment(new SequenceI[]
+            { sq }), false);
+    System.out.println(toStockholm);
+
+    // bleh - java.util.Regex sucks
+    assertTrue(toStockholm.contains(expected_descr),
+            "Couldn't locate expected description srting in generated Stockholm file.");
+
+    AlignmentI fromStockholm = af.readFile(toStockholm,
+            DataSourceType.PASTE, FileFormat.Stockholm);
+    SequenceI importedSeq = fromStockholm.getSequenceAt(0);
+    assertEquals("Description did not get reimported.", expected_descr,
+            importedSeq.getDescription());
+  }
+
   /**
    * test alignment data in given file can be imported, exported and reimported
    * with no dataloss
@@ -274,6 +299,11 @@ public class StockholmFileTest
     // check Alignment annotation
     AlignmentAnnotation[] aa_new = al_input.getAlignmentAnnotation();
     AlignmentAnnotation[] aa_original = al.getAlignmentAnnotation();
+    boolean expectProteinSS = !al.isNucleotide();
+    assertTrue(
+            "Alignments not both "
+                    + (al.isNucleotide() ? "nucleotide" : "protein"),
+            al_input.isNucleotide() == al.isNucleotide());
 
     // note - at moment we do not distinguish between alignment without any
     // annotation rows and alignment with no annotation row vector
@@ -292,6 +322,13 @@ public class StockholmFileTest
           assertEqualSecondaryStructure(
                   "Different alignment annotation at position " + i,
                   aa_original[i], aa_new[i], allowNullAnnotation);
+          if (aa_original[i].hasIcons)
+          {
+            assertTrue(
+                    "Secondary structure expected to be "
+                            + (expectProteinSS ? "protein" : "nucleotide"),
+                    expectProteinSS == !aa_original[i].isRNA());
+          }
           // compare graphGroup or graph properties - needed to verify JAL-1299
           assertEquals("Graph type not identical.", aa_original[i].graph,
                   aa_new[i].graph);