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lafitalafita
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Merge branch 'master' into cesymm
Conflicts: biojava-structure-gui/src/main/java/org/biojava/nbio/structure/symmetry/gui/SymmetryDisplay.java biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
2 parents 57015e9 + 9d1d5ed commit 9b1d123

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‎biojava-aa-prop/pom.xml‎

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@@ -19,15 +19,17 @@
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<build>
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<plugins>
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<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-compiler-plugin</artifactId>
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<artifactId>maven-jar-plugin</artifactId>
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<configuration>
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<excludes>
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<exclude>demo/**.java</exclude>
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<exclude>demo/**</exclude>
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</excludes>
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</configuration>
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</plugin>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-assembly-plugin</artifactId>

‎biojava-alignment/pom.xml‎

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</properties>
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<build>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-compiler-plugin</artifactId>
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<configuration>
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<source>${jdk.version}</source>
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<target>${jdk.version}</target>
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<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jar-plugin</artifactId>
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<configuration>
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<excludes>
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<exclude>demo/**.java</exclude>
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<exclude>demo/**</exclude>
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</excludes>
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</configuration>
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</plugin>
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</configuration>
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</plugin>
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</plugins>
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</build>
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<dependencies>

‎biojava-core/pom.xml‎

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<build>
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<plugins>
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-compiler-plugin</artifactId>
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<configuration>
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<source>${jdk.version}</source>
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<target>${jdk.version}</target>
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<debug>true</debug>
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</configuration>
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</plugin>
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<!-- Excluding demo package is required for avoiding namespace clashes (demo package is in all modules) for signing the jar. See issue #387 -->
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<plugin>
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<groupId>org.apache.maven.plugins</groupId>
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<artifactId>maven-jar-plugin</artifactId>
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<configuration>
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<excludes>
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<exclude>demo/**</exclude>
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</excludes>
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</configuration>
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</plugin>
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</plugins>
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</build>
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<dependencies>

‎biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java‎

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@@ -32,6 +32,7 @@
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import org.biojava.nbio.core.sequence.location.template.Point;
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import org.biojava.nbio.core.sequence.template.*;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Iterator;
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* @author Mark Chapman
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* @param <C> each element of the {@link Sequence} is a {@link Compound} of type C
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*/
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public class SimpleAlignedSequence<S extends Sequence<C>, C extends Compound> implements AlignedSequence<S, C> {
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public class SimpleAlignedSequence<S extends Sequence<C>, C extends Compound> implements Serializable, AlignedSequence<S, C> {
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private static final String gap = "-";
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private static final long serialVersionUID = 1L;
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private static final String gap = "-";
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// always stored
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private AlignedSequence<S, C> prev;

‎biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfile.java‎

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import org.biojava.nbio.core.sequence.template.CompoundSet;
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import org.biojava.nbio.core.sequence.template.Sequence;
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import java.io.Serializable;
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import java.util.*;
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* @param <S> each element of the alignment {@link Profile} is of type S
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* @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
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*/
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public class SimpleProfile<S extends Sequence<C>, C extends Compound> implements Profile<S, C> {
53+
public class SimpleProfile<S extends Sequence<C>, C extends Compound> implements Serializable, Profile<S, C> {
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private static final long serialVersionUID = 1L;
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private List<AlignedSequence<S, C>> list;
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private List<S> originals;
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private int length;

‎biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleProfilePair.java‎

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public class SimpleProfilePair<S extends Sequence<C>, C extends Compound> extends SimpleProfile<S, C>
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implements ProfilePair<S, C> {
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private Profile<S, C> query, target;
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private static final long serialVersionUID = 1L;
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private Profile<S, C> query, target;
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/**
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* Creates a pair profile for the given profiles.

‎biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleSequencePair.java‎

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public class SimpleSequencePair<S extends Sequence<C>, C extends Compound> extends SimpleProfile<S, C>
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implements SequencePair<S, C> {
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private static final long serialVersionUID = 1L;
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private int identicals = -1, similars = -1;
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/**

‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/SimplePoint.java‎

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*/
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package org.biojava.nbio.core.sequence.location;
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import java.io.Serializable;
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import org.biojava.nbio.core.sequence.location.template.Point;
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import org.biojava.nbio.core.util.Equals;
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import org.biojava.nbio.core.util.Hashcoder;
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*
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* @author ayates
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*/
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public class SimplePoint implements Point {
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public class SimplePoint implements Serializable, Point {
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private int position;
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private static final long serialVersionUID = 1L;
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private int position;
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private boolean unknown;
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private boolean uncertain;
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‎biojava-core/src/main/java/org/biojava/nbio/core/sequence/location/template/AbstractLocation.java‎

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import org.biojava.nbio.core.sequence.views.ReversedSequenceView;
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import org.biojava.nbio.core.util.Hashcoder;
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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.Iterator;
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* @author ayates
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* @author Paolo Pavan
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*/
51-
public abstract class AbstractLocation implements Location {
52+
public abstract class AbstractLocation implements Serializable, Location {
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53-
//TODO Need to have the Sequence lookup resolver here; see the next one as well
54+
private static final long serialVersionUID = 1L;
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//TODO Need to have the Sequence lookup resolver here; see the next one as well
5457
//TODO Need a way of late binding of start/stop
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5659
private Point start;

‎biojava-core/src/main/java/org/biojava/nbio/core/util/InputStreamProvider.java‎

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@@ -78,8 +78,10 @@ public InputStreamProvider() {
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}
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/** get an InputStream for this file
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*
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/**
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* Get an InputStream for given file path.
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* The caller is responsible for closing the stream or otherwise
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* a resource leak can occur.
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* @param pathToFile the path of the file.
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* @return an InputStream for the file located at the path.
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* @throws IOException
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144146
}
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/** get an InputStream for the file
148-
*
149+
/**
150+
* Get an InputStream for the file.
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* The caller is responsible for closing the stream or otherwise
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* a resource leak can occur.
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* @param f a File
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* @return an InputStream for the file
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* @throws IOException
@@ -229,7 +233,8 @@ else if ( fileName.endsWith(".Z")) {
229233
}
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232-
/** Wrapper for new FileInputStream. if System.property biojava.cache.files is set, will try to load files from memory cache.
236+
/**
237+
* Wrapper for new FileInputStream. if System.property biojava.cache.files is set, will try to load files from memory cache.
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*
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* @param f
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* @return

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