+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.analysis.scoremodels;
-import org.testng.annotations.Test;
-import org.testng.AssertJUnit;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
public class FeatureScoreModelTest
{
public static String alntestFile = "FER1_MESCR/72-76 DVYIL\nFER1_SPIOL/71-75 DVYIL\nFER3_RAPSA/21-25 DVYVL\nFER1_MAIZE/73-77 DVYIL\n";
- int[] sf1 = new int[]
- { 74, 74, 73, 73, 23, 23, -1, -1 };
+ int[] sf1 = new int[] { 74, 74, 73, 73, 23, 23, -1, -1 };
- int[] sf2 = new int[]
- { -1, -1, 74, 75, -1, -1, 76, 77 };
+ int[] sf2 = new int[] { -1, -1, 74, 75, -1, -1, 76, 77 };
- int[] sf3 = new int[]
- { -1, -1, -1, -1, -1, -1, 76, 77 };
+ int[] sf3 = new int[] { -1, -1, -1, -1, -1, -1, 76, 77 };
- @Test
- public void testFeatureScoreModel() throws Exception
+ public AlignFrame getTestAlignmentFrame()
{
- AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(alntestFile,
- FormatAdapter.PASTE);
+ AlignFrame alf = new FileLoader(false).LoadFileWaitTillLoaded(
+ alntestFile, FormatAdapter.PASTE);
AlignmentI al = alf.getViewport().getAlignment();
- AssertJUnit.assertEquals(4, al.getHeight());
- AssertJUnit.assertEquals(5, al.getWidth());
+ Assert.assertEquals(al.getHeight(), 4);
+ Assert.assertEquals(al.getWidth(), 5);
for (int i = 0; i < 4; i++)
{
SequenceI ds = al.getSequenceAt(i).getDatasetSequence();
alf.getFeatureRenderer().setVisible("sf2");
alf.getFeatureRenderer().setVisible("sf3");
alf.getFeatureRenderer().findAllFeatures(true);
- AssertJUnit.assertEquals("Number of feature types", 3, alf
- .getFeatureRenderer().getDisplayedFeatureTypes().length);
- AssertJUnit.assertTrue(alf.getCurrentView().areFeaturesDisplayed());
+ Assert.assertEquals(alf.getFeatureRenderer().getDisplayedFeatureTypes()
+ .size(), 3, "Number of feature types");
+ Assert.assertTrue(alf.getCurrentView().areFeaturesDisplayed());
+ return alf;
+ }
+
+ @Test(groups = { "Functional" })
+ public void testFeatureScoreModel() throws Exception
+ {
+ AlignFrame alf = getTestAlignmentFrame();
+ FeatureScoreModel fsm = new FeatureScoreModel();
+ Assert.assertTrue(fsm.configureFromAlignmentView(alf
+ .getCurrentView().getAlignPanel()));
+ alf.selectAllSequenceMenuItem_actionPerformed(null);
+ float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
+ true));
+ Assert.assertTrue(dm[0][2] == 0f,
+ "FER1_MESCR (0) should be identical with RAPSA (2)");
+ Assert.assertTrue(dm[0][1] > dm[0][2],
+ "FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)");
+ }
+
+ @Test(groups = { "Functional" })
+ public void testFeatureScoreModel_hiddenFirstColumn() throws Exception
+ {
+ AlignFrame alf = getTestAlignmentFrame();
+ // hiding first two columns shouldn't affect the tree
+ alf.getViewport().hideColumns(0, 1);
FeatureScoreModel fsm = new FeatureScoreModel();
- AssertJUnit.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
+ Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
.getAlignPanel()));
alf.selectAllSequenceMenuItem_actionPerformed(null);
float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
true));
- AssertJUnit.assertTrue("FER1_MESCR should be identical with RAPSA (2)",
- dm[0][2] == 0f);
- AssertJUnit.assertTrue(
- "FER1_MESCR should be further from SPIOL (1) than it is from RAPSA (2)",
- dm[0][1] > dm[0][2]);
+ Assert.assertTrue(dm[0][2] == 0f,
+ "FER1_MESCR (0) should be identical with RAPSA (2)");
+ Assert.assertTrue(dm[0][1] > dm[0][2],
+ "FER1_MESCR (0) should be further from SPIOL (1) than it is from RAPSA (2)");
+ }
+ @Test(groups = { "Functional" })
+ public void testFeatureScoreModel_HiddenColumns() throws Exception
+ {
+ AlignFrame alf = getTestAlignmentFrame();
+ // hide columns and check tree changes
+ alf.getViewport().hideColumns(3, 4);
+ alf.getViewport().hideColumns(0, 1);
+ FeatureScoreModel fsm = new FeatureScoreModel();
+ Assert.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
+ .getAlignPanel()));
+ alf.selectAllSequenceMenuItem_actionPerformed(null);
+ float[][] dm = fsm.findDistances(alf.getViewport().getAlignmentView(
+ true));
+ Assert.assertTrue(dm[0][2] == 0f,
+ "After hiding last two columns FER1_MESCR (0) should still be identical with RAPSA (2)");
+ Assert.assertTrue(dm[0][1] == 0f,
+ "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)");
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff