+/*
+ assertEquals(case7, case9);
+ * 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.datamodel;
-import static org.junit.Assert.assertTrue;
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertFalse;
+import static org.testng.Assert.assertNotEquals;
+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 org.junit.After;
-import org.junit.Before;
-import org.junit.Test;
+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
{
- @Before
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ }
+
+ @BeforeMethod(alwaysRun = true)
public void setUp() throws Exception
{
}
- @After
+ @AfterMethod(alwaysRun = true)
public void tearDown() throws Exception
{
}
- @Test
- public void test()
+ @Test(groups = { "Functional" })
+ public void testEquals()
{
- try
- {
-
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");
+
+ /*
+ * assertEquals will invoke PDBEntry.equals()
+ */
+ assertFalse(pdbEntry.equals(null));
+ assertFalse(pdbEntry.equals("a"));
+ assertEquals(case1, pdbEntry);
+ assertEquals(case2, pdbEntry);
+ assertNotEquals(case3, pdbEntry);
+ assertNotEquals(case4, pdbEntry);
+ assertNotEquals(case5, pdbEntry);
+ assertNotEquals(case6, pdbEntry);
+ assertNotEquals(case7, 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.setProperty("chain_code", "a");
+ assertFalse(pdbEntry.equals(case1));
+ assertFalse(case1.equals(pdbEntry));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testSetChainCode()
+ {
+ PDBEntry pdbEntry = new PDBEntry("1xyz", null, PDBEntry.Type.PDB,
+ "x/y/z/File");
+ assertNull(pdbEntry.getChainCode());
+
+ pdbEntry.setChainCode("a");
+ assertEquals("a", pdbEntry.getChainCode());
+
+ pdbEntry.setChainCode(null);
+ assertNull(pdbEntry.getChainCode());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testGetType()
+ {
+ assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("FILE"));
+ assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("File"));
+ assertSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("file"));
+ assertNotSame(PDBEntry.Type.FILE, PDBEntry.Type.getType("file "));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testTypeMatches()
+ {
+ // TODO Type.matches() is not used - delete?
+ assertTrue(PDBEntry.Type.FILE.matches("FILE"));
+ assertTrue(PDBEntry.Type.FILE.matches("File"));
+ assertTrue(PDBEntry.Type.FILE.matches("file"));
+ assertFalse(PDBEntry.Type.FILE.matches("FILE "));
+ }
- // System.out.println(">>>> Testing case 1");
- assertTrue(pdbEntry.equals(case1));
- // System.out.println(">>>> Testing case 2");
- assertTrue(pdbEntry.equals(case2));
- // System.out.println(">>>> Testing case 3");
- assertTrue(!pdbEntry.equals(case3));
- // System.out.println(">>>> Testing case 4");
- assertTrue(!pdbEntry.equals(case4));
- // System.out.println(">>>> Testing case 5");
- assertTrue(!pdbEntry.equals(case5));
- // System.out.println(">>>> Testing case 6");
- assertTrue(!pdbEntry.equals(case6));
- // System.out.println(">>>> Testing case 7");
- assertTrue(!pdbEntry.equals(case7));
- // System.out.println(">>>> Testing case 8");
- assertTrue(pdbEntry.equals(case8));
- } catch (Exception e)
+ @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");
+
+ /*
+ * different id but authoritative
+ */
+ pdb1 = new PDBEntry("af:1xyz", "A", null, "a/b/c/File");
+ pdb2 = new PDBEntry("af-1xyz", "A", null, "a/b/c/File");
+ pdb1.setAuthoritative(true);
+
+ assertTrue(pdb1.isAuthoritative());
+ assertFalse(pdb2.isAuthoritative());
+ // can update pdb1 (authoritative) from pdb2 (non-authoritative)
+ assertTrue(pdb1.updateFrom(pdb2));
+ // but the ID must remain the same
+ assertEquals(pdb1.getId(),"af:1xyz");
+
+ }
+
+ @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
{
- e.printStackTrace();
+ pdb = new PDBEntry(new DBRefEntry("PDBe", "0", "1A70"));
+ fail("Expected exception");
+ } catch (IllegalArgumentException e)
+ {
+ // expected;
}
-
}
}
git://source.jalview.org / jalview.git / blobdiff