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JAL-2018 export graduated feature colours correctly
[jalview.git] / test / jalview / io / FeaturesFileTest.java
diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 385e049..81d5b05 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -26,6 +26,7 @@ import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.api.FeatureRenderer;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceDummy;
@@ -412,4 +413,73 @@ public class FeaturesFileTest
             parseResult);
     checkDatasetfromSimpleGff3(dataset);
   }
+
+  @Test(groups = { "Functional" })
+  public void testPrintJalviewFormat() throws Exception
+  {
+    File f = new File("examples/uniref50.fa");
+    AlignmentI al = readAlignmentFile(f);
+    AlignFrame af = new AlignFrame(al, 500, 500);
+    Map<String, Object> colours = af.getFeatureRenderer()
+            .getFeatureColours();
+    String features = "METAL\tcc9900\n"
+            + "GAMMA-TURN\tred|0,255,255|20.0|95.0|below|66.0\n"
+            + "Pfam\tred\n"
+            + "STARTGROUP\tuniprot\n"
+            + "Iron\tFER_CAPAA\t-1\t39\t39\tMETAL\n"
+            + "Turn\tFER_CAPAA\t-1\t36\t38\tGAMMA-TURN\n"
+            + "<html>Pfam domain<a href=\"http://pfam.sanger.ac.uk/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\n"
+            + "ENDGROUP\tuniprot\n";
+    FeaturesFile featuresFile = new FeaturesFile(features,
+            FormatAdapter.PASTE);
+    featuresFile.parse(al.getDataset(), colours, false);
+
+    /*
+     * first with no features displayed
+     */
+    FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
+    Map<String, Object> visible = fr
+            .getDisplayedFeatureCols();
+    String exported = featuresFile.printJalviewFormat(
+            al.getSequencesArray(), visible);
+    String expected = "No Features Visible";
+    assertEquals(expected, exported);
+
+    /*
+     * set METAL (in uniprot group) and GAMMA-TURN visible, but not Pfam
+     */
+    fr.setVisible("METAL");
+    fr.setVisible("GAMMA-TURN");
+    visible = fr.getDisplayedFeatureCols();
+    exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
+            visible);
+    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"
+            + "ENDGROUP\tuniprot\n";
+    assertEquals(expected, exported);
+
+    /*
+     * now set Pfam visible
+     */
+    fr.setVisible("Pfam");
+    visible = fr.getDisplayedFeatureCols();
+    exported = featuresFile.printJalviewFormat(al.getSequencesArray(),
+            visible);
+    /*
+     * note the order of feature types is uncontrolled - derives from
+     * FeaturesDisplayed.featuresDisplayed which is a HashSet
+     */
+    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"
+            + "<html>Pfam domain<a href=\"http://pfam.sanger.ac.uk/family/PF00111\">Pfam_3_4</a></html>\tFER_CAPAA\t-1\t20\t20\tPfam\t0.0\n"
+            + "ENDGROUP\tuniprot\n";
+    assertEquals(expected, exported);
+  }
 }