test/jalview/schemes/FeatureColourTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.schemes;
  22
  23 import static org.testng.AssertJUnit.assertEquals;
  24 import static org.testng.AssertJUnit.assertFalse;
  25 import static org.testng.AssertJUnit.assertNull;
  26 import static org.testng.AssertJUnit.assertTrue;
  27 import static org.testng.AssertJUnit.fail;
  28 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
  29
  30 import jalview.api.FeatureColourI;
  31 import jalview.datamodel.SequenceFeature;
  32 import jalview.gui.JvOptionPane;
  33 import jalview.util.ColorUtils;
  34 import jalview.util.Format;
  35
  36 import java.awt.Color;
  37
  38 import org.testng.annotations.BeforeClass;
  39 import org.testng.annotations.Test;
  40
  41 public class FeatureColourTest
  42 {
  43
  44   @BeforeClass(alwaysRun = true)
  45   public void setUpJvOptionPane()
  46   {
  47     JvOptionPane.setInteractiveMode(false);
  48     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  49   }
  50
  51   @Test(groups = { "Functional" })
  52   public void testConstructors()
  53   {
  54     FeatureColourI fc = new FeatureColour();
  55     assertNull(fc.getColour());
  56     assertTrue(fc.isSimpleColour());
  57     assertFalse(fc.isColourByLabel());
  58     assertFalse(fc.isGraduatedColour());
  59     assertFalse(fc.isColourByAttribute());
  60     assertEquals(Color.white, fc.getMinColour());
  61     assertEquals(Color.black, fc.getMaxColour());
  62
  63     fc = new FeatureColour(Color.RED);
  64     assertEquals(Color.red, fc.getColour());
  65     assertTrue(fc.isSimpleColour());
  66     assertFalse(fc.isColourByLabel());
  67     assertFalse(fc.isGraduatedColour());
  68     assertFalse(fc.isColourByAttribute());
  69     assertEquals(ColorUtils.bleachColour(Color.RED, 0.9f),
  70             fc.getMinColour());
  71     assertEquals(Color.RED, fc.getMaxColour());
  72
  73   }
  74
  75   @Test(groups = { "Functional" })
  76   public void testCopyConstructor()
  77   {
  78     /*
  79      * plain colour
  80      */
  81     FeatureColour fc = new FeatureColour(Color.RED);
  82     FeatureColour fc1 = new FeatureColour(fc);
  83     assertTrue(fc1.getColour().equals(Color.RED));
  84     assertFalse(fc1.isGraduatedColour());
  85     assertFalse(fc1.isColourByLabel());
  86     assertFalse(fc1.isColourByAttribute());
  87     assertNull(fc1.getAttributeName());
  88
  89     /*
  90      * min-max colour
  91      */
  92     fc = new FeatureColour(null, Color.gray, Color.black, Color.gray, 10f,
  93             20f);
  94     fc.setAboveThreshold(true);
  95     fc.setThreshold(12f);
  96     fc1 = new FeatureColour(fc);
  97     assertTrue(fc1.isGraduatedColour());
  98     assertFalse(fc1.isColourByLabel());
  99     assertTrue(fc1.isAboveThreshold());
 100     assertFalse(fc1.isColourByAttribute());
 101     assertNull(fc1.getAttributeName());
 102     assertEquals(12f, fc1.getThreshold());
 103     assertEquals(Color.gray, fc1.getMinColour());
 104     assertEquals(Color.black, fc1.getMaxColour());
 105     assertEquals(Color.gray, fc1.getNoColour());
 106     assertEquals(10f, fc1.getMin());
 107     assertEquals(20f, fc1.getMax());
 108
 109     /*
 110      * min-max-noValue colour
 111      */
 112     fc = new FeatureColour(Color.red, Color.gray, Color.black, Color.green,
 113             10f, 20f);
 114     fc.setAboveThreshold(true);
 115     fc.setThreshold(12f);
 116     fc1 = new FeatureColour(fc);
 117     assertTrue(fc1.isGraduatedColour());
 118     assertFalse(fc1.isColourByLabel());
 119     assertFalse(fc1.isSimpleColour());
 120     assertFalse(fc1.isColourByAttribute());
 121     assertNull(fc1.getAttributeName());
 122     assertTrue(fc1.isAboveThreshold());
 123     assertEquals(12f, fc1.getThreshold());
 124     assertEquals(Color.gray, fc1.getMinColour());
 125     assertEquals(Color.black, fc1.getMaxColour());
 126     assertEquals(Color.green, fc1.getNoColour());
 127     assertEquals(Color.red, fc1.getColour());
 128     assertEquals(10f, fc1.getMin());
 129     assertEquals(20f, fc1.getMax());
 130
 131     /*
 132      * colour by label
 133      */
 134     fc = new FeatureColour();
 135     fc.setColourByLabel(true);
 136     fc1 = new FeatureColour(fc);
 137     assertTrue(fc1.isColourByLabel());
 138     assertFalse(fc1.isGraduatedColour());
 139     assertFalse(fc1.isColourByAttribute());
 140     assertNull(fc1.getAttributeName());
 141
 142     /*
 143      * colour by attribute (label)
 144      */
 145     fc = new FeatureColour();
 146     fc.setColourByLabel(true);
 147     fc.setAttributeName("AF");
 148     fc1 = new FeatureColour(fc);
 149     assertTrue(fc1.isColourByLabel());
 150     assertFalse(fc1.isGraduatedColour());
 151     assertTrue(fc1.isColourByAttribute());
 152     assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName());
 153
 154     /*
 155      * colour by attribute (value)
 156      */
 157     fc = new FeatureColour(Color.yellow, Color.gray, Color.black,
 158             Color.green, 10f, 20f);
 159     fc.setAboveThreshold(true);
 160     fc.setThreshold(12f);
 161     fc.setAttributeName("AF");
 162     fc1 = new FeatureColour(fc);
 163     assertTrue(fc1.isGraduatedColour());
 164     assertFalse(fc1.isColourByLabel());
 165     assertTrue(fc1.isColourByAttribute());
 166     assertFalse(fc1.isSimpleColour());
 167     assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName());
 168     assertTrue(fc1.isAboveThreshold());
 169     assertEquals(12f, fc1.getThreshold());
 170     assertEquals(Color.gray, fc1.getMinColour());
 171     assertEquals(Color.black, fc1.getMaxColour());
 172     assertEquals(Color.green, fc1.getNoColour());
 173     assertEquals(Color.yellow, fc1.getColour());
 174     assertEquals(10f, fc1.getMin());
 175     assertEquals(20f, fc1.getMax());
 176
 177     /*
 178      * modify original attribute label and check that copy doesn't change
 179      */
 180     fc.setAttributeName("MAF", "AF");
 181     assertArrayEquals(new String[] { "AF" }, fc1.getAttributeName());
 182
 183   }
 184
 185   @Test(groups = { "Functional" })
 186   public void testGetColor_simpleColour()
 187   {
 188     FeatureColour fc = new FeatureColour(Color.RED);
 189     assertEquals(Color.RED,
 190             fc.getColor(new SequenceFeature("Cath", "", 1, 2, 0f, null)));
 191   }
 192
 193   @Test(groups = { "Functional" })
 194   public void testGetColor_colourByLabel()
 195   {
 196     FeatureColour fc = new FeatureColour();
 197     fc.setColourByLabel(true);
 198     SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 1f,
 199             null);
 200     Color expected = ColorUtils.createColourFromName("desc");
 201     assertEquals(expected, fc.getColor(sf));
 202   }
 203
 204   @Test(groups = { "Functional" })
 205   public void testGetColor_Graduated()
 206   {
 207     /*
 208      * graduated colour from
 209      * score 0 to 100
 210      * gray(128, 128, 128) to red(255, 0, 0)
 211      */
 212     FeatureColour fc = new FeatureColour(null, Color.GRAY, Color.RED, null,
 213             0f, 100f);
 214     // feature score is 75 which is 3/4 of the way from GRAY to RED
 215     SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 75f,
 216             null);
 217     // the colour gradient is computed in float values from 0-1 (where 1 == 255)
 218     float red = 128 / 255f + 3 / 4f * (255 - 128) / 255f;
 219     float green = 128 / 255f + 3 / 4f * (0 - 128) / 255f;
 220     float blue = 128 / 255f + 3 / 4f * (0 - 128) / 255f;
 221     Color expected = new Color(red, green, blue);
 222     assertEquals(expected, fc.getColor(sf));
 223   }
 224
 225   @Test(groups = { "Functional" })
 226   public void testGetColor_aboveBelowThreshold()
 227   {
 228     // gradient from [50, 150] from WHITE(255, 255, 255) to BLACK(0, 0, 0)
 229     FeatureColour fc = new FeatureColour(null, Color.WHITE, Color.BLACK,
 230             Color.white, 50f, 150f);
 231     SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 70f,
 232             null);
 233
 234     /*
 235      * feature with score of Float.NaN is always assigned minimum colour
 236      */
 237     SequenceFeature sf2 = new SequenceFeature("type", "desc", 0, 20,
 238             Float.NaN, null);
 239
 240     fc.setThreshold(100f); // ignore for now
 241     assertEquals(new Color(204, 204, 204), fc.getColor(sf));
 242     assertEquals(Color.white, fc.getColor(sf2));
 243
 244     fc.setAboveThreshold(true); // feature lies below threshold
 245     assertNull(fc.getColor(sf));
 246     assertEquals(Color.white, fc.getColor(sf2));
 247
 248     fc.setBelowThreshold(true);
 249     fc.setThreshold(70f);
 250     assertNull(fc.getColor(sf)); // feature score == threshold - hidden
 251     assertEquals(Color.white, fc.getColor(sf2));
 252     fc.setThreshold(69f);
 253     assertNull(fc.getColor(sf)); // feature score > threshold - hidden
 254     assertEquals(Color.white, fc.getColor(sf2));
 255   }
 256
 257   /**
 258    * Test output of feature colours to Jalview features file format
 259    */
 260   @Test(groups = { "Functional" })
 261   public void testToJalviewFormat()
 262   {
 263     /*
 264      * plain colour - to RGB hex code
 265      */
 266     FeatureColour fc = new FeatureColour(Color.RED);
 267     String redHex = Format.getHexString(Color.RED);
 268     String hexColour = redHex;
 269     assertEquals("domain\t" + hexColour, fc.toJalviewFormat("domain"));
 270
 271     /*
 272      * colour by label (no threshold)
 273      */
 274     fc = new FeatureColour();
 275     fc.setColourByLabel(true);
 276     assertEquals("domain\tlabel", fc.toJalviewFormat("domain"));
 277
 278     /*
 279      * colour by attribute text (no threshold)
 280      */
 281     fc = new FeatureColour();
 282     fc.setColourByLabel(true);
 283     fc.setAttributeName("CLIN_SIG");
 284     assertEquals("domain\tattribute|CLIN_SIG",
 285             fc.toJalviewFormat("domain"));
 286
 287     /*
 288      * colour by label (autoscaled) (an odd state you can reach by selecting
 289      * 'above threshold', then deselecting 'threshold is min/max' then 'colour
 290      * by label')
 291      */
 292     fc.setAttributeName((String[]) null);
 293     fc.setAutoScaled(true);
 294     assertEquals("domain\tlabel", fc.toJalviewFormat("domain"));
 295
 296     /*
 297      * colour by label (above threshold)
 298      */
 299     fc.setAutoScaled(false);
 300     fc.setThreshold(12.5f);
 301     fc.setAboveThreshold(true);
 302     // min/max values are output though not used by this scheme
 303     assertEquals("domain\tlabel|||0.0|0.0|above|12.5",
 304             fc.toJalviewFormat("domain"));
 305
 306     /*
 307      * colour by label (below threshold)
 308      */
 309     fc.setBelowThreshold(true);
 310     assertEquals("domain\tlabel|||0.0|0.0|below|12.5",
 311             fc.toJalviewFormat("domain"));
 312
 313     /*
 314      * colour by attributes text (below threshold)
 315      */
 316     fc.setBelowThreshold(true);
 317     fc.setAttributeName("CSQ", "Consequence");
 318     assertEquals("domain\tattribute|CSQ:Consequence|||0.0|0.0|below|12.5",
 319             fc.toJalviewFormat("domain"));
 320
 321     /*
 322      * graduated colour by score, no threshold
 323      * - default constructor sets noValueColor = minColor
 324      */
 325     fc = new FeatureColour(null, Color.GREEN, Color.RED, Color.GREEN, 12f,
 326             25f);
 327     String greenHex = Format.getHexString(Color.GREEN);
 328     String expected = String.format(
 329             "domain\tscore|%s|%s|noValueMin|abso|12.0|25.0|none", greenHex,
 330             redHex);
 331     assertEquals(expected, fc.toJalviewFormat("domain"));
 332
 333     /*
 334      * graduated colour by score, no threshold, no value gets min colour
 335      */
 336     fc = new FeatureColour(Color.RED, Color.GREEN, Color.RED, Color.GREEN,
 337             12f, 25f);
 338     expected = String.format(
 339             "domain\tscore|%s|%s|noValueMin|abso|12.0|25.0|none", greenHex,
 340             redHex);
 341     assertEquals(expected, fc.toJalviewFormat("domain"));
 342
 343     /*
 344      * graduated colour by score, no threshold, no value gets max colour
 345      */
 346     fc = new FeatureColour(Color.RED, Color.GREEN, Color.RED, Color.RED,
 347             12f, 25f);
 348     expected = String.format(
 349             "domain\tscore|%s|%s|noValueMax|abso|12.0|25.0|none", greenHex,
 350             redHex);
 351     assertEquals(expected, fc.toJalviewFormat("domain"));
 352
 353     /*
 354      * colour ranges over the actual score ranges (not min/max)
 355      */
 356     fc.setAutoScaled(true);
 357     expected = String.format(
 358             "domain\tscore|%s|%s|noValueMax|12.0|25.0|none", greenHex,
 359             redHex);
 360     assertEquals(expected, fc.toJalviewFormat("domain"));
 361
 362     /*
 363      * graduated colour by score, below threshold
 364      */
 365     fc.setThreshold(12.5f);
 366     fc.setBelowThreshold(true);
 367     expected = String.format(
 368             "domain\tscore|%s|%s|noValueMax|12.0|25.0|below|12.5", greenHex,
 369             redHex);
 370     assertEquals(expected, fc.toJalviewFormat("domain"));
 371
 372     /*
 373      * graduated colour by score, above threshold
 374      */
 375     fc.setThreshold(12.5f);
 376     fc.setAboveThreshold(true);
 377     fc.setAutoScaled(false);
 378     expected = String.format(
 379             "domain\tscore|%s|%s|noValueMax|abso|12.0|25.0|above|12.5",
 380             greenHex, redHex);
 381     assertEquals(expected, fc.toJalviewFormat("domain"));
 382
 383     /*
 384      * graduated colour by attribute, above threshold
 385      */
 386     fc.setAttributeName("CSQ", "AF");
 387     fc.setAboveThreshold(true);
 388     fc.setAutoScaled(false);
 389     expected = String.format(
 390             "domain\tattribute|CSQ:AF|%s|%s|noValueMax|abso|12.0|25.0|above|12.5",
 391             greenHex, redHex);
 392     assertEquals(expected, fc.toJalviewFormat("domain"));
 393   }
 394
 395   /**
 396    * Test parsing of feature colours from Jalview features file format
 397    */
 398   @Test(groups = { "Functional" })
 399   public void testParseJalviewFeatureColour()
 400   {
 401     /*
 402      * simple colour by name
 403      */
 404     FeatureColourI fc = FeatureColour.parseJalviewFeatureColour("red");
 405     assertTrue(fc.isSimpleColour());
 406     assertEquals(Color.RED, fc.getColour());
 407
 408     /*
 409      * simple colour by hex code
 410      */
 411     fc = FeatureColour
 412             .parseJalviewFeatureColour(Format.getHexString(Color.RED));
 413     assertTrue(fc.isSimpleColour());
 414     assertEquals(Color.RED, fc.getColour());
 415
 416     /*
 417      * simple colour by rgb triplet
 418      */
 419     fc = FeatureColour.parseJalviewFeatureColour("255,0,0");
 420     assertTrue(fc.isSimpleColour());
 421     assertEquals(Color.RED, fc.getColour());
 422
 423     /*
 424      * malformed colour
 425      */
 426     try
 427     {
 428       fc = FeatureColour.parseJalviewFeatureColour("oops");
 429       fail("expected exception");
 430     } catch (IllegalArgumentException e)
 431     {
 432       assertEquals("Invalid colour descriptor: oops", e.getMessage());
 433     }
 434
 435     /*
 436      * colour by label (no threshold)
 437      */
 438     fc = FeatureColour.parseJalviewFeatureColour("label");
 439     assertTrue(fc.isColourByLabel());
 440     assertFalse(fc.hasThreshold());
 441
 442     /*
 443      * colour by label (with threshold)
 444      */
 445     fc = FeatureColour
 446             .parseJalviewFeatureColour("label|||0.0|0.0|above|12.0");
 447     assertTrue(fc.isColourByLabel());
 448     assertTrue(fc.isAboveThreshold());
 449     assertEquals(12.0f, fc.getThreshold());
 450
 451     /*
 452      * colour by attribute text (no threshold)
 453      */
 454     fc = FeatureColour.parseJalviewFeatureColour("attribute|CLIN_SIG");
 455     assertTrue(fc.isColourByAttribute());
 456     assertTrue(fc.isColourByLabel());
 457     assertFalse(fc.hasThreshold());
 458     assertArrayEquals(new String[] { "CLIN_SIG" }, fc.getAttributeName());
 459
 460     /*
 461      * colour by attributes text (with score threshold)
 462      */
 463     fc = FeatureColour.parseJalviewFeatureColour(
 464             "attribute|CSQ:Consequence|||0.0|0.0|above|12.0");
 465     assertTrue(fc.isColourByLabel());
 466     assertTrue(fc.isColourByAttribute());
 467     assertArrayEquals(new String[] { "CSQ", "Consequence" },
 468             fc.getAttributeName());
 469     assertTrue(fc.isAboveThreshold());
 470     assertEquals(12.0f, fc.getThreshold());
 471
 472     /*
 473      * graduated colour by score (with colour names) (no threshold)
 474      */
 475     fc = FeatureColour.parseJalviewFeatureColour("red|green|10.0|20.0");
 476     assertTrue(fc.isGraduatedColour());
 477     assertFalse(fc.hasThreshold());
 478     assertEquals(Color.RED, fc.getMinColour());
 479     assertEquals(Color.GREEN, fc.getMaxColour());
 480     assertEquals(Color.RED, fc.getNoColour());
 481     assertEquals(10f, fc.getMin());
 482     assertEquals(20f, fc.getMax());
 483     assertTrue(fc.isAutoScaled());
 484
 485     /*
 486      * the same, with 'no value colour' specified as max
 487      */
 488     fc = FeatureColour
 489             .parseJalviewFeatureColour("red|green|novaluemax|10.0|20.0");
 490     assertEquals(Color.RED, fc.getMinColour());
 491     assertEquals(Color.GREEN, fc.getMaxColour());
 492     assertEquals(Color.GREEN, fc.getNoColour());
 493     assertEquals(10f, fc.getMin());
 494     assertEquals(20f, fc.getMax());
 495
 496     /*
 497      * the same, with 'no value colour' specified as min
 498      */
 499     fc = FeatureColour
 500             .parseJalviewFeatureColour("red|green|novalueMin|10.0|20.0");
 501     assertEquals(Color.RED, fc.getMinColour());
 502     assertEquals(Color.GREEN, fc.getMaxColour());
 503     assertEquals(Color.RED, fc.getNoColour());
 504     assertEquals(10f, fc.getMin());
 505     assertEquals(20f, fc.getMax());
 506
 507     /*
 508      * the same, with 'no value colour' specified as none
 509      */
 510     fc = FeatureColour
 511             .parseJalviewFeatureColour("red|green|novaluenone|10.0|20.0");
 512     assertEquals(Color.RED, fc.getMinColour());
 513     assertEquals(Color.GREEN, fc.getMaxColour());
 514     assertNull(fc.getNoColour());
 515     assertEquals(10f, fc.getMin());
 516     assertEquals(20f, fc.getMax());
 517
 518     /*
 519      * the same, with invalid 'no value colour'
 520      */
 521     try
 522     {
 523       fc = FeatureColour
 524               .parseJalviewFeatureColour("red|green|blue|10.0|20.0");
 525       fail("expected exception");
 526     } catch (IllegalArgumentException e)
 527     {
 528       assertEquals(
 529               "Couldn't parse the minimum value for graduated colour ('blue')",
 530               e.getMessage());
 531     }
 532
 533     /*
 534      * graduated colour (explicitly by 'score') (no threshold)
 535      */
 536     fc = FeatureColour
 537             .parseJalviewFeatureColour("Score|red|green|10.0|20.0");
 538     assertTrue(fc.isGraduatedColour());
 539     assertFalse(fc.hasThreshold());
 540     assertEquals(Color.RED, fc.getMinColour());
 541     assertEquals(Color.GREEN, fc.getMaxColour());
 542     assertEquals(10f, fc.getMin());
 543     assertEquals(20f, fc.getMax());
 544     assertTrue(fc.isAutoScaled());
 545
 546     /*
 547      * graduated colour by attribute (no threshold)
 548      */
 549     fc = FeatureColour
 550             .parseJalviewFeatureColour("attribute|AF|red|green|10.0|20.0");
 551     assertTrue(fc.isGraduatedColour());
 552     assertTrue(fc.isColourByAttribute());
 553     assertArrayEquals(new String[] { "AF" }, fc.getAttributeName());
 554     assertFalse(fc.hasThreshold());
 555     assertEquals(Color.RED, fc.getMinColour());
 556     assertEquals(Color.GREEN, fc.getMaxColour());
 557     assertEquals(10f, fc.getMin());
 558     assertEquals(20f, fc.getMax());
 559     assertTrue(fc.isAutoScaled());
 560
 561     /*
 562      * graduated colour by score (colours by hex code) (above threshold)
 563      */
 564     String descriptor = String.format("%s|%s|10.0|20.0|above|15",
 565             Format.getHexString(Color.RED),
 566             Format.getHexString(Color.GREEN));
 567     fc = FeatureColour.parseJalviewFeatureColour(descriptor);
 568     assertTrue(fc.isGraduatedColour());
 569     assertTrue(fc.hasThreshold());
 570     assertTrue(fc.isAboveThreshold());
 571     assertEquals(15f, fc.getThreshold());
 572     assertEquals(Color.RED, fc.getMinColour());
 573     assertEquals(Color.GREEN, fc.getMaxColour());
 574     assertEquals(10f, fc.getMin());
 575     assertEquals(20f, fc.getMax());
 576     assertTrue(fc.isAutoScaled());
 577
 578     /*
 579      * graduated colour by attributes (below threshold)
 580      */
 581     fc = FeatureColour.parseJalviewFeatureColour(
 582             "attribute|CSQ:AF|red|green|10.0|20.0|below|13");
 583     assertTrue(fc.isGraduatedColour());
 584     assertTrue(fc.isColourByAttribute());
 585     assertArrayEquals(new String[] { "CSQ", "AF" }, fc.getAttributeName());
 586     assertTrue(fc.hasThreshold());
 587     assertTrue(fc.isBelowThreshold());
 588     assertEquals(13f, fc.getThreshold());
 589     assertEquals(Color.RED, fc.getMinColour());
 590     assertEquals(Color.GREEN, fc.getMaxColour());
 591     assertEquals(10f, fc.getMin());
 592     assertEquals(20f, fc.getMax());
 593     assertTrue(fc.isAutoScaled());
 594
 595     /*
 596      * graduated colour (by RGB triplet) (below threshold), absolute scale
 597      */
 598     descriptor = "255,0,0|0,255,0|abso|10.0|20.0|below|15";
 599     fc = FeatureColour.parseJalviewFeatureColour(descriptor);
 600     assertTrue(fc.isGraduatedColour());
 601     assertFalse(fc.isAutoScaled());
 602     assertTrue(fc.hasThreshold());
 603     assertTrue(fc.isBelowThreshold());
 604     assertEquals(15f, fc.getThreshold());
 605     assertEquals(Color.RED, fc.getMinColour());
 606     assertEquals(Color.GREEN, fc.getMaxColour());
 607     assertEquals(10f, fc.getMin());
 608     assertEquals(20f, fc.getMax());
 609
 610     descriptor = "blue|255,0,255|absolute|20.0|95.0|below|66.0";
 611     fc = FeatureColour.parseJalviewFeatureColour(descriptor);
 612     assertTrue(fc.isGraduatedColour());
 613   }
 614
 615   @Test(groups = { "Functional" })
 616   public void testGetColor_colourByAttributeText()
 617   {
 618     FeatureColour fc = new FeatureColour();
 619     fc.setColourByLabel(true);
 620     fc.setAttributeName("consequence");
 621     SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 1f,
 622             null);
 623
 624     /*
 625      * if feature has no such attribute, use 'no value' colour
 626      */
 627     assertEquals(FeatureColour.DEFAULT_NO_COLOUR, fc.getColor(sf));
 628
 629     /*
 630      * if feature has attribute, generate colour from value
 631      */
 632     sf.setValue("consequence", "benign");
 633     Color expected = ColorUtils.createColourFromName("benign");
 634     assertEquals(expected, fc.getColor(sf));
 635   }
 636
 637   @Test(groups = { "Functional" })
 638   public void testGetColor_GraduatedByAttributeValue()
 639   {
 640     /*
 641      * graduated colour based on attribute value for AF
 642      * given a min-max range of 0-100
 643      */
 644     FeatureColour fc = new FeatureColour(Color.white,
 645             new Color(50, 100, 150), new Color(150, 200, 250), Color.yellow,
 646             0f, 100f);
 647     String attName = "AF";
 648     fc.setAttributeName(attName);
 649
 650     /*
 651      * first case: feature lacks the attribute - use 'no value' colour
 652      */
 653     SequenceFeature sf = new SequenceFeature("type", "desc", 0, 20, 75f,
 654             null);
 655     assertEquals(Color.yellow, fc.getColor(sf));
 656
 657     /*
 658      * second case: attribute present but not numeric - treat as if absent
 659      */
 660     sf.setValue(attName, "twelve");
 661     assertEquals(Color.yellow, fc.getColor(sf));
 662
 663     /*
 664      * third case: valid attribute value
 665      */
 666     sf.setValue(attName, "20.0");
 667     Color expected = new Color(70, 120, 170);
 668     assertEquals(expected, fc.getColor(sf));
 669   }
 670
 671   @Test(groups = { "Functional" })
 672   public void testIsOutwithThreshold()
 673   {
 674     FeatureColourI fc = new FeatureColour(Color.red);
 675     SequenceFeature sf = new SequenceFeature("METAL", "desc", 10, 12, 1.2f,
 676             "grp");
 677     assertFalse(fc.isOutwithThreshold(null));
 678     assertFalse(fc.isOutwithThreshold(sf));
 679
 680     fc = new FeatureColour(null, Color.white, Color.black, Color.green, 0f,
 681             10f);
 682     assertFalse(fc.isOutwithThreshold(sf)); // no threshold
 683
 684     fc.setAboveThreshold(true);
 685     fc.setThreshold(1f);
 686     assertFalse(fc.isOutwithThreshold(sf)); // feature score 1.2 is above 1
 687
 688     fc.setThreshold(2f);
 689     assertTrue(fc.isOutwithThreshold(sf)); // feature score 1.2 is not above 2
 690
 691     fc.setBelowThreshold(true);
 692     assertFalse(fc.isOutwithThreshold(sf)); // feature score 1.2 is below 2
 693
 694     fc.setThreshold(1f);
 695     assertTrue(fc.isOutwithThreshold(sf)); // feature score 1.2 is not below 1
 696
 697     /*
 698      * with attribute value threshold
 699      */
 700     fc.setAttributeName("AC");
 701     assertFalse(fc.isOutwithThreshold(sf)); // missing attribute AC is ignored
 702
 703     sf.setValue("AC", "-1");
 704     assertFalse(fc.isOutwithThreshold(sf)); // value -1 is below 1
 705
 706     sf.setValue("AC", "1");
 707     assertTrue(fc.isOutwithThreshold(sf)); // value 1 is not below 1
 708
 709     sf.setValue("AC", "junk");
 710     assertFalse(fc.isOutwithThreshold(sf)); // bad value is ignored
 711   }
 712
 713   /**
 714    * Test description of feature colour suitable for a tooltip
 715    */
 716   @Test(groups = { "Functional" })
 717   public void testGetDescription()
 718   {
 719     /*
 720      * plain colour
 721      */
 722     FeatureColour fc = new FeatureColour(Color.RED);
 723     assertEquals(
 724             String.format("r=%d,g=%d,b=%d", Color.RED.getRed(),
 725                     Color.red.getGreen(), Color.red.getBlue()),
 726             fc.getDescription());
 727
 728     /*
 729      * colour by label (no threshold)
 730      */
 731     fc = new FeatureColour();
 732     fc.setColourByLabel(true);
 733     assertEquals("By Label", fc.getDescription());
 734
 735     /*
 736      * colour by attribute text (no threshold)
 737      */
 738     fc = new FeatureColour();
 739     fc.setColourByLabel(true);
 740     fc.setAttributeName("CLIN_SIG");
 741     assertEquals("By CLIN_SIG", fc.getDescription());
 742
 743     /*
 744      * colour by label (above score threshold)
 745      */
 746     fc = new FeatureColour();
 747     fc.setColourByLabel(true);
 748     fc.setAutoScaled(false);
 749     fc.setThreshold(12.5f);
 750     fc.setAboveThreshold(true);
 751     assertEquals("By Label (Score > 12.5)", fc.getDescription());
 752
 753     /*
 754      * colour by label (below score threshold)
 755      */
 756     fc.setBelowThreshold(true);
 757     assertEquals("By Label (Score < 12.5)", fc.getDescription());
 758
 759     /*
 760      * colour by attributes text (below score threshold)
 761      */
 762     fc.setBelowThreshold(true);
 763     fc.setAttributeName("CSQ", "Consequence");
 764     assertEquals("By CSQ:Consequence (Score < 12.5)", fc.getDescription());
 765
 766     /*
 767      * graduated colour by score, no threshold
 768      */
 769     fc = new FeatureColour(null, Color.GREEN, Color.RED, null, 12f, 25f);
 770     assertEquals("By Score", fc.getDescription());
 771
 772     /*
 773      * graduated colour by score, below threshold
 774      */
 775     fc.setThreshold(12.5f);
 776     fc.setBelowThreshold(true);
 777     assertEquals("By Score (< 12.5)", fc.getDescription());
 778
 779     /*
 780      * graduated colour by score, above threshold
 781      */
 782     fc.setThreshold(12.5f);
 783     fc.setAboveThreshold(true);
 784     fc.setAutoScaled(false);
 785     assertEquals("By Score (> 12.5)", fc.getDescription());
 786
 787     /*
 788      * graduated colour by attribute, no threshold
 789      */
 790     fc.setAttributeName("CSQ", "AF");
 791     fc.setAboveThreshold(false);
 792     fc.setAutoScaled(false);
 793     assertEquals("By CSQ:AF", fc.getDescription());
 794
 795     /*
 796      * graduated colour by attribute, above threshold
 797      */
 798     fc.setAboveThreshold(true);
 799     fc.setAutoScaled(false);
 800     assertEquals("By CSQ:AF (> 12.5)", fc.getDescription());
 801   }
 802 }