test/jalview/analysis/AverageDistanceEngineTest.java

   1 package jalview.analysis;
   2
   3 import java.io.File;
   4 import java.io.FileInputStream;
   5 import java.io.IOException;
   6 import java.io.InputStream;
   7 import java.util.List;
   8 import java.util.Map;
   9
  10 import org.junit.Assert;
  11 import org.testng.annotations.BeforeClass;
  12 import org.testng.annotations.BeforeMethod;
  13 import org.testng.annotations.Test;
  14
  15 import jalview.bin.Cache;
  16 import jalview.bin.Console;
  17 import jalview.datamodel.AlignmentAnnotation;
  18 import jalview.datamodel.AlignmentI;
  19 import jalview.datamodel.ContactMatrixI;
  20 import jalview.datamodel.SequenceI;
  21 import jalview.gui.AlignFrame;
  22 import jalview.gui.JvOptionPane;
  23 import jalview.io.DataSourceType;
  24 import jalview.io.FastaFile;
  25 import jalview.io.FileLoader;
  26 import jalview.io.FormatAdapter;
  27 import jalview.util.Platform;
  28 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
  29
  30 public class AverageDistanceEngineTest
  31 {
  32
  33     @BeforeClass(alwaysRun = true)
  34     public void setUpJvOptionPane()
  35     {
  36       JvOptionPane.setInteractiveMode(false);
  37       JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  38     }
  39
  40     @BeforeMethod(alwaysRun = true)
  41     public void loadProperties()
  42     {
  43       Cache.loadProperties("test/jalview/bin/TestProps.jvprops");
  44     }
  45     @Test
  46     public void testUPGMAEngine() throws Exception
  47     {
  48       AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded("examples/test_fab41.result/sample.a3m",DataSourceType.FILE);
  49       AlignmentI seqs = af.getViewport().getAlignment();
  50       SequenceI target = seqs.getSequenceAt(0);
  51       File testPAE = new File("examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json");
  52       List<Object> pae_obj = (List<Object>) Platform.parseJSON(new FileInputStream(testPAE));
  53       if (pae_obj == null)
  54       {
  55         Assert.fail("JSON PAE file did not parse properly.");
  56       }
  57       ContactMatrixI matrix = new PAEContactMatrix(target,
  58               (Map<String, Object>) pae_obj.get(0));
  59       AlignmentAnnotation aa = target.addContactList(matrix);
  60       long start = System.currentTimeMillis();
  61       AverageDistanceEngine clusterer = new AverageDistanceEngine(af.getViewport(), null, matrix);
  62       System.out.println("built a tree in "+(System.currentTimeMillis()-start)*0.001+" seconds.");
  63       StringBuffer sb = new StringBuffer();
  64       System.out.println("Newick string\n"+      new jalview.io.NewickFile(clusterer.getTopNode(),true,true).print());
  65
  66     }
  67
  68 }