+++ /dev/null
-package jalview.renderer;
-
-import static org.testng.AssertJUnit.assertEquals;
-import static org.testng.AssertJUnit.assertFalse;
-import static org.testng.AssertJUnit.assertTrue;
-
-import jalview.analysis.Conservation;
-import jalview.datamodel.Profile;
-import jalview.datamodel.ProfileI;
-import jalview.datamodel.Profiles;
-import jalview.datamodel.ProfilesI;
-import jalview.datamodel.ResidueCount;
-import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceI;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.PIDColourScheme;
-import jalview.schemes.ResidueProperties;
-import jalview.schemes.UserColourScheme;
-import jalview.schemes.ZappoColourScheme;
-
-import java.awt.Color;
-import java.util.Collections;
-
-import org.testng.annotations.Test;
-
-public class ResidueShaderTest
-{
-
- @Test(groups = "Functional")
- public void testAboveThreshold()
- {
- /*
- * make up profiles for this alignment:
- * AR-Q
- * AR--
- * SR-T
- * SR-T
- */
- ProfileI[] profiles = new ProfileI[4];
- profiles[0] = new Profile(4, 0, 2, "AS");
- profiles[1] = new Profile(4, 0, 4, "R");
- profiles[2] = new Profile(4, 4, 0, "");
- profiles[3] = new Profile(4, 1, 2, "T");
- ResidueShader ccs = new ResidueShader(new PIDColourScheme());
- ccs.setConsensus(new Profiles(profiles));
-
- /*
- * no threshold
- */
- ccs.setThreshold(0, true);
- assertTrue(ccs.aboveThreshold('a', 0));
- assertTrue(ccs.aboveThreshold('S', 0));
- assertTrue(ccs.aboveThreshold('W', 0));
- assertTrue(ccs.aboveThreshold('R', 1));
- assertTrue(ccs.aboveThreshold('W', 2));
- assertTrue(ccs.aboveThreshold('t', 3));
- assertTrue(ccs.aboveThreshold('Q', 3));
-
- /*
- * with threshold, include gaps
- */
- ccs.setThreshold(60, false);
- assertFalse(ccs.aboveThreshold('a', 0));
- assertFalse(ccs.aboveThreshold('S', 0));
- assertTrue(ccs.aboveThreshold('R', 1));
- assertFalse(ccs.aboveThreshold('W', 2));
- assertFalse(ccs.aboveThreshold('t', 3)); // 50% < 60%
-
- /*
- * with threshold, ignore gaps
- */
- ccs.setThreshold(60, true);
- assertFalse(ccs.aboveThreshold('a', 0));
- assertFalse(ccs.aboveThreshold('S', 0));
- assertTrue(ccs.aboveThreshold('R', 1));
- assertFalse(ccs.aboveThreshold('W', 2));
- assertTrue(ccs.aboveThreshold('t', 3)); // 67% > 60%
- }
-
- /**
- * Test colour bleaching based on conservation score and conservation slider.
- * Scores of 10 or 11 should leave colours unchanged. Gap is always white.
- */
- @Test(groups = "Functional")
- public void testApplyConservation()
- {
- ResidueShader ccs = new ResidueShader(new PIDColourScheme());
-
- // no conservation present - no fading
- assertEquals(Color.RED, ccs.applyConservation(Color.RED, 12));
-
- /*
- * stub Conservation to return a given consensus string
- */
- final String consSequence = "0123456789+*-";
- Conservation cons = new Conservation(null,
- Collections.<SequenceI> emptyList(), 0, 0)
- {
- @Override
- public SequenceI getConsSequence()
- {
- return new Sequence("seq", consSequence);
- }
- };
- ccs.setConservation(cons);
-
- // column out of range:
- assertEquals(Color.RED,
- ccs.applyConservation(Color.RED, consSequence.length()));
-
- /*
- * with 100% threshold, 'fade factor' is
- * (11-score)/10 * 100/20 = (11-score)/2
- * which is >= 1 for all scores i.e. all fade to white except +, *
- */
- ccs.setConservationInc(100);
- assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 0));
- assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 1));
- assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 2));
- assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 3));
- assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 4));
- assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 5));
- assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 6));
- assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 7));
- assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 8));
- assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 9));
- assertEquals(Color.RED, ccs.applyConservation(Color.RED, 10));
- assertEquals(Color.RED, ccs.applyConservation(Color.RED, 11));
- assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 12));
-
- /*
- * with 0% threshold, there should be no fading
- */
- ccs.setConservationInc(0);
- assertEquals(Color.RED, ccs.applyConservation(Color.RED, 0));
- assertEquals(Color.RED, ccs.applyConservation(Color.RED, 1));
- assertEquals(Color.RED, ccs.applyConservation(Color.RED, 2));
- assertEquals(Color.RED, ccs.applyConservation(Color.RED, 3));
- assertEquals(Color.RED, ccs.applyConservation(Color.RED, 4));
- assertEquals(Color.RED, ccs.applyConservation(Color.RED, 5));
- assertEquals(Color.RED, ccs.applyConservation(Color.RED, 6));
- assertEquals(Color.RED, ccs.applyConservation(Color.RED, 7));
- assertEquals(Color.RED, ccs.applyConservation(Color.RED, 8));
- assertEquals(Color.RED, ccs.applyConservation(Color.RED, 9));
- assertEquals(Color.RED, ccs.applyConservation(Color.RED, 10));
- assertEquals(Color.RED, ccs.applyConservation(Color.RED, 11));
- assertEquals(Color.WHITE, ccs.applyConservation(Color.RED, 12)); // gap
-
- /*
- * with 40% threshold, 'fade factor' is
- * (11-score)/10 * 40/20 = (11-score)/5
- * which is {>1, >1, >1, >1, >1, >1, 1, 0.8, 0.6, 0.4} for score 0-9
- * e.g. score 7 colour fades 80% of the way to white (255, 255, 255)
- */
- ccs.setConservationInc(40);
- Color colour = new Color(155, 105, 55);
- assertEquals(Color.WHITE, ccs.applyConservation(colour, 0));
- assertEquals(Color.WHITE, ccs.applyConservation(colour, 1));
- assertEquals(Color.WHITE, ccs.applyConservation(colour, 2));
- assertEquals(Color.WHITE, ccs.applyConservation(colour, 3));
- assertEquals(Color.WHITE, ccs.applyConservation(colour, 4));
- assertEquals(Color.WHITE, ccs.applyConservation(colour, 5));
- assertEquals(Color.WHITE, ccs.applyConservation(colour, 6));
- assertEquals(new Color(235, 225, 215), ccs.applyConservation(colour, 7));
- assertEquals(new Color(215, 195, 175), ccs.applyConservation(colour, 8));
- assertEquals(new Color(195, 165, 135), ccs.applyConservation(colour, 9));
- assertEquals(colour, ccs.applyConservation(colour, 10));
- assertEquals(colour, ccs.applyConservation(colour, 11));
- assertEquals(Color.WHITE, ccs.applyConservation(colour, 12));
- }
-
- @Test(groups = "Functional")
- public void testFindColour_gapColour()
- {
- /*
- * normally, a gap is coloured white
- */
- ResidueShader rs = new ResidueShader(new ZappoColourScheme());
- assertEquals(Color.white, rs.findColour(' ', 7, null));
-
- /*
- * a User Colour Scheme may specify a bespoke gap colour
- */
- Color[] colours = new Color[ResidueProperties.maxProteinIndex + 1];
- colours[5] = Color.blue; // Q colour
- colours[23] = Color.red; // gap colour
- ColourSchemeI cs = new UserColourScheme(colours);
- rs = new ResidueShader(cs);
-
- assertEquals(Color.red, rs.findColour(' ', 7, null));
- assertEquals(Color.blue, rs.findColour('Q', 7, null));
-
- /*
- * stub Conservation to return a given consensus string
- */
- final String consSequence = "0123456789+*-";
- Conservation cons = new Conservation(null,
- Collections.<SequenceI> emptyList(), 0, 0)
- {
- @Override
- public SequenceI getConsSequence()
- {
- return new Sequence("seq", consSequence);
- }
- };
- rs.setConservation(cons);
-
- /*
- * with 0% threshold, there should be no fading
- */
- rs.setConservationInc(0);
- assertEquals(Color.red, rs.findColour(' ', 7, null));
- assertEquals(Color.blue, rs.findColour('Q', 7, null));
-
- /*
- * with 40% threshold, 'fade factor' is
- * (11-score)/10 * 40/20 = (11-score)/5
- * so position 7, score 7 fades 80% of the way to white (255, 255, 255)
- */
- rs.setConservationInc(40);
-
- /*
- * gap colour is unchanged for Conservation
- */
- assertEquals(Color.red, rs.findColour(' ', 7, null));
- assertEquals(Color.red, rs.findColour('-', 7, null));
- assertEquals(Color.red, rs.findColour('.', 7, null));
-
- /*
- * residue colour is faded 80% of the way from
- * blue(0, 0, 255) to white(255, 255, 255)
- * making (204, 204, 255)
- */
- assertEquals(new Color(204, 204, 255), rs.findColour('Q', 7, null));
-
- /*
- * turn off By Conservation, apply Above Identity Threshold
- * providing a stub Consensus that has modal residue "Q" with pid 60%
- */
- rs.setConservationApplied(false);
- ProfilesI consensus = getStubConsensus("Q", 60f);
- rs.setConsensus(consensus);
-
- // with consensus pid (60) above threshold (50), colours are unchanged
- rs.setThreshold(50, false);
- assertEquals(Color.blue, rs.findColour('Q', 7, null));
- assertEquals(Color.red, rs.findColour('-', 7, null));
-
- // with consensus pid (60) below threshold (70),
- // residue colour becomes white, gap colour is unchanged
- rs.setThreshold(70, false);
- assertEquals(Color.white, rs.findColour('Q', 7, null));
- assertEquals(Color.red, rs.findColour('-', 7, null));
- }
-
- /**
- * @param modalResidue
- * @param pid
- * @return
- */
- protected ProfilesI getStubConsensus(final String modalResidue,
- final float pid)
- {
- ProfilesI consensus = new ProfilesI() {
-
- @Override
- public ProfileI get(int i)
- {
- return new ProfileI() {
- @Override
- public void setCounts(ResidueCount residueCounts)
- {
- }
-
- @Override
- public float getPercentageIdentity(boolean ignoreGaps)
- {
- return pid;
- }
-
- @Override
- public ResidueCount getCounts()
- {
- return null;
- }
-
- @Override
- public int getHeight()
- {
- return 0;
- }
-
- @Override
- public int getGapped()
- {
- return 0;
- }
-
- @Override
- public int getMaxCount()
- {
- return 0;
- }
-
- @Override
- public String getModalResidue()
- {
- return modalResidue;
- }
-
- @Override
- public int getNonGapped()
- {
- return 0;
- }};
- }
-
- @Override
- public int getStartColumn()
- {
- return 0;
- }
-
- @Override
- public int getEndColumn()
- {
- return 0;
- }
-
- };
- return consensus;
- }
-}
git://source.jalview.org / jalview.git / blobdiff