JAL-2611 reinstate missed merge - again!

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

diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 0cfe46a..cc7dca0 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -34,17 +34,26 @@ import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
 
 import java.awt.Color;
 import java.io.File;
 import java.io.IOException;
 import java.util.Map;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class FeaturesFileTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   private static String simpleGffFile = "examples/testdata/simpleGff3.gff";
 
   @Test(groups = { "Functional" })
@@ -66,9 +75,13 @@ public class FeaturesFileTest
      * updated - JAL-1904), and verify (some) feature group colours
      */
     colours = af.getFeatureRenderer().getFeatureColours();
-    assertEquals("26 feature group colours not found", 26, colours.size());
+    assertEquals("27 feature group colours not found", 27, colours.size());
     assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
     assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
+    FeatureColourI kdColour = colours.get("kdHydrophobicity");
+    assertTrue(kdColour.isGraduatedColour());
+    assertTrue(kdColour.isAboveThreshold());
+    assertEquals(-2f, kdColour.getThreshold());
 
     /*
      * verify (some) features on sequences
@@ -153,7 +166,8 @@ public class FeaturesFileTest
     Map<String, FeatureColourI> colours = af.getFeatureRenderer()
             .getFeatureColours();
     // GFF2 uses space as name/value separator in column 9
-    String gffData = "METAL\tcc9900\n" + "GFF\n"
+    String gffData = "METAL\tcc9900\n"
+            + "GFF\n"
             + "FER_CAPAA\tuniprot\tMETAL\t44\t45\t4.0\t.\t.\tNote Iron-sulfur; Note 2Fe-2S\n"
             + "FER1_SOLLC\tuniprot\tPfam\t55\t130\t2.0\t.\t.";
     FeaturesFile featuresFile = new FeaturesFile(gffData,
@@ -304,7 +318,7 @@ public class FeaturesFileTest
   {
     assertEquals("no sequences extracted from GFF3 file", 2,
             dataset.getHeight());
-  
+
     SequenceI seq1 = dataset.findName("seq1");
     SequenceI seq2 = dataset.findName("seq2");
     assertNotNull(seq1);
@@ -335,7 +349,7 @@ public class FeaturesFileTest
             "Expected at least one CDNA/Protein mapping for seq1",
             dataset.getCodonFrame(seq1) != null
                     && dataset.getCodonFrame(seq1).size() > 0);
-  
+
   }
 
   @Test(groups = { "Functional" })
@@ -408,8 +422,7 @@ public class FeaturesFileTest
      * first with no features displayed
      */
     FeatureRenderer fr = af.alignPanel.getFeatureRenderer();
-    Map<String, FeatureColourI> visible = fr
-            .getDisplayedFeatureCols();
+    Map<String, FeatureColourI> visible = fr.getDisplayedFeatureCols();
     String exported = featuresFile.printJalviewFormat(
             al.getSequencesArray(), visible);
     String expected = "No Features Visible";