Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

[jalview.git] / test / jalview / analysis / AverageDistanceEngineTest.java

diff --git a/test/jalview/analysis/AverageDistanceEngineTest.java b/test/jalview/analysis/AverageDistanceEngineTest.java
index 6d9ab50..760e0ba 100644 (file)
--- a/test/jalview/analysis/AverageDistanceEngineTest.java
+++ b/test/jalview/analysis/AverageDistanceEngineTest.java
@@ -32,66 +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)
     {
-      Cache.loadProperties("test/jalview/bin/TestProps.jvprops");
+      float cut = (float) (thr / height);
+      System.out.println("Threshold " + cut + " for height=" + height);
+      groups = clusterer.groupNodes(cut);
     }
-    @Test
-    public void testUPGMAEngine() throws Exception
+    else
     {
-      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)
-      {
-        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);
-      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());
-      
-      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{
-        groups=new ArrayList<BinaryNode>();
-        groups.add(clusterer.getTopNode());
-      }
-      int n=1;
-      for (BinaryNode root:groups)
+      groups = new ArrayList<BinaryNode>();
+      groups.add(clusterer.getTopNode());
+    }
+    int n = 1;
+    for (BinaryNode root : groups)
+    {
+      System.out.println("Cluster " + n++);
+      for (BinaryNode leaf : clusterer.findLeaves(root))
       {
-        System.out.println("Cluster "+n++);
-        for (BinaryNode leaf:clusterer.findLeaves(root))
-        {
-          System.out.print(" "+leaf.getName());
-        }
-        System.out.println("\\");
+        System.out.print(" " + leaf.getName());
       }
-      
+      System.out.println("\\");
     }
+  }
 
 }