X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotatedPDBFileInputTest.java;h=b8c12c6260c98bd49487350de11ae96b8944b845;hb=528c0f1815bc67b54618ad5b16c2162946974caf;hp=b4a8bf67f9216c62772d2b117ff13e5aa41c1503;hpb=4ab35f51d8e04f4e468db6d47a604fe552944899;p=jalview.git

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index b4a8bf6..b8c12c6 100644
--- 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;
@@ -11,13 +31,11 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.structure.StructureMapping;
-import jalview.structure.StructureSelectionManager;
+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;
@@ -28,11 +46,15 @@ public class AnnotatedPDBFileInputTest
 
   AlignmentI al;
 
-  String pdbStr = "examples/1gaq.txt";
-
   String pdbId;
 
- @BeforeMethod(alwaysRun = true)
+  /**
+   * Ensure 'process secondary structure from PDB and add annotations' are set
+   * in preferences, and load PDB example file 1gaq
+   * 
+   * @throws Exception
+   */
+  @BeforeMethod(alwaysRun = true)
   public void setup() throws Exception
   {
     Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
@@ -40,14 +62,17 @@ public class AnnotatedPDBFileInputTest
     Cache.applicationProperties.setProperty("ADD_SS_ANN",
             Boolean.TRUE.toString());
     FileLoader loader = new FileLoader(false);
-    AlignFrame af = loader.LoadFileWaitTillLoaded(pdbStr,
+    AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
             FormatAdapter.FILE);
     al = af.getViewport().getAlignment();
     pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
             .get(0).getId();
+    StructureImportSettings.setDefaultStructureFileFormat("PDB");
+    // StructureImportSettings
+    // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void checkNoDuplicates()
   {
     // not strictly a requirement, but strange things may happen if multiple
@@ -60,14 +85,13 @@ 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]);
       }
     }
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void checkPDBannotationSource()
   {
 
@@ -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));
+        }
       }
     }
   }
@@ -85,14 +113,9 @@ public class AnnotatedPDBFileInputTest
   /**
    * Check sequence features have been added
    */
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void checkPDBSequenceFeatures()
   {
-    StructureSelectionManager ssm = StructureSelectionManager
-            .getStructureSelectionManager(Desktop.instance);
-    StructureMapping[] mappings = ssm.getMapping("1gaq");
-    // suspect we really want to make assertions on sequence features
-    // in these mappings' sequencess
     /*
      * 1GAQ/A
      */
@@ -124,7 +147,7 @@ public class AnnotatedPDBFileInputTest
     assertEquals("TYR: 314  1gaqC", sf[295].getDescription());
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void checkAnnotationWiring()
   {
     assertTrue(al.getAlignmentAnnotation() != null);
@@ -159,22 +182,21 @@ public class AnnotatedPDBFileInputTest
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Jalview.main(new String[]
- { "-props",
+    jalview.bin.Jalview.main(new String[] { "-props",
         "test/jalview/io/testProps.jvprops" });
   }
 
   /**
    * @throws java.lang.Exception
    */
-  @AfterClass
+  @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
     jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
 
   }
 
-  @Test(groups ={ "Functional" })
+  @Test(groups = { "Functional" })
   public void testJalviewProjectRelocationAnnotation() throws Exception
   {
 
@@ -199,7 +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() + " "
@@ -212,8 +235,7 @@ public class AnnotatedPDBFileInputTest
                   && MCview.PDBfile.isCalcIdHandled(ana.getCalcId()))
           {
             exists = true;
-            if (MCview.PDBfile.isCalcIdForFile(ana,
-                    pdbentry.getId()))
+            if (MCview.PDBfile.isCalcIdForFile(ana, pdbentry.getId()))
             {
               found = true;
             }