Merge branch 'develop' into features/JAL-2094_colourInterface

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

diff --git a/test/jalview/io/FeaturesFileTest.java b/test/jalview/io/FeaturesFileTest.java
index 2f5d0c5..bf5bb3d 100644 (file)
--- a/test/jalview/io/FeaturesFileTest.java
+++ b/test/jalview/io/FeaturesFileTest.java
@@ -34,8 +34,8 @@ import jalview.datamodel.SequenceDummy;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.schemes.Colour;
 
-import java.awt.Color;
 import java.io.File;
 import java.io.IOException;
 import java.util.Map;
@@ -67,8 +67,8 @@ public class FeaturesFileTest
      */
     colours = af.getFeatureRenderer().getFeatureColours();
     assertEquals("26 feature group colours not found", 26, colours.size());
-    assertEquals(colours.get("Cath").getColour(), new Color(0x93b1d1));
-    assertEquals(colours.get("ASX-MOTIF").getColour(), new Color(0x6addbb));
+    assertEquals(colours.get("Cath").getColour(), new Colour(0x93b1d1));
+    assertEquals(colours.get("ASX-MOTIF").getColour(), new Colour(0x6addbb));
 
     /*
      * verify (some) features on sequences
@@ -164,7 +164,7 @@ public class FeaturesFileTest
     // verify colours read or synthesized
     colours = af.getFeatureRenderer().getFeatureColours();
     assertEquals("1 feature group colours not found", 1, colours.size());
-    assertEquals(colours.get("METAL").getColour(), new Color(0xcc9900));
+    assertEquals(colours.get("METAL").getColour(), new Colour(0xcc9900));
 
     // verify feature on FER_CAPAA
     SequenceFeature[] sfs = al.getSequenceAt(0).getDatasetSequence()
@@ -205,6 +205,44 @@ public class FeaturesFileTest
   }
 
   /**
+   * Test various ways of describing a feature colour scheme
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" })
+  public void testParseGraduatedColourScheme() throws Exception
+  {
+    FeaturesFile ff = new FeaturesFile();
+
+    // colour by label:
+    FeatureColourI gc = ff.parseGraduatedColourScheme(
+            "BETA-TURN-IR\t9a6a94", "label");
+    assertTrue(gc.isColourByLabel());
+    assertEquals(Colour.white, gc.getMinColour());
+    assertEquals(Colour.black, gc.getMaxColour());
+    assertTrue(gc.isAutoScaled());
+
+    // using colour name, rgb, etc:
+    String spec = "blue|255,0,255|absolute|20.0|95.0|below|66.0";
+    gc = ff.parseGraduatedColourScheme("BETA-TURN-IR\t" + spec, spec);
+    assertFalse(gc.isColourByLabel());
+    assertEquals(Colour.blue, gc.getMinColour());
+    assertEquals(new Colour(255, 0, 255), gc.getMaxColour());
+    assertFalse(gc.isAutoScaled());
+    // assertFalse(gc.getTolow());
+    assertEquals(20.0f, gc.getMin(), 0.001f);
+    assertEquals(95.0f, gc.getMax(), 0.001f);
+    assertTrue(gc.isBelowThreshold());
+    assertEquals(66.0f, gc.getThreshold(), 0.001f);
+
+    // inverse gradient high to low:
+    spec = "blue|255,0,255|95.0|20.0|below|66.0";
+    gc = ff.parseGraduatedColourScheme("BETA-TURN-IR\t" + spec, spec);
+    assertTrue(gc.isAutoScaled());
+    // assertTrue(gc..getTolow());
+  }
+
+  /**
    * Test parsing a features file with GFF formatted content only
    * 
    * @throws Exception