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;
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);
public void testFeatureScoreModel() throws Exception
{
AlignFrame alf = getTestAlignmentFrame();
- FeatureDistanceModel fsm = new FeatureDistanceModel();
- assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
- .getAlignPanel()));
+ ScoreModelI sm = new FeatureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
- MatrixI dm = fsm.findDistances(
+ MatrixI dm = sm.findDistances(
alf.getViewport().getAlignmentView(true),
SimilarityParams.Jalview);
assertEquals(dm.getValue(0, 2), 0d,
AlignFrame alf = getTestAlignmentFrame();
// hiding first two columns shouldn't affect the tree
alf.getViewport().hideColumns(0, 1);
- FeatureDistanceModel fsm = new FeatureDistanceModel();
- assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
- .getAlignPanel()));
+ ScoreModelI sm = new FeatureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
- MatrixI dm = fsm.findDistances(
+ MatrixI dm = sm.findDistances(
alf.getViewport().getAlignmentView(true),
SimilarityParams.Jalview);
assertEquals(dm.getValue(0, 2), 0d,
// hide columns and check tree changes
alf.getViewport().hideColumns(3, 4);
alf.getViewport().hideColumns(0, 1);
- FeatureDistanceModel fsm = new FeatureDistanceModel();
- 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);
- MatrixI dm = fsm.findDistances(
+ MatrixI dm = sm.findDistances(
alf.getViewport().getAlignmentView(true),
SimilarityParams.Jalview);
assertEquals(
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)
+ 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)
+ 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)
+ 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)
+ 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)
+ 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)
+ Assert.assertEquals(af.getFeatureRenderer().findFeaturesAtColumn(aseq, 6)
.size(), 0);
}
alf.setShowSeqFeatures(true);
alf.getFeatureRenderer().findAllFeatures(true);
- FeatureDistanceModel fsm = new FeatureDistanceModel();
- assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
- .getAlignPanel()));
+ ScoreModelI sm = new FeatureDistanceModel();
+ sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+ alf.getCurrentView().getAlignPanel());
alf.selectAllSequenceMenuItem_actionPerformed(null);
- MatrixI distances = fsm.findDistances(alf.getViewport()
- .getAlignmentView(true), SimilarityParams.Jalview);
+ 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);
- // these left to fail pending resolution of
- // JAL-2424 (dividing score by 6, not 5)
- assertEquals(distances.getValue(0, 1), 1f);
- assertEquals(distances.getValue(1, 0), 1f);
+
+ 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