JAL-2189 format tests

[jalview.git] / test / jalview / io / AnnotatedPDBFileInputTest.java

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index f02226e..b8c12c6 100644 (file)
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.io;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -11,10 +31,11 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
 
 import java.io.File;
 
-import org.junit.Assert;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
@@ -46,6 +67,9 @@ public class AnnotatedPDBFileInputTest
     al = af.getViewport().getAlignment();
     pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
             .get(0).getId();
+    StructureImportSettings.setDefaultStructureFileFormat("PDB");
+    // StructureImportSettings
+    // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
   }
 
   @Test(groups = { "Functional" })
@@ -61,8 +85,8 @@ public class AnnotatedPDBFileInputTest
     {
       for (int q = p + 1; q < avec.length; q++)
       {
-        Assert.assertNotEquals("Found a duplicate annotation row "
-                + avec[p].label, avec[p], avec[q]);
+        assertTrue("Found a duplicate annotation row " + avec[p].label,
+                avec[p] != avec[q]);
       }
     }
   }
@@ -77,7 +101,11 @@ public class AnnotatedPDBFileInputTest
       {
 
         System.out.println("CalcId: " + aa.getCalcId());
-        assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+        if (StructureImportSettings.getDefaultPDBFileParser().equals(
+                StructureParser.JALVIEW_PARSER))
+        {
+          assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+        }
       }
     }
   }
@@ -161,7 +189,7 @@ public class AnnotatedPDBFileInputTest
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
@@ -193,8 +221,8 @@ public class AnnotatedPDBFileInputTest
         sq = sq.getDatasetSequence();
       }
       assertNotNull(sq.getAllPDBEntries());
-      assertEquals("Expected only one PDB ID",
-              sq.getAllPDBEntries().size(), 1);
+      assertEquals("Expected only one PDB ID", 1, sq.getAllPDBEntries()
+              .size());
       for (PDBEntry pdbentry : sq.getAllPDBEntries())
       {
         System.err.println("PDB Entry " + pdbentry.getId() + " "