X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fdatamodel%2FPDBEntryTest.java;h=198cde3ac7e25a750e8e6cb5ffb9a07953c0717f;hb=3a8dc0dd7261853a53c7e4c3cde1b6d53d0e3e93;hp=cf944b287ecb5a3e21beae904be8fe64e69f3e85;hpb=3becb23b055e6b17b372c04be015bb205251ae9f;p=jalview.git

diff --git a/test/jalview/datamodel/PDBEntryTest.java b/test/jalview/datamodel/PDBEntryTest.java
index cf944b2..198cde3 100644
--- a/test/jalview/datamodel/PDBEntryTest.java
+++ b/test/jalview/datamodel/PDBEntryTest.java
@@ -1,4 +1,5 @@
 /*
+    assertEquals(case7, case9);
  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
  * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
@@ -27,15 +28,27 @@ import static org.testng.Assert.assertNotSame;
 import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
+import static org.testng.Assert.fail;
+
+import jalview.datamodel.PDBEntry.Type;
+import jalview.gui.JvOptionPane;
 
 //import org.testng.Assert;
 import org.testng.annotations.AfterMethod;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 public class PDBEntryTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
   {
@@ -52,23 +65,34 @@ public class PDBEntryTest
     PDBEntry pdbEntry = new PDBEntry("1xyz", "A", PDBEntry.Type.PDB,
             "x/y/z/File");
 
+    // id comparison is not case sensitive
     PDBEntry case1 = new PDBEntry("1XYZ", "A", PDBEntry.Type.PDB,
             "x/y/z/File");
+    // chain code comparison is not case sensitive
     PDBEntry case2 = new PDBEntry("1xyz", "a", PDBEntry.Type.PDB,
             "x/y/z/File");
+    // different type
     PDBEntry case3 = new PDBEntry("1xyz", "A", PDBEntry.Type.FILE,
             "x/y/z/File");
+    // different everything
     PDBEntry case4 = new PDBEntry(null, null, null, null);
+    // null id
     PDBEntry case5 = new PDBEntry(null, "A", PDBEntry.Type.PDB,
             "x/y/z/File");
+    // null chain
     PDBEntry case6 = new PDBEntry("1xyz", null, PDBEntry.Type.PDB,
             "x/y/z/File");
+    // null type
     PDBEntry case7 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
+    // null file
     PDBEntry case8 = new PDBEntry("1xyz", "A", PDBEntry.Type.PDB, null);
+    // identical to case7
     PDBEntry case9 = new PDBEntry("1xyz", "A", null, "x/y/z/File");
+    // different file only
+    PDBEntry case10 = new PDBEntry("1xyz", "A", null, "a/b/c/File");
 
     /*
-     * assertions will invoke PDBEntry.equals()
+     * assertEquals will invoke PDBEntry.equals()
      */
     assertFalse(pdbEntry.equals(null));
     assertFalse(pdbEntry.equals("a"));
@@ -79,13 +103,22 @@ public class PDBEntryTest
     assertNotEquals(case5, pdbEntry);
     assertNotEquals(case6, pdbEntry);
     assertNotEquals(case7, pdbEntry);
-    assertEquals(case8, pdbEntry);
+    assertNotEquals(case8, pdbEntry);
+    assertEquals(case7, case9);
+    assertNotEquals(case9, case10);
+
+    // add properties
+    case7.setProperty("hello", "world");
+    assertNotEquals(case7, case9);
+    case9.setProperty("hello", "world");
     assertEquals(case7, case9);
+    case9.setProperty("hello", "WORLD");
+    assertNotEquals(case7, case9);
 
     /*
      * change string wrapper property to string...
      */
-    case1.getProperty().put("chain_code", "a");
+    case1.setProperty("chain_code", "a");
     assertFalse(pdbEntry.equals(case1));
     assertFalse(case1.equals(pdbEntry));
   }
@@ -122,4 +155,156 @@ public class PDBEntryTest
     assertTrue(PDBEntry.Type.FILE.matches("file"));
     assertFalse(PDBEntry.Type.FILE.matches("FILE "));
   }
+
+  @Test(groups = { "Functional" })
+  public void testUpdateFrom()
+  {
+    PDBEntry pdb1 = new PDBEntry("3A6S", null, null, null);
+    PDBEntry pdb2 = new PDBEntry("3A6S", null, null, null);
+    assertTrue(pdb1.updateFrom(pdb2));
+
+    /*
+     * mismatch of pdb id not allowed
+     */
+    pdb2 = new PDBEntry("1A70", "A", null, null);
+    assertFalse(pdb1.updateFrom(pdb2));
+    assertNull(pdb1.getChainCode());
+
+    /*
+     * match of pdb id is not case sensitive
+     */
+    pdb2 = new PDBEntry("3a6s", "A", null, null);
+    assertTrue(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getChainCode(), "A");
+    assertEquals(pdb1.getId(), "3A6S");
+
+    /*
+     * add chain - with differing case for id
+     */
+    pdb1 = new PDBEntry("3A6S", null, null, null);
+    pdb2 = new PDBEntry("3a6s", "A", null, null);
+    assertTrue(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getChainCode(), "A");
+
+    /*
+     * change of chain is not allowed
+     */
+    pdb2 = new PDBEntry("3A6S", "B", null, null);
+    assertFalse(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getChainCode(), "A");
+
+    /*
+     * change chain from null
+     */
+    pdb1 = new PDBEntry("3A6S", null, null, null);
+    pdb2 = new PDBEntry("3A6S", "B", null, null);
+    assertTrue(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getChainCode(), "B");
+
+    /*
+     * set file and type
+     */
+    pdb2 = new PDBEntry("3A6S", "B", Type.FILE, "filePath");
+    assertTrue(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getFile(), "filePath");
+    assertEquals(pdb1.getType(), Type.FILE.toString());
+    assertEquals(pdb1.getChainCode(),"B");
+    /*
+     * change of file is not allowed
+     */
+    pdb1 = new PDBEntry("3A6S", null, null, "file1");
+    pdb2 = new PDBEntry("3A6S", "A", null, "file2");
+    assertFalse(pdb1.updateFrom(pdb2));
+    assertNull(pdb1.getChainCode());
+    assertEquals(pdb1.getFile(), "file1");
+
+    /*
+     * set type without change of file
+     */
+    pdb1 = new PDBEntry("3A6S", null, null, "file1");
+    pdb2 = new PDBEntry("3A6S", null, Type.PDB, "file1");
+    assertTrue(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getType(), Type.PDB.toString());
+
+    /*
+     * set file with differing case of id and chain code
+     */
+    pdb1 = new PDBEntry("3A6S", "A", null, null);
+    pdb2 = new PDBEntry("3a6s", "a", Type.PDB, "file1");
+    assertTrue(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getType(), Type.PDB.toString());
+    assertEquals(pdb1.getId(), "3A6S"); // unchanged
+    assertEquals(pdb1.getFile(), "file1"); // updated
+    assertEquals(pdb1.getChainCode(), "A"); // unchanged
+
+    /*
+     * changing nothing returns true
+     */
+    pdb1 = new PDBEntry("3A6S", "A", Type.PDB, "file1");
+    pdb2 = new PDBEntry("3A6S", null, null, null);
+    assertTrue(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getChainCode(), "A");
+    assertEquals(pdb1.getType(), Type.PDB.toString());
+    assertEquals(pdb1.getFile(), "file1");
+
+    /*
+     * add and update properties only
+     */
+    pdb1 = new PDBEntry("3A6S", null, null, null);
+    pdb2 = new PDBEntry("3A6S", null, null, null);
+    pdb1.setProperty("destination", "mars");
+    pdb1.setProperty("hello", "world");
+    pdb2.setProperty("hello", "moon");
+    pdb2.setProperty("goodbye", "world");
+    assertTrue(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getProperty("destination"), "mars");
+    assertEquals(pdb1.getProperty("hello"), "moon");
+    assertEquals(pdb1.getProperty("goodbye"), "world");
+
+    /*
+     * add properties only
+     */
+    pdb1 = new PDBEntry("3A6S", null, null, null);
+    pdb2 = new PDBEntry("3A6S", null, null, null);
+    pdb2.setProperty("hello", "moon");
+    assertTrue(pdb1.updateFrom(pdb2));
+    assertEquals(pdb1.getProperty("hello"), "moon");
+  }
+
+  @Test(groups = { "Functional" })
+  public void testConstructor_fromDbref()
+  {
+    PDBEntry pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70"));
+    assertEquals(pdb.getId(), "1A70");
+    assertNull(pdb.getChainCode());
+    assertNull(pdb.getType());
+    assertNull(pdb.getFile());
+
+    /*
+     * from dbref with chain code appended
+     */
+    pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70B"));
+    assertEquals(pdb.getId(), "1A70");
+    assertEquals(pdb.getChainCode(), "B");
+
+    /*
+     * from dbref with overlong accession
+     */
+    pdb = new PDBEntry(new DBRefEntry("PDB", "0", "1A70BC"));
+    assertEquals(pdb.getId(), "1A70BC");
+    assertNull(pdb.getChainCode());
+
+    /*
+     * from dbref which is not for PDB
+     */
+    try
+    {
+      pdb = new PDBEntry(new DBRefEntry("PDBe", "0", "1A70"));
+      fail("Expected exception");
+    } catch (IllegalArgumentException e)
+    {
+      // expected;
+    }
+  }
+
 }