X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fanalysis%2FAverageDistanceEngineTest.java;h=760e0ba9ff6b8ae2f20462af4b265038bec38bed;hb=refs%2Fheads%2Fimprovement%2FJAL-3847_some_attempts_to_set_gradle_and_groovy_versions;hp=3697efd8c550f2100383c781c77871cae664813d;hpb=8fbc01654883e68f8843ad6632efaabfaf21692e;p=jalview.git

diff --git a/test/jalview/analysis/AverageDistanceEngineTest.java b/test/jalview/analysis/AverageDistanceEngineTest.java
index 3697efd..760e0ba 100644
--- a/test/jalview/analysis/AverageDistanceEngineTest.java
+++ b/test/jalview/analysis/AverageDistanceEngineTest.java
@@ -4,6 +4,7 @@ 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;
 
@@ -16,6 +17,7 @@ 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;
@@ -30,39 +32,77 @@ import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 public class AverageDistanceEngineTest
 {
 
-    @BeforeClass(alwaysRun = true)
-    public void setUpJvOptionPane()
+  @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<Object> pae_obj = (List<Object>) Platform
+            .parseJSON(new FileInputStream(testPAE));
+    if (pae_obj == null)
     {
-      JvOptionPane.setInteractiveMode(false);
-      JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+      Assert.fail("JSON PAE file did not parse properly.");
     }
+    ContactMatrixI matrix = new PAEContactMatrix(target,
+            (Map<String, Object>) pae_obj.get(0));
+    AlignmentAnnotation aa = target.addContactList(matrix);
+    System.out.println("Matrix has max=" + matrix.getMax() + " and min="
+            + matrix.getMin());
+    long start = System.currentTimeMillis();
+    AverageDistanceEngine clusterer = new AverageDistanceEngine(
+            af.getViewport(), null, matrix, false);
+    System.out.println("built a tree in "
+            + (System.currentTimeMillis() - start) * 0.001 + " seconds.");
+    StringBuffer sb = new StringBuffer();
+    System.out.println("Newick string\n"
+            + new jalview.io.NewickFile(clusterer.getTopNode(), true, true)
+                    .print());
 
-    @BeforeMethod(alwaysRun = true)
-    public void loadProperties()
+    double height = clusterer.findHeight(clusterer.getTopNode());
+    // compute height fraction to cut
+    // PAE matrixes are absolute measure in angstrom, so
+    // cluster all regions within threshold (e.g. 2A) - if height above
+    // threshold. Otherwise all nodes are in one cluster
+    double thr = .2;
+    List<BinaryNode> groups;
+    if (height > thr)
+    {
+      float cut = (float) (thr / height);
+      System.out.println("Threshold " + cut + " for height=" + height);
+      groups = clusterer.groupNodes(cut);
+    }
+    else
     {
-      Cache.loadProperties("test/jalview/bin/TestProps.jvprops");
+      groups = new ArrayList<BinaryNode>();
+      groups.add(clusterer.getTopNode());
     }
-    @Test
-    public void testUPGMAEngine() throws Exception
+    int n = 1;
+    for (BinaryNode root : groups)
     {
-      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<Object> pae_obj = (List<Object>) Platform.parseJSON(new FileInputStream(testPAE));
-      if (pae_obj == null)
+      System.out.println("Cluster " + n++);
+      for (BinaryNode leaf : clusterer.findLeaves(root))
       {
-        Assert.fail("JSON PAE file did not parse properly.");
+        System.out.print(" " + leaf.getName());
       }
-      ContactMatrixI matrix = new PAEContactMatrix(target,
-              (Map<String, Object>) pae_obj.get(0));
-      AlignmentAnnotation aa = target.addContactList(matrix);
-      long start = System.currentTimeMillis();
-      AverageDistanceEngine clusterer = new AverageDistanceEngine(af.getViewport(), null, matrix);
-      System.out.println("built a tree in "+(System.currentTimeMillis()-start)*0.001+" seconds.");
-      StringBuffer sb = new StringBuffer(); 
-      System.out.println("Newick string\n"+      new jalview.io.NewickFile(clusterer.getTopNode(),true,true).print());
-      
+      System.out.println("\\");
     }
+  }
 
 }