From eb22bb5a2b5a58777db94ee65700c86d7484916e Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Fri, 8 Jun 2018 16:19:47 +0200 Subject: [PATCH 1/6] Fix duplicate code introduced by merge --- .../core/alignment/template/AlignedSequence.java | 16 ---------------- 1 file changed, 16 deletions(-) diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java index 985e11bf30..748bf593ad 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/template/AlignedSequence.java @@ -158,20 +158,4 @@ enum Step { COMPOUND, GAP } */ boolean isGap(int alignmentIndex); - /** - * Returns number of gap positions (gap openings and extensions) in the sequence. This could be determined from the {@link Location} - * information or from gap {@link Compound}s, which may not necessarily result in the same number. - * - * @return number of gap positions in the sequence - */ - int getNumGapPositions(); - - /** - * Returns the coverage, as a fraction between 0 and 1, of this {@link AlignedSequence} with respect to the original sequence. - * This is equivalent to ({@link #getLength()} - {@link #getNumGapPositions()}) / getOriginalSequence().getLength(). - * - * @return coverage of the original sequence by the aligned sequence - */ - double getCoverage(); - } From 0a3d660677d33220988006a5b0aa28d9cb67dc3d Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Mon, 18 Jun 2018 15:23:34 +0200 Subject: [PATCH 2/6] Make BioJava compile under java9 --- .../biojava/nbio/core/sequence/io/embl/EmblId.java | 3 --- biojava-protein-disorder/pom.xml | 4 ++++ biojava-structure/pom.xml | 5 +++++ pom.xml | 11 ++++++++--- 4 files changed, 17 insertions(+), 6 deletions(-) diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblId.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblId.java index 4c93427767..f89c79762c 100644 --- a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblId.java +++ b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/io/embl/EmblId.java @@ -20,8 +20,6 @@ */ package org.biojava.nbio.core.sequence.io.embl; -import jdk.nashorn.internal.ir.annotations.Immutable; - /** * This class contains the processed data of embl file * Primary accession number @@ -35,7 +33,6 @@ * @author Noor Aldeen Al Mbaidin * @since 5.0.0 */ -@Immutable public class EmblId { diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index ae653bdf00..f8ed94471a 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -84,6 +84,10 @@ org.apache.logging.log4j log4j-core + + javax.xml.bind + jaxb-api + diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 6c63cbf2d2..3f29d97c92 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -62,6 +62,11 @@ 1.1.0 + + javax.xml.bind + jaxb-api + + diff --git a/pom.xml b/pom.xml index 8f01d73591..f1eb533df9 100644 --- a/pom.xml +++ b/pom.xml @@ -32,8 +32,8 @@ - 1.8 - 1.8 + 9 + 9 UTF-8 UTF-8 @@ -507,6 +507,11 @@ forester 1.038 + + javax.xml.bind + jaxb-api + 2.3.0 + @@ -518,7 +523,7 @@ true true true - 1.8 + ${jdk.version} false true From 65b18b57bb1ddf192bd583985ef1ee118ed9b29c Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Wed, 20 Jun 2018 11:00:48 +0200 Subject: [PATCH 3/6] Update travis JDK --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 6be4786ae3..f9a66a457b 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,6 +1,6 @@ language: java jdk: - - oraclejdk8 + - oraclejdk9 sudo: required cache: directories: From 519a4b7858274ff84dafa4ebfea4fc521e59912a Mon Sep 17 00:00:00 2001 From: Spencer Bliven Date: Wed, 20 Jun 2018 11:01:03 +0200 Subject: [PATCH 4/6] Update maven plugin versions. --- pom.xml | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/pom.xml b/pom.xml index f1eb533df9..92a0e4a933 100644 --- a/pom.xml +++ b/pom.xml @@ -171,7 +171,7 @@ maven-dependency-plugin - 3.0.2 + 3.1.1 maven-jar-plugin @@ -179,11 +179,11 @@ there are some config changes required. see https://github.com/biojava/biojava/issues/531 --> - 3.0.2 + 3.1.0 maven-scm-plugin - 1.9.5 + 1.10.0 maven-source-plugin @@ -191,7 +191,7 @@ maven-failsafe-plugin - 2.21.0 + 2.22.0 net.sf @@ -201,7 +201,7 @@ org.jvnet.jaxb2.maven2 maven-jaxb2-plugin - 0.13.1 + 0.14.0 org.apache.maven.plugins @@ -224,7 +224,7 @@ org.apache.maven.plugins maven-javadoc-plugin - 3.0.0 + 3.0.1 -Xdoclint:none @@ -242,7 +242,7 @@ org.apache.maven.plugins maven-shade-plugin - 3.1.0 + 3.1.1 maven-assembly-plugin @@ -280,18 +280,18 @@ org.apache.maven.plugins maven-checkstyle-plugin - 2.17 + 3.0.0 org.apache.maven.plugins maven-resources-plugin - 3.0.2 + 3.1.0 maven-enforcer-plugin - 3.0.0-M1 + 3.0.0-M2 enforce-java @@ -316,12 +316,12 @@ org.apache.maven.plugins maven-surefire-plugin - 2.21.0 + 2.22.0 org.apache.maven.plugins maven-site-plugin - 3.7 + 3.7.1 From 44176e9a0709f7558fba5a1e73fd24bf7fb28f7c Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Fri, 7 Sep 2018 13:57:48 -0700 Subject: [PATCH 5/6] Explicit jaxb dependencies so that biojava can compile/run in all jdks up to 11 --- biojava-structure/pom.xml | 14 ++++++++++++++ pom.xml | 15 +++++++++++++++ 2 files changed, 29 insertions(+) diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 3d5adc40df..6db447ae6f 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -62,10 +62,24 @@ 1.1.0 + javax.xml.bind jaxb-api + + com.sun.xml.bind + jaxb-core + + + com.sun.xml.bind + jaxb-impl + + + javax.activation + activation + diff --git a/pom.xml b/pom.xml index 4a59004073..3d9e561ebc 100644 --- a/pom.xml +++ b/pom.xml @@ -512,6 +512,21 @@ jaxb-api 2.3.0 + + com.sun.xml.bind + jaxb-core + 2.3.0 + + + com.sun.xml.bind + jaxb-impl + 2.3.0 + + + javax.activation + activation + 1.1.1 + From 5affcac6191e3af6c9005f1a4f43cd2d95980950 Mon Sep 17 00:00:00 2001 From: Jose Manuel Duarte Date: Fri, 7 Sep 2018 14:32:05 -0700 Subject: [PATCH 6/6] Keeping the java 8 compliance level (compiled byte code is 8). Still it works under 9, 10, 11 JREs --- pom.xml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/pom.xml b/pom.xml index 3d9e561ebc..83082896ee 100644 --- a/pom.xml +++ b/pom.xml @@ -32,8 +32,9 @@ - 9 - 9 + + 1.8 + 1.8 UTF-8 UTF-8