X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fio%2FAnnotatedPDBFileInputTest.java;h=e14a4782a8ba51f04dc6fffc698a52f292fc5986;hb=44be050a48b372e5e29c74a0b838c73269501e0e;hp=d07f28c59c628928d517bb9b9742b1c0c4103488;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index d07f28c..e14a478 100644
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -30,11 +30,14 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
 import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureImportSettings.StructureParser;
 
 import java.io.File;
+import java.util.List;
 
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
@@ -44,6 +47,13 @@ import org.testng.annotations.Test;
 public class AnnotatedPDBFileInputTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   AlignmentI al;
 
   String pdbId;
@@ -119,32 +129,35 @@ public class AnnotatedPDBFileInputTest
     /*
      * 1GAQ/A
      */
-    SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
-    assertEquals(296, sf.length);
-    assertEquals("RESNUM", sf[0].getType());
-    assertEquals("GLU:  19  1gaqA", sf[0].getDescription());
-    assertEquals("RESNUM", sf[295].getType());
-    assertEquals("TYR: 314  1gaqA", sf[295].getDescription());
+    List<SequenceFeature> sf = al.getSequenceAt(0).getSequenceFeatures();
+    SequenceFeatures.sortFeatures(sf, true);
+    assertEquals(296, sf.size());
+    assertEquals("RESNUM", sf.get(0).getType());
+    assertEquals("GLU:  19  1gaqA", sf.get(0).getDescription());
+    assertEquals("RESNUM", sf.get(295).getType());
+    assertEquals("TYR: 314  1gaqA", sf.get(295).getDescription());
 
     /*
      * 1GAQ/B
      */
     sf = al.getSequenceAt(1).getSequenceFeatures();
-    assertEquals(98, sf.length);
-    assertEquals("RESNUM", sf[0].getType());
-    assertEquals("ALA:   1  1gaqB", sf[0].getDescription());
-    assertEquals("RESNUM", sf[97].getType());
-    assertEquals("ALA:  98  1gaqB", sf[97].getDescription());
+    SequenceFeatures.sortFeatures(sf, true);
+    assertEquals(98, sf.size());
+    assertEquals("RESNUM", sf.get(0).getType());
+    assertEquals("ALA:   1  1gaqB", sf.get(0).getDescription());
+    assertEquals("RESNUM", sf.get(97).getType());
+    assertEquals("ALA:  98  1gaqB", sf.get(97).getDescription());
 
     /*
      * 1GAQ/C
      */
     sf = al.getSequenceAt(2).getSequenceFeatures();
-    assertEquals(296, sf.length);
-    assertEquals("RESNUM", sf[0].getType());
-    assertEquals("GLU:  19  1gaqC", sf[0].getDescription());
-    assertEquals("RESNUM", sf[295].getType());
-    assertEquals("TYR: 314  1gaqC", sf[295].getDescription());
+    SequenceFeatures.sortFeatures(sf, true);
+    assertEquals(296, sf.size());
+    assertEquals("RESNUM", sf.get(0).getType());
+    assertEquals("GLU:  19  1gaqC", sf.get(0).getDescription());
+    assertEquals("RESNUM", sf.get(295).getType());
+    assertEquals("TYR: 314  1gaqC", sf.get(295).getDescription());
   }
 
   @Test(groups = { "Functional" })