X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotatedPDBFileInputTest.java;h=c0038a1905c9c9830ef613c20b9ad39882b1dea6;hb=d7e95f458ebcbbdcc13f8b07357542ab2d7e4547;hp=30b6d55a59e727dda27a7d7978d45a9d9ed8974e;hpb=dd9db815930b8918c6177b1a4c61706250cd595f;p=jalview.git

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index 30b6d55..c0038a1 100644
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -1,44 +1,89 @@
+/*
+ * 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.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 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.Vector;
+import java.util.List;
 
-import org.junit.AfterClass;
-import org.junit.Before;
-import org.junit.BeforeClass;
-import org.junit.Test;
+import org.junit.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
 
 public class AnnotatedPDBFileInputTest
 {
 
-  AlignmentI al;
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
 
-  String pdbStr = "examples/1gaq.txt";
+  AlignmentI al;
 
   String pdbId;
 
-  @Before
+  /**
+   * 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",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+            Boolean.TRUE.toString());
     FileLoader loader = new FileLoader(false);
-    AlignFrame af = loader.LoadFileWaitTillLoaded(pdbStr,
-            FormatAdapter.FILE);
+    AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
+            DataSourceType.FILE);
     al = af.getViewport().getAlignment();
-    pdbId = ((PDBEntry) al.getSequenceAt(0).getDatasetSequence().getPDBId()
-            .get(0)).getId();
+    pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
+            .get(0).getId();
+    StructureImportSettings.setDefaultStructureFileFormat("PDB");
+    // StructureImportSettings
+    // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void checkNoDuplicates()
   {
     // not strictly a requirement, but strange things may happen if multiple
@@ -51,29 +96,73 @@ public class AnnotatedPDBFileInputTest
     {
       for (int q = p + 1; q < avec.length; q++)
       {
-        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
+  @Test(groups = { "Functional" }, enabled = false)
   public void checkPDBannotationSource()
   {
-
+    Assert.fail(
+            "This test is incorrect - does not verify that JmolParser's annotation rows can be recognised as generated by the Jmol parser.");
     for (SequenceI asq : al.getSequences())
     {
       for (AlignmentAnnotation aa : asq.getAnnotation())
       {
 
         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));
+        }
       }
     }
   }
 
-  @Test
+  /**
+   * Check sequence features have been added
+   */
+  @Test(groups = { "Functional" })
+  public void checkPDBSequenceFeatures()
+  {
+    /*
+     * 1GAQ/A
+     */
+    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();
+    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();
+    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" })
   public void checkAnnotationWiring()
   {
     assertTrue(al.getAlignmentAnnotation() != null);
@@ -105,24 +194,24 @@ public class AnnotatedPDBFileInputTest
   /**
    * @throws java.lang.Exception
    */
-  @BeforeClass
+  @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Jalview.main(new String[]
-    { "-props", "test/src/jalview/io/testProps.jvprops" });
+    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
+  @Test(groups = { "Functional" })
   public void testJalviewProjectRelocationAnnotation() throws Exception
   {
 
@@ -130,14 +219,14 @@ public class AnnotatedPDBFileInputTest
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
-            inFile, FormatAdapter.FILE);
+            inFile, DataSourceType.FILE);
     assertTrue("Didn't read input file " + inFile, af != null);
     assertTrue("Failed to store as a project.",
-            af.saveAlignment(tfile, "Jalview"));
+            af.saveAlignment(tfile, FileFormat.Jalview));
     af.closeMenuItem_actionPerformed(true);
     af = null;
     af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
-            FormatAdapter.FILE);
+            DataSourceType.FILE);
     assertTrue("Failed to import new project", af != null);
     for (SequenceI asq : af.getViewport().getAlignment().getSequences())
     {
@@ -146,9 +235,10 @@ public class AnnotatedPDBFileInputTest
       {
         sq = sq.getDatasetSequence();
       }
-      assertNotNull(sq.getPDBId());
-      assertEquals("Expected only one PDB ID", sq.getPDBId().size(), 1);
-      for (PDBEntry pdbentry : (Vector<PDBEntry>) sq.getPDBId())
+      assertNotNull(sq.getAllPDBEntries());
+      assertEquals("Expected only one PDB ID", 1, sq.getAllPDBEntries()
+              .size());
+      for (PDBEntry pdbentry : sq.getAllPDBEntries())
       {
         System.err.println("PDB Entry " + pdbentry.getId() + " "
                 + pdbentry.getFile());
@@ -160,8 +250,7 @@ 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;
             }