package jalview.analysis.scoremodels;
import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+import jalview.api.analysis.ScoreModelI;
+import jalview.api.analysis.SimilarityParamsI;
+import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentView;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
+import jalview.math.MatrixI;
import java.util.Arrays;
*/
public AlignFrame getTestAlignmentFrame()
{
- AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
- alntestFile, DataSourceType.PASTE);
+ AlignFrame alf = new FileLoader(false)
+ .LoadFileWaitTillLoaded(alntestFile, DataSourceType.PASTE);
AlignmentI al = alf.getViewport().getAlignment();
Assert.assertEquals(al.getHeight(), 4);
Assert.assertEquals(al.getWidth(), 5);
SequenceI ds = al.getSequenceAt(i).getDatasetSequence();
if (sf1[i * 2] > 0)
{
- ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", "sf1",
- sf1[i * 2], sf1[i * 2 + 1], "sf1"));
+ ds.addSequenceFeature(new SequenceFeature("sf1", "sf1", sf1[i * 2],
+ sf1[i * 2 + 1], "sf1"));
}
if (sf2[i * 2] > 0)
{
- ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", "sf2",
- sf2[i * 2], sf2[i * 2 + 1], "sf2"));
+ ds.addSequenceFeature(new SequenceFeature("sf2", "sf2", sf2[i * 2],
+ sf2[i * 2 + 1], "sf2"));
}
if (sf3[i * 2] > 0)
{
- ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", "sf3",
- sf3[i * 2], sf3[i * 2 + 1], "sf3"));
+ ds.addSequenceFeature(new SequenceFeature("sf3", "sf3", sf3[i * 2],
+ sf3[i * 2 + 1], "sf3"));
}
}
alf.setShowSeqFeatures(true);
alf.getFeatureRenderer().setVisible("sf2");
alf.getFeatureRenderer().setVisible("sf3");
alf.getFeatureRenderer().findAllFeatures(true);
- Assert.assertEquals(alf.getFeatureRenderer().getDisplayedFeatureTypes()
- .size(), 3, "Number of feature types");
- Assert.assertTrue(alf.getCurrentView().areFeaturesDisplayed());
+ Assert.assertEquals(
+ alf.getFeatureRenderer().getDisplayedFeatureTypes().size(), 3,
+ "Number of feature types");
+ assertTrue(alf.getCurrentView().areFeaturesDisplayed());
return alf;
}
public void testFeatureScoreModel() throws Exception
{
AlignFrame alf = getTestAlignmentFrame();
- FeatureDistanceModel fsm = new FeatureDistanceModel();
- Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
- .getAlignPanel()));
+ ScoreModelI sm = new FeatureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
- float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
- true));
- Assert.assertTrue(dm[0][2] == 0f,
+ MatrixI dm = sm.findDistances(alf.getViewport().getAlignmentView(true),
+ SimilarityParams.Jalview);
+ assertEquals(dm.getValue(0, 2), 0d,
"FER1_MESCR (0) should be identical with RAPSA (2)");
- Assert.assertTrue(dm[0][1] > dm[0][2],
+ assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
"FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)");
}
AlignFrame alf = getTestAlignmentFrame();
// hiding first two columns shouldn't affect the tree
alf.getViewport().hideColumns(0, 1);
- FeatureDistanceModel fsm = new FeatureDistanceModel();
- Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
- .getAlignPanel()));
+ ScoreModelI sm = new FeatureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
- float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
- true));
- Assert.assertTrue(dm[0][2] == 0f,
+ MatrixI dm = sm.findDistances(alf.getViewport().getAlignmentView(true),
+ SimilarityParams.Jalview);
+ assertEquals(dm.getValue(0, 2), 0d,
"FER1_MESCR (0) should be identical with RAPSA (2)");
- Assert.assertTrue(dm[0][1] > dm[0][2],
+ assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
"FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)");
}
// hide columns and check tree changes
alf.getViewport().hideColumns(3, 4);
alf.getViewport().hideColumns(0, 1);
- FeatureDistanceModel fsm = new FeatureDistanceModel();
- Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
- .getAlignPanel()));
+ // getName() can become static in Java 8
+ ScoreModelI sm = new FeatureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
- float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
- true));
- Assert.assertTrue(
- dm[0][2] == 0f,
+ MatrixI dm = sm.findDistances(alf.getViewport().getAlignmentView(true),
+ SimilarityParams.Jalview);
+ assertEquals(dm.getValue(0, 2), 0d,
"After hiding last two columns FER1_MESCR (0) should still be identical with RAPSA (2)");
- Assert.assertTrue(
- dm[0][1] == 0f,
+ assertEquals(dm.getValue(0, 1), 0d,
"After hiding last two columns FER1_MESCR (0) should now also be identical with SPIOL (1)");
for (int s = 0; s < 3; s++)
{
- Assert.assertTrue(dm[s][3] > 0f, "After hiding last two columns "
- + alf.getViewport().getAlignment().getSequenceAt(s).getName()
- + "(" + s + ") should still be distinct from FER1_MAIZE (3)");
+ assertTrue(dm.getValue(s, 3) > 0d,
+ "After hiding last two columns "
+ + alf.getViewport().getAlignment().getSequenceAt(s)
+ .getName()
+ + "(" + s
+ + ") should still be distinct from FER1_MAIZE (3)");
}
}
SequenceFeature sf = null;
sf = new SequenceFeature("disulphide bond", "", 2, 5, Float.NaN, "");
aseq.addSequenceFeature(sf);
- Assert.assertTrue(sf.isContactFeature());
+ assertTrue(sf.isContactFeature());
af.refreshFeatureUI(true);
af.getFeatureRenderer().setAllVisible(Arrays.asList("disulphide bond"));
- Assert.assertEquals(af.getFeatureRenderer().getDisplayedFeatureTypes()
- .size(), 1, "Should be just one feature type displayed");
+ Assert.assertEquals(
+ af.getFeatureRenderer().getDisplayedFeatureTypes().size(), 1,
+ "Should be just one feature type displayed");
// step through and check for pointwise feature presence/absence
- Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 1)
- .size(), 0);
+ Assert.assertEquals(
+ af.getFeatureRenderer().findFeaturesAtColumn(aseq, 1).size(),
+ 0);
// step through and check for pointwise feature presence/absence
- Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 2)
- .size(), 1);
+ Assert.assertEquals(
+ af.getFeatureRenderer().findFeaturesAtColumn(aseq, 2).size(),
+ 1);
// step through and check for pointwise feature presence/absence
- Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 3)
- .size(), 0);
+ Assert.assertEquals(
+ af.getFeatureRenderer().findFeaturesAtColumn(aseq, 3).size(),
+ 0);
// step through and check for pointwise feature presence/absence
- Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 4)
- .size(), 0);
+ Assert.assertEquals(
+ af.getFeatureRenderer().findFeaturesAtColumn(aseq, 4).size(),
+ 0);
// step through and check for pointwise feature presence/absence
- Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 5)
- .size(), 1);
+ Assert.assertEquals(
+ af.getFeatureRenderer().findFeaturesAtColumn(aseq, 5).size(),
+ 1);
// step through and check for pointwise feature presence/absence
- Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtRes(aseq, 6)
- .size(), 0);
+ Assert.assertEquals(
+ af.getFeatureRenderer().findFeaturesAtColumn(aseq, 6).size(),
+ 0);
}
@Test(groups = { "Functional" })
* 20120 (two features of the same type doesn't affect score)
* giving an average (pairwise distance) of 5/5 or 1.0
*/
- s1.addSequenceFeature(new SequenceFeature("domain", null, 1, 3, 0f,
- null));
- s1.addSequenceFeature(new SequenceFeature("variant", null, 2, 4, 0f,
- null));
- s1.addSequenceFeature(new SequenceFeature("variant", null, 3, 5, 0f,
- null));
- s2.addSequenceFeature(new SequenceFeature("domain", null, 2, 4, 0f,
- null));
- s2.addSequenceFeature(new SequenceFeature("variant", null, 1, 2, 0f,
- null));
- s2.addSequenceFeature(new SequenceFeature("variant", null, 5, 5, 0f,
- null));
+ s1.addSequenceFeature(
+ new SequenceFeature("domain", null, 1, 3, 0f, null));
+ s1.addSequenceFeature(
+ new SequenceFeature("variant", null, 2, 4, 0f, null));
+ s1.addSequenceFeature(
+ new SequenceFeature("variant", null, 3, 5, 0f, null));
+ s2.addSequenceFeature(
+ new SequenceFeature("domain", null, 2, 4, 0f, null));
+ s2.addSequenceFeature(
+ new SequenceFeature("variant", null, 1, 2, 0f, null));
+ s2.addSequenceFeature(
+ new SequenceFeature("variant", null, 5, 5, 0f, null));
alf.setShowSeqFeatures(true);
alf.getFeatureRenderer().findAllFeatures(true);
- FeatureDistanceModel fsm = new FeatureDistanceModel();
- Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
- .getAlignPanel()));
+ ScoreModelI sm = new FeatureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
- float[][] distances = fsm.findDistances(alf.getViewport()
- .getAlignmentView(true));
- assertEquals(distances.length, 2);
- assertEquals(distances[0][0], 0f);
- assertEquals(distances[1][1], 0f);
- // these left to fail pending resolution of
- // JAL-2424 (dividing score by 6, not 5)
- assertEquals(distances[0][1], 1f);
- assertEquals(distances[1][0], 1f);
+ AlignmentView alignmentView = alf.getViewport().getAlignmentView(true);
+ MatrixI distances = sm.findDistances(alignmentView,
+ SimilarityParams.Jalview);
+ assertEquals(distances.width(), 2);
+ assertEquals(distances.height(), 2);
+ assertEquals(distances.getValue(0, 0), 0d);
+ assertEquals(distances.getValue(1, 1), 0d);
+
+ assertEquals(distances.getValue(0, 1), 1d,
+ "expected identical pairs. (check normalisation for similarity score)");
+ assertEquals(distances.getValue(1, 0), 1d);
+ }
+
+ /**
+ * Verify computed distances with varying parameter options
+ */
+ @Test(groups = "Functional")
+ public void testFindDistances_withParams()
+ {
+ AlignFrame af = setupAlignmentView();
+ AlignViewport viewport = af.getViewport();
+ AlignmentView view = viewport.getAlignmentView(false);
+
+ ScoreModelI sm = new FeatureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ af.alignPanel);
+
+ /*
+ * feature distance model always normalises by region width
+ * gap-gap is always included (but scores zero)
+ * the only variable parameter is 'includeGaps'
+ */
+
+ /*
+ * include gaps
+ * score = 3 + 3 + 0 + 2 + 3 + 2 = 13/6
+ */
+ SimilarityParamsI params = new SimilarityParams(true, true, true, true);
+ MatrixI distances = sm.findDistances(view, params);
+ assertEquals(distances.getValue(0, 0), 0d);
+ assertEquals(distances.getValue(1, 1), 0d);
+ assertEquals(distances.getValue(0, 1), 13d / 6); // should be 13d/6
+ assertEquals(distances.getValue(1, 0), 13d / 6);
+
+ /*
+ * exclude gaps
+ * score = 3 + 3 + 0 + 0 + 0 + 0 = 6/6
+ */
+ params = new SimilarityParams(true, true, false, true);
+ distances = sm.findDistances(view, params);
+ assertEquals(distances.getValue(0, 1), 6d / 6);// should be 6d/6
+ }
+
+ /**
+ * <pre>
+ * Set up
+ * column 1 2 3 4 5 6
+ * seq s1 F R - K - S
+ * seq s2 F S - - L
+ * s1 chain c c c c
+ * s1 domain d d d d
+ * s2 chain c c c
+ * s2 metal m m m
+ * s2 Pfam P P P
+ * scores: 3 3 0 2 3 2
+ * </pre>
+ *
+ * @return
+ */
+ protected AlignFrame setupAlignmentView()
+ {
+ /*
+ * for now, using space for gap to match callers of
+ * AlignmentView.getSequenceStrings()
+ * may change this to '-' (with corresponding change to matrices)
+ */
+ SequenceI s1 = new Sequence("s1", "FR K S");
+ SequenceI s2 = new Sequence("s2", "FS L");
+
+ s1.addSequenceFeature(
+ new SequenceFeature("chain", null, 1, 4, 0f, null));
+ s1.addSequenceFeature(
+ new SequenceFeature("domain", null, 1, 4, 0f, null));
+ s2.addSequenceFeature(
+ new SequenceFeature("chain", null, 1, 3, 0f, null));
+ s2.addSequenceFeature(
+ new SequenceFeature("metal", null, 1, 3, 0f, null));
+ s2.addSequenceFeature(
+ new SequenceFeature("Pfam", null, 1, 3, 0f, null));
+ AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
+ AlignFrame af = new AlignFrame(al, 300, 300);
+ af.setShowSeqFeatures(true);
+ af.getFeatureRenderer().findAllFeatures(true);
+ return af;
}
}
git://source.jalview.org / jalview.git / blobdiff