X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fschemes%2FFeatureColourTest.java;h=1a6a5f342e8ec9bb8b1fda575657e243ccd12f33;hb=refs%2Fheads%2Fbug%2FJAL-3120restoreFeatureColour;hp=db4fe4096a42e70a3b06a095c9f5b1c8df433ad9;hpb=586870ac526e851e3589fd8880a4a2fc090bbcc3;p=jalview.git diff --git a/test/jalview/schemes/FeatureColourTest.java b/test/jalview/schemes/FeatureColourTest.java index db4fe40..1a6a5f3 100644 --- a/test/jalview/schemes/FeatureColourTest.java +++ b/test/jalview/schemes/FeatureColourTest.java @@ -25,7 +25,9 @@ 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 static org.testng.internal.junit.ArrayAsserts.assertArrayEquals; +import jalview.api.FeatureColourI; import jalview.datamodel.SequenceFeature; import jalview.gui.JvOptionPane; import jalview.util.ColorUtils; @@ -33,8 +35,6 @@ import jalview.util.Format; import java.awt.Color; -import junit.extensions.PA; - import org.testng.annotations.BeforeClass; import org.testng.annotations.Test; @@ -49,6 +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() { /* @@ -65,7 +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); @@ -84,12 +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()); @@ -97,6 +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()); @@ -121,12 +149,13 @@ public class FeatureColourTest assertTrue(fc1.isColourByLabel()); assertFalse(fc1.isGraduatedColour()); assertTrue(fc1.isColourByAttribute()); - assertEquals("AF", fc1.getAttributeName()); + assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName()); /* * 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"); @@ -134,104 +163,19 @@ public class FeatureColourTest assertTrue(fc1.isGraduatedColour()); assertFalse(fc1.isColourByLabel()); assertTrue(fc1.isColourByAttribute()); - assertEquals("AF", fc1.getAttributeName()); + 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 - */ - fc1.setAttributeName("AF"); - fc1 = new FeatureColour(fc1, 13f, 36f); - assertTrue(fc1.isGraduatedColour()); - assertFalse(fc1.isColourByLabel()); - assertTrue(fc1.isColourByAttribute()); - assertEquals("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()); - assertEquals("AC", fc1.getAttributeName()); - assertEquals(13f, fc1.getMin()); - assertEquals(36f, fc1.getMax()); - } - - @Test(groups = { "Functional" }) public void testGetColor_simpleColour() { FeatureColour fc = new FeatureColour(Color.RED); @@ -258,7 +202,8 @@ 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); @@ -274,8 +219,8 @@ 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); @@ -324,20 +269,29 @@ 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")); @@ -349,38 +303,83 @@ public class FeatureColourTest fc.toJalviewFormat("domain")); /* - * graduated colour, no threshold + * colour by attributes text (below threshold) */ - fc = new FeatureColour(Color.GREEN, Color.RED, 12f, 25f); + 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(null, Color.GREEN, Color.RED, Color.GREEN, 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.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); + assertEquals(expected, fc.toJalviewFormat("domain")); + + /* + * graduated colour by score, no threshold, no value gets max colour + */ + 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) */ 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")); } @@ -394,7 +393,7 @@ 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()); @@ -442,7 +441,28 @@ 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()); @@ -454,7 +474,35 @@ public class FeatureColourTest assertTrue(fc.isAutoScaled()); /* - * graduated colour (by hex code) (above threshold) + * 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 score (colours by hex code) (above threshold) */ String descriptor = String.format("%s|%s|10.0|20.0|above|15", Format.getHexString(Color.RED), @@ -471,9 +519,26 @@ 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()); @@ -485,8 +550,7 @@ 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()); } @@ -520,8 +584,9 @@ 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);