JAL-1919 Added improvement to ensure consistence of annotations parsed via JmolParser...

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

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index f02226e..d3d9ff8 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());
+        if (StructureImportSettings.getDefaultPDBFileParser().equals(
+                StructureParser.JALVIEW_PARSER))
+        {
         assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+        }
       }
     }
   }
@@ -94,9 +122,9 @@ public class AnnotatedPDBFileInputTest
     SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
     assertEquals(296, sf.length);
     assertEquals("RESNUM", sf[0].getType());
-    assertEquals("GLU:  19  1gaqA", sf[0].getDescription());
+    assertEquals("GLU:19 1gaqA", sf[0].getDescription());
     assertEquals("RESNUM", sf[295].getType());
-    assertEquals("TYR: 314  1gaqA", sf[295].getDescription());
+    assertEquals("TYR:314 1gaqA", sf[295].getDescription());
 
     /*
      * 1GAQ/B
@@ -104,9 +132,9 @@ public class AnnotatedPDBFileInputTest
     sf = al.getSequenceAt(1).getSequenceFeatures();
     assertEquals(98, sf.length);
     assertEquals("RESNUM", sf[0].getType());
-    assertEquals("ALA:   1  1gaqB", sf[0].getDescription());
+    assertEquals("ALA:1 1gaqB", sf[0].getDescription());
     assertEquals("RESNUM", sf[97].getType());
-    assertEquals("ALA:  98  1gaqB", sf[97].getDescription());
+    assertEquals("ALA:98 1gaqB", sf[97].getDescription());
 
     /*
      * 1GAQ/C
@@ -114,9 +142,9 @@ public class AnnotatedPDBFileInputTest
     sf = al.getSequenceAt(2).getSequenceFeatures();
     assertEquals(296, sf.length);
     assertEquals("RESNUM", sf[0].getType());
-    assertEquals("GLU:  19  1gaqC", sf[0].getDescription());
+    assertEquals("GLU:19 1gaqC", sf[0].getDescription());
     assertEquals("RESNUM", sf[295].getType());
-    assertEquals("TYR: 314  1gaqC", sf[295].getDescription());
+    assertEquals("TYR:314 1gaqC", sf[295].getDescription());
   }
 
   @Test(groups = { "Functional" })
@@ -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);