import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
+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;
.getAlignPanel()));
alf.selectAllSequenceMenuItem_actionPerformed(null);
- MatrixI dm = fsm
- .findDistances(alf.getViewport().getAlignmentView(
- true));
+ MatrixI dm = fsm.findDistances(
+ alf.getViewport().getAlignmentView(true),
+ SimilarityParams.Jalview);
assertEquals(dm.getValue(0, 2), 0d,
"FER1_MESCR (0) should be identical with RAPSA (2)");
assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
.getAlignPanel()));
alf.selectAllSequenceMenuItem_actionPerformed(null);
- MatrixI dm = fsm
- .findDistances(alf.getViewport().getAlignmentView(
- true));
+ MatrixI dm = fsm.findDistances(
+ alf.getViewport().getAlignmentView(true),
+ SimilarityParams.Jalview);
assertEquals(dm.getValue(0, 2), 0d,
"FER1_MESCR (0) should be identical with RAPSA (2)");
assertTrue(dm.getValue(0, 1) > dm.getValue(0, 2),
assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
.getAlignPanel()));
alf.selectAllSequenceMenuItem_actionPerformed(null);
- MatrixI dm = fsm
- .findDistances(alf.getViewport().getAlignmentView(
- true));
+ MatrixI dm = fsm.findDistances(
+ alf.getViewport().getAlignmentView(true),
+ SimilarityParams.Jalview);
assertEquals(
dm.getValue(0, 2),
0d,
alf.selectAllSequenceMenuItem_actionPerformed(null);
MatrixI distances = fsm.findDistances(alf.getViewport()
- .getAlignmentView(true));
+ .getAlignmentView(true), 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)
+ // JAL-2424 (computing score as 5/6, should be 5/5)
assertEquals(distances.getValue(0, 1), 1f);
assertEquals(distances.getValue(1, 0), 1f);
}
+ /**
+ * 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);
+
+ FeatureDistanceModel sm = new FeatureDistanceModel();
+ sm.configureFromAlignmentView(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
+ // FIXME out by 1 error in cpwidth JAL-2424 - dividing by 7
+ */
+ 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 / 7); // should be 13d/6
+ assertEquals(distances.getValue(1, 0), 13d / 7);
+
+ /*
+ * exclude gaps
+ * score = 3 + 3 + 0 + 0 + 0 + 0 = 6/6
+ // FIXME out by 1 error in cpwidth JAL-2424 - dividing by 7
+ */
+ params = new SimilarityParams(true, true, false, true);
+ distances = sm.findDistances(view, params);
+ assertEquals(distances.getValue(0, 1), 6d / 7);// 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;
+ }
+
}