Merge pull request #676 from biojava/serialize

lafita · web-flow · commit ee3a2d4ff796 · 2017-07-06T14:38:44.000+01:00
Serialize all the Structure objects
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/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 {
 
 	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/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/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/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
@@ -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 {
 
 	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/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 {
 
 
 	/**
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
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
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
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
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
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureSerialization.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestStructureSerialization.java

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`