X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotatedPDBFileInputTest.java;h=899a990cd603d675dd7fa5002a9f43a5ca24680e;hb=838e4f91d4a53dd315640dbc9ff6ef7a815ee576;hp=7e994095d406cf72fafb6df23069b34c86555261;hpb=e05ad4f9199d673b327277d1266d97f3a51419ae;p=jalview.git

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index 7e99409..899a990 100644
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -1,44 +1,74 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 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.gui.AlignFrame;
 
 import java.io.File;
-import java.util.Vector;
 
-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;
 
-  String pdbStr = "examples/2GIS.pdb";
-
   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,
+    AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
             FormatAdapter.FILE);
     al = af.getViewport().getAlignment();
-    pdbId = ((PDBEntry) al.getSequenceAt(0).getDatasetSequence().getPDBId()
-            .get(0)).getId();
+    pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
+            .get(0).getId();
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void checkNoDuplicates()
   {
     // not strictly a requirement, but strange things may happen if multiple
@@ -51,14 +81,13 @@ 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]);
+        Assert.assertNotEquals("Found a duplicate annotation row "
+                + avec[p].label, avec[p], avec[q]);
       }
     }
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void checkPDBannotationSource()
   {
 
@@ -68,12 +97,49 @@ public class AnnotatedPDBFileInputTest
       {
 
         System.out.println("CalcId: " + aa.getCalcId());
-        assertTrue(MCview.PDBfile.isCalcIdForFile(aa.getCalcId(), pdbId));
+        assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
       }
     }
   }
 
-  @Test
+  /**
+   * Check sequence features have been added
+   */
+  @Test(groups = { "Functional" })
+  public void checkPDBSequenceFeatures()
+  {
+    /*
+     * 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());
+
+    /*
+     * 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());
+
+    /*
+     * 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());
+  }
+
+  @Test(groups = { "Functional" })
   public void checkAnnotationWiring()
   {
     assertTrue(al.getAlignmentAnnotation() != null);
@@ -105,11 +171,11 @@ 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" });
   }
 
   /**
@@ -122,11 +188,11 @@ public class AnnotatedPDBFileInputTest
 
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testJalviewProjectRelocationAnnotation() throws Exception
   {
 
-    String inFile = "examples/2GIS.pdb";
+    String inFile = "examples/1gaq.txt";
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
@@ -146,9 +212,10 @@ 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",
+              sq.getAllPDBEntries().size(), 1);
+      for (PDBEntry pdbentry : sq.getAllPDBEntries())
       {
         System.err.println("PDB Entry " + pdbentry.getId() + " "
                 + pdbentry.getFile());
@@ -160,8 +227,7 @@ public class AnnotatedPDBFileInputTest
                   && MCview.PDBfile.isCalcIdHandled(ana.getCalcId()))
           {
             exists = true;
-            if (MCview.PDBfile.isCalcIdForFile(ana.getCalcId(),
-                    pdbentry.getId()))
+            if (MCview.PDBfile.isCalcIdForFile(ana, pdbentry.getId()))
             {
               found = true;
             }