X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fschemes%2FFeatureColourTest.java;h=a96caec9a3d9b542ab19585ec0f641ad1ad5a3b9;hb=4c43b10447a141c73446fc2bc368b06245a675c3;hp=72c29d344da0feaf0728733286445df9dcd5125d;hpb=9e926ac4305fd9dff38b6e079e55b4f50664d544;p=jalview.git

diff --git a/test/jalview/schemes/FeatureColourTest.java b/test/jalview/schemes/FeatureColourTest.java
index 72c29d3..a96caec 100644
--- a/test/jalview/schemes/FeatureColourTest.java
+++ b/test/jalview/schemes/FeatureColourTest.java
@@ -27,6 +27,7 @@ import static org.testng.AssertJUnit.assertTrue;
 import static org.testng.AssertJUnit.fail;
 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
 
+import jalview.api.FeatureColourI;
 import jalview.datamodel.SequenceFeature;
 import jalview.gui.JvOptionPane;
 import jalview.util.ColorUtils;
@@ -325,20 +326,29 @@ public class FeatureColourTest
     assertEquals("domain\tlabel", fc.toJalviewFormat("domain"));
 
     /*
+     * colour by attribute text (no threshold)
+     */
+    fc = new FeatureColour();
+    fc.setColourByLabel(true);
+    fc.setAttributeName("CLIN_SIG");
+    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
      * by label')
      */
+    fc.setAttributeName((String[]) null);
     fc.setAutoScaled(true);
     assertEquals("domain\tlabel", fc.toJalviewFormat("domain"));
 
     /*
-     * colour by label (above threshold) (min/max values are output though not
-     * used by this scheme)
+     * colour by label (above threshold) 
      */
     fc.setAutoScaled(false);
     fc.setThreshold(12.5f);
     fc.setAboveThreshold(true);
+    // min/max values are output though not used by this scheme
     assertEquals("domain\tlabel|||0.0|0.0|above|12.5",
             fc.toJalviewFormat("domain"));
 
@@ -350,38 +360,80 @@ public class FeatureColourTest
             fc.toJalviewFormat("domain"));
 
     /*
-     * graduated colour, no threshold
+     * colour by attributes text (below threshold)
+     */
+    fc.setBelowThreshold(true);
+    fc.setAttributeName("CSQ", "Consequence");
+    assertEquals("domain\tattribute|CSQ:Consequence|||0.0|0.0|below|12.5",
+            fc.toJalviewFormat("domain"));
+
+    /*
+     * graduated colour by score, no threshold
+     * - default constructor sets noValueColor = minColor
      */
     fc = new FeatureColour(Color.GREEN, Color.RED, 12f, 25f);
     String greenHex = Format.getHexString(Color.GREEN);
-    String expected = String.format("domain\t%s|%s|abso|12.0|25.0|none",
-            greenHex, redHex);
+    String expected = String.format(
+            "domain\tscore|%s|%s|noValueMin|abso|12.0|25.0|none", greenHex,
+            redHex);
+    assertEquals(expected, fc.toJalviewFormat("domain"));
+
+    /*
+     * graduated colour by score, no threshold, no value gets min colour
+     */
+    fc = new FeatureColour(Color.GREEN, Color.RED, Color.GREEN, 12f, 25f);
+    expected = String.format(
+            "domain\tscore|%s|%s|noValueMin|abso|12.0|25.0|none", greenHex,
+            redHex);
     assertEquals(expected, fc.toJalviewFormat("domain"));
 
     /*
+     * graduated colour by score, no threshold, no value gets max colour
+     */
+    fc = new FeatureColour(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)
      */
     fc.setAutoScaled(true);
-    expected = String.format("domain\t%s|%s|12.0|25.0|none", greenHex,
+    expected = String.format(
+            "domain\tscore|%s|%s|noValueMax|12.0|25.0|none", greenHex,
             redHex);
     assertEquals(expected, fc.toJalviewFormat("domain"));
 
     /*
-     * graduated colour below threshold
+     * graduated colour by score, below threshold
      */
     fc.setThreshold(12.5f);
     fc.setBelowThreshold(true);
-    expected = String.format("domain\t%s|%s|12.0|25.0|below|12.5",
+    expected = String.format(
+            "domain\tscore|%s|%s|noValueMax|12.0|25.0|below|12.5",
             greenHex, redHex);
     assertEquals(expected, fc.toJalviewFormat("domain"));
 
     /*
-     * graduated colour above threshold
+     * graduated colour by score, above threshold
      */
     fc.setThreshold(12.5f);
     fc.setAboveThreshold(true);
     fc.setAutoScaled(false);
-    expected = String.format("domain\t%s|%s|abso|12.0|25.0|above|12.5",
+    expected = String.format(
+            "domain\tscore|%s|%s|noValueMax|abso|12.0|25.0|above|12.5",
+            greenHex, redHex);
+    assertEquals(expected, fc.toJalviewFormat("domain"));
+
+    /*
+     * graduated colour by attribute, above threshold
+     */
+    fc.setAttributeName("CSQ", "AF");
+    fc.setAboveThreshold(true);
+    fc.setAutoScaled(false);
+    expected = String.format(
+            "domain\tattribute|CSQ:AF|%s|%s|noValueMax|abso|12.0|25.0|above|12.5",
             greenHex, redHex);
     assertEquals(expected, fc.toJalviewFormat("domain"));
   }
@@ -395,7 +447,7 @@ public class FeatureColourTest
     /*
      * simple colour by name
      */
-    FeatureColour fc = FeatureColour.parseJalviewFeatureColour("red");
+    FeatureColourI fc = FeatureColour.parseJalviewFeatureColour("red");
     assertTrue(fc.isSimpleColour());
     assertEquals(Color.RED, fc.getColour());
 
@@ -443,19 +495,117 @@ public class FeatureColourTest
     assertEquals(12.0f, fc.getThreshold());
 
     /*
-     * graduated colour (by name) (no threshold)
+     * colour by attribute text (no threshold)
+     */
+    fc = FeatureColour.parseJalviewFeatureColour("attribute|CLIN_SIG");
+    assertTrue(fc.isColourByAttribute());
+    assertTrue(fc.isColourByLabel());
+    assertFalse(fc.hasThreshold());
+    assertArrayEquals(new String[] { "CLIN_SIG" }, fc.getAttributeName());
+
+    /*
+     * colour by attributes text (with score threshold)
+     */
+    fc = FeatureColour.parseJalviewFeatureColour(
+            "attribute|CSQ:Consequence|||0.0|0.0|above|12.0");
+    assertTrue(fc.isColourByLabel());
+    assertTrue(fc.isColourByAttribute());
+    assertArrayEquals(new String[] { "CSQ", "Consequence" },
+            fc.getAttributeName());
+    assertTrue(fc.isAboveThreshold());
+    assertEquals(12.0f, fc.getThreshold());
+
+    /*
+     * graduated colour by score (with colour names) (no threshold)
      */
     fc = FeatureColour.parseJalviewFeatureColour("red|green|10.0|20.0");
     assertTrue(fc.isGraduatedColour());
     assertFalse(fc.hasThreshold());
     assertEquals(Color.RED, fc.getMinColour());
     assertEquals(Color.GREEN, fc.getMaxColour());
+    assertEquals(Color.RED, fc.getNoColour());
+    assertEquals(10f, fc.getMin());
+    assertEquals(20f, fc.getMax());
+    assertTrue(fc.isAutoScaled());
+
+    /*
+     * the same, with 'no value colour' specified as max
+     */
+    fc = FeatureColour
+            .parseJalviewFeatureColour("red|green|novaluemax|10.0|20.0");
+    assertEquals(Color.RED, fc.getMinColour());
+    assertEquals(Color.GREEN, fc.getMaxColour());
+    assertEquals(Color.GREEN, fc.getNoColour());
+    assertEquals(10f, fc.getMin());
+    assertEquals(20f, fc.getMax());
+
+    /*
+     * the same, with 'no value colour' specified as min
+     */
+    fc = FeatureColour
+            .parseJalviewFeatureColour("red|green|novalueMin|10.0|20.0");
+    assertEquals(Color.RED, fc.getMinColour());
+    assertEquals(Color.GREEN, fc.getMaxColour());
+    assertEquals(Color.RED, fc.getNoColour());
+    assertEquals(10f, fc.getMin());
+    assertEquals(20f, fc.getMax());
+
+    /*
+     * the same, with 'no value colour' specified as none
+     */
+    fc = FeatureColour
+            .parseJalviewFeatureColour("red|green|novaluenone|10.0|20.0");
+    assertEquals(Color.RED, fc.getMinColour());
+    assertEquals(Color.GREEN, fc.getMaxColour());
+    assertNull(fc.getNoColour());
+    assertEquals(10f, fc.getMin());
+    assertEquals(20f, fc.getMax());
+
+    /*
+     * the same, with invalid 'no value colour'
+     */
+    try
+    {
+      fc = FeatureColour
+              .parseJalviewFeatureColour("red|green|blue|10.0|20.0");
+      fail("expected exception");
+    } catch (IllegalArgumentException e)
+    {
+      assertEquals(
+              "Couldn't parse the minimum value for graduated colour ('blue')",
+              e.getMessage());
+    }
+
+    /*
+     * graduated colour (explicitly by 'score') (no threshold)
+     */
+    fc = FeatureColour
+            .parseJalviewFeatureColour("Score|red|green|10.0|20.0");
+    assertTrue(fc.isGraduatedColour());
+    assertFalse(fc.hasThreshold());
+    assertEquals(Color.RED, fc.getMinColour());
+    assertEquals(Color.GREEN, fc.getMaxColour());
+    assertEquals(10f, fc.getMin());
+    assertEquals(20f, fc.getMax());
+    assertTrue(fc.isAutoScaled());
+
+    /*
+     * graduated colour by attribute (no threshold)
+     */
+    fc = FeatureColour
+            .parseJalviewFeatureColour("attribute|AF|red|green|10.0|20.0");
+    assertTrue(fc.isGraduatedColour());
+    assertTrue(fc.isColourByAttribute());
+    assertArrayEquals(new String[] { "AF" }, fc.getAttributeName());
+    assertFalse(fc.hasThreshold());
+    assertEquals(Color.RED, fc.getMinColour());
+    assertEquals(Color.GREEN, fc.getMaxColour());
     assertEquals(10f, fc.getMin());
     assertEquals(20f, fc.getMax());
     assertTrue(fc.isAutoScaled());
 
     /*
-     * graduated colour (by hex code) (above threshold)
+     * graduated colour by score (colours by hex code) (above threshold)
      */
     String descriptor = String.format("%s|%s|10.0|20.0|above|15",
             Format.getHexString(Color.RED),
@@ -472,9 +622,26 @@ public class FeatureColourTest
     assertTrue(fc.isAutoScaled());
 
     /*
+     * graduated colour by attributes (below threshold)
+     */
+    fc = FeatureColour.parseJalviewFeatureColour(
+            "attribute|CSQ:AF|red|green|10.0|20.0|below|13");
+    assertTrue(fc.isGraduatedColour());
+    assertTrue(fc.isColourByAttribute());
+    assertArrayEquals(new String[] { "CSQ", "AF" }, fc.getAttributeName());
+    assertTrue(fc.hasThreshold());
+    assertTrue(fc.isBelowThreshold());
+    assertEquals(13f, fc.getThreshold());
+    assertEquals(Color.RED, fc.getMinColour());
+    assertEquals(Color.GREEN, fc.getMaxColour());
+    assertEquals(10f, fc.getMin());
+    assertEquals(20f, fc.getMax());
+    assertTrue(fc.isAutoScaled());
+
+    /*
      * graduated colour (by RGB triplet) (below threshold), absolute scale
      */
-    descriptor = String.format("255,0,0|0,255,0|abso|10.0|20.0|below|15");
+    descriptor = "255,0,0|0,255,0|abso|10.0|20.0|below|15";
     fc = FeatureColour.parseJalviewFeatureColour(descriptor);
     assertTrue(fc.isGraduatedColour());
     assertFalse(fc.isAutoScaled());
@@ -486,8 +653,7 @@ public class FeatureColourTest
     assertEquals(10f, fc.getMin());
     assertEquals(20f, fc.getMax());
 
-    descriptor = String
-            .format("blue|255,0,255|absolute|20.0|95.0|below|66.0");
+    descriptor = "blue|255,0,255|absolute|20.0|95.0|below|66.0";
     fc = FeatureColour.parseJalviewFeatureColour(descriptor);
     assertTrue(fc.isGraduatedColour());
   }