import jalview.util.CaseInsensitiveString;
+import java.util.Collections;
+import java.util.Enumeration;
import java.util.Hashtable;
public class PDBEntry
{
+
+ /**
+ * constant for storing chain code in properties table
+ */
+ private static final String CHAIN_ID = "chain_code";
+
- Hashtable<String, Object> properties;
++ private Hashtable<String, Object> properties;
++
+ private static final int PDB_ID_LENGTH = 4;
private String file;
}
}
- /**
- * constant for storing chain code in properties table
- */
- private static final String CHAIN_ID = "chain_code";
-
- Hashtable properties;
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#equals(java.lang.Object)
+ /**
+ * Answers true if obj is a PDBEntry with the same id and chain code (both
+ * ignoring case), file, type and properties
*/
@Override
public boolean equals(Object obj)
public PDBEntry(String pdbId, String chain, PDBEntry.Type type,
String filePath)
{
+ init(pdbId, chain, type, filePath);
+ }
+
+ /**
+ * @param pdbId
+ * @param chain
- * @param type
++ * @param entryType
+ * @param filePath
+ */
- void init(String pdbId, String chain, PDBEntry.Type type, String filePath)
++ void init(String pdbId, String chain, PDBEntry.Type entryType, String filePath)
+ {
this.id = pdbId;
-- this.type = type == null ? null : type.toString();
++ this.type = entryType == null ? null : entryType.toString();
this.file = filePath;
setChainCode(chain);
}
}
}
+ /**
+ * Make a PDBEntry from a DBRefEntry. The accession code is used for the PDB
+ * id, but if it is 5 characters in length, the last character is removed and
+ * set as the chain code instead.
+ *
+ * @param dbr
+ */
+ public PDBEntry(DBRefEntry dbr)
+ {
+ if (!DBRefSource.PDB.equals(dbr.getSource()))
+ {
+ throw new IllegalArgumentException("Invalid source: "
+ + dbr.getSource());
+ }
+
+ String pdbId = dbr.getAccessionId();
+ String chainCode = null;
+ if (pdbId.length() == PDB_ID_LENGTH + 1)
+ {
+ char chain = pdbId.charAt(PDB_ID_LENGTH);
+ if (('a' <= chain && chain <= 'z') || ('A' <= chain && chain <= 'Z'))
+ {
+ pdbId = pdbId.substring(0, PDB_ID_LENGTH);
+ chainCode = String.valueOf(chain);
+ }
+ }
+ init(pdbId, chainCode, null, null);
+ }
+
- public void setFile(String file)
+ public void setFile(String f)
{
- this.file = file;
+ this.file = f;
}
public String getFile()
}
/**
+ * Getter provided for Castor binding only. Application code should call
+ * getProperty() or getProperties() instead.
+ *
+ * @deprecated
+ * @see #getProperty(String)
+ * @see #getProperties()
+ * @see jalview.ws.dbsources.Uniprot#getUniprotEntries
+ * @return
+ */
+ @Deprecated
+ public Hashtable<String, Object> getProps()
+ {
+ return properties;
+ }
+
+ /**
+ * Setter provided for Castor binding only. Application code should call
+ * setProperty() instead.
+ *
+ * @deprecated
+ * @return
+ */
+ @Deprecated
+ public void setProps(Hashtable<String, Object> props)
+ {
+ properties = props;
+ }
+
+ /**
- * update entry with details from another entry concerning the same PDB
- * ID/file spec.
+ * Answers true if this object is either equivalent to, or can be 'improved'
+ * by, the given entry.
+ * <p>
+ * If newEntry has the same id (ignoring case), and doesn't have a conflicting
+ * file spec or chain code, then update this entry from its file and/or chain
+ * code.
*
* @param newEntry
* @return true if modifications were made
*/
- protected boolean updateFrom(PDBEntry newEntry)
+ public boolean updateFrom(PDBEntry newEntry)
{
- boolean modified = false;
+ if (this.equals(newEntry))
+ {
+ return true;
+ }
+
+ String newId = newEntry.getId();
+ if (newId == null || getId() == null)
+ {
+ return false; // shouldn't happen
+ }
+
+ /*
- * id (less any chain code) has to match (ignoring case)
++ * id has to match (ignoring case)
+ */
+ if (!getId().equalsIgnoreCase(newId))
+ {
+ return false;
+ }
+
+ /*
+ * Don't update if associated with different structure files
+ */
+ String newFile = newEntry.getFile();
+ if (newFile != null && getFile() != null && !newFile.equals(getFile()))
+ {
+ return false;
+ }
- if (getFile() == null)
+ /*
+ * Don't update if associated with different chains (ignoring case)
+ */
+ String newChain = newEntry.getChainCode();
+ if (newChain != null && newChain.length() > 0 && getChainCode() != null
+ && getChainCode().length() > 0
+ && !getChainCode().equalsIgnoreCase(newChain))
{
- // update file and type of file
- modified = newEntry.getFile() != null;
- setFile(newEntry.getFile());
+ return false;
}
- if (newEntry.getType() != null && newEntry.getFile() != null
- && newEntry.getFile().equals(getFile()))
+
+ /*
+ * set file path if not already set
+ */
+ String newType = newEntry.getType();
+ if (getFile() == null && newFile != null)
+ {
+ setFile(newFile);
+ setType(newType);
+ }
+
+ /*
+ * set file type if new entry has it and we don't
+ * (for the case where file was not updated)
+ */
+ if (getType() == null && newType != null)
{
- setType(newEntry.getType());
+ setType(newType);
}
- if (getChainCode() == null
- || (getChainCode() != null && getChainCode().length() == 0 && newEntry
- .getChainCode() != null))
+
+ /*
+ * set chain if not already set (we excluded differing
+ * chains earlier) (ignoring case change only)
+ */
+ if (newChain != null && newChain.length() > 0
+ && !newChain.equalsIgnoreCase(getChainCode()))
{
- modified |= (getChainCode() == null || !newEntry.getChainCode()
- .equals(getChainCode()));
- setChainCode(newEntry.getChainCode());
+ setChainCode(newChain);
}
- if (newEntry.properties != null)
+
+ /*
- * copy any new properties; notice this may include chain_code,
- * but we excluded differing chain codes earlier
++ * copy any new or modified properties
+ */
- if (newEntry.getProperty() != null)
++ Enumeration<String> newProps = newEntry.getProperties();
++ while (newProps.hasMoreElements())
{
- for (Entry<String, Object> entry : newEntry.properties.entrySet())
- if (properties == null)
++ /*
++ * copy properties unless value matches; this defends against changing
++ * the case of chain_code which is wrapped in a CaseInsensitiveString
++ */
++ String key = newProps.nextElement();
++ Object value = newEntry.getProperty(key);
++ if (!value.equals(getProperty(key)))
{
- if (!entry.getValue().equals(getProperty(entry.getKey())))
- {
- modified = true;
- }
- setProperty(entry.getKey(), entry.getValue());
- properties = new Hashtable();
- }
- for (Object p : newEntry.getProperty().keySet())
- {
- /*
- * copy properties unless value matches; this defends against changing
- * the case of chain_code which is wrapped in a CaseInsensitiveString
- */
- Object value = newEntry.getProperty().get(p);
- if (!value.equals(properties.get(p)))
- {
- properties.put(p, newEntry.getProperty().get(p));
- }
++ setProperty(key, value);
}
}
- return modified;
+ return true;
}
}
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 jalview.datamodel.PDBEntry.Type;
-import java.util.Hashtable;
-
//import org.testng.Assert;
import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeMethod;
assertNotEquals(case5, pdbEntry);
assertNotEquals(case6, pdbEntry);
assertNotEquals(case7, pdbEntry);
- assertEquals(case8, pdbEntry);
+ assertNotEquals(case8, pdbEntry);
assertEquals(case7, case9);
+ assertNotEquals(case9, case10);
+
+ // add properties
- case7.getProperty().put("hello", "world");
++ case7.setProperty("hello", "world");
+ assertNotEquals(case7, case9);
- case9.getProperty().put("hello", "world");
++ case9.setProperty("hello", "world");
+ assertEquals(case7, case9);
- case9.getProperty().put("hello", "WORLD");
++ case9.setProperty("hello", "WORLD");
+ assertNotEquals(case7, case9);
/*
* change string wrapper property to string...
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 "));
+ }
+
+ @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());
+
+ /*
+ * 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);
- // ughh properties not null if chain code has been set...
- // JAL-2196 addresses this
- pdb1.properties = new Hashtable();
- pdb2.properties = new Hashtable();
- pdb1.properties.put("destination", "mars");
- pdb1.properties.put("hello", "world");
- pdb2.properties.put("hello", "moon");
- pdb2.properties.put("goodbye", "world");
++ pdb1.setProperty("destination", "mars");
++ pdb1.setProperty("hello", "world");
++ pdb2.setProperty("hello", "moon");
++ pdb2.setProperty("goodbye", "world");
+ assertTrue(pdb1.updateFrom(pdb2));
- assertEquals(pdb1.properties.get("destination"), "mars");
- assertEquals(pdb1.properties.get("hello"), "moon");
- assertEquals(pdb1.properties.get("goodbye"), "world");
++ 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.properties = new Hashtable();
- pdb2.properties.put("hello", "moon");
++ pdb2.setProperty("hello", "moon");
+ assertTrue(pdb1.updateFrom(pdb2));
- assertEquals(pdb1.properties.get("hello"), "moon");
++ 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;
+ }
+ }
+
}
git://source.jalview.org / jalview.git / commitdiff