X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fschemes%2FFeatureColourTest.java;h=c16d5411f6a6313647696dfb38add903aea7620e;hb=refs%2Fheads%2Ftask%2FJAL-2662;hp=81357fa29b8379406a3b9311dc68471df233cb9d;hpb=0b1c761dfaa8242f122cf868e8897a06ec6eb727;p=jalview.git

diff --git a/test/jalview/schemes/FeatureColourTest.java b/test/jalview/schemes/FeatureColourTest.java
index 81357fa..c16d541 100644
--- a/test/jalview/schemes/FeatureColourTest.java
+++ b/test/jalview/schemes/FeatureColourTest.java
@@ -1,17 +1,88 @@
+/*
+ * 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.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
 {
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @Test(groups = { "Functional" })
+  public void testCopyConstructor()
+  {
+    /*
+     * 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());
+
+    /*
+     * min-max colour
+     */
+    fc = new FeatureColour(Color.gray, Color.black, 10f, 20f);
+    fc.setAboveThreshold(true);
+    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());
+
+    /*
+     * colour by label
+     */
+    fc = new FeatureColour();
+    fc.setColourByLabel(true);
+    fc1 = new FeatureColour(fc);
+    assertTrue(fc1.isColourByLabel());
+    assertFalse(fc1.isGraduatedColour());
+  }
+
   @Test(groups = { "Functional" })
   public void testIsColored_simpleColour()
   {
@@ -76,14 +147,15 @@ 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,
@@ -112,4 +184,193 @@ public class FeatureColourTest
     assertFalse(fc.isColored(sf));
     assertEquals(new Color(204, 204, 204), fc.getColor(sf));
   }
+
+  /**
+   * 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());
+  }
 }