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URL: http://github.com/biojava/biojava/commit/fed00d0f189681ec11c5ce882176f423f577e80b

ylesheet" href="https://github.githubassets.com/assets/global-d18f184ea1a06a2c.css" /> Merge pull request #510 from DevFactory/release--comparators-should-b… · biojava/biojava@fed00d0 · GitHub
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Merge pull request #510 from DevFactory/release--comparators-should-be-Serializable-fix-1
squid:S2063 - Comparators should be Serializable
2 parents 4d9fe73 + 23136cb commit fed00d0

15 files changed

Lines changed: 46 additions & 18 deletions

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‎biojava-alignment/src/main/java/org/biojava/nbio/alignment/routines/AlignerHelper.java‎

Lines changed: 4 additions & 1 deletion
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@@ -25,6 +25,7 @@
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import org.biojava.nbio.core.alignment.template.AlignedSequence.Step;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.Comparator;
@@ -207,7 +208,9 @@ public Anchor(int queryIndex, int targetIndex) {
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this.queryIndex = queryIndex;
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this.targetIndex = targetIndex;
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}
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public static class QueryIndexComparator implements Comparator<Anchor> {
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public static class QueryIndexComparator implements Comparator<Anchor>, Serializable {
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private static final long serialVersionUID = 1;
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@Override
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public int compare(Anchor o1, Anchor o2) {
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return o1.getQueryIndex() - o2.getQueryIndex();

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/CDSComparator.java‎

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@@ -23,11 +23,13 @@
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package org.biojava.nbio.core.sequence;
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import java.io.Serializable;
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import java.util.Comparator;
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public class CDSComparator implements Comparator<CDSSequence>{
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public class CDSComparator implements Comparator<CDSSequence>, Serializable{
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private static final long serialVersionUID = 1;
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/**
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* Used to sort two CDSSequences where Negative Strand makes it tough

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/ExonComparator.java‎

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@@ -23,6 +23,7 @@
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package org.biojava.nbio.core.sequence;
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import java.io.Serializable;
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import java.util.Comparator;
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@@ -31,8 +32,8 @@
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* where a negative stranded gene should go the other direction. Need to think about this?
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* @author Scooter Willis <willishf at gmail dot com>
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*/
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public class ExonComparator implements Comparator<ExonSequence>{
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public class ExonComparator implements Comparator<ExonSequence>, Serializable{
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private static final long serialVersionUID = 1;
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@Override
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public int compare(ExonSequence o1, ExonSequence o2) {

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/SequenceComparator.java‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -24,14 +24,15 @@
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import org.biojava.nbio.core.sequence.template.AbstractSequence;
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import java.io.Serializable;
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import java.util.Comparator;
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/**
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* Used to sort sequences
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* @author Scooter Willis <willishf at gmail dot com>
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*/
33-
public class SequenceComparator implements Comparator<AbstractSequence<?>>{
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public class SequenceComparator implements Comparator<AbstractSequence<?>>, Serializable{
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private static final long serialVersionUID = 1;
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@Override
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public int compare(AbstractSequence<?> o1, AbstractSequence<?> o2) {

‎biojava-genome/src/main/java/org/biojava/nbio/genome/parsers/gff/FeatureList.java‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -22,6 +22,7 @@
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import org.biojava.nbio.core.sequence.DNASequence;
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import java.io.Serializable;
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import java.util.*;
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import java.util.Map.Entry;
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@@ -467,7 +468,8 @@ public String toString() {
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/**
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* used by sort routine
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*/
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private class FeatureComparator implements Comparator<FeatureI> {
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private class FeatureComparator implements Comparator<FeatureI>, Serializable {
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private static final long serialVersionUID = 1;
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@Override
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public int compare(FeatureI a, FeatureI b) {

‎biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/MyTableRowSorter.java‎

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@@ -26,6 +26,7 @@
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import javax.swing.table.TableModel;
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import javax.swing.table.TableRowSorter;
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import java.io.Serializable;
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import java.util.Comparator;
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public class MyTableRowSorter extends TableRowSorter<TableModel>
@@ -46,7 +47,8 @@ public Comparator<?> getComparator(int column)
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}
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class MyComparator implements Comparator<String> {
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class MyComparator implements Comparator<String>, Serializable {
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private static final long serialVersionUID = 1;
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int column;
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public MyComparator(int column){

‎biojava-structure/src/main/java/org/biojava/nbio/structure/AtomPositionMap.java‎

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@@ -23,6 +23,7 @@
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package org.biojava.nbio.structure;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.Comparator;
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import java.util.HashMap;
@@ -119,7 +120,8 @@ public boolean matches(Group group) {
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* @param <V>
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* The value type
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*/
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private static class ValueComparator<T, V extends Comparable<V>> implements Comparator<T> {
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private static class ValueComparator<T, V extends Comparable<V>> implements Comparator<T>, Serializable {
124+
private static final long serialVersionUID = 1;
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private Map<T, V> map;
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‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/helper/IdxComparator.java‎

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@@ -19,10 +19,12 @@
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package org.biojava.nbio.structure.align.helper;
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import java.io.Serializable;
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import java.util.Comparator;
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public class IdxComparator implements Comparator<int[]>
25+
public class IdxComparator implements Comparator<int[]>, Serializable
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{
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private static final long serialVersionUID = 1;
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@Override
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public int compare(int[] o1, int[] o2)

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/AltAligComparator.java‎

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@@ -22,6 +22,7 @@
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*/
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package org.biojava.nbio.structure.align.pairwise;
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import java.io.Serializable;
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import java.util.Comparator;
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@@ -31,8 +32,8 @@
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* @author Andreas Prlic
3233
*
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*/
34-
public class AltAligComparator implements Comparator<AlternativeAlignment> {
35-
35+
public class AltAligComparator implements Comparator<AlternativeAlignment>, Serializable {
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private static final long serialVersionUID = 1;
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public AltAligComparator() {
3839
super();

‎biojava-structure/src/main/java/org/biojava/nbio/structure/align/pairwise/FragmentJoiner.java‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -31,6 +31,7 @@
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import org.biojava.nbio.structure.align.helper.JointFragments;
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import org.biojava.nbio.structure.jama.Matrix;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.Collections;
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import java.util.Comparator;
@@ -535,7 +536,8 @@ private double testAdd(Atom[] ca1, Atom[] ca2, JointFragments fragments, int pst
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class JointFragmentsComparator
538-
implements Comparator<JointFragments> {
539+
implements Comparator<JointFragments>, Serializable {
540+
private static final long serialVersionUID = 1;
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@Override
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public int compare(JointFragments one, JointFragments two) {

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