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 java.awt.Color;
   8 import java.io.File;
   9 import java.io.IOException;
  10 import java.util.HashMap;
  11
  12 import org.testng.annotations.Test;
  13
  14 import jalview.api.FeatureColourI;
  15 import jalview.datamodel.SequenceFeature;
  16 import jalview.datamodel.SequenceI;
  17 import jalview.datamodel.features.FeatureMatcher;
  18 import jalview.datamodel.features.FeatureMatcherSet;
  19 import jalview.datamodel.features.FeatureMatcherSetI;
  20 import jalview.io.DataSourceType;
  21 import jalview.io.FileLoader;
  22 import jalview.schemes.FeatureColour;
  23 import jalview.schemes.FeatureColourTest;
  24 import jalview.util.matcher.Condition;
  25 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
  26
  27 public class FeatureSettingsTest
  28 {
  29   /**
  30    * Test a roundtrip of save and reload of feature colours and filters as XML
  31    *
  32    * @throws IOException
  33    */
  34   @Test(groups = "Functional")
  35   public void testSaveLoad() throws IOException
  36   {
  37     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
  38             ">Seq1\nACDEFGHIKLM", DataSourceType.PASTE);
  39     SequenceI seq1 = af.getViewport().getAlignment().getSequenceAt(0);
  40
  41     /*
  42      * add some features to the sequence
  43      */
  44     int score = 1;
  45     addFeatures(seq1, "type1", score++);
  46     addFeatures(seq1, "type2", score++);
  47     addFeatures(seq1, "type3", score++);
  48     addFeatures(seq1, "type4", score++);
  49     addFeatures(seq1, "type5", score++);
  50
  51     /*
  52      * set colour schemes for features
  53      */
  54     FeatureRendererModel fr = af.getFeatureRenderer();
  55
  56     // type1: red
  57     fr.setColour("type1", new FeatureColour(Color.red));
  58
  59     // type2: by label
  60     FeatureColourI byLabel = new FeatureColour();
  61     byLabel.setColourByLabel(true);
  62     fr.setColour("type2", byLabel);
  63
  64     // type3: by score above threshold
  65     FeatureColourI byScore = new FeatureColour(null, Color.BLACK,
  66             Color.BLUE, null, 1, 10);
  67     byScore.setAboveThreshold(true);
  68     byScore.setThreshold(2f);
  69     fr.setColour("type3", byScore);
  70
  71     // type4: by attribute AF
  72     FeatureColourI byAF = new FeatureColour();
  73     byAF.setColourByLabel(true);
  74     byAF.setAttributeName("AF");
  75     fr.setColour("type4", byAF);
  76
  77     // type5: by attribute CSQ:PolyPhen below threshold
  78     FeatureColourI byPolyPhen = new FeatureColour(null, Color.BLACK,
  79             Color.BLUE, null, 1, 10);
  80     byPolyPhen.setBelowThreshold(true);
  81     byPolyPhen.setThreshold(3f);
  82     byPolyPhen.setAttributeName("CSQ", "PolyPhen");
  83     fr.setColour("type5", byPolyPhen);
  84
  85     /*
  86      * set filters for feature types
  87      */
  88
  89     // filter type1 features by (label contains "x")
  90     FeatureMatcherSetI filterByX = new FeatureMatcherSet();
  91     filterByX.and(FeatureMatcher.byLabel(Condition.Contains, "x"));
  92     fr.setFeatureFilter("type1", filterByX);
  93
  94     // filter type2 features by (score <= 2.4 and score > 1.1)
  95     FeatureMatcherSetI filterByScore = new FeatureMatcherSet();
  96     filterByScore.and(FeatureMatcher.byScore(Condition.LE, "2.4"));
  97     filterByScore.and(FeatureMatcher.byScore(Condition.GT, "1.1"));
  98     fr.setFeatureFilter("type2", filterByScore);
  99
 100     // filter type3 features by (AF contains X OR CSQ:PolyPhen != 0)
 101     FeatureMatcherSetI filterByXY = new FeatureMatcherSet();
 102     filterByXY
 103             .and(FeatureMatcher.byAttribute(Condition.Contains, "X", "AF"));
 104     filterByXY.or(FeatureMatcher.byAttribute(Condition.NE, "0", "CSQ",
 105             "PolyPhen"));
 106     fr.setFeatureFilter("type3", filterByXY);
 107
 108     /*
 109      * save colours and filters to an XML file
 110      */
 111     File coloursFile = File.createTempFile("testSaveLoad", ".fc");
 112     coloursFile.deleteOnExit();
 113     FeatureSettings fs = new FeatureSettings(af);
 114     fs.save(coloursFile);
 115
 116     /*
 117      * change feature colours and filters
 118      */
 119     FeatureColourI pink = new FeatureColour(Color.pink);
 120     fr.setColour("type1", pink);
 121     fr.setColour("type2", pink);
 122     fr.setColour("type3", pink);
 123     fr.setColour("type4", pink);
 124     fr.setColour("type5", pink);
 125
 126     FeatureMatcherSetI filter2 = new FeatureMatcherSet();
 127     filter2.and(FeatureMatcher.byLabel(Condition.NotContains, "y"));
 128     fr.setFeatureFilter("type1", filter2);
 129     fr.setFeatureFilter("type2", filter2);
 130     fr.setFeatureFilter("type3", filter2);
 131     fr.setFeatureFilter("type4", filter2);
 132     fr.setFeatureFilter("type5", filter2);
 133
 134     /*
 135      * reload colours and filters from file and verify they are restored
 136      */
 137     fs.load(coloursFile);
 138     FeatureColourI fc = fr.getFeatureStyle("type1");
 139     assertTrue(fc.isSimpleColour());
 140     assertEquals(fc.getColour(), Color.red);
 141     fc = fr.getFeatureStyle("type2");
 142     assertTrue(fc.isColourByLabel());
 143     fc = fr.getFeatureStyle("type3");
 144     assertTrue(fc.isGraduatedColour());
 145     assertNull(fc.getAttributeName());
 146     assertTrue(fc.isAboveThreshold());
 147     assertEquals(fc.getThreshold(), 2f);
 148     fc = fr.getFeatureStyle("type4");
 149     assertTrue(fc.isColourByLabel());
 150     assertTrue(fc.isColourByAttribute());
 151     assertEquals(fc.getAttributeName(), new String[] { "AF" });
 152     fc = fr.getFeatureStyle("type5");
 153     assertTrue(fc.isGraduatedColour());
 154     assertTrue(fc.isColourByAttribute());
 155     assertEquals(fc.getAttributeName(), new String[] { "CSQ", "PolyPhen" });
 156     assertTrue(fc.isBelowThreshold());
 157     assertEquals(fc.getThreshold(), 3f);
 158
 159     assertEquals(fr.getFeatureFilter("type1").toStableString(), "Label Contains x");
 160     assertEquals(fr.getFeatureFilter("type2").toStableString(),
 161             "(Score LE 2.4) AND (Score GT 1.1)");
 162     assertEquals(fr.getFeatureFilter("type3").toStableString(),
 163             "(AF Contains X) OR (CSQ:PolyPhen NE 0)");
 164   }
 165
 166   /**
 167    * Adds two features of the given type to the given sequence, also setting the
 168    * score as the value of attribute "AF" and sub-attribute "CSQ:PolyPhen"
 169    *
 170    * @param seq
 171    * @param featureType
 172    * @param score
 173    */
 174   private void addFeatures(SequenceI seq, String featureType, int score)
 175   {
 176     addFeature(seq, featureType, score++);
 177     addFeature(seq, featureType, score);
 178   }
 179
 180   private void addFeature(SequenceI seq, String featureType, int score)
 181   {
 182     SequenceFeature sf = new SequenceFeature(featureType, "desc", 1, 2,
 183             score, "grp");
 184     sf.setValue("AF", score);
 185     sf.setValue("CSQ", new HashMap<String, String>()
 186     {
 187       {
 188         put("PolyPhen", Integer.toString(score));
 189       }
 190     });
 191     seq.addSequenceFeature(sf);
 192   }
 193
 194   /**
 195    * @see FeatureColourTest#testGetDescription()
 196    * @throws IOException
 197    */
 198   @Test(groups = "Functional")
 199   public void testGetColorTooltip() throws IOException
 200   {
 201     assertNull(FeatureSettings.getColorTooltip(null, false));
 202
 203     /*
 204      * simple colour
 205      */
 206     FeatureColourI fc = new FeatureColour(Color.black);
 207     String simpleTooltip = "Click to edit, right-click for menu";
 208     assertEquals(FeatureSettings.getColorTooltip(fc, true), simpleTooltip);
 209     assertNull(FeatureSettings.getColorTooltip(fc, false));
 210
 211     /*
 212      * graduated colour tooltip includes description of colour
 213      */
 214     fc.setColourByLabel(true);
 215     assertEquals(FeatureSettings.getColorTooltip(fc, false),
 216             "<html>By Label</html>");
 217     assertEquals(FeatureSettings.getColorTooltip(fc, true),
 218             "<html>By Label<br>" + simpleTooltip + "</br></html>");
 219
 220     /*
 221      * graduated colour with threshold is html-encoded
 222      */
 223     fc = new FeatureColour(null, Color.red, Color.blue, null, 2f, 10f);
 224     fc.setBelowThreshold(true);
 225     fc.setThreshold(4f);
 226     assertEquals(FeatureSettings.getColorTooltip(fc, false),
 227             "<html>By Score (&lt; 4.0)</html>");
 228     assertEquals(FeatureSettings.getColorTooltip(fc, true),
 229             "<html>By Score (&lt; 4.0)<br>" + simpleTooltip
 230                     + "</br></html>");
 231
 232     fc.setAboveThreshold(true);
 233     assertEquals(FeatureSettings.getColorTooltip(fc, false),
 234             "<html>By Score (&gt; 4.0)</html>");
 235     assertEquals(FeatureSettings.getColorTooltip(fc, true),
 236             "<html>By Score (&gt; 4.0)<br>" + simpleTooltip
 237                     + "</br></html>");
 238   }
 239 }