test/jalview/gui/FeatureSettingsTest.java

   1 package jalview.gui;
   2
   3 import static org.testng.Assert.assertEquals;
   4 import static org.testng.Assert.assertNull;
   5 import static org.testng.Assert.assertTrue;
   6
   7 import jalview.api.FeatureColourI;
   8 import jalview.datamodel.SequenceFeature;
   9 import jalview.datamodel.SequenceI;
  10 import jalview.datamodel.features.FeatureMatcher;
  11 import jalview.datamodel.features.FeatureMatcherSet;
  12 import jalview.datamodel.features.FeatureMatcherSetI;
  13 import jalview.io.DataSourceType;
  14 import jalview.io.FileLoader;
  15 import jalview.schemes.FeatureColour;
  16 import jalview.util.matcher.Condition;
  17
  18 import java.awt.Color;
  19 import java.io.File;
  20 import java.io.IOException;
  21 import java.util.HashMap;
  22
  23 import org.testng.annotations.Test;
  24
  25 public class FeatureSettingsTest
  26 {
  27   /**
  28    * Test a roundtrip of save and reload of feature colours and filters as XML
  29    *
  30    * @throws IOException
  31    */
  32   @Test(groups = "Functional")
  33   public void testSaveLoad() throws IOException
  34   {
  35     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
  36             ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
  37     SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
  38
  39     /*
  40      * add some features to the sequence
  41      */
  42     int score = 1;
  43     addFeatures(seq1, "type1", score++);
  44     addFeatures(seq1, "type2", score++);
  45     addFeatures(seq1, "type3", score++);
  46     addFeatures(seq1, "type4", score++);
  47     addFeatures(seq1, "type5", score++);
  48
  49     /*
  50      * set colour schemes for features
  51      */
  52     FeatureRenderer fr = af.getFeatureRenderer();
  53
  54     // type1: red
  55     fr.setColour("type1", new FeatureColour(Color.red));
  56
  57     // type2: by label
  58     FeatureColourI byLabel = new FeatureColour();
  59     byLabel.setColourByLabel(true);
  60     fr.setColour("type2", byLabel);
  61
  62     // type3: by score above threshold
  63     FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
  64             Color.BLUE, null, 1, 10);
  65     byScore.setAboveThreshold(true);
  66     byScore.setThreshold(2f);
  67     fr.setColour("type3", byScore);
  68
  69     // type4: by attribute AF
  70     FeatureColourI byAF = new FeatureColour();
  71     byAF.setColourByLabel(true);
  72     byAF.setAttributeName("AF");
  73     fr.setColour("type4", byAF);
  74
  75     // type5: by attribute CSQ:PolyPhen below threshold
  76     FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
  77             Color.BLUE, null, 1, 10);
  78     byPolyPhen.setBelowThreshold(true);
  79     byPolyPhen.setThreshold(3f);
  80     byPolyPhen.setAttributeName("CSQ", "PolyPhen");
  81     fr.setColour("type5", byPolyPhen);
  82
  83     /*
  84      * set filters for feature types
  85      */
  86
  87     // filter type1 features by (label contains "x")
  88     FeatureMatcherSetI filterByX = new FeatureMatcherSet();
  89     filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
  90     fr.setFeatureFilter("type1", filterByX);
  91
  92     // filter type2 features by (score <= 2.4 and score > 1.1)
  93     FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
  94     filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
  95     filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
  96     fr.setFeatureFilter("type2", filterByScore);
  97
  98     // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
  99     FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
 100     filterByXY
 101             .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
 102     filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
 103             "PolyPhen"));
 104     fr.setFeatureFilter("type3", filterByXY);
 105
 106     /*
 107      * save colours and filters to an XML file
 108      */
 109     File coloursFile = File.createTempFile("testSaveLoad", ".fc");
 110     coloursFile.deleteOnExit();
 111     FeatureSettings fs = new FeatureSettings(af);
 112     fs.save(coloursFile);
 113
 114     /*
 115      * change feature colours and filters
 116      */
 117     FeatureColourI pink = new FeatureColour(Color.pink);
 118     fr.setColour("type1", pink);
 119     fr.setColour("type2", pink);
 120     fr.setColour("type3", pink);
 121     fr.setColour("type4", pink);
 122     fr.setColour("type5", pink);
 123
 124     FeatureMatcherSetI filter2 = new FeatureMatcherSet();
 125     filter2.and(FeatureMatcher.byLabel(Condition.NotContains, "y"));
 126     fr.setFeatureFilter("type1", filter2);
 127     fr.setFeatureFilter("type2", filter2);
 128     fr.setFeatureFilter("type3", filter2);
 129     fr.setFeatureFilter("type4", filter2);
 130     fr.setFeatureFilter("type5", filter2);
 131
 132     /*
 133      * reload colours and filters from file and verify they are restored
 134      */
 135     fs.load(coloursFile);
 136     FeatureColourI fc = fr.getFeatureStyle("type1");
 137     assertTrue(fc.isSimpleColour());
 138     assertEquals(fc.getColour(), Color.red);
 139     fc = fr.getFeatureStyle("type2");
 140     assertTrue(fc.isColourByLabel());
 141     fc = fr.getFeatureStyle("type3");
 142     assertTrue(fc.isGraduatedColour());
 143     assertNull(fc.getAttributeName());
 144     assertTrue(fc.isAboveThreshold());
 145     assertEquals(fc.getThreshold(), 2f);
 146     fc = fr.getFeatureStyle("type4");
 147     assertTrue(fc.isColourByLabel());
 148     assertTrue(fc.isColourByAttribute());
 149     assertEquals(fc.getAttributeName(), new String[] { "AF" });
 150     fc = fr.getFeatureStyle("type5");
 151     assertTrue(fc.isGraduatedColour());
 152     assertTrue(fc.isColourByAttribute());
 153     assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
 154     assertTrue(fc.isBelowThreshold());
 155     assertEquals(fc.getThreshold(), 3f);
 156
 157     assertEquals(fr.getFeatureFilter("type1").toStableString(), "Label Contains x");
 158     assertEquals(fr.getFeatureFilter("type2").toStableString(),
 159             "(Score LE 2.4) AND (Score GT 1.1)");
 160     assertEquals(fr.getFeatureFilter("type3").toStableString(),
 161             "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)");
 162   }
 163
 164   /**
 165    * Adds two features of the given type to the given sequence, also setting the
 166    * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
 167    *
 168    * @param seq
 169    * @param featureType
 170    * @param score
 171    */
 172   private void addFeatures(SequenceI seq, String featureType, int score)
 173   {
 174     addFeature(seq, featureType, score++);
 175     addFeature(seq, featureType, score);
 176   }
 177
 178   private void addFeature(SequenceI seq, String featureType, int score)
 179   {
 180     SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
 181             score, "grp");
 182     sf.setValue("AF", score);
 183     sf.setValue("CSQ", new HashMap<String, String>()
 184     {
 185       {
 186         put("PolyPhen", Integer.toString(score));
 187       }
 188     });
 189     seq.addSequenceFeature(sf);
 190   }
 191 }