+++ /dev/null
-package jalview.gui;
-
-import static org.testng.Assert.assertEquals;
-import static org.testng.Assert.assertNull;
-import static org.testng.Assert.assertTrue;
-
-import jalview.api.FeatureColourI;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.FeatureMatcher;
-import jalview.datamodel.features.FeatureMatcherSet;
-import jalview.datamodel.features.FeatureMatcherSetI;
-import jalview.io.DataSourceType;
-import jalview.io.FileLoader;
-import jalview.schemes.FeatureColour;
-import jalview.schemes.FeatureColourTest;
-import jalview.util.matcher.Condition;
-
-import java.awt.Color;
-import java.io.File;
-import java.io.IOException;
-import java.util.HashMap;
-
-import org.testng.annotations.Test;
-
-public class FeatureSettingsTest
-{
- /**
- * Test a roundtrip of save and reload of feature colours and filters as XML
- *
- * @throws IOException
- */
- @Test(groups = "Functional")
- public void testSaveLoad() throws IOException
- {
- AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
- ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
- SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
-
- /*
- * add some features to the sequence
- */
- int score = 1;
- addFeatures(seq1, "type1", score++);
- addFeatures(seq1, "type2", score++);
- addFeatures(seq1, "type3", score++);
- addFeatures(seq1, "type4", score++);
- addFeatures(seq1, "type5", score++);
-
- /*
- * set colour schemes for features
- */
- FeatureRenderer fr = af.getFeatureRenderer();
-
- // type1: red
- fr.setColour("type1", new FeatureColour(Color.red));
-
- // type2: by label
- FeatureColourI byLabel = new FeatureColour();
- byLabel.setColourByLabel(true);
- fr.setColour("type2", byLabel);
-
- // type3: by score above threshold
- FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
- Color.BLUE, null, 1, 10);
- byScore.setAboveThreshold(true);
- byScore.setThreshold(2f);
- fr.setColour("type3", byScore);
-
- // type4: by attribute AF
- FeatureColourI byAF = new FeatureColour();
- byAF.setColourByLabel(true);
- byAF.setAttributeName("AF");
- fr.setColour("type4", byAF);
-
- // type5: by attribute CSQ:PolyPhen below threshold
- FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
- Color.BLUE, null, 1, 10);
- byPolyPhen.setBelowThreshold(true);
- byPolyPhen.setThreshold(3f);
- byPolyPhen.setAttributeName("CSQ", "PolyPhen");
- fr.setColour("type5", byPolyPhen);
-
- /*
- * set filters for feature types
- */
-
- // filter type1 features by (label contains "x")
- FeatureMatcherSetI filterByX = new FeatureMatcherSet();
- filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
- fr.setFeatureFilter("type1", filterByX);
-
- // filter type2 features by (score <= 2.4 and score > 1.1)
- FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
- filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
- filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
- fr.setFeatureFilter("type2", filterByScore);
-
- // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
- FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
- filterByXY
- .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
- filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
- "PolyPhen"));
- fr.setFeatureFilter("type3", filterByXY);
-
- /*
- * save colours and filters to an XML file
- */
- File coloursFile = File.createTempFile("testSaveLoad", ".fc");
- coloursFile.deleteOnExit();
- FeatureSettings fs = new FeatureSettings(af);
- fs.save(coloursFile);
-
- /*
- * change feature colours and filters
- */
- FeatureColourI pink = new FeatureColour(Color.pink);
- fr.setColour("type1", pink);
- fr.setColour("type2", pink);
- fr.setColour("type3", pink);
- fr.setColour("type4", pink);
- fr.setColour("type5", pink);
-
- FeatureMatcherSetI filter2 = new FeatureMatcherSet();
- filter2.and(FeatureMatcher.byLabel(Condition.NotContains, "y"));
- fr.setFeatureFilter("type1", filter2);
- fr.setFeatureFilter("type2", filter2);
- fr.setFeatureFilter("type3", filter2);
- fr.setFeatureFilter("type4", filter2);
- fr.setFeatureFilter("type5", filter2);
-
- /*
- * reload colours and filters from file and verify they are restored
- */
- fs.load(coloursFile);
- FeatureColourI fc = fr.getFeatureStyle("type1");
- assertTrue(fc.isSimpleColour());
- assertEquals(fc.getColour(), Color.red);
- fc = fr.getFeatureStyle("type2");
- assertTrue(fc.isColourByLabel());
- fc = fr.getFeatureStyle("type3");
- assertTrue(fc.isGraduatedColour());
- assertNull(fc.getAttributeName());
- assertTrue(fc.isAboveThreshold());
- assertEquals(fc.getThreshold(), 2f);
- fc = fr.getFeatureStyle("type4");
- assertTrue(fc.isColourByLabel());
- assertTrue(fc.isColourByAttribute());
- assertEquals(fc.getAttributeName(), new String[] { "AF" });
- fc = fr.getFeatureStyle("type5");
- assertTrue(fc.isGraduatedColour());
- assertTrue(fc.isColourByAttribute());
- assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
- assertTrue(fc.isBelowThreshold());
- assertEquals(fc.getThreshold(), 3f);
-
- assertEquals(fr.getFeatureFilter("type1").toStableString(), "Label Contains x");
- assertEquals(fr.getFeatureFilter("type2").toStableString(),
- "(Score LE 2.4) AND (Score GT 1.1)");
- assertEquals(fr.getFeatureFilter("type3").toStableString(),
- "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)");
- }
-
- /**
- * Adds two features of the given type to the given sequence, also setting the
- * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
- *
- * @param seq
- * @param featureType
- * @param score
- */
- private void addFeatures(SequenceI seq, String featureType, int score)
- {
- addFeature(seq, featureType, score++);
- addFeature(seq, featureType, score);
- }
-
- private void addFeature(SequenceI seq, String featureType, int score)
- {
- SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
- score, "grp");
- sf.setValue("AF", score);
- sf.setValue("CSQ", new HashMap<String, String>()
- {
- {
- put("PolyPhen", Integer.toString(score));
- }
- });
- seq.addSequenceFeature(sf);
- }
-
- /**
- * @see FeatureColourTest#testGetDescription()
- * @throws IOException
- */
- @Test(groups = "Functional")
- public void testGetColorTooltip() throws IOException
- {
- assertNull(FeatureSettings.getColorTooltip(null, false));
-
- /*
- * simple colour
- */
- FeatureColourI fc = new FeatureColour(Color.black);
- String simpleTooltip = "Click to edit, right-click for menu";
- assertEquals(FeatureSettings.getColorTooltip(fc, true), simpleTooltip);
- assertNull(FeatureSettings.getColorTooltip(fc, false));
-
- /*
- * graduated colour tooltip includes description of colour
- */
- fc.setColourByLabel(true);
- assertEquals(FeatureSettings.getColorTooltip(fc, false),
- "<html>By Label</html>");
- assertEquals(FeatureSettings.getColorTooltip(fc, true),
- "<html>By Label<br>" + simpleTooltip + "</br></html>");
-
- /*
- * graduated colour with threshold is html-encoded
- */
- fc = new FeatureColour(null, Color.red, Color.blue, null, 2f, 10f);
- fc.setBelowThreshold(true);
- fc.setThreshold(4f);
- assertEquals(FeatureSettings.getColorTooltip(fc, false),
- "<html>By Score (< 4.0)</html>");
- assertEquals(FeatureSettings.getColorTooltip(fc, true),
- "<html>By Score (< 4.0)<br>" + simpleTooltip
- + "</br></html>");
-
- fc.setAboveThreshold(true);
- assertEquals(FeatureSettings.getColorTooltip(fc, false),
- "<html>By Score (> 4.0)</html>");
- assertEquals(FeatureSettings.getColorTooltip(fc, true),
- "<html>By Score (> 4.0)<br>" + simpleTooltip
- + "</br></html>");
- }
-}
git://source.jalview.org / jalview.git / blobdiff