Fix biojava#452 update ECOD javadoc

lafita · lafita · commit 1511d931cdb6 · 2016-04-22T10:48:40.000+02:00
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java
@@ -47,8 +47,8 @@
  * The most common warning is caused by residue ranges with missing terminal CA atoms,
  * which cause a warning to print.
  *
- * develop83 and earlier versions also had a number of invalid ranges, which cause
- * error messages to print.
+ * develop134, 127, 84 and earlier versions also had a number of invalid ranges, which
+ * cause error messages to print.
  *
  * Filtering log4j messages to the 'error' level will filter all but the most
  * grievous errors.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDatabase.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDatabase.java
@@ -23,7 +23,7 @@
 import java.io.IOException;
 import java.util.List;
 
-/** General API for interacting with CATH.
+/** General API for interacting with ECOD.
  *
  * @author Spencer Bliven
  */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodDomain.java
@@ -29,6 +29,18 @@
 import java.util.Set;
 
 /**
+ * An EcodDomain contains all the information of the ECOD database: id, 
+ * classification groups (from higher to lower in the tree: X,H,T,F), PDB code,
+ * chain, residue ranges and status (manual or automatic classification).
+ * <p>
+ * For detailed explanation about the ECOD information see the original article
+ * at: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4256011.
+ * <pre>
+ * Cheng H, Schaeffer RD, Liao Y, et al. 
+ * ECOD: An Evolutionary Classification of Protein Domains. 
+ * Elofsson A, ed. PLoS Computational Biology. 2014;10(12):e1003926.
+ * </pre>
+ * 
  * @author Spencer Bliven
  *
  */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ecod/EcodFactory.java
@@ -29,29 +29,29 @@
 import java.util.Map.Entry;
 
 import org.biojava.nbio.structure.align.util.UserConfiguration;
-import org.biojava.nbio.structure.cath.CathDatabase;
-import org.biojava.nbio.structure.cath.CathInstallation;
+import org.biojava.nbio.structure.cath.CathFactory;
 import org.biojava.nbio.structure.scop.ScopFactory;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
 /**
- * Controls global {@link CathDatabase CathDatabases} being used.
- * Implements a multiton pattern through {@link #getCathDatabase(String)},
- * and a singleton pattern through {@link #getCathDatabase()}.
+ * Controls global {@link EcodDatabase EcodDatabases} being used.
+ * Implements a multiton pattern through {@link #getEcodDatabase(String)},
+ * and a singleton pattern through {@link #getEcodDatabase()}.
  * @author Spencer Bliven
  * @see ScopFactory
- * @see CathInstallation
+ * @see CathFactory
+ * @see EcodInstallation
  */
 public class EcodFactory {
 
-	private static Logger logger = LoggerFactory.getLogger(EcodFactory.class);
-
-	public static String DEFAULT_VERSION = EcodInstallation.DEFAULT_VERSION;
+	private static final Logger logger = LoggerFactory.getLogger(EcodFactory.class);
+	
+	public static final String DEFAULT_VERSION = EcodInstallation.DEFAULT_VERSION;
 
 	private static Map<String, SoftReference<EcodDatabase>> versionedEcodDBs =
 			Collections.synchronizedMap(new HashMap<String, SoftReference<EcodDatabase>>());
-	private static String defaultVersion = DEFAULT_VERSION;
+	private static String defaultVersion = EcodInstallation.DEFAULT_VERSION;
 
 	/**
 	 * Returns the (singleton) database for the current default version

Original file line number	Diff line number	Diff line change
`@@ -47,8 +47,8 @@`
`47`	`47`	`* The most common warning is caused by residue ranges with missing terminal CA atoms,`
`48`	`48`	`* which cause a warning to print.`
`49`	`49`	`*`
`50`		`- * develop83 and earlier versions also had a number of invalid ranges, which cause`
`51`		`- * error messages to print.`
	`50`	`+ * develop134, 127, 84 and earlier versions also had a number of invalid ranges, which`
	`51`	`+ * cause error messages to print.`
`52`	`52`	`*`
`53`	`53`	`* Filtering log4j messages to the 'error' level will filter all but the most`
`54`	`54`	`* grievous errors.`
Original file line number	Diff line number	Diff line change
`@@ -23,7 +23,7 @@`
`23`	`23`	`import java.io.IOException;`
`24`	`24`	`import java.util.List;`
`25`	`25`
`26`		`-/** General API for interacting with CATH.`
	`26`	`+/** General API for interacting with ECOD.`
`27`	`27`	`*`
`28`	`28`	`* @author Spencer Bliven`
`29`	`29`	`*/`