Make other structure classes serializable

lafita · lafita · commit 738d347b1412 · 2017-06-29T11:40:10.000-07:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Atom.java
@@ -23,7 +23,6 @@
  */
 package org.biojava.nbio.structure;
 
-import java.io.Serializable;
 import java.util.List;
 
 import javax.vecmath.Point3d;
@@ -42,7 +41,7 @@
  * @since 1.4
  *
  */
-public interface Atom extends Cloneable, PDBRecord, Serializable {
+public interface Atom extends Cloneable, PDBRecord {
 
 	/**
 	 * Set atom name, e.g. "CA".
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/AtomImpl.java
@@ -38,7 +38,7 @@
  * @since 1.4
  * @version %I% %G%
  */
-public class AtomImpl implements Atom, PDBRecord {
+public class AtomImpl implements Atom {
 
 	private static final long serialVersionUID = -2258364127420562883L;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ChainImpl.java
@@ -35,7 +35,6 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.Serializable;
 import java.util.*;
 
 
@@ -47,7 +46,7 @@
  * @author Jules Jacobsen
  * @since 1.4
  */
-public class ChainImpl implements Chain, Serializable {
+public class ChainImpl implements Chain {
 
 	private final static Logger logger = LoggerFactory.getLogger(ChainImpl.class);
 
@@ -712,7 +711,7 @@ public boolean isWaterOnly() {
 	public boolean isPureNonPolymer() {
 		for (Group g : getAtomGroups()) {
 
-			ChemComp cc = g.getChemComp();
+			//ChemComp cc = g.getChemComp();
 
 			if ( 	g.isPolymeric() &&
 					!g.isHetAtomInFile() ) {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/DBRef.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/DBRef.java
@@ -25,7 +25,6 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.Serializable;
 import java.lang.reflect.Method;
 import java.util.Formatter;
 import java.util.Locale;
@@ -38,7 +37,7 @@
  * @since 4:56:14 PM
  * @version %I% %G%
  */
-public class DBRef implements PDBRecord, Serializable{
+public class DBRef implements PDBRecord {
 
 	private final static Logger logger = LoggerFactory.getLogger(DBRef.class);
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Element.java
@@ -22,7 +22,6 @@
  */
 package org.biojava.nbio.structure;
 
-import java.io.Serializable;
 import java.util.HashMap;
 import java.util.Map;
 
@@ -40,7 +39,7 @@
  *
  */
 
-public enum Element implements Serializable {
+public enum Element {
 
 	// most frequently used elements first
 	H(1, 1, 39, 1.10f, 0.32f, 1, 1, 1, 1, 1, 1.008f, 0, 1, new int[] {1}, 2.20f, ElementType.OTHER_NONMETAL),
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ElementType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ElementType.java
@@ -23,8 +23,6 @@
 
 package org.biojava.nbio.structure;
 
-import java.io.Serializable;
-
 /**
  * ElementType is an enumeration of the types of elements found in the periodic table.
  * Each element type is further classified into Metal, Metalloid, and Non-Metal.
@@ -36,7 +34,7 @@
  * @since 3.0
  */
 
-public enum ElementType implements Serializable {
+public enum ElementType {
 
 	METALLOID(false),
 	OTHER_NONMETAL(false),
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityInfo.java
@@ -20,8 +20,6 @@
  * Created on 22.01.2007
  *
  */
-
-
 package org.biojava.nbio.structure;
 
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/EntityType.java
@@ -1,7 +1,5 @@
 package org.biojava.nbio.structure;
 
-import java.io.Serializable;
-
 /**
  *  
  * The type of entity (polymer, non-polymer, water, macrolide)
@@ -19,7 +17,7 @@
  * @author Jose Duarte
  *
  */
-public enum EntityType implements Serializable {
+public enum EntityType {
 
 	/**
 	 * Polymeric entities: poly-peptides and nucleotide chains
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/JournalArticle.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/JournalArticle.java
@@ -29,7 +29,7 @@
  * @author Jules Jacobsen
  * @since 1.7
  */
-public class JournalArticle implements Serializable{
+public class JournalArticle implements Serializable {
 
 	private static final long serialVersionUID = 5062668226159515468L;
 	private List<Author> authorList = new ArrayList<Author>();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Model.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Model.java
@@ -1,5 +1,6 @@
 package org.biojava.nbio.structure;
 
+import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -14,8 +15,10 @@
  * @author Andreas Prlic
  * @since 5.0
  */
-public class Model {
+public class Model implements Serializable {
 	
+	private static final long serialVersionUID = 5320613424668781882L;
+
 	private static final Logger logger = LoggerFactory.getLogger(Model.class);
 
     private List<Chain> polyChains;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/NucleotideImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/NucleotideImpl.java
@@ -31,7 +31,7 @@
  * @since 1.4
  * @version %I% %G%
  */
-public class NucleotideImpl extends HetatomImpl implements Group, Cloneable {
+public class NucleotideImpl extends HetatomImpl {
 
 	private static final long serialVersionUID = -7467726932980288712L;
 	/** this is a "nucleotide", a special occurance of a Hetatom. */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBHeader.java
@@ -41,7 +41,7 @@
  * @since 1.6
  *
  */
-public class PDBHeader implements PDBRecord, Serializable{
+public class PDBHeader implements PDBRecord {
 
 	private static final long serialVersionUID = -5834326174085429508L;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBRecord.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PDBRecord.java
@@ -20,12 +20,15 @@
  */
 package org.biojava.nbio.structure;
 
-/** An interface implemented by all classes that represent PDB records
+import java.io.Serializable;
+
+/** 
+ * An interface implemented by all classes that represent PDB records.
  *
  * @author Andreas Prlic
  * @since 1.6
  */
-public interface PDBRecord {
+public interface PDBRecord extends Serializable {
 
 	/** Returns a PDB file like representation of this record.
 	 *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/PassthroughIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/PassthroughIdentifier.java
@@ -32,6 +32,8 @@
  */
 public class PassthroughIdentifier implements StructureIdentifier {
 
+	private static final long serialVersionUID = -2773111624414448950L;
+	
 	private String identifier;
 	public PassthroughIdentifier(String identifier) {
 		this.identifier = identifier;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueNumber.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueNumber.java
@@ -27,7 +27,8 @@
 import java.io.Serializable;
 import java.io.StringWriter;
 
-/** Everything that is needed to uniquely describe a residue position
+/** 
+ * Everything that is needed to uniquely describe a residue position
  *
  * @author Andreas Prlic
  *
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Site.java
@@ -20,7 +20,6 @@
 
 package org.biojava.nbio.structure;
 
-import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Locale;
@@ -37,7 +36,7 @@
  * @author Amr AL-Hossary
  * @author Jules Jacobsen
  */
-public class Site implements PDBRecord, Serializable, Comparable<Site> {
+public class Site implements PDBRecord, Comparable<Site> {
 
 	private static final long serialVersionUID = -4577047072916341237L;
 	private static final String lineEnd = System.getProperty("line.separator");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StandardAminoAcid.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StandardAminoAcid.java
@@ -30,8 +30,8 @@
 import java.util.zip.GZIPInputStream;
 
 
-/** A class that provides a set of standard amino acids.
- *
+/** 
+ * A class that provides a set of standard amino acids.
  *
  *
  * @author Andreas Prlic
@@ -49,7 +49,6 @@ public final class StandardAminoAcid {
 	 * Cannot be instantiated.
 	 */
 	private StandardAminoAcid() {
-		super();
 	}
 
 	/**
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIO.java
@@ -27,8 +27,6 @@
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.io.MMCIFFileReader;
 import org.biojava.nbio.structure.io.PDBFileReader;
-//import org.slf4j.Logger;
-//import org.slf4j.LoggerFactory;
 
 /**
  * A class that provides static access methods for easy lookup of protein structure related components
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureIdentifier.java
@@ -24,6 +24,7 @@
 package org.biojava.nbio.structure;
 
 import java.io.IOException;
+import java.io.Serializable;
 
 import org.biojava.nbio.structure.align.util.AtomCache;
 
@@ -42,7 +43,7 @@
  * @author dmyersturnbull
  * @author Spencer Bliven
  */
-public interface StructureIdentifier {
+public interface StructureIdentifier extends Serializable {
 
 	/**
 	 * Get the String form of this identifier.
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureImpl.java
@@ -23,7 +23,6 @@
  */
 package org.biojava.nbio.structure;
 
-import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.ListIterator;
@@ -43,7 +42,7 @@
  * @since 1.4
  * @version %I% %G%
  */
-public class StructureImpl implements Structure, Serializable {
+public class StructureImpl implements Structure {
 
 	private static final long serialVersionUID = -8344837138032851348L;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
@@ -52,7 +52,8 @@
 /**
  * A class that provides some tool methods.
  *
- * @author Andreas Prlic, Jules Jacobsen
+ * @author Andreas Prlic
+ * @author Jules Jacobsen
  * @since 1.0
  */
 public class StructureTools {
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/SubstructureIdentifier.java
@@ -24,7 +24,6 @@
 package org.biojava.nbio.structure;
 
 import java.io.IOException;
-import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.Arrays;
 import java.util.LinkedList;
@@ -69,7 +68,7 @@
  * @author dmyersturnbull
  * @author Spencer Bliven
  */
-public class SubstructureIdentifier implements Serializable, StructureIdentifier {
+public class SubstructureIdentifier implements StructureIdentifier {
 
 	private static final long serialVersionUID = 1L;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
@@ -63,6 +63,9 @@
  *
  */
 public class URLIdentifier implements StructureIdentifier {
+
+	private static final long serialVersionUID = -5161230822868926035L;
+
 	private static final Logger logger = LoggerFactory.getLogger(URLIdentifier.class);
 
 	// Used for guessing the PDB ID from the filename
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SSBondImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/SSBondImpl.java
@@ -23,7 +23,6 @@
 
 package org.biojava.nbio.structure.io;
 
-import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -32,15 +31,12 @@
 
 /**
  * A simple bean to store disulfide bridge information, the SSBOND records in the PDB files.
- *
  * The two residues specified here are CYS residues that form a Disulfide bridge.
  *
- *
- *
  * @author Andreas Prlic
  *
  */
-public class SSBondImpl implements PDBRecord, Serializable, Cloneable {
+public class SSBondImpl implements PDBRecord, Cloneable {
 
 	private static final long serialVersionUID = -8663681100691188647L;
 
@@ -60,7 +56,6 @@ public SSBondImpl(){
 	@Override
 	public String toPDB(){
 
-
 		StringBuffer buf = new StringBuffer();
 		toPDB(buf);
 		return buf.toString();

Original file line number	Diff line number	Diff line change
`@@ -20,8 +20,6 @@`
`20`	`20`	`* Created on 22.01.2007`
`21`	`21`	`*`
`22`	`22`	`*/`
`23`		`-`
`24`		`-`
`25`	`23`	`package org.biojava.nbio.structure;`
`26`	`24`
`27`	`25`
Original file line number	Diff line number	Diff line change
`@@ -1,7 +1,5 @@`
`1`	`1`	`package org.biojava.nbio.structure;`
`2`	`2`
`3`		`-import java.io.Serializable;`
`4`		`-`
`5`	`3`	`/**`
`6`	`4`	`*`
`7`	`5`	`* The type of entity (polymer, non-polymer, water, macrolide)`
`@@ -19,7 +17,7 @@`
`19`	`17`	`* @author Jose Duarte`
`20`	`18`	`*`
`21`	`19`	`*/`
`22`		`-public enum EntityType implements Serializable {`
	`20`	`+public enum EntityType {`
`23`	`21`
`24`	`22`	`/**`
`25`	`23`	`* Polymeric entities: poly-peptides and nucleotide chains`