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.schemes.FeatureColourTest;
  17 import jalview.util.matcher.Condition;
  18
  19 import java.awt.Color;
  20 import java.io.File;
  21 import java.io.IOException;
  22 import java.util.HashMap;
  23
  24 import org.testng.annotations.Test;
  25
  26 public class FeatureSettingsTest
  27 {
  28   /**
  29    * Test a roundtrip of save and reload of feature colours and filters as XML
  30    *
  31    * @throws IOException
  32    */
  33   @Test(groups = "Functional")
  34   public void testSaveLoad() throws IOException
  35   {
  36     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
  37             ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
  38     SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
  39
  40     /*
  41      * add some features to the sequence
  42      */
  43     int score = 1;
  44     addFeatures(seq1, "type1", score++);
  45     addFeatures(seq1, "type2", score++);
  46     addFeatures(seq1, "type3", score++);
  47     addFeatures(seq1, "type4", score++);
  48     addFeatures(seq1, "type5", score++);
  49
  50     /*
  51      * set colour schemes for features
  52      */
  53     FeatureRenderer fr = af.getFeatureRenderer();
  54
  55     // type1: red
  56     fr.setColour("type1", new FeatureColour(Color.red));
  57
  58     // type2: by label
  59     FeatureColourI byLabel = new FeatureColour();
  60     byLabel.setColourByLabel(true);
  61     fr.setColour("type2", byLabel);
  62
  63     // type3: by score above threshold
  64     FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
  65             Color.BLUE, null, 1, 10);
  66     byScore.setAboveThreshold(true);
  67     byScore.setThreshold(2f);
  68     fr.setColour("type3", byScore);
  69
  70     // type4: by attribute AF
  71     FeatureColourI byAF = new FeatureColour();
  72     byAF.setColourByLabel(true);
  73     byAF.setAttributeName("AF");
  74     fr.setColour("type4", byAF);
  75
  76     // type5: by attribute CSQ:PolyPhen below threshold
  77     FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
  78             Color.BLUE, null, 1, 10);
  79     byPolyPhen.setBelowThreshold(true);
  80     byPolyPhen.setThreshold(3f);
  81     byPolyPhen.setAttributeName("CSQ", "PolyPhen");
  82     fr.setColour("type5", byPolyPhen);
  83
  84     /*
  85      * set filters for feature types
  86      */
  87
  88     // filter type1 features by (label contains "x")
  89     FeatureMatcherSetI filterByX = new FeatureMatcherSet();
  90     filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
  91     fr.setFeatureFilter("type1", filterByX);
  92
  93     // filter type2 features by (score <= 2.4 and score > 1.1)
  94     FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
  95     filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
  96     filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
  97     fr.setFeatureFilter("type2", filterByScore);
  98
  99     // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
 100     FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
 101     filterByXY
 102             .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
 103     filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
 104             "PolyPhen"));
 105     fr.setFeatureFilter("type3", filterByXY);
 106
 107     /*
 108      * save colours and filters to an XML file
 109      */
 110     File coloursFile = File.createTempFile("testSaveLoad", ".fc");
 111     coloursFile.deleteOnExit();
 112     FeatureSettings fs = new FeatureSettings(af);
 113     fs.save(coloursFile);
 114
 115     /*
 116      * change feature colours and filters
 117      */
 118     FeatureColourI pink = new FeatureColour(Color.pink);
 119     fr.setColour("type1", pink);
 120     fr.setColour("type2", pink);
 121     fr.setColour("type3", pink);
 122     fr.setColour("type4", pink);
 123     fr.setColour("type5", pink);
 124
 125     FeatureMatcherSetI filter2 = new FeatureMatcherSet();
 126     filter2.and(FeatureMatcher.byLabel(Condition.NotContains, "y"));
 127     fr.setFeatureFilter("type1", filter2);
 128     fr.setFeatureFilter("type2", filter2);
 129     fr.setFeatureFilter("type3", filter2);
 130     fr.setFeatureFilter("type4", filter2);
 131     fr.setFeatureFilter("type5", filter2);
 132
 133     /*
 134      * reload colours and filters from file and verify they are restored
 135      */
 136     fs.load(coloursFile);
 137     FeatureColourI fc = fr.getFeatureStyle("type1");
 138     assertTrue(fc.isSimpleColour());
 139     assertEquals(fc.getColour(), Color.red);
 140     fc = fr.getFeatureStyle("type2");
 141     assertTrue(fc.isColourByLabel());
 142     fc = fr.getFeatureStyle("type3");
 143     assertTrue(fc.isGraduatedColour());
 144     assertNull(fc.getAttributeName());
 145     assertTrue(fc.isAboveThreshold());
 146     assertEquals(fc.getThreshold(), 2f);
 147     fc = fr.getFeatureStyle("type4");
 148     assertTrue(fc.isColourByLabel());
 149     assertTrue(fc.isColourByAttribute());
 150     assertEquals(fc.getAttributeName(), new String[] { "AF" });
 151     fc = fr.getFeatureStyle("type5");
 152     assertTrue(fc.isGraduatedColour());
 153     assertTrue(fc.isColourByAttribute());
 154     assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
 155     assertTrue(fc.isBelowThreshold());
 156     assertEquals(fc.getThreshold(), 3f);
 157
 158     assertEquals(fr.getFeatureFilter("type1").toStableString(), "Label Contains x");
 159     assertEquals(fr.getFeatureFilter("type2").toStableString(),
 160             "(Score LE 2.4) AND (Score GT 1.1)");
 161     assertEquals(fr.getFeatureFilter("type3").toStableString(),
 162             "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)");
 163   }
 164
 165   /**
 166    * Adds two features of the given type to the given sequence, also setting the
 167    * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
 168    *
 169    * @param seq
 170    * @param featureType
 171    * @param score
 172    */
 173   private void addFeatures(SequenceI seq, String featureType, int score)
 174   {
 175     addFeature(seq, featureType, score++);
 176     addFeature(seq, featureType, score);
 177   }
 178
 179   private void addFeature(SequenceI seq, String featureType, int score)
 180   {
 181     SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
 182             score, "grp");
 183     sf.setValue("AF", score);
 184     sf.setValue("CSQ", new HashMap<String, String>()
 185     {
 186       {
 187         put("PolyPhen", Integer.toString(score));
 188       }
 189     });
 190     seq.addSequenceFeature(sf);
 191   }
 192
 193   /**
 194    * @see FeatureColourTest#testGetDescription()
 195    * @throws IOException
 196    */
 197   @Test(groups = "Functional")
 198   public void testGetColorTooltip() throws IOException
 199   {
 200     assertNull(FeatureSettings.getColorTooltip(null));
 201
 202     /*
 203      * simple colour
 204      */
 205     FeatureColourI fc = new FeatureColour(Color.black);
 206     String simpleTooltip = "Click to edit, right-click for menu";
 207     assertEquals(FeatureSettings.getColorTooltip(fc), simpleTooltip);
 208
 209     /*
 210      * graduated colour tooltip includes description of colour
 211      */
 212     fc.setColourByLabel(true);
 213     assertEquals(FeatureSettings.getColorTooltip(fc),
 214             "<html>By Label<br>" + simpleTooltip + "</br></html>");
 215
 216     /*
 217      * graduated colour with threshold is html-encoded
 218      */
 219     fc = new FeatureColour(null, Color.red, Color.blue, null, 2f, 10f);
 220     fc.setBelowThreshold(true);
 221     fc.setThreshold(4f);
 222     assertEquals(FeatureSettings.getColorTooltip(fc),
 223             "<html>By Score (&lt; 4.0)<br>" + simpleTooltip
 224                     + "</br></html>");
 225     fc.setAboveThreshold(true);
 226     assertEquals(FeatureSettings.getColorTooltip(fc),
 227             "<html>By Score (&gt; 4.0)<br>" + simpleTooltip
 228                     + "</br></html>");
 229   }
 230 }