X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Frbvi%2Fchimera%2FJalviewChimeraView.java;h=734f7ebd19fc54adfd3ff54487a51db49286d937;hb=ec8f3cedf60fb1feed6d34de6b49f6bfa78b9dd8;hp=d85bb104a1055c5d55373b03216deecb661853d1;hpb=5965127c38ff1a35d10d806c4b4537cdc1e39579;p=jalview.git

diff --git a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
index d85bb10..734f7eb 100644
--- a/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
+++ b/test/jalview/ext/rbvi/chimera/JalviewChimeraView.java
@@ -39,6 +39,7 @@ import jalview.gui.JvOptionPane;
 import jalview.gui.Preferences;
 import jalview.gui.StructureViewer;
 import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
 import jalview.structure.StructureMapping;
 import jalview.structure.StructureSelectionManager;
@@ -50,7 +51,6 @@ import java.io.File;
 import java.io.IOException;
 import java.util.List;
 import java.util.Vector;
-import jalview.io.DataSourceType;
 
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.AfterMethod;
@@ -217,7 +217,7 @@ public class JalviewChimeraView
      * (or possibly 52-145 to 1-94 - see JAL-2319)
      */
     StructureSelectionManager ssm = binding.getSsm();
-    String pdbFile = binding.getPdbFile()[0];
+    String pdbFile = binding.getStructureFiles()[0];
     StructureMapping[] mappings = ssm.getMapping(pdbFile);
     assertTrue(mappings[0].getMappingDetailsOutput().contains("SIFTS"),
             "Failed to perform SIFTS mapping");
@@ -440,15 +440,18 @@ public class JalviewChimeraView
     binding.copyStructureAttributesToFeatures("phi", af.getViewport()
             .getAlignPanel());
     fr.setVisible("phi");
-    List<SequenceFeature> fs = fr.findFeaturesAtRes(fer2Arath, 54);
+    List<SequenceFeature> fs = fer2Arath.getFeatures().findFeatures(54, 54);
     assertEquals(fs.size(), 3);
-    assertEquals(fs.get(0).getType(), "RESNUM");
-    assertEquals(fs.get(1).getType(), "phi");
-    assertEquals(fs.get(2).getType(), "phi");
-    assertEquals(fs.get(1).getDescription(), "A"); // chain
-    assertEquals(fs.get(2).getDescription(), "B");
-    assertEquals(fs.get(1).getScore(), -131.0713f, 0.001f);
-    assertEquals(fs.get(2).getScore(), -127.39512, 0.001f);
+    /*
+     * order of returned features is not guaranteed
+     */
+    assertTrue("RESNUM".equals(fs.get(0).getType())
+            || "RESNUM".equals(fs.get(1).getType())
+            || "RESNUM".equals(fs.get(2).getType()));
+    assertTrue(fs.contains(new SequenceFeature("phi", "A", 54, 54,
+            -131.0713f, "Chimera")));
+    assertTrue(fs.contains(new SequenceFeature("phi", "B", 54, 54,
+            -127.39512f, "Chimera")));
 
     /*
      * tear down - also in AfterMethod
@@ -470,7 +473,8 @@ public class JalviewChimeraView
           int res, String featureType)
   {
     String where = "at position " + res;
-    List<SequenceFeature> fs = fr.findFeaturesAtRes(seq, res);
+    List<SequenceFeature> fs = seq.getFeatures().findFeatures(res, res);
+
     assertEquals(fs.size(), 2, where);
     assertEquals(fs.get(0).getType(), "RESNUM", where);
     SequenceFeature sf = fs.get(1);