Make BioJava Structure objects serializable

lafita · lafita · commit 2d99f574b429 · 2017-06-29T10:57:19.000-07:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/AminoAcidImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/AminoAcidImpl.java
@@ -23,8 +23,6 @@
  */
 package org.biojava.nbio.structure;
 
-import java.io.Serializable;
-
 /**
  * AminoAcid inherits most from Hetatom.  Adds a few AminoAcid
  * specific methods.
@@ -34,7 +32,7 @@
  * @version %I% %G%
  *
  */
-public class AminoAcidImpl extends HetatomImpl implements AminoAcid, Serializable {
+public class AminoAcidImpl extends HetatomImpl implements AminoAcid {
 
 	private static final long serialVersionUID = -6018854413829044230L;
 
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
@@ -23,6 +23,7 @@
  */
 package org.biojava.nbio.structure;
 
+import java.io.Serializable;
 import java.util.List;
 
 import javax.vecmath.Point3d;
@@ -41,7 +42,7 @@
  * @since 1.4
  *
  */
-public interface Atom extends Cloneable, PDBRecord {
+public interface Atom extends Cloneable, PDBRecord, Serializable {
 
 	/**
 	 * 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
@@ -25,7 +25,6 @@
 
 import org.biojava.nbio.structure.io.FileConvert;
 
-import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -39,7 +38,7 @@
  * @since 1.4
  * @version %I% %G%
  */
-public class AtomImpl implements Atom, Serializable, PDBRecord {
+public class AtomImpl implements Atom, PDBRecord {
 
 	private static final long serialVersionUID = -2258364127420562883L;
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Bond.java
@@ -20,14 +20,16 @@
  */
 package org.biojava.nbio.structure;
 
+import java.io.Serializable;
+
 /**
  * A simple bond -- it stores information about two atoms as well as information
  * about its bond order.
  *
  * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
  * @author Ulysse Carion
  */
-public interface Bond {
+public interface Bond extends Serializable {
 
 	/**
 	 * Gets atom 'A' of this bond. There is no meaning to which atom is 'A' and
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java
@@ -20,7 +20,6 @@
  */
 package org.biojava.nbio.structure;
 
-import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.List;
 
@@ -31,7 +30,7 @@
  * @author Jules Jacobsen <jacobsen@ebi.ac.uk>
  * @author Ulysse Carion
  */
-public class BondImpl implements Serializable, Bond {
+public class BondImpl implements Bond {
 
 	private static final long serialVersionUID = 8836120946858134380L;
 	private Atom atomA;
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Chain.java
@@ -27,6 +27,7 @@
 import org.biojava.nbio.structure.io.FileParsingParameters;
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 
+import java.io.Serializable;
 import java.util.List;
 
 /**
@@ -48,7 +49,7 @@
  * @version %I% %G%
  * @since 1.4
  */
-public interface Chain {
+public interface Chain extends Serializable {
 
 	/** returns an identical copy of this Chain.
 	 * @return  an identical copy of this Chain
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Group.java
@@ -25,6 +25,7 @@
 
 import org.biojava.nbio.structure.io.mmcif.model.ChemComp;
 
+import java.io.Serializable;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
@@ -51,7 +52,7 @@
  * @version %I% %G%
  *
  */
-public interface Group {
+public interface Group extends Serializable {
 
 	/** Group property key for secondary structure annotation */
 	public static final String SEC_STRUC = "secstruc";
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java
@@ -31,7 +31,6 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import java.io.Serializable;
 import java.util.*;
 
 /**
@@ -45,7 +44,7 @@
  * @version %I% %G%
  * @since 1.4
  */
-public class HetatomImpl implements Group,Serializable {
+public class HetatomImpl implements Group {
 
 	private static final Logger logger = LoggerFactory.getLogger(HetatomImpl.class);
 
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
@@ -22,9 +22,6 @@
  *
  */
 package org.biojava.nbio.structure;
-import java.io.Serializable;
-
-
 
 /**
  * A nucleotide group is almost the same as a Hetatm group.
@@ -34,7 +31,7 @@
  * @since 1.4
  * @version %I% %G%
  */
-public class NucleotideImpl extends HetatomImpl implements Group, Serializable, Cloneable {
+public class NucleotideImpl extends HetatomImpl implements Group, Cloneable {
 
 	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/Structure.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/Structure.java
@@ -26,6 +26,7 @@
 import org.biojava.nbio.structure.io.FileConvert;
 import org.biojava.nbio.structure.io.PDBFileReader;
 
+import java.io.Serializable;
 import java.util.List;
 
 
@@ -165,7 +166,7 @@
  * @since 1.4
  * @version %I% %G%
  */
-public interface Structure extends Cloneable {
+public interface Structure extends Cloneable, Serializable {
 
 
 	/**
