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JAL-2490 tidy code and tests for feature export 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 be5e68d..70a5f16 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -421,33 +421,31 @@ public class FeaturesFileTest
     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
     Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
     String exported = featuresFile.printJalviewFormat(
-            al.getSequencesArray(), visible, true, false);
+            al.getSequencesArray(), visible, false);
     String expected = "No Features Visible";
     assertEquals(expected, exported);
 
     /*
      * include non-positional features
      */
-    af.getViewport().setShowNPFeats(true);
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
-            visible, true, true);
+            visible, true);
     expected = "\nSTARTGROUP\tuniprot\nCath\tFER_CAPAA\t-1\t0\t0\tDomain\t0.0\nENDGROUP\tuniprot\n";
     assertEquals(expected, exported);
 
     /*
      * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
      */
-    af.getViewport().setShowNPFeats(false);
     fr.setVisible("METAL");
     fr.setVisible("GAMMA-TURN");
     visible = fr.getDisplayedFeatureCols();
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
-            visible, true, false);
+            visible, false);
     expected = "METAL\tcc9900\n"
             + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
             + "\nSTARTGROUP\tuniprot\n"
-            + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
             + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\t0.0\n"
+            + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
             + "ENDGROUP\tuniprot\n";
     assertEquals(expected, exported);
 
@@ -457,17 +455,16 @@ public class FeaturesFileTest
     fr.setVisible("Pfam");
     visible = fr.getDisplayedFeatureCols();
     exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
-            visible, true, false);
+            visible, false);
     /*
-     * note the order of feature types is uncontrolled - derives from
-     * FeaturesDisplayed.featuresDisplayed which is a HashSet
+     * features are output within group, ordered by sequence and by type
      */
     expected = "METAL\tcc9900\n"
             + "Pfam\tff0000\n"
             + "GAMMA-TURN\tff0000|00ffff|20.0|95.0|below|66.0\n"
             + "\nSTARTGROUP\tuniprot\n"
-            + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\t0.0\n"
             + "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";
     assertEquals(expected, exported);