X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fschemes%2FFeatureColourTest.java;h=7a72c1510ad83ab88b49bc037c157e40dd3c385c;hb=2066caec85bf0b332d924472fcfdbdaa07f56f1e;hp=81357fa29b8379406a3b9311dc68471df233cb9d;hpb=0b1c761dfaa8242f122cf868e8897a06ec6eb727;p=jalview.git

diff --git a/test/jalview/schemes/FeatureColourTest.java b/test/jalview/schemes/FeatureColourTest.java
index 81357fa..7a72c15 100644
--- a/test/jalview/schemes/FeatureColourTest.java
+++ b/test/jalview/schemes/FeatureColourTest.java
@@ -1,72 +1,95 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.schemes;
 
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertNull;
 import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.fail;
 
 import jalview.datamodel.SequenceFeature;
+import jalview.gui.JvOptionPane;
+import jalview.util.ColorUtils;
+import jalview.util.Format;
 
 import java.awt.Color;
 
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.Test;
 
 public class FeatureColourTest
 {
-  @Test(groups = { "Functional" })
-  public void testIsColored_simpleColour()
-  {
-    FeatureColour fc = new FeatureColour(Color.RED);
-    assertTrue(fc.isColored(new SequenceFeature()));
-  }
 
-  @Test(groups = { "Functional" })
-  public void testIsColored_colourByLabel()
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
   {
-    FeatureColour fc = new FeatureColour();
-    fc.setColourByLabel(true);
-    assertTrue(fc.isColored(new SequenceFeature()));
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
   @Test(groups = { "Functional" })
-  public void testIsColored_aboveThreshold()
+  public void testCopyConstructor()
   {
-    // graduated colour range from score 20 to 100
-    FeatureColour fc = new FeatureColour(Color.WHITE, Color.BLACK, 20f,
-            100f);
-
-    // score 0 is adjusted to bottom of range
-    SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 0f,
-            null);
-    assertTrue(fc.isColored(sf));
-    assertEquals(Color.WHITE, fc.getColor(sf));
-
-    // score 120 is adjusted to top of range
-    sf.setScore(120f);
-    assertEquals(Color.BLACK, fc.getColor(sf));
-
-    // value below threshold is still rendered
-    // setting threshold has no effect yet...
-    fc.setThreshold(60f);
-    sf.setScore(36f);
-    assertTrue(fc.isColored(sf));
-    assertEquals(new Color(204, 204, 204), fc.getColor(sf));
+    /*
+     * plain colour
+     */
+    FeatureColour fc = new FeatureColour(Color.RED);
+    FeatureColour fc1 = new FeatureColour(fc);
+    assertTrue(fc1.getColour().equals(Color.RED));
+    assertFalse(fc1.isGraduatedColour());
+    assertFalse(fc1.isColourByLabel());
 
-    // now apply threshold:
+    /*
+     * min-max colour
+     */
+    fc = new FeatureColour(Color.gray, Color.black, 10f, 20f);
     fc.setAboveThreshold(true);
-    assertFalse(fc.isColored(sf));
-    // colour is still returned though ?!?
-    assertEquals(new Color(204, 204, 204), fc.getColor(sf));
+    fc.setThreshold(12f);
+    fc1 = new FeatureColour(fc);
+    assertTrue(fc1.isGraduatedColour());
+    assertFalse(fc1.isColourByLabel());
+    assertTrue(fc1.isAboveThreshold());
+    assertEquals(12f, fc1.getThreshold());
+    assertEquals(Color.gray, fc1.getMinColour());
+    assertEquals(Color.black, fc1.getMaxColour());
+    assertEquals(10f, fc1.getMin());
+    assertEquals(20f, fc1.getMax());
 
-    sf.setScore(84); // above threshold now
-    assertTrue(fc.isColored(sf));
-    assertEquals(new Color(51, 51, 51), fc.getColor(sf));
+    /*
+     * colour by label
+     */
+    fc = new FeatureColour();
+    fc.setColourByLabel(true);
+    fc1 = new FeatureColour(fc);
+    assertTrue(fc1.isColourByLabel());
+    assertFalse(fc1.isGraduatedColour());
   }
 
   @Test(groups = { "Functional" })
   public void testGetColor_simpleColour()
   {
     FeatureColour fc = new FeatureColour(Color.RED);
-    assertEquals(Color.RED, fc.getColor(new SequenceFeature()));
+    assertEquals(Color.RED,
+            fc.getColor(new SequenceFeature("Cath", "", 1, 2, 0f, null)));
   }
 
   @Test(groups = { "Functional" })
@@ -76,14 +99,15 @@ public class FeatureColourTest
     fc.setColourByLabel(true);
     SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 1f,
             null);
-    Color expected = UserColourScheme.createColourFromName("desc");
+    Color expected = ColorUtils.createColourFromName("desc");
     assertEquals(expected, fc.getColor(sf));
   }
 
   @Test(groups = { "Functional" })
   public void testGetColor_Graduated()
   {
-    // graduated colour from score 0 to 100, gray(128, 128, 128) to red(255, 0, 0)
+    // graduated colour from score 0 to 100, gray(128, 128, 128) to red(255, 0,
+    // 0)
     FeatureColour fc = new FeatureColour(Color.GRAY, Color.RED, 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,
@@ -97,19 +121,223 @@ public class FeatureColourTest
   }
 
   @Test(groups = { "Functional" })
-  public void testGetColor_belowThreshold()
+  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);
     SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 70f,
             null);
+
+    /*
+     * feature with score of Float.NaN is always assigned minimum colour
+     */
+    SequenceFeature sf2 = new SequenceFeature("type", "desc", 0, 20,
+            Float.NaN, null);
+
     fc.setThreshold(100f); // ignore for now
-    assertTrue(fc.isColored(sf));
     assertEquals(new Color(204, 204, 204), fc.getColor(sf));
+    assertEquals(Color.white, fc.getColor(sf2));
 
     fc.setAboveThreshold(true); // feature lies below threshold
-    assertFalse(fc.isColored(sf));
-    assertEquals(new Color(204, 204, 204), fc.getColor(sf));
+    assertNull(fc.getColor(sf));
+    assertEquals(Color.white, fc.getColor(sf2));
+
+    fc.setBelowThreshold(true);
+    fc.setThreshold(70f);
+    assertNull(fc.getColor(sf)); // feature score == threshold - hidden
+    assertEquals(Color.white, fc.getColor(sf2));
+    fc.setThreshold(69f);
+    assertNull(fc.getColor(sf)); // feature score > threshold - hidden
+    assertEquals(Color.white, fc.getColor(sf2));
+  }
+
+  /**
+   * Test output of feature colours to Jalview features file format
+   */
+  @Test(groups = { "Functional" })
+  public void testToJalviewFormat()
+  {
+    /*
+     * plain colour - to RGB hex code
+     */
+    FeatureColour fc = new FeatureColour(Color.RED);
+    String redHex = Format.getHexString(Color.RED);
+    String hexColour = redHex;
+    assertEquals("domain\t" + hexColour, fc.toJalviewFormat("domain"));
+
+    /*
+     * colour by label (no threshold)
+     */
+    fc = new FeatureColour();
+    fc.setColourByLabel(true);
+    assertEquals("domain\tlabel", 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.setAutoScaled(true);
+    assertEquals("domain\tlabel", fc.toJalviewFormat("domain"));
+
+    /*
+     * colour by label (above threshold) (min/max values are output though not
+     * used by this scheme)
+     */
+    fc.setAutoScaled(false);
+    fc.setThreshold(12.5f);
+    fc.setAboveThreshold(true);
+    assertEquals("domain\tlabel|||0.0|0.0|above|12.5",
+            fc.toJalviewFormat("domain"));
+
+    /*
+     * colour by label (below threshold)
+     */
+    fc.setBelowThreshold(true);
+    assertEquals("domain\tlabel|||0.0|0.0|below|12.5",
+            fc.toJalviewFormat("domain"));
+
+    /*
+     * graduated colour, no threshold
+     */
+    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);
+    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,
+            redHex);
+    assertEquals(expected, fc.toJalviewFormat("domain"));
+
+    /*
+     * graduated colour below threshold
+     */
+    fc.setThreshold(12.5f);
+    fc.setBelowThreshold(true);
+    expected = String.format("domain\t%s|%s|12.0|25.0|below|12.5",
+            greenHex, redHex);
+    assertEquals(expected, fc.toJalviewFormat("domain"));
+
+    /*
+     * graduated colour 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",
+            greenHex, redHex);
+    assertEquals(expected, fc.toJalviewFormat("domain"));
+  }
+
+  /**
+   * Test parsing of feature colours from Jalview features file format
+   */
+  @Test(groups = { "Functional" })
+  public void testParseJalviewFeatureColour()
+  {
+    /*
+     * simple colour by name
+     */
+    FeatureColour fc = FeatureColour.parseJalviewFeatureColour("red");
+    assertTrue(fc.isSimpleColour());
+    assertEquals(Color.RED, fc.getColour());
+
+    /*
+     * simple colour by hex code
+     */
+    fc = FeatureColour.parseJalviewFeatureColour(Format
+            .getHexString(Color.RED));
+    assertTrue(fc.isSimpleColour());
+    assertEquals(Color.RED, fc.getColour());
+
+    /*
+     * simple colour by rgb triplet
+     */
+    fc = FeatureColour.parseJalviewFeatureColour("255,0,0");
+    assertTrue(fc.isSimpleColour());
+    assertEquals(Color.RED, fc.getColour());
+
+    /*
+     * malformed colour
+     */
+    try
+    {
+      fc = FeatureColour.parseJalviewFeatureColour("oops");
+      fail("expected exception");
+    } catch (IllegalArgumentException e)
+    {
+      assertEquals("Invalid colour descriptor: oops", e.getMessage());
+    }
+
+    /*
+     * colour by label (no threshold)
+     */
+    fc = FeatureColour.parseJalviewFeatureColour("label");
+    assertTrue(fc.isColourByLabel());
+    assertFalse(fc.hasThreshold());
+
+    /*
+     * colour by label (with threshold)
+     */
+    fc = FeatureColour
+            .parseJalviewFeatureColour("label|||0.0|0.0|above|12.0");
+    assertTrue(fc.isColourByLabel());
+    assertTrue(fc.isAboveThreshold());
+    assertEquals(12.0f, fc.getThreshold());
+
+    /*
+     * graduated colour (by name) (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(10f, fc.getMin());
+    assertEquals(20f, fc.getMax());
+    assertTrue(fc.isAutoScaled());
+
+    /*
+     * graduated colour (by hex code) (above threshold)
+     */
+    String descriptor = String.format("%s|%s|10.0|20.0|above|15",
+            Format.getHexString(Color.RED),
+            Format.getHexString(Color.GREEN));
+    fc = FeatureColour.parseJalviewFeatureColour(descriptor);
+    assertTrue(fc.isGraduatedColour());
+    assertTrue(fc.hasThreshold());
+    assertTrue(fc.isAboveThreshold());
+    assertEquals(15f, 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");
+    fc = FeatureColour.parseJalviewFeatureColour(descriptor);
+    assertTrue(fc.isGraduatedColour());
+    assertFalse(fc.isAutoScaled());
+    assertTrue(fc.hasThreshold());
+    assertTrue(fc.isBelowThreshold());
+    assertEquals(15f, fc.getThreshold());
+    assertEquals(Color.RED, fc.getMinColour());
+    assertEquals(Color.GREEN, fc.getMaxColour());
+    assertEquals(10f, fc.getMin());
+    assertEquals(20f, fc.getMax());
+
+    descriptor = String
+            .format("blue|255,0,255|absolute|20.0|95.0|below|66.0");
+    fc = FeatureColour.parseJalviewFeatureColour(descriptor);
+    assertTrue(fc.isGraduatedColour());
   }
 }