test/jalview/renderer/seqfeatures/FeatureRendererTest.java

   1 package jalview.renderer.seqfeatures;
   2
   3 import static org.testng.Assert.assertEquals;
   4 import static org.testng.Assert.assertFalse;
   5 import static org.testng.Assert.assertTrue;
   6
   7 import jalview.api.AlignViewportI;
   8 import jalview.api.FeatureColourI;
   9 import jalview.datamodel.SequenceFeature;
  10 import jalview.datamodel.SequenceI;
  11 import jalview.gui.AlignFrame;
  12 import jalview.io.DataSourceType;
  13 import jalview.io.FileLoader;
  14 import jalview.schemes.FeatureColour;
  15
  16 import java.awt.Color;
  17 import java.util.ArrayList;
  18 import java.util.Arrays;
  19 import java.util.List;
  20 import java.util.Map;
  21
  22 import org.testng.annotations.Test;
  23
  24 public class FeatureRendererTest
  25 {
  26
  27   @Test(groups = "Functional")
  28   public void testFindAllFeatures()
  29   {
  30     String seqData = ">s1\nabcdef\n>s2\nabcdef\n>s3\nabcdef\n>s4\nabcdef\n";
  31     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
  32             DataSourceType.PASTE);
  33     AlignViewportI av = af.getViewport();
  34     FeatureRenderer fr = new FeatureRenderer(av);
  35
  36     /*
  37      * with no features
  38      */
  39     fr.findAllFeatures(true);
  40     assertTrue(fr.getRenderOrder().isEmpty());
  41     assertTrue(fr.getFeatureGroups().isEmpty());
  42
  43     List<SequenceI> seqs = av.getAlignment().getSequences();
  44
  45     // add a non-positional feature - should be ignored by FeatureRenderer
  46     SequenceFeature sf1 = new SequenceFeature("Type", "Desc", 0, 0, 1f,
  47             "Group");
  48     seqs.get(0).addSequenceFeature(sf1);
  49     fr.findAllFeatures(true);
  50     // ? bug - types and groups added for non-positional features
  51     List<String> types = fr.getRenderOrder();
  52     List<String> groups = fr.getFeatureGroups();
  53     assertEquals(types.size(), 0);
  54     assertFalse(types.contains("Type"));
  55     assertEquals(groups.size(), 0);
  56     assertFalse(groups.contains("Group"));
  57
  58     // add some positional features
  59     seqs.get(1).addSequenceFeature(
  60             new SequenceFeature("Pfam", "Desc", 5, 9, 1f, "PfamGroup"));
  61     seqs.get(2).addSequenceFeature(
  62             new SequenceFeature("Pfam", "Desc", 14, 22, 2f, "RfamGroup"));
  63     // bug in findAllFeatures - group not checked for a known feature type
  64     seqs.get(2).addSequenceFeature(
  65             new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN,
  66                     "RfamGroup"));
  67     // existing feature type with null group
  68     seqs.get(3).addSequenceFeature(
  69             new SequenceFeature("Rfam", "Desc", 5, 9, Float.NaN, null));
  70     // new feature type with null group
  71     seqs.get(3).addSequenceFeature(
  72             new SequenceFeature("Scop", "Desc", 5, 9, Float.NaN, null));
  73     // null value for type produces NullPointerException
  74     fr.findAllFeatures(true);
  75     types = fr.getRenderOrder();
  76     groups = fr.getFeatureGroups();
  77     assertEquals(types.size(), 3);
  78     assertFalse(types.contains("Type"));
  79     assertTrue(types.contains("Pfam"));
  80     assertTrue(types.contains("Rfam"));
  81     assertTrue(types.contains("Scop"));
  82     assertEquals(groups.size(), 2);
  83     assertFalse(groups.contains("Group"));
  84     assertTrue(groups.contains("PfamGroup"));
  85     assertTrue(groups.contains("RfamGroup"));
  86     assertFalse(groups.contains(null)); // null group is ignored
  87
  88     /*
  89      * check min-max values
  90      */
  91     Map<String, float[][]> minMax = fr.getMinMax();
  92     assertEquals(minMax.size(), 1); // non-positional and NaN not stored
  93     assertEquals(minMax.get("Pfam")[0][0], 1f); // positional min
  94     assertEquals(minMax.get("Pfam")[0][1], 2f); // positional max
  95
  96     // increase max for Pfam, add scores for Rfam
  97     seqs.get(0).addSequenceFeature(
  98             new SequenceFeature("Pfam", "Desc", 14, 22, 8f, "RfamGroup"));
  99     seqs.get(1).addSequenceFeature(
 100             new SequenceFeature("Rfam", "Desc", 5, 9, 6f, "RfamGroup"));
 101     fr.findAllFeatures(true);
 102     // note minMax is not a defensive copy, shouldn't expose this
 103     assertEquals(minMax.size(), 2);
 104     assertEquals(minMax.get("Pfam")[0][0], 1f);
 105     assertEquals(minMax.get("Pfam")[0][1], 8f);
 106     assertEquals(minMax.get("Rfam")[0][0], 6f);
 107     assertEquals(minMax.get("Rfam")[0][1], 6f);
 108
 109     /*
 110      * check render order (last is on top)
 111      */
 112     List<String> renderOrder = fr.getRenderOrder();
 113     assertEquals(renderOrder, Arrays.asList("Scop", "Rfam", "Pfam"));
 114
 115     /*
 116      * change render order (todo: an easier way)
 117      * nb here last comes first in the data array
 118      */
 119     Object[][] data = new Object[3][];
 120     FeatureColourI colour = new FeatureColour(Color.RED);
 121     data[0] = new Object[] { "Rfam", colour, true };
 122     data[1] = new Object[] { "Pfam", colour, false };
 123     data[2] = new Object[] { "Scop", colour, false };
 124     fr.setFeaturePriority(data);
 125     assertEquals(fr.getRenderOrder(), Arrays.asList("Scop", "Pfam", "Rfam"));
 126     assertEquals(fr.getDisplayedFeatureTypes(), Arrays.asList("Rfam"));
 127
 128     /*
 129      * add a new feature type: should go on top of render order as visible,
 130      * other feature ordering and visibility should be unchanged
 131      */
 132     seqs.get(2).addSequenceFeature(
 133             new SequenceFeature("Metal", "Desc", 14, 22, 8f, "MetalGroup"));
 134     fr.findAllFeatures(true);
 135     assertEquals(fr.getRenderOrder(),
 136             Arrays.asList("Scop", "Pfam", "Rfam", "Metal"));
 137     assertEquals(fr.getDisplayedFeatureTypes(),
 138             Arrays.asList("Rfam", "Metal"));
 139   }
 140
 141   @Test(groups = "Functional")
 142   public void testFindFeaturesAtColumn()
 143   {
 144     String seqData = ">s1/4-29\n-ab--cdefghijklmnopqrstuvwxyz\n";
 145     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
 146             DataSourceType.PASTE);
 147     AlignViewportI av = af.getViewport();
 148     FeatureRenderer fr = new FeatureRenderer(av);
 149     SequenceI seq = av.getAlignment().getSequenceAt(0);
 150
 151     /*
 152      * with no features
 153      */
 154     List<SequenceFeature> features = fr.findFeaturesAtColumn(seq, 3);
 155     assertTrue(features.isEmpty());
 156
 157     /*
 158      * add features
 159      */
 160     SequenceFeature sf1 = new SequenceFeature("Type1", "Desc", 0, 0, 1f,
 161             "Group"); // non-positional
 162     seq.addSequenceFeature(sf1);
 163     SequenceFeature sf2 = new SequenceFeature("Type2", "Desc", 8, 18, 1f,
 164             "Group1");
 165     seq.addSequenceFeature(sf2);
 166     SequenceFeature sf3 = new SequenceFeature("Type3", "Desc", 8, 18, 1f,
 167             "Group2");
 168     seq.addSequenceFeature(sf3);
 169     SequenceFeature sf4 = new SequenceFeature("Type3", "Desc", 8, 18, 1f,
 170             null); // null group is always treated as visible
 171     seq.addSequenceFeature(sf4);
 172
 173     /*
 174      * add contact features
 175      */
 176     SequenceFeature sf5 = new SequenceFeature("Disulphide Bond", "Desc", 7,
 177             15, 1f, "Group1");
 178     seq.addSequenceFeature(sf5);
 179     SequenceFeature sf6 = new SequenceFeature("Disulphide Bond", "Desc", 7,
 180             15, 1f, "Group2");
 181     seq.addSequenceFeature(sf6);
 182     SequenceFeature sf7 = new SequenceFeature("Disulphide Bond", "Desc", 7,
 183             15, 1f, null);
 184     seq.addSequenceFeature(sf7);
 185
 186     // feature spanning B--C
 187     SequenceFeature sf8 = new SequenceFeature("Type1", "Desc", 5, 6, 1f,
 188             "Group");
 189     seq.addSequenceFeature(sf8);
 190     // contact feature B/C
 191     SequenceFeature sf9 = new SequenceFeature("Disulphide Bond", "Desc", 5,
 192             6, 1f, "Group");
 193     seq.addSequenceFeature(sf9);
 194
 195     /*
 196      * let feature renderer discover features (and make visible)
 197      */
 198     fr.findAllFeatures(true);
 199     features = fr.findFeaturesAtColumn(seq, 15); // all positional
 200     assertEquals(features.size(), 6);
 201     assertTrue(features.contains(sf2));
 202     assertTrue(features.contains(sf3));
 203     assertTrue(features.contains(sf4));
 204     assertTrue(features.contains(sf5));
 205     assertTrue(features.contains(sf6));
 206     assertTrue(features.contains(sf7));
 207
 208     /*
 209      * at a non-contact position
 210      */
 211     features = fr.findFeaturesAtColumn(seq, 14);
 212     assertEquals(features.size(), 3);
 213     assertTrue(features.contains(sf2));
 214     assertTrue(features.contains(sf3));
 215     assertTrue(features.contains(sf4));
 216
 217     /*
 218      * make "Type2" not displayed
 219      */
 220     Object[][] data = new Object[4][];
 221     FeatureColourI colour = new FeatureColour(Color.RED);
 222     data[0] = new Object[] { "Type1", colour, true };
 223     data[1] = new Object[] { "Type2", colour, false };
 224     data[2] = new Object[] { "Type3", colour, true };
 225     data[3] = new Object[] { "Disulphide Bond", colour, true };
 226     fr.setFeaturePriority(data);
 227
 228     features = fr.findFeaturesAtColumn(seq, 15);
 229     assertEquals(features.size(), 5); // no sf2
 230     assertTrue(features.contains(sf3));
 231     assertTrue(features.contains(sf4));
 232     assertTrue(features.contains(sf5));
 233     assertTrue(features.contains(sf6));
 234     assertTrue(features.contains(sf7));
 235
 236     /*
 237      * make "Group2" not displayed
 238      */
 239     fr.setGroupVisibility("Group2", false);
 240
 241     features = fr.findFeaturesAtColumn(seq, 15);
 242     assertEquals(features.size(), 3); // no sf2, sf3, sf6
 243     assertTrue(features.contains(sf4));
 244     assertTrue(features.contains(sf5));
 245     assertTrue(features.contains(sf7));
 246
 247     // features 'at' a gap between b and c
 248     // - returns enclosing feature BC but not contact feature B/C
 249     features = fr.findFeaturesAtColumn(seq, 4);
 250     assertEquals(features.size(), 1);
 251     assertTrue(features.contains(sf8));
 252     features = fr.findFeaturesAtColumn(seq, 5);
 253     assertEquals(features.size(), 1);
 254     assertTrue(features.contains(sf8));
 255   }
 256
 257   @Test(groups = "Functional")
 258   public void testFilterFeaturesForDisplay()
 259   {
 260     String seqData = ">s1\nabcdef\n";
 261     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
 262             DataSourceType.PASTE);
 263     AlignViewportI av = af.getViewport();
 264     FeatureRenderer fr = new FeatureRenderer(av);
 265
 266     List<SequenceFeature> features = new ArrayList<>();
 267     fr.filterFeaturesForDisplay(features, null); // empty list, does nothing
 268
 269     SequenceI seq = av.getAlignment().getSequenceAt(0);
 270     SequenceFeature sf1 = new SequenceFeature("Cath", "", 6, 8, "group1");
 271     seq.addSequenceFeature(sf1);
 272     SequenceFeature sf2 = new SequenceFeature("Cath", "", 5, 11, "group2");
 273     seq.addSequenceFeature(sf2);
 274     SequenceFeature sf3 = new SequenceFeature("Cath", "", 5, 11, "group3");
 275     seq.addSequenceFeature(sf3);
 276     SequenceFeature sf4 = new SequenceFeature("Cath", "", 6, 8, "group4");
 277     seq.addSequenceFeature(sf4);
 278     SequenceFeature sf5 = new SequenceFeature("Cath", "", 6, 9, "group4");
 279     seq.addSequenceFeature(sf5);
 280
 281     fr.findAllFeatures(true);
 282
 283     features = seq.getSequenceFeatures();
 284     assertEquals(features.size(), 5);
 285     assertTrue(features.contains(sf1));
 286     assertTrue(features.contains(sf2));
 287     assertTrue(features.contains(sf3));
 288     assertTrue(features.contains(sf4));
 289     assertTrue(features.contains(sf5));
 290
 291     /*
 292      * filter out duplicate (co-located) features
 293      * note: which gets removed is not guaranteed
 294      */
 295     fr.filterFeaturesForDisplay(features, new FeatureColour(Color.blue));
 296     assertEquals(features.size(), 3);
 297     assertTrue(features.contains(sf1) || features.contains(sf4));
 298     assertFalse(features.contains(sf1) && features.contains(sf4));
 299     assertTrue(features.contains(sf2) || features.contains(sf3));
 300     assertFalse(features.contains(sf2) && features.contains(sf3));
 301     assertTrue(features.contains(sf5));
 302
 303     /*
 304      * hide group 3 - sf3 is removed, sf2 is retained
 305      */
 306     fr.setGroupVisibility("group3", false);
 307     features = seq.getSequenceFeatures();
 308     fr.filterFeaturesForDisplay(features, new FeatureColour(Color.blue));
 309     assertEquals(features.size(), 3);
 310     assertTrue(features.contains(sf1) || features.contains(sf4));
 311     assertFalse(features.contains(sf1) && features.contains(sf4));
 312     assertTrue(features.contains(sf2));
 313     assertFalse(features.contains(sf3));
 314     assertTrue(features.contains(sf5));
 315
 316     /*
 317      * hide group 2, show group 3 - sf2 is removed, sf3 is retained
 318      */
 319     fr.setGroupVisibility("group2", false);
 320     fr.setGroupVisibility("group3", true);
 321     features = seq.getSequenceFeatures();
 322     fr.filterFeaturesForDisplay(features, null);
 323     assertEquals(features.size(), 3);
 324     assertTrue(features.contains(sf1) || features.contains(sf4));
 325     assertFalse(features.contains(sf1) && features.contains(sf4));
 326     assertFalse(features.contains(sf2));
 327     assertTrue(features.contains(sf3));
 328     assertTrue(features.contains(sf5));
 329
 330     /*
 331      * no filtering of co-located features with graduated colour scheme
 332      * sf2 is removed as its group is hidden
 333      */
 334     features = seq.getSequenceFeatures();
 335     fr.filterFeaturesForDisplay(features, new FeatureColour(Color.black,
 336             Color.white, 0f, 1f));
 337     assertEquals(features.size(), 4);
 338     assertTrue(features.contains(sf1));
 339     assertTrue(features.contains(sf3));
 340     assertTrue(features.contains(sf4));
 341     assertTrue(features.contains(sf5));
 342
 343     /*
 344      * filtering of co-located features with colour by label
 345      */
 346     features = seq.getSequenceFeatures();
 347     FeatureColour fc = new FeatureColour(Color.black);
 348     fc.setColourByLabel(true);
 349     fr.filterFeaturesForDisplay(features, fc);
 350     assertEquals(features.size(), 3);
 351     assertTrue(features.contains(sf1) || features.contains(sf4));
 352     assertFalse(features.contains(sf1) && features.contains(sf4));
 353     assertFalse(features.contains(sf2));
 354     assertTrue(features.contains(sf3));
 355     assertTrue(features.contains(sf5));
 356   }
 357 }