/*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.analysis;
import java.io.File;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
import org.junit.Assert;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
import jalview.bin.Cache;
import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.BinaryNode;
import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.SequenceI;
import jalview.gui.AlignFrame;
import jalview.gui.JvOptionPane;
import jalview.io.DataSourceType;
import jalview.io.FastaFile;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.util.Platform;
import jalview.ws.datamodel.alphafold.PAEContactMatrix;
public class AverageDistanceEngineTest
{
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
JvOptionPane.setInteractiveMode(false);
JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
}
@BeforeMethod(alwaysRun = true)
public void loadProperties()
{
Cache.loadProperties("test/jalview/bin/TestProps.jvprops");
}
@Test(groups = { "Functional" })
public void testUPGMAEngine() throws Exception
{
AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
"examples/test_fab41.result/sample.a3m", DataSourceType.FILE);
AlignmentI seqs = af.getViewport().getAlignment();
SequenceI target = seqs.getSequenceAt(0);
File testPAE = new File(
"examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json");
List