Some more removals

josemduarte · josemduarte · commit 31d29b5f42b2 · 2020-07-03T19:05:55.000-07:00
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/webstart/WebStartMain.java
@@ -25,7 +25,6 @@
 import org.biojava.nbio.structure.align.StructureAlignmentFactory;
 import org.biojava.nbio.structure.align.ce.CeCPMain;
 import org.biojava.nbio.structure.align.ce.CeMain;
-import org.biojava.nbio.structure.align.client.FarmJobParameters;
 import org.biojava.nbio.structure.align.client.JFatCatClient;
 import org.biojava.nbio.structure.align.client.PdbPair;
 import org.biojava.nbio.structure.align.fatcat.FatCatFlexible;
@@ -38,6 +37,7 @@
 import org.biojava.nbio.structure.align.model.AFPChain;
 import org.biojava.nbio.structure.align.seq.SmithWaterman3Daligner;
 import org.biojava.nbio.structure.align.util.AtomCache;
+import org.biojava.nbio.structure.align.util.ResourceManager;
 import org.biojava.nbio.structure.align.util.UserConfiguration;
 
 import javax.swing.*;
@@ -47,6 +47,13 @@
 public class WebStartMain
 {
 
+	private static final ResourceManager resourceManager;
+	private static final String DEFAULT_SERVER_URL;
+	static {
+		resourceManager = ResourceManager.getResourceManager("jfatcat");
+		DEFAULT_SERVER_URL = resourceManager.getString("server.url");
+	}
+
 	static UserConfiguration userConfig;
 
 	/**
@@ -113,7 +120,7 @@ public void run() {
 			return;
 		}
 
-		String serverLocation = FarmJobParameters.DEFAULT_SERVER_URL;
+		String serverLocation = DEFAULT_SERVER_URL;
 
 		if ( args.length  > 3 ) {
 			// we have 4 arguments.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/CountProgressListener.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/CountProgressListener.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobParameters.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/FarmJobParameters.java
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/PdbPair.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/PdbPair.java
@@ -22,7 +22,8 @@
 
 import org.biojava.nbio.structure.StructureException;
 
-/** A pair for structure alignment
+/**
+ * A pair for structure alignment
  *
  * @author Andreas Prlic
  *
@@ -31,11 +32,13 @@
  */
 public class PdbPair implements Comparable<PdbPair> {
 
-	StructureName name1;
-	StructureName name2;
+	private StructureName name1;
+	private StructureName name2;
+
 	public PdbPair(String name1, String name2) {
 		this(new StructureName(name1),new StructureName(name2));
 	}
+
 	public PdbPair(StructureName name1, StructureName name2) {
 		super();
 		this.name1 = name1;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/client/StructureName.java
@@ -67,7 +67,7 @@
  * information may be loaded from one of the factory classes:
  * {@link CathFactory},{@link ScopFactory}, etc.
  *
- * @see #getName the name. e.g. 4hhb, 4hhb.A, d4hhba_, PDP:4HHBAa etc.
+ * @see #getIdentifier() the name. e.g. 4hhb, 4hhb.A, d4hhba_, PDP:4HHBAa etc.
  */
 
 public class StructureName implements Comparable<StructureName>, Serializable, StructureIdentifier {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/ResourceManager.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/util/ResourceManager.java
@@ -27,14 +27,14 @@
 
 
 
-/** A class that manages the Strings that are defined in the spice.properties file.
+/**
+ * A class that manages the Strings that are defined in the spice.properties file.
  * This will be usefull for internationalisation.
  *
  * TODO: provide .properties files for other locales.
  * e.g. jfatcat_de_DE.properties, etc.
  *
  * @author Andreas Prlic
- * @since 1:43:04 PM
  * @version %I% %G%
  */
 public class ResourceManager {

Original file line number	Diff line number	Diff line change
`@@ -67,7 +67,7 @@`
`67`	`67`	`* information may be loaded from one of the factory classes:`
`68`	`68`	`* {@link CathFactory},{@link ScopFactory}, etc.`
`69`	`69`	`*`
`70`		`- * @see #getName the name. e.g. 4hhb, 4hhb.A, d4hhba_, PDP:4HHBAa etc.`
	`70`	`+ * @see #getIdentifier() the name. e.g. 4hhb, 4hhb.A, d4hhba_, PDP:4HHBAa etc.`
`71`	`71`	`*/`
`72`	`72`
`73`	`73`	`public class StructureName implements Comparable<StructureName>, Serializable, StructureIdentifier {`
Original file line number	Diff line number	Diff line change
`@@ -27,14 +27,14 @@`
`27`	`27`
`28`	`28`
`29`	`29`
`30`		`-/** A class that manages the Strings that are defined in the spice.properties file.`
	`30`	`+/**`
	`31`	`+ * A class that manages the Strings that are defined in the spice.properties file.`
`31`	`32`	`* This will be usefull for internationalisation.`
`32`	`33`	`*`
`33`	`34`	`* TODO: provide .properties files for other locales.`
`34`	`35`	`* e.g. jfatcat_de_DE.properties, etc.`
`35`	`36`	`*`
`36`	`37`	`* @author Andreas Prlic`
`37`		`- * @since 1:43:04 PM`
`38`	`38`	`* @version %I% %G%`
`39`	`39`	`*/`
`40`	`40`	`public class ResourceManager {`