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;
assertTrue(fc1.isGraduatedColour());
assertFalse(fc1.isColourByLabel());
assertTrue(fc1.isColourByAttribute());
- assertEquals(new String[] { "AF" }, fc1.getAttributeName());
+ assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName());
assertEquals(13f, fc1.getMin());
assertEquals(36f, fc1.getMax());
assertFalse((boolean) PA.getValue(fc1, "isHighToLow"));
assertFalse(fc1.isGraduatedColour());
assertTrue(fc1.isColourByLabel());
assertTrue(fc1.isColourByAttribute());
- assertEquals("AC", fc1.getAttributeName());
+ assertArrayEquals(new String[] { "AC" }, fc1.getAttributeName());
assertEquals(13f, fc1.getMin());
assertEquals(36f, fc1.getMax());
}
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"));
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"));
}
/*
* simple colour by name
*/
- FeatureColour fc = FeatureColour.parseJalviewFeatureColour("red");
+ FeatureColourI fc = FeatureColour.parseJalviewFeatureColour("red");
assertTrue(fc.isSimpleColour());
assertEquals(Color.RED, fc.getColour());
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());
/*
- * graduated colour (by hex code) (above threshold)
+ * 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 score (colours by hex code) (above threshold)
*/
String descriptor = String.format("%s|%s|10.0|20.0|above|15",
Format.getHexString(Color.RED),
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());
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());
}
git://source.jalview.org / jalview.git / blobdiff