X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fschemes%2FFeatureColourTest.java;h=42b898db0fd8bd8a57138cde4b519a6a63b616bf;hb=43d97319aebb52a38c58fe201198f593d312b940;hp=99542ae3532df95a7427f0bf0dff0e6726a9c01f;hpb=dcfba29a940c44003581f28e6da481450aa86575;p=jalview.git

diff --git a/test/jalview/schemes/FeatureColourTest.java b/test/jalview/schemes/FeatureColourTest.java
index 99542ae..42b898d 100644
--- a/test/jalview/schemes/FeatureColourTest.java
+++ b/test/jalview/schemes/FeatureColourTest.java
@@ -38,8 +38,6 @@ import java.awt.Color;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
-import junit.extensions.PA;
-
 public class FeatureColourTest
 {
 
@@ -51,6 +49,30 @@ public class FeatureColourTest
   }
 
   @Test(groups = { "Functional" })
+  public void testConstructors()
+  {
+    FeatureColourI fc = new FeatureColour();
+    assertNull(fc.getColour());
+    assertTrue(fc.isSimpleColour());
+    assertFalse(fc.isColourByLabel());
+    assertFalse(fc.isGraduatedColour());
+    assertFalse(fc.isColourByAttribute());
+    assertEquals(Color.white, fc.getMinColour());
+    assertEquals(Color.black, fc.getMaxColour());
+
+    fc = new FeatureColour(Color.RED);
+    assertEquals(Color.red, fc.getColour());
+    assertTrue(fc.isSimpleColour());
+    assertFalse(fc.isColourByLabel());
+    assertFalse(fc.isGraduatedColour());
+    assertFalse(fc.isColourByAttribute());
+    assertEquals(ColorUtils.bleachColour(Color.RED, 0.9f),
+            fc.getMinColour());
+    assertEquals(Color.RED, fc.getMaxColour());
+
+  }
+
+  @Test(groups = { "Functional" })
   public void testCopyConstructor()
   {
     /*
@@ -67,7 +89,8 @@ public class FeatureColourTest
     /*
      * min-max colour
      */
-    fc = new FeatureColour(Color.gray, Color.black, 10f, 20f);
+    fc = new FeatureColour(null, Color.gray, Color.black, Color.gray, 10f,
+            20f);
     fc.setAboveThreshold(true);
     fc.setThreshold(12f);
     fc1 = new FeatureColour(fc);
@@ -86,12 +109,14 @@ public class FeatureColourTest
     /*
      * min-max-noValue colour
      */
-    fc = new FeatureColour(Color.gray, Color.black, Color.green, 10f, 20f);
+    fc = new FeatureColour(Color.red, Color.gray, Color.black, Color.green,
+            10f, 20f);
     fc.setAboveThreshold(true);
     fc.setThreshold(12f);
     fc1 = new FeatureColour(fc);
     assertTrue(fc1.isGraduatedColour());
     assertFalse(fc1.isColourByLabel());
+    assertFalse(fc1.isSimpleColour());
     assertFalse(fc1.isColourByAttribute());
     assertNull(fc1.getAttributeName());
     assertTrue(fc1.isAboveThreshold());
@@ -99,6 +124,7 @@ public class FeatureColourTest
     assertEquals(Color.gray, fc1.getMinColour());
     assertEquals(Color.black, fc1.getMaxColour());
     assertEquals(Color.green, fc1.getNoColour());
+    assertEquals(Color.red, fc1.getColour());
     assertEquals(10f, fc1.getMin());
     assertEquals(20f, fc1.getMax());
 
@@ -128,7 +154,8 @@ public class FeatureColourTest
     /*
      * colour by attribute (value)
      */
-    fc = new FeatureColour(Color.gray, Color.black, Color.green, 10f, 20f);
+    fc = new FeatureColour(Color.yellow, Color.gray, Color.black,
+            Color.green, 10f, 20f);
     fc.setAboveThreshold(true);
     fc.setThreshold(12f);
     fc.setAttributeName("AF");
@@ -136,101 +163,23 @@ public class FeatureColourTest
     assertTrue(fc1.isGraduatedColour());
     assertFalse(fc1.isColourByLabel());
     assertTrue(fc1.isColourByAttribute());
+    assertFalse(fc1.isSimpleColour());
     assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName());
     assertTrue(fc1.isAboveThreshold());
     assertEquals(12f, fc1.getThreshold());
     assertEquals(Color.gray, fc1.getMinColour());
     assertEquals(Color.black, fc1.getMaxColour());
     assertEquals(Color.green, fc1.getNoColour());
+    assertEquals(Color.yellow, fc1.getColour());
     assertEquals(10f, fc1.getMin());
     assertEquals(20f, fc1.getMax());
-  }
-
-  @Test(groups = { "Functional" })
-  public void testCopyConstructor_minMax()
-  {
-    /*
-     * graduated colour
-     */
-    FeatureColour fc = new FeatureColour(Color.BLUE, Color.RED, 1f, 5f);
-    assertTrue(fc.isGraduatedColour());
-    assertFalse(fc.isColourByLabel());
-    assertFalse(fc.isColourByAttribute());
-    assertNull(fc.getAttributeName());
-    assertEquals(1f, fc.getMin());
-    assertEquals(5f, fc.getMax());
-
-    /*
-     * update min-max bounds
-     */
-    FeatureColour fc1 = new FeatureColour(fc, 2f, 6f);
-    assertTrue(fc1.isGraduatedColour());
-    assertFalse(fc1.isColourByLabel());
-    assertFalse(fc1.isColourByAttribute());
-    assertNull(fc1.getAttributeName());
-    assertEquals(2f, fc1.getMin());
-    assertEquals(6f, fc1.getMax());
-    assertFalse((boolean) PA.getValue(fc1, "isHighToLow"));
-
-    /*
-     * update min-max bounds - high to low
-     */
-    fc1 = new FeatureColour(fc, 23f, 16f);
-    assertTrue(fc1.isGraduatedColour());
-    assertFalse(fc1.isColourByLabel());
-    assertFalse(fc1.isColourByAttribute());
-    assertNull(fc1.getAttributeName());
-    assertEquals(23f, fc1.getMin());
-    assertEquals(16f, fc1.getMax());
-    assertTrue((boolean) PA.getValue(fc1, "isHighToLow"));
 
     /*
-     * graduated colour by attribute
+     * modify original attribute label and check that copy doesn't change
      */
-    fc1.setAttributeName("AF");
-    fc1 = new FeatureColour(fc1, 13f, 36f);
-    assertTrue(fc1.isGraduatedColour());
-    assertFalse(fc1.isColourByLabel());
-    assertTrue(fc1.isColourByAttribute());
+    fc.setAttributeName("MAF", "AF");
     assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName());
-    assertEquals(13f, fc1.getMin());
-    assertEquals(36f, fc1.getMax());
-    assertFalse((boolean) PA.getValue(fc1, "isHighToLow"));
-
-    /*
-     * colour by label
-     */
-    fc = new FeatureColour(Color.BLUE, Color.RED, 1f, 5f);
-    fc.setColourByLabel(true);
-    assertFalse(fc.isGraduatedColour());
-    assertTrue(fc.isColourByLabel());
-    assertFalse(fc.isColourByAttribute());
-    assertNull(fc.getAttributeName());
-    assertEquals(1f, fc.getMin());
-    assertEquals(5f, fc.getMax());
-
-    /*
-     * update min-max bounds
-     */
-    fc1 = new FeatureColour(fc, 2f, 6f);
-    assertFalse(fc1.isGraduatedColour());
-    assertTrue(fc1.isColourByLabel());
-    assertFalse(fc1.isColourByAttribute());
-    assertNull(fc1.getAttributeName());
-    assertEquals(2f, fc1.getMin());
-    assertEquals(6f, fc1.getMax());
 
-    /*
-     * colour by attribute text
-     */
-    fc1.setAttributeName("AC");
-    fc1 = new FeatureColour(fc1, 13f, 36f);
-    assertFalse(fc1.isGraduatedColour());
-    assertTrue(fc1.isColourByLabel());
-    assertTrue(fc1.isColourByAttribute());
-    assertArrayEquals(new String[] { "AC" }, fc1.getAttributeName());
-    assertEquals(13f, fc1.getMin());
-    assertEquals(36f, fc1.getMax());
   }
 
   @Test(groups = { "Functional" })
@@ -260,7 +209,8 @@ public class FeatureColourTest
      * score 0 to 100
      * gray(128, 128, 128) to red(255, 0, 0)
      */
-    FeatureColour fc = new FeatureColour(Color.GRAY, Color.RED, 0f, 100f);
+    FeatureColour fc = new FeatureColour(null, Color.GRAY, Color.RED, null,
+            0f, 100f);
     // feature score is 75 which is 3/4 of the way from GRAY to RED
     SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 75f,
             null);
@@ -276,8 +226,8 @@ public class FeatureColourTest
   public void testGetColor_aboveBelowThreshold()
   {
     // gradient from [50, 150] from WHITE(255, 255, 255) to BLACK(0, 0, 0)
-    FeatureColour fc = new FeatureColour(Color.WHITE, Color.BLACK, 50f,
-            150f);
+    FeatureColour fc = new FeatureColour(null, Color.WHITE, Color.BLACK,
+            Color.white, 50f, 150f);
     SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 70f,
             null);
 
@@ -331,8 +281,9 @@ public class FeatureColourTest
     fc = new FeatureColour();
     fc.setColourByLabel(true);
     fc.setAttributeName("CLIN_SIG");
-    assertEquals("domain\tattribute|CLIN_SIG", fc.toJalviewFormat("domain"));
-    
+    assertEquals("domain\tattribute|CLIN_SIG",
+            fc.toJalviewFormat("domain"));
+
     /*
      * colour by label (autoscaled) (an odd state you can reach by selecting
      * 'above threshold', then deselecting 'threshold is min/max' then 'colour
@@ -371,7 +322,8 @@ public class FeatureColourTest
      * graduated colour by score, no threshold
      * - default constructor sets noValueColor = minColor
      */
-    fc = new FeatureColour(Color.GREEN, Color.RED, 12f, 25f);
+    fc = new FeatureColour(null, Color.GREEN, Color.RED, Color.GREEN, 12f,
+            25f);
     String greenHex = Format.getHexString(Color.GREEN);
     String expected = String.format(
             "domain\tscore|%s|%s|noValueMin|abso|12.0|25.0|none", greenHex,
@@ -381,7 +333,8 @@ public class FeatureColourTest
     /*
      * graduated colour by score, no threshold, no value gets min colour
      */
-    fc = new FeatureColour(Color.GREEN, Color.RED, Color.GREEN, 12f, 25f);
+    fc = new FeatureColour(Color.RED, Color.GREEN, Color.RED, Color.GREEN,
+            12f, 25f);
     expected = String.format(
             "domain\tscore|%s|%s|noValueMin|abso|12.0|25.0|none", greenHex,
             redHex);
@@ -390,12 +343,13 @@ public class FeatureColourTest
     /*
      * graduated colour by score, no threshold, no value gets max colour
      */
-    fc = new FeatureColour(Color.GREEN, Color.RED, Color.RED, 12f, 25f);
+    fc = new FeatureColour(Color.RED, Color.GREEN, Color.RED, Color.RED,
+            12f, 25f);
     expected = String.format(
             "domain\tscore|%s|%s|noValueMax|abso|12.0|25.0|none", greenHex,
             redHex);
     assertEquals(expected, fc.toJalviewFormat("domain"));
-    
+
     /*
      * colour ranges over the actual score ranges (not min/max)
      */
@@ -411,8 +365,8 @@ public class FeatureColourTest
     fc.setThreshold(12.5f);
     fc.setBelowThreshold(true);
     expected = String.format(
-            "domain\tscore|%s|%s|noValueMax|12.0|25.0|below|12.5",
-            greenHex, redHex);
+            "domain\tscore|%s|%s|noValueMax|12.0|25.0|below|12.5", greenHex,
+            redHex);
     assertEquals(expected, fc.toJalviewFormat("domain"));
 
     /*
@@ -454,8 +408,8 @@ public class FeatureColourTest
     /*
      * simple colour by hex code
      */
-    fc = FeatureColour.parseJalviewFeatureColour(Format
-            .getHexString(Color.RED));
+    fc = FeatureColour
+            .parseJalviewFeatureColour(Format.getHexString(Color.RED));
     assertTrue(fc.isSimpleColour());
     assertEquals(Color.RED, fc.getColour());
 
@@ -687,8 +641,9 @@ public class FeatureColourTest
      * graduated colour based on attribute value for AF
      * given a min-max range of 0-100
      */
-    FeatureColour fc = new FeatureColour(new Color(50, 100, 150),
-            new Color(150, 200, 250), Color.yellow, 0f, 100f);
+    FeatureColour fc = new FeatureColour(Color.white,
+            new Color(50, 100, 150), new Color(150, 200, 250), Color.yellow,
+            0f, 100f);
     String attName = "AF";
     fc.setAttributeName(attName);
 
@@ -713,6 +668,48 @@ public class FeatureColourTest
     assertEquals(expected, fc.getColor(sf));
   }
 
+  @Test(groups = { "Functional" })
+  public void testIsOutwithThreshold()
+  {
+    FeatureColourI fc = new FeatureColour(Color.red);
+    SequenceFeature sf = new SequenceFeature("METAL", "desc", 10, 12, 1.2f,
+            "grp");
+    assertFalse(fc.isOutwithThreshold(null));
+    assertFalse(fc.isOutwithThreshold(sf));
+
+    fc = new FeatureColour(null, Color.white, Color.black, Color.green, 0f,
+            10f);
+    assertFalse(fc.isOutwithThreshold(sf)); // no threshold
+
+    fc.setAboveThreshold(true);
+    fc.setThreshold(1f);
+    assertFalse(fc.isOutwithThreshold(sf)); // feature score 1.2 is above 1
+
+    fc.setThreshold(2f);
+    assertTrue(fc.isOutwithThreshold(sf)); // feature score 1.2 is not above 2
+
+    fc.setBelowThreshold(true);
+    assertFalse(fc.isOutwithThreshold(sf)); // feature score 1.2 is below 2
+
+    fc.setThreshold(1f);
+    assertTrue(fc.isOutwithThreshold(sf)); // feature score 1.2 is not below 1
+
+    /*
+     * with attribute value threshold
+     */
+    fc.setAttributeName("AC");
+    assertFalse(fc.isOutwithThreshold(sf)); // missing attribute AC is ignored
+
+    sf.setValue("AC", "-1");
+    assertFalse(fc.isOutwithThreshold(sf)); // value -1 is below 1
+
+    sf.setValue("AC", "1");
+    assertTrue(fc.isOutwithThreshold(sf)); // value 1 is not below 1
+
+    sf.setValue("AC", "junk");
+    assertFalse(fc.isOutwithThreshold(sf)); // bad value is ignored
+  }
+
   /**
    * Test description of feature colour suitable for a tooltip
    */
@@ -727,14 +724,14 @@ public class FeatureColourTest
             String.format("r=%d,g=%d,b=%d", Color.RED.getRed(),
                     Color.red.getGreen(), Color.red.getBlue()),
             fc.getDescription());
-  
+
     /*
      * colour by label (no threshold)
      */
     fc = new FeatureColour();
     fc.setColourByLabel(true);
     assertEquals("By Label", fc.getDescription());
-  
+
     /*
      * colour by attribute text (no threshold)
      */
@@ -742,7 +739,7 @@ public class FeatureColourTest
     fc.setColourByLabel(true);
     fc.setAttributeName("CLIN_SIG");
     assertEquals("By CLIN_SIG", fc.getDescription());
-  
+
     /*
      * colour by label (above score threshold) 
      */
@@ -751,47 +748,41 @@ public class FeatureColourTest
     fc.setAutoScaled(false);
     fc.setThreshold(12.5f);
     fc.setAboveThreshold(true);
-    assertEquals("By Label (Score > 12.5)",
-            fc.getDescription());
-  
+    assertEquals("By Label (Score > 12.5)", fc.getDescription());
+
     /*
      * colour by label (below score threshold)
      */
     fc.setBelowThreshold(true);
-    assertEquals("By Label (Score < 12.5)",
-            fc.getDescription());
-  
+    assertEquals("By Label (Score < 12.5)", fc.getDescription());
+
     /*
      * colour by attributes text (below score threshold)
      */
     fc.setBelowThreshold(true);
     fc.setAttributeName("CSQ", "Consequence");
-    assertEquals(
-            "By CSQ:Consequence (Score < 12.5)",
-            fc.getDescription());
-  
+    assertEquals("By CSQ:Consequence (Score < 12.5)", fc.getDescription());
+
     /*
      * graduated colour by score, no threshold
      */
-    fc = new FeatureColour(Color.GREEN, Color.RED, 12f, 25f);
+    fc = new FeatureColour(null, Color.GREEN, Color.RED, null, 12f, 25f);
     assertEquals("By Score", fc.getDescription());
-  
+
     /*
      * graduated colour by score, below threshold
      */
     fc.setThreshold(12.5f);
     fc.setBelowThreshold(true);
-    assertEquals("By Score (< 12.5)",
-            fc.getDescription());
-  
+    assertEquals("By Score (< 12.5)", fc.getDescription());
+
     /*
      * graduated colour by score, above threshold
      */
     fc.setThreshold(12.5f);
     fc.setAboveThreshold(true);
     fc.setAutoScaled(false);
-    assertEquals("By Score (> 12.5)",
-            fc.getDescription());
+    assertEquals("By Score (> 12.5)", fc.getDescription());
 
     /*
      * graduated colour by attribute, no threshold
@@ -800,13 +791,12 @@ public class FeatureColourTest
     fc.setAboveThreshold(false);
     fc.setAutoScaled(false);
     assertEquals("By CSQ:AF", fc.getDescription());
-  
+
     /*
      * graduated colour by attribute, above threshold
      */
     fc.setAboveThreshold(true);
     fc.setAutoScaled(false);
-    assertEquals("By CSQ:AF (> 12.5)",
-            fc.getDescription());
+    assertEquals("By CSQ:AF (> 12.5)", fc.getDescription());
   }
 }