+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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 jalview.datamodel.AlignmentI;
{
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(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testFeatureScoreModel() throws Exception
{
- 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());
.getFeatureRenderer().getDisplayedFeatureTypes().length);
AssertJUnit.assertTrue(alf.getCurrentView().areFeaturesDisplayed());
FeatureScoreModel fsm = new FeatureScoreModel();
- AssertJUnit.assertTrue(fsm.configureFromAlignmentView(alf.getCurrentView()
- .getAlignPanel()));
+ AssertJUnit.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]);
+ AssertJUnit
+ .assertTrue(
+ "FER1_MESCR should be further from SPIOL (1) than it is from RAPSA (2)",
+ dm[0][1] > dm[0][2]);
}
}