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.BinaryNode;
  20 import jalview.datamodel.ContactMatrixI;
  21 import jalview.datamodel.SequenceI;
  22 import jalview.gui.AlignFrame;
  23 import jalview.gui.JvOptionPane;
  24 import jalview.io.DataSourceType;
  25 import jalview.io.FastaFile;
  26 import jalview.io.FileLoader;
  27 import jalview.io.FormatAdapter;
  28 import jalview.util.Platform;
  29 import jalview.ws.datamodel.alphafold.PAEContactMatrix;
  30
  31 public class AverageDistanceEngineTest
  32 {
  33
  34     @BeforeClass(alwaysRun = true)
  35     public void setUpJvOptionPane()
  36     {
  37       JvOptionPane.setInteractiveMode(false);
  38       JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  39     }
  40
  41     @BeforeMethod(alwaysRun = true)
  42     public void loadProperties()
  43     {
  44       Cache.loadProperties("test/jalview/bin/TestProps.jvprops");
  45     }
  46     @Test
  47     public void testUPGMAEngine() throws Exception
  48     {
  49       AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded("examples/test_fab41.result/sample.a3m",DataSourceType.FILE);
  50       AlignmentI seqs = af.getViewport().getAlignment();
  51       SequenceI target = seqs.getSequenceAt(0);
  52       File testPAE = new File("examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json");
  53       List<Object> pae_obj = (List<Object>) Platform.parseJSON(new FileInputStream(testPAE));
  54       if (pae_obj == null)
  55       {
  56         Assert.fail("JSON PAE file did not parse properly.");
  57       }
  58       ContactMatrixI matrix = new PAEContactMatrix(target,
  59               (Map<String, Object>) pae_obj.get(0));
  60       AlignmentAnnotation aa = target.addContactList(matrix);
  61       long start = System.currentTimeMillis();
  62       AverageDistanceEngine clusterer = new AverageDistanceEngine(af.getViewport(), null, matrix);
  63       System.out.println("built a tree in "+(System.currentTimeMillis()-start)*0.001+" seconds.");
  64       StringBuffer sb = new StringBuffer();
  65       System.out.println("Newick string\n"+      new jalview.io.NewickFile(clusterer.getTopNode(),true,true).print());
  66
  67       clusterer.findHeight(clusterer.getTopNode());
  68       List<BinaryNode> groups = clusterer.groupNodes(0.8f);
  69       int n=1;
  70       for (BinaryNode root:groups)
  71       {
  72         System.out.println("Cluster "+n++);
  73         for (BinaryNode leaf:clusterer.findLeaves(root))
  74         {
  75           System.out.print(" "+leaf.getName());
  76         }
  77         System.out.println("\\");
  78       }
  79
  80     }
  81
  82 }