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JAL-2490 test coverage of empty and null feature group in Jalview format
[jalview.git] / test / jalview / io / FeaturesFileTest.java
diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index d59c6bb..b88c2ee 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -420,6 +420,21 @@ public class FeaturesFileTest
     featuresFile.parse(al.getDataset(), colours, false);
 
     /*
+     * add positional and non-positional features with null and
+     * empty feature group to check handled correctly
+     */
+    SequenceI seq = al.getSequenceAt(1); // FER_CAPAN
+    seq.addSequenceFeature(new SequenceFeature("Pfam", "desc1", 0, 0, 1.3f,
+            null));
+    seq.addSequenceFeature(new SequenceFeature("Pfam", "desc2", 4, 9,
+            Float.NaN, null));
+    seq = al.getSequenceAt(2); // FER1_SOLLC
+    seq.addSequenceFeature(new SequenceFeature("Pfam", "desc3", 0, 0,
+            Float.NaN, ""));
+    seq.addSequenceFeature(new SequenceFeature("Pfam", "desc4", 5, 8,
+            -2.6f, ""));
+
+    /*
      * first with no features displayed, exclude non-positional features
      */
     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
@@ -437,7 +452,10 @@ public class FeaturesFileTest
     visibleGroups.add("uniprot");
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
             visible, visibleGroups, true);
-    expected = "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n\nSTARTGROUP\tuniprot\nENDGROUP\tuniprot\n";
+    expected = "Cath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\n"
+            + "desc1\tFER_CAPAN\t-1\t0\t0\tPfam\t1.3\n"
+            + "desc3\tFER1_SOLLC\t-1\t0\t0\tPfam\n" // NaN is not output
+            + "\nSTARTGROUP\tuniprot\nENDGROUP\tuniprot\n";
     assertEquals(expected, exported);
 
     /*
@@ -473,7 +491,11 @@ public class FeaturesFileTest
             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
             + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
             + "<html>Pfam domain<a href=\"http://pfam.xfam.org/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
-            + "ENDGROUP\tuniprot\n";
+            + "ENDGROUP\tuniprot\n"
+            // null / empty group features output after features in named
+            // groups:
+            + "desc2\tFER_CAPAN\t-1\t4\t9\tPfam\n"
+            + "desc4\tFER1_SOLLC\t-1\t5\t8\tPfam\t-2.6\n";
     assertEquals(expected, exported);
   }