[med-svn] r23335 - in trunk/packages/biojava4-live/tags: . 4.2.4+dfsg-2/debian 4.2.4+dfsg-2/debian/patches
Olivier Sallou
osallou at moszumanska.debian.org
Tue Dec 20 10:42:50 UTC 2016
Author: osallou
Date: 2016-12-20 10:42:49 +0000 (Tue, 20 Dec 2016)
New Revision: 23335
Added:
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/README.source
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/build.xml
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/changelog
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/control
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/get-orig-source
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_ascii_characters_mapping
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_import
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_itext_class_updates
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/ignore_fake_tests
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/remove_openchart_use
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/series
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/skip_network_related_tests
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/use_simple_json
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/watch
Removed:
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/README.source
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/build.xml
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/changelog
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/control
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/get-orig-source
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_ascii_characters_mapping
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_import
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_itext_class_updates
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/series
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/skip_network_related_tests
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/use_simple_json
trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/watch
Log:
[svn-buildpackage] Tagging biojava4-live 4.2.4+dfsg-2
Deleted: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/README.source
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/README.source 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/README.source 2016-12-20 10:42:49 UTC (rev 23335)
@@ -1,16 +0,0 @@
-biojava for Debian
-------------------
-
-Biojava uses the forester library version 0.955.
-The source version is hosted in Biojava repo only and does not
-match any release available in forester web site. To manage,
-a specific biojava4-forester library is created.
-
-Same for jcolorbrewer
-
-The get-orig-source embeds this library version in the code.
-
-json.org dependency is replaced by json-simple with a patch for biojava3-ws.
-Future release will use json-lib
-
-Some tests are skipped due to errors dependending on context (nfs dirs), remote access required....
Copied: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/README.source (from rev 23275, trunk/packages/biojava4-live/trunk/debian/README.source)
===================================================================
--- trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/README.source (rev 0)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/README.source 2016-12-20 10:42:49 UTC (rev 23335)
@@ -0,0 +1,16 @@
+biojava for Debian
+------------------
+
+Biojava uses the forester library version 0.955.
+The source version is hosted in maven/biojava repo only and does not
+match any release available in forester web site. To manage,
+a specific biojava4-forester library is created.
+
+Same for jcolorbrewer
+
+The get-orig-source embeds this library version in the code.
+
+json.org dependency is replaced by json-simple with a patch for biojava3-ws.
+Future release will use json-lib
+
+Some tests are skipped due to errors dependending on context (nfs dirs), remote access required....
Deleted: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/build.xml
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/build.xml 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/build.xml 2016-12-20 10:42:49 UTC (rev 23335)
@@ -1,122 +0,0 @@
-<?xml version="1.0" ?>
-<project name="BJLIB" default="jar" basedir=".">
- <!-- Directory structure -->
- <property name="build.dir" location="../build/BJLIB"/>
- <property name="test.dir" location="../buildtest/BJLIB"/>
- <property name="dist.dir" location="../dist"/>
- <property name="src.dir" location="src/main/java"/>
- <property name="resources.dir" location="src/main/resources"/>
- <property name="test.src.dir" location="src/test/java"/>
- <property name="test.resources.dir" location="src/test/resources"/>
- <property name="lib.dir" location="/usr/share/java"/>
- <property name="docs.dir" location="../javadoc"/>
- <property name="docs.lib.dir" location="../doc/BJLIB"/>
- <property name="class.dir" location="${build.dir}/classes"/>
- <property name="test.class.dir" location="${test.dir}/classes"/>
-
- <property name="project.name" value="biojava"/>
- <property name="debug" value="true"/>
- <property name="optimized" value="true"/>
- <property name="project.version" value="1.8.2"/>
- <property environment="env"/>
- <property name="project.jarfile.name" value="BJLIB.jar"/>
-
- <property name="class.path" value="${lib.dir}/commons-logging.jar ${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections3.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/junit4.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar ${lib.dir}/Jmol.jar /usr/share/icedtea-web/netx.jar ${lib.dir}/hamcrest.jar ${lib.dir}/json_simple.jar ${lib.dir}/commons-codec.jar ${lib.dir}/itext5.jar ${lib.dir}/Jmol.jar ${lib.dir}/log4j2.jar ${lib.dir}/json-simple.jar ${lib.dir}/slf4j-api.jar ${lib.dir}/log4j-over-slf4j.jar ${lib.dir}/commons-math.jar ${lib.dir}/xmlunit.jar"/>
-
- <path id="compile.classpath">
- <fileset dir="${lib.dir}">
- <include name="commons-cli.jar"/>
- <include name="xmlunit.jar"/>
- <include name="commons-collections3.jar"/>
- <include name="commons-dbcp.jar"/>
- <include name="commons-logging.jar"/>
- <include name="commons-pool.jar"/>
- <include name="commons-codec.jar"/>
- <include name="commons-math.jar"/>
- <include name="itext5.jar"/>
- <include name="Jmol.jar"/>
- <include name="junit4.jar"/>
- <include name="guava.jar"/>
- <include name="jgrapht0.8.jar"/>
- <include name="JmolApplet.jar"/>
- <include name="hamcrest.jar"/>
- <include name="json-simple.jar"/>
- <include name="log4j2.jar"/>
- <include name="slf4j-api.jar"/>
- <include name="log4j-over-slf4j.jar"/>
- </fileset>
- <fileset dir="${dist.dir}">
- <include name="*.jar"/>
- </fileset>
- <fileset dir="/usr/share/icedtea-web">
- <include name="netx.jar"/>
- </fileset>
- </path>
-
-
- <target name="clean">
- <echo level="info">Cleaning build directories</echo>
- <delete verbose="true" includeEmptyDirs="true">
- <fileset dir="${build.dir}" includes="**"/>
- <fileset dir="${dist.dir}" includes="${project.name}*.jar"/>
- </delete>
- </target>
-
- <target name="javadocs">
- <mkdir dir="${docs.dir}"/>
- <mkdir dir="${docs.lib.dir}"/>
- <javadoc destdir="${docs.lib.dir}" sourcepath="${src.dir}" packagenames="org.*" encoding="UTF-8">
- <link href="http://java.sun.com/j2se/1.6.0/docs/api/"/>
- </javadoc>
- </target>
-
- <target name="compile">
- <mkdir dir="${class.dir}"/>
- <mkdir dir="${dist.dir}"/>
- <javac srcdir="${src.dir}" destdir="${class.dir}" classpathref="compile.classpath" debug="${debug}" optimize="${optimized}" nowarn="true" source="1.6" target="1.6">
- </javac>
- <copy todir="${class.dir}" failonerror="false">
- <fileset dir="${resources.dir}"/>
- </copy>
- </target>
-
- <target name="compile-test">
- <mkdir dir="${test.class.dir}"/>
- <javac srcdir="${test.src.dir}" destdir="${test.class.dir}" classpathref="compile.classpath" debug="${debug}" optimize="${optimized}" nowarn="true">
- </javac>
- <copy todir="${test.class.dir}" failonerror="false">
- <fileset dir="${test.resources.dir}"/>
- </copy>
- <copy todir="${test.class.dir}" failonerror="false">
- <fileset dir="${src.dir}"/>
- </copy>
- </target>
-
- <path id="test.classpath">
- <path refid="compile.classpath"/>
- <pathelement location="${test.class.dir}" />
- </path>
-
- <target name="test" depends="compile-test">
- <junit haltonfailure="yes" printsummary="yes" fork="true">
- <classpath refid="test.classpath"/>
- <formatter type="plain" usefile="false" />
- <batchtest>
- <fileset dir="${test.class.dir}" includes="**/*Test.class" excludes="**/Abstract*.class" />
- </batchtest>
- </junit>
- </target>
-
- <target name="jar" depends="compile">
- <jar destfile="${dist.dir}/${project.jarfile.name}" basedir="${class.dir}" >
- <manifest>
- <attribute name="Built-By" value="Debian-Med team"/>
- <attribute name="Class-Path" value="${class.path}"/>
- <attribute name="Specification-Title" value="BioJava"/>
- <attribute name="Specification-Version" value="${project.version}"/>
- </manifest>
- </jar>
- </target>
-
-</project>
-
Copied: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/build.xml (from rev 23275, trunk/packages/biojava4-live/trunk/debian/build.xml)
===================================================================
--- trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/build.xml (rev 0)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/build.xml 2016-12-20 10:42:49 UTC (rev 23335)
@@ -0,0 +1,122 @@
+<?xml version="1.0" ?>
+<project name="BJLIB" default="jar" basedir=".">
+ <!-- Directory structure -->
+ <property name="build.dir" location="../build/BJLIB"/>
+ <property name="test.dir" location="../buildtest/BJLIB"/>
+ <property name="dist.dir" location="../dist"/>
+ <property name="src.dir" location="src/main/java"/>
+ <property name="resources.dir" location="src/main/resources"/>
+ <property name="test.src.dir" location="src/test/java"/>
+ <property name="test.resources.dir" location="src/test/resources"/>
+ <property name="lib.dir" location="/usr/share/java"/>
+ <property name="docs.dir" location="../javadoc"/>
+ <property name="docs.lib.dir" location="../doc/BJLIB"/>
+ <property name="class.dir" location="${build.dir}/classes"/>
+ <property name="test.class.dir" location="${test.dir}/classes"/>
+
+ <property name="project.name" value="biojava"/>
+ <property name="debug" value="true"/>
+ <property name="optimized" value="true"/>
+ <property name="project.version" value="1.8.2"/>
+ <property environment="env"/>
+ <property name="project.jarfile.name" value="BJLIB.jar"/>
+
+ <property name="class.path" value="${lib.dir}/commons-logging.jar ${lib.dir}/commons-cli.jar ${lib.dir}/commons-collections3.jar ${lib.dir}/commons-dbcp.jar ${lib.dir}/junit4.jar ${lib.dir}/commons-pool.jar ${lib.dir}/guava.jar ${lib.dir}/jgrapht0.8.jar ${lib.dir}/Jmol.jar /usr/share/icedtea-web/netx.jar ${lib.dir}/hamcrest.jar ${lib.dir}/json_simple.jar ${lib.dir}/commons-codec.jar ${lib.dir}/itext5.jar ${lib.dir}/Jmol.jar ${lib.dir}/log4j2.jar ${lib.dir}/json-simple.jar ${lib.dir}/slf4j-api.jar ${lib.dir}/log4j-over-slf4j.jar ${lib.dir}/commons-math.jar ${lib.dir}/xmlunit.jar"/>
+
+ <path id="compile.classpath">
+ <fileset dir="${lib.dir}">
+ <include name="commons-cli.jar"/>
+ <include name="xmlunit.jar"/>
+ <include name="commons-collections3.jar"/>
+ <include name="commons-dbcp.jar"/>
+ <include name="commons-logging.jar"/>
+ <include name="commons-pool.jar"/>
+ <include name="commons-codec.jar"/>
+ <include name="commons-math.jar"/>
+ <include name="itext5.jar"/>
+ <include name="Jmol.jar"/>
+ <include name="junit4.jar"/>
+ <include name="guava.jar"/>
+ <include name="jgrapht0.8.jar"/>
+ <include name="JmolApplet.jar"/>
+ <include name="hamcrest.jar"/>
+ <include name="json-simple.jar"/>
+ <include name="log4j2.jar"/>
+ <include name="slf4j-api.jar"/>
+ <include name="log4j-over-slf4j.jar"/>
+ </fileset>
+ <fileset dir="${dist.dir}">
+ <include name="*.jar"/>
+ </fileset>
+ <fileset dir="/usr/share/icedtea-web">
+ <include name="netx.jar"/>
+ </fileset>
+ </path>
+
+
+ <target name="clean">
+ <echo level="info">Cleaning build directories</echo>
+ <delete verbose="true" includeEmptyDirs="true">
+ <fileset dir="${build.dir}" includes="**"/>
+ <fileset dir="${dist.dir}" includes="${project.name}*.jar"/>
+ </delete>
+ </target>
+
+ <target name="javadocs">
+ <mkdir dir="${docs.dir}"/>
+ <mkdir dir="${docs.lib.dir}"/>
+ <javadoc destdir="${docs.lib.dir}" sourcepath="${src.dir}" packagenames="org.*" encoding="UTF-8">
+ <link href="http://java.sun.com/j2se/1.6.0/docs/api/"/>
+ </javadoc>
+ </target>
+
+ <target name="compile">
+ <mkdir dir="${class.dir}"/>
+ <mkdir dir="${dist.dir}"/>
+ <javac srcdir="${src.dir}" destdir="${class.dir}" classpathref="compile.classpath" debug="${debug}" optimize="${optimized}" nowarn="true" source="1.7" target="1.7">
+ </javac>
+ <copy todir="${class.dir}" failonerror="false">
+ <fileset dir="${resources.dir}"/>
+ </copy>
+ </target>
+
+ <target name="compile-test">
+ <mkdir dir="${test.class.dir}"/>
+ <javac srcdir="${test.src.dir}" destdir="${test.class.dir}" classpathref="compile.classpath" debug="${debug}" optimize="${optimized}" nowarn="true">
+ </javac>
+ <copy todir="${test.class.dir}" failonerror="false">
+ <fileset dir="${test.resources.dir}"/>
+ </copy>
+ <copy todir="${test.class.dir}" failonerror="false">
+ <fileset dir="${src.dir}"/>
+ </copy>
+ </target>
+
+ <path id="test.classpath">
+ <path refid="compile.classpath"/>
+ <pathelement location="${test.class.dir}" />
+ </path>
+
+ <target name="test" depends="compile-test">
+ <junit haltonfailure="yes" printsummary="yes" fork="true">
+ <classpath refid="test.classpath"/>
+ <formatter type="plain" usefile="false" />
+ <batchtest>
+ <fileset dir="${test.class.dir}" includes="**/*Test.class" excludes="**/Abstract*.class" />
+ </batchtest>
+ </junit>
+ </target>
+
+ <target name="jar" depends="compile">
+ <jar destfile="${dist.dir}/${project.jarfile.name}" basedir="${class.dir}" >
+ <manifest>
+ <attribute name="Built-By" value="Debian-Med team"/>
+ <attribute name="Class-Path" value="${class.path}"/>
+ <attribute name="Specification-Title" value="BioJava"/>
+ <attribute name="Specification-Version" value="${project.version}"/>
+ </manifest>
+ </jar>
+ </target>
+
+</project>
+
Deleted: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/changelog
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/changelog 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/changelog 2016-12-20 10:42:49 UTC (rev 23335)
@@ -1,37 +0,0 @@
-biojava4-live (4.1.0+dfsg-4) unstable; urgency=medium
-
- * Team upload.
- * d/rules: export LC_ALL=C.UTF-8
- * Fix clean target
- * d/watch: do not report beta versions
- * d/rules: tolerate test failures of biojava-core which happens in stretch
- sbuild environments for no obvious reasons
- Closes: #843712
- * cme fix dpkg-control
- * debhelper 10
-
- -- Andreas Tille <tille at debian.org> Thu, 24 Nov 2016 14:45:01 +0100
-
-biojava4-live (4.1.0+dfsg-3) unstable; urgency=medium
-
- * Fix FTBS unmappable characters (Closes: #795849).
-
- -- Olivier Sallou <osallou at debian.org> Mon, 17 Aug 2015 14:54:33 +0000
-
-biojava4-live (4.1.0+dfsg-2) unstable; urgency=medium
-
- * Remove some network related tests (Closes: #795685).
-
- -- Olivier Sallou <osallou at debian.org> Sun, 16 Aug 2015 16:33:47 +0200
-
-biojava4-live (4.1.0+dfsg-1) unstable; urgency=medium
-
- * New upstream release
-
- -- Olivier Sallou <osallou at debian.org> Wed, 12 Aug 2015 09:32:50 +0200
-
-biojava4-live (4.0.0+dfsg-1) unstable; urgency=medium
-
- * BioJava4 packaging (Closes: #776704).
-
- -- Olivier Sallou <osallou at debian.org> Fri, 30 Jan 2015 17:24:21 +0100
Copied: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/changelog (from rev 23334, trunk/packages/biojava4-live/trunk/debian/changelog)
===================================================================
--- trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/changelog (rev 0)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/changelog 2016-12-20 10:42:49 UTC (rev 23335)
@@ -0,0 +1,50 @@
+biojava4-live (4.2.4+dfsg-2) unstable; urgency=medium
+
+ * d/control: add jgrapht as required dependency instead of suggests
+ (Closes: #848768)
+
+ -- Olivier Sallou <osallou at debian.org> Tue, 20 Dec 2016 10:48:01 +0100
+
+biojava4-live (4.2.4+dfsg-1) unstable; urgency=medium
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> Mon, 05 Dec 2016 09:37:13 +0100
+
+biojava4-live (4.1.0+dfsg-4) unstable; urgency=medium
+
+ * Team upload.
+ * d/rules: export LC_ALL=C.UTF-8
+ * Fix clean target
+ * d/watch: do not report beta versions
+ * d/rules: tolerate test failures of biojava-core which happens in stretch
+ sbuild environments for no obvious reasons
+ Closes: #843712
+ * cme fix dpkg-control
+ * debhelper 10
+
+ -- Andreas Tille <tille at debian.org> Thu, 24 Nov 2016 14:45:01 +0100
+
+biojava4-live (4.1.0+dfsg-3) unstable; urgency=medium
+
+ * Fix FTBS unmappable characters (Closes: #795849).
+
+ -- Olivier Sallou <osallou at debian.org> Mon, 17 Aug 2015 14:54:33 +0000
+
+biojava4-live (4.1.0+dfsg-2) unstable; urgency=medium
+
+ * Remove some network related tests (Closes: #795685).
+
+ -- Olivier Sallou <osallou at debian.org> Sun, 16 Aug 2015 16:33:47 +0200
+
+biojava4-live (4.1.0+dfsg-1) unstable; urgency=medium
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 12 Aug 2015 09:32:50 +0200
+
+biojava4-live (4.0.0+dfsg-1) unstable; urgency=medium
+
+ * BioJava4 packaging (Closes: #776704).
+
+ -- Olivier Sallou <osallou at debian.org> Fri, 30 Jan 2015 17:24:21 +0100
Deleted: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/control
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/control 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/control 2016-12-20 10:42:49 UTC (rev 23335)
@@ -1,100 +0,0 @@
-Source: biojava4-live
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Olivier Sallou <osallou at debian.org>
-Section: java
-Priority: optional
-Build-Depends: debhelper (>= 10),
- ant
-Build-Depends-Indep: libcommons-dbcp-java,
- libhsqldb-java,
- libcommons-collections3-java,
- libcommons-pool-java,
- libcommons-logging-java,
- libcommons-math-java,
- libcommons-cli-java,
- libguava-java (>= 17.0),
- libcommons-codec-java,
- libitext5-java (>= 5.4.1),
- libjmol-java,
- default-jdk (>= 1:1.6),
- junit4,
- javahelper,
- ant-optional,
- icedtea-netx,
- libhamcrest-java,
- libjson-simple-java (>= 1.1.1),
- liblog4j2-java,
- libslf4j-java,
- libxmlunit-java
-Standards-Version: 3.9.8
-Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/biojava4-live/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/biojava4-live/trunk/
-Homepage: http://www.biojava.org
-
-Package: libbiojava4.0-java
-Architecture: all
-Depends: ${java:Depends},
- ${misc:Depends},
- libcommons-pool-java,
- libcommons-collections3-java,
- libcommons-dbcp-java,
- libcommons-logging-java,
- libhsqldb-java,
- libbytecode-java,
- icedtea-netx,
- libjson-simple-java,
- libcommons-codec-java,
- libitext5-java (>= 5.4.1),
- libjmol-java,
- liblog4j2-java,
- libguava-java (>= 17.0),
- libslf4j-java,
- libcommons-math-java
-Suggests: java-virtual-machine,
- libjgrapht-java,
- libbiojava4-java,
- libbiojava4-java-doc
-Description: Java API to biological data and applications (version 4)
- This package presents the Open Source Java API to biological databases
- and a series of mostly sequence-based algorithms.
- .
- BioJava is an open-source project dedicated to providing a Java framework
- for processing biological data. It includes objects for manipulating
- sequences, file parsers, server support, access to BioSQL
- and Ensembl databases, and powerful analysis and statistical routines
- including a dynamic programming toolkit.
-
-Package: libbiojava4-java
-Architecture: all
-Depends: libbiojava4.0-java,
- ${misc:Depends}
-Provides: libbiojava4-java
-Description: Java API to biological data and applications (default version)
- BioJava is an open-source project dedicated to providing a Java framework
- for processing biological data. It includes objects for manipulating
- sequences, file parsers, server support, access to BioSQL
- and Ensembl databases, and powerful analysis and statistical routines
- including a dynamic programming toolkit.
- .
- BioJava is provided by a vibrant community which meets annually at
- the Bioinformatics Open Source Conference (BOSC) that traditionally
- accompanies the Intelligent Systems in Molecular Biology (ISMB)
- meeting. Much like BioPerl, the employment of this library is valuable
- for everybody active in the field because of the many tricks of the
- trade one learns just by communicating on the mailing list.
- .
- This is a wrapper package which should enable smooth upgrades to new
- versions.
-
-Package: libbiojava4-java-doc
-Architecture: all
-Section: doc
-Depends: ${misc:Depends}
-Suggests: libbiojava4-java-demos,
- libbiojava4-java
-Description: [Biology] Documentation for BioJava
- BioJava is an open-source project dedicated to providing a Java framework
- for processing biological data.
- .
- This package contains the HTML documentation describing the API of BioJava
- which was generated automatically by JavaDoc.
Copied: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/control (from rev 23333, trunk/packages/biojava4-live/trunk/debian/control)
===================================================================
--- trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/control (rev 0)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/control 2016-12-20 10:42:49 UTC (rev 23335)
@@ -0,0 +1,101 @@
+Source: biojava4-live
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
+Section: java
+Priority: optional
+Build-Depends: debhelper (>= 10),
+ ant
+Build-Depends-Indep: libcommons-dbcp-java,
+ libhsqldb-java,
+ libcommons-collections3-java,
+ libcommons-pool-java,
+ libcommons-logging-java,
+ libcommons-math-java,
+ libcommons-cli-java,
+ libguava-java (>= 17.0),
+ libcommons-codec-java,
+ libitext5-java (>= 5.4.1),
+ libjmol-java,
+ default-jdk (>= 1:1.6),
+ junit4,
+ javahelper,
+ ant-optional,
+ icedtea-netx,
+ libhamcrest-java,
+ libjson-simple-java (>= 1.1.1),
+ liblog4j2-java,
+ libslf4j-java,
+ libxmlunit-java,
+ libjgrapht-java
+Standards-Version: 3.9.8
+Vcs-Browser: https://anonscm.debian.org/viewvc/debian-med/trunk/packages/biojava4-live/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/biojava4-live/trunk/
+Homepage: http://www.biojava.org
+
+Package: libbiojava4.0-java
+Architecture: all
+Depends: ${java:Depends},
+ ${misc:Depends},
+ libcommons-pool-java,
+ libcommons-collections3-java,
+ libcommons-dbcp-java,
+ libcommons-logging-java,
+ libhsqldb-java,
+ libbytecode-java,
+ icedtea-netx,
+ libjson-simple-java,
+ libcommons-codec-java,
+ libitext5-java (>= 5.4.1),
+ libjmol-java,
+ liblog4j2-java,
+ libguava-java (>= 17.0),
+ libslf4j-java,
+ libcommons-math-java,
+ libjgrapht-java
+Suggests: java-virtual-machine,
+ libbiojava4-java,
+ libbiojava4-java-doc
+Description: Java API to biological data and applications (version 4)
+ This package presents the Open Source Java API to biological databases
+ and a series of mostly sequence-based algorithms.
+ .
+ BioJava is an open-source project dedicated to providing a Java framework
+ for processing biological data. It includes objects for manipulating
+ sequences, file parsers, server support, access to BioSQL
+ and Ensembl databases, and powerful analysis and statistical routines
+ including a dynamic programming toolkit.
+
+Package: libbiojava4-java
+Architecture: all
+Depends: libbiojava4.0-java,
+ ${misc:Depends}
+Provides: libbiojava4-java
+Description: Java API to biological data and applications (default version)
+ BioJava is an open-source project dedicated to providing a Java framework
+ for processing biological data. It includes objects for manipulating
+ sequences, file parsers, server support, access to BioSQL
+ and Ensembl databases, and powerful analysis and statistical routines
+ including a dynamic programming toolkit.
+ .
+ BioJava is provided by a vibrant community which meets annually at
+ the Bioinformatics Open Source Conference (BOSC) that traditionally
+ accompanies the Intelligent Systems in Molecular Biology (ISMB)
+ meeting. Much like BioPerl, the employment of this library is valuable
+ for everybody active in the field because of the many tricks of the
+ trade one learns just by communicating on the mailing list.
+ .
+ This is a wrapper package which should enable smooth upgrades to new
+ versions.
+
+Package: libbiojava4-java-doc
+Architecture: all
+Section: doc
+Depends: ${misc:Depends}
+Suggests: libbiojava4-java-demos,
+ libbiojava4-java
+Description: [Biology] Documentation for BioJava
+ BioJava is an open-source project dedicated to providing a Java framework
+ for processing biological data.
+ .
+ This package contains the HTML documentation describing the API of BioJava
+ which was generated automatically by JavaDoc.
Deleted: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/get-orig-source
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/get-orig-source 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/get-orig-source 2016-12-20 10:42:49 UTC (rev 23335)
@@ -1,48 +0,0 @@
-#!/bin/bash
-
-set -e
-
-PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
-VERSION=`uscan --verbose --force-download |
- grep "Newest version on remote site is .* local version is .*" |
- head -n 1 |
- sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"`
-
-
-mkdir -p ../tarballs
-
-cd ../tarballs
-UTAR="biojava-${VERSION}.tar.gz"
-mv ../${UTAR} .
-tar -xzf ${UTAR}
-
-mv biojava-biojava-${VERSION} $PKG-${VERSION}.orig # .orig is requested by Developers Reference 3.4.4 §6.7.8.2
-
-cd $PKG-${VERSION}.orig
- rm -rf target
- rm -rf biojava/dist/*.jar
-
-mkdir -p biojava-forester/src/main/java
-cd biojava-forester/src/main/java
- #wget http://www.biojava.org/download/maven/org/forester/forester-1.005-sources/1.005/forester-1.005-sources-1.005.jar
- wget http://www.biojava.org/download/maven/org/forester/forester-lgpl/1.005/forester-lgpl-1.005-sources.jar
- #jar xf forester-1.005-sources-1.005.jar
- jar xf forester-lgpl-1.005-sources.jar
- find . -name *.class | xargs rm -f
- rm -f resources/*.jar
- rm forester-lgpl-1.005-sources.jar
- #rm forester-1.005-sources-1.005.jar
-cd ../../../..
-mkdir -p biojava-jcolorbrewer/src/main/java
-cd biojava-jcolorbrewer/src/main/java
- wget -O jcolorbrewer-5.2-sources.jar "https://search.maven.org/remotecontent?filepath=org/biojava/jcolorbrewer/5.2/jcolorbrewer-5.2-sources.jar"
- jar xf jcolorbrewer-5.2-sources.jar
- rm jcolorbrewer-5.2-sources.jar
-cd ../../../..
-cd ..
-
-BZIP2="--best" tar -cjf ${PKG}_${VERSION}+dfsg.orig.tar.bz2 ${PKG}-${VERSION}.orig
-rm -rf ${PKG}-${VERSION}.orig
-
-rm ${UTAR}
-
Copied: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/get-orig-source (from rev 23275, trunk/packages/biojava4-live/trunk/debian/get-orig-source)
===================================================================
--- trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/get-orig-source (rev 0)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/get-orig-source 2016-12-20 10:42:49 UTC (rev 23335)
@@ -0,0 +1,50 @@
+#!/bin/bash
+
+set -e
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`uscan --verbose --force-download |
+ grep "Newest version of biojava4-live on remote site is .* local version is .*" |
+ head -n 1 |
+ sed "s/.*Newest version of biojava4-live on remote site is \([a-z0-9.]\+\),.*/\1/"`
+
+mkdir -p ../tarballs
+
+cd ../tarballs
+UTAR="biojava-${VERSION}.tar.gz"
+mv ../${UTAR} .
+tar -xzf ${UTAR}
+
+mv biojava-biojava-${VERSION} $PKG-${VERSION}.orig # .orig is requested by Developers Reference 3.4.4 §6.7.8.2
+
+cd $PKG-${VERSION}.orig
+ rm -rf target
+ rm -rf biojava/dist/*.jar
+
+mkdir -p biojava-forester/src/main/java
+cd biojava-forester/src/main/java
+ #wget http://www.biojava.org/download/maven/org/forester/forester-1.005-sources/1.005/forester-1.005-sources-1.005.jar
+ #wget http://www.biojava.org/download/maven/org/forester/forester-lgpl/1.005/forester-lgpl-1.005-sources.jar
+ wget -O forester-1.038-sources.jar "https://search.maven.org/remotecontent?filepath=org/biojava/thirdparty/forester/1.038/forester-1.038-sources.jar"
+ #jar xf forester-1.005-sources-1.005.jar
+ #jar xf forester-lgpl-1.005-sources.jar
+ jar xf forester-1.038-sources.jar
+ find . -name *.class | xargs rm -f
+ rm -f resources/*.jar
+ rm forester-1.038-sources.jar
+ #rm forester-lgpl-1.005-sources.jar
+ #rm forester-1.005-sources-1.005.jar
+cd ../../../..
+mkdir -p biojava-jcolorbrewer/src/main/java
+cd biojava-jcolorbrewer/src/main/java
+ wget -O jcolorbrewer-5.2-sources.jar "https://search.maven.org/remotecontent?filepath=org/biojava/jcolorbrewer/5.2/jcolorbrewer-5.2-sources.jar"
+ jar xf jcolorbrewer-5.2-sources.jar
+ rm jcolorbrewer-5.2-sources.jar
+cd ../../../..
+cd ..
+
+BZIP2="--best" tar -cjf ${PKG}_${VERSION}+dfsg.orig.tar.bz2 ${PKG}-${VERSION}.orig
+rm -rf ${PKG}-${VERSION}.orig
+
+rm ${UTAR}
+
Deleted: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_ascii_characters_mapping
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_ascii_characters_mapping 2016-12-20 10:42:49 UTC (rev 23335)
@@ -1,105 +0,0 @@
-Subject: ASCII error in pbuilder
-Description: unmappable character for encoding ASCII
-Author: Olivier Sallou <osallou at debian.org>
-Last-Updated: 2012-12-05
-Forwarded: yes
-Bug: http://code.google.com/p/forester/issues/detail?id=1
---- a/biojava-forester/src/main/java/org/forester/test/Test.java
-+++ b/biojava-forester/src/main/java/org/forester/test/Test.java
-@@ -1310,7 +1310,7 @@
- return false;
- }
- if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
-- .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) {
-+ .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489-493." ) ) ) {
- return false;
- }
- if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
---- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SuperPosition.java
-+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/geometry/SuperPosition.java
-@@ -162,7 +162,6 @@
-
- /**
- * Returns the TM-Score for two superimposed sets of coordinates
-- * Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)
- * @param x coordinate set 1
- * @param y coordinate set 2
- * @param lengthNative total length of native sequence
---- a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java
-+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/core/QuatSuperpositionScorer.java
-@@ -36,7 +36,6 @@
- /**
- * Returns minimum, mean, and maximum RMSD and TM-Score for two superimposed sets of subunits
- *
-- * TM score: Yang Zhang and Jeffrey Skolnick, PROTEINS: Structure, Function, and Bioinformatics 57:702–710 (2004)
- * @param subunits subunits to be scored
- * @param transformation transformation matrix
- * @param permutations permutation that determines which subunits are superposed
---- a/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java
-+++ b/biojava-structure/src/main/java/org/biojava/nbio/structure/ResidueRangeAndLength.java
-@@ -30,7 +30,6 @@
- /**
- * A chain, a start residue, and an end residue.
- *
-- * Also stores a length. Because of insertion codes, this length is not necessarily {@code end − start}.
- */
- public class ResidueRangeAndLength extends ResidueRange {
- private static final Logger logger = LoggerFactory.getLogger(ResidueRangeAndLength.class);
---- a/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java
-+++ b/biojava-modfinder/src/main/java/org/biojava/nbio/phosphosite/Dataset.java
-@@ -29,13 +29,13 @@
- import java.util.List;
-
- /**
-- * Phosphosite is available under the PhosphoSitePlus® is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License and is freely available for non-commercial purposes from
-+ * Phosphosite is available under the PhosphoSitePlus is licensed under Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License and is freely available for non-commercial purposes from
- *
- * http://www.phosphosite.org/staticDownloads.do
- *
-- * Please acknowledge PhosphoSitePlus®, www.phosphosite.org" at appropriate locations.
-+ * Please acknowledge PhosphoSitePlus, www.phosphosite.org" at appropriate locations.
- *
-- * Please cite : “Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261–70.”.
-+ * Please cite : "Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261-70.".
- *
- (
- *
-@@ -111,7 +111,7 @@
- public void download(){
-
- System.out.println("Downloading data from www.phosposite.org. Data is under CC-BY-NC-SA license. Please link to site and cite: ");
-- System.out.println("Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261–70.");
-+ System.out.println("Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M (2012) PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 40(Database issue), D261-70.");
-
- File dir = getLocalDir();
-
---- a/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java
-+++ b/biojava-ontology/src/main/java/org/biojava/nbio/ontology/utils/Annotatable.java
-@@ -74,7 +74,7 @@
- * immutable Annotation instances that are built from scratch each time.
- * @author Matthew Pocock
- * @author <a href="mailto:kdj at sanger.ac.uk">Keith James</a> (docs).
-- * @author Kalle N�slund (docs)
-+ * @author Kalle Nslund (docs)
- * @see org.biojavax.RichAnnotatable
- * @since 1.0
- */
---- a/biojava-structure-gui/src/main/java/demo/DemoOrientBioAssembly.java
-+++ b/biojava-structure-gui/src/main/java/demo/DemoOrientBioAssembly.java
-@@ -57,11 +57,11 @@
- 2WPD has 2 local symmetries.
-
- Other examples with a single local symmetry are:
-- 4F88 – local C8
-- 1LTI – local C5
-- 2W6E – local C3
-- 2LXC – local C2
-- 3OE7 – local C3
-+ 4F88 - local C8
-+ 1LTI - local C5
-+ 2W6E - local C3
-+ 2LXC - local C2
-+ 3OE7 - local C3
-
- Local Pseudosymmetry, structure only
-
Copied: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_ascii_characters_mapping (from rev 23275, trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping)
===================================================================
--- trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_ascii_characters_mapping (rev 0)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_ascii_characters_mapping 2016-12-20 10:42:49 UTC (rev 23335)
@@ -0,0 +1,17 @@
+Subject: ASCII error in pbuilder
+Description: unmappable character for encoding ASCII
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2012-12-05
+Forwarded: yes
+Bug: http://code.google.com/p/forester/issues/detail?id=1
+--- a/biojava-forester/src/main/java/org/forester/test/Test.java
++++ b/biojava-forester/src/main/java/org/forester/test/Test.java
+@@ -2080,7 +2080,7 @@
+ return false;
+ }
+ if ( !( t3_rt.getNode( "root node" ).getNodeData().getReference().getDescription()
+- .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489–493." ) ) ) {
++ .equals( "Aguinaldo, A. M. A.; J. M. Turbeville, L. S. Linford, M. C. Rivera, J. R. Garey, R. A. Raff, & J. A. Lake (1997). \"Evidence for a clade of nematodes, arthropods and other moulting animals\". Nature 387 (6632): 489-493." ) ) ) {
+ return false;
+ }
+ if ( !t3_rt.getNode( "root node" ).getNodeData().getTaxonomy().getTaxonomyCode().equals( "ECDYS" ) ) {
Deleted: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_import
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/fix_import 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_import 2016-12-20 10:42:49 UTC (rev 23335)
@@ -1,31 +0,0 @@
-Subject: missing imports
-Description: some classes are not imported
-Author: Olivier Sallou
-Last-Updated: 2015-01-31
-Forwarded: no
---- a/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
-+++ b/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
-@@ -44,6 +44,13 @@
- import org.biojava.nbio.structure.io.FastaStructureParser;
- import org.biojava.nbio.structure.io.StructureSequenceMatcher;
-
-+import org.biojava.nbio.structure.StructureException;
-+import org.biojava.nbio.structure.Structure;
-+import org.biojava.nbio.structure.StructureTools;
-+import org.biojava.nbio.structure.Atom;
-+import org.biojava.nbio.structure.ResidueNumber;
-+
-+
- /**
- * Demo of how to use the {@link FastaStructureParser} class to read protein
- * structures from a FASTA file.
---- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MyJmolStatusListener.java
-+++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MyJmolStatusListener.java
-@@ -130,7 +130,6 @@
- }
-
-
-- @Override
- public Map<String, Object> getProperty(String arg0) {
- // TODO Auto-generated method stub
- return null;
Copied: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_import (from rev 23275, trunk/packages/biojava4-live/trunk/debian/patches/fix_import)
===================================================================
--- trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_import (rev 0)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_import 2016-12-20 10:42:49 UTC (rev 23335)
@@ -0,0 +1,31 @@
+Subject: missing imports
+Description: some classes are not imported
+Author: Olivier Sallou
+Last-Updated: 2015-01-31
+Forwarded: no
+--- a/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
++++ b/biojava-structure-gui/src/main/java/demo/DemoAlignmentFromFasta.java
+@@ -44,6 +44,13 @@
+ import org.biojava.nbio.structure.io.FastaStructureParser;
+ import org.biojava.nbio.structure.io.StructureSequenceMatcher;
+
++import org.biojava.nbio.structure.StructureException;
++import org.biojava.nbio.structure.Structure;
++import org.biojava.nbio.structure.StructureTools;
++import org.biojava.nbio.structure.Atom;
++import org.biojava.nbio.structure.ResidueNumber;
++
++
+ /**
+ * Demo of how to use the {@link FastaStructureParser} class to read protein
+ * structures from a FASTA file.
+--- a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MyJmolStatusListener.java
++++ b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/MyJmolStatusListener.java
+@@ -131,7 +131,6 @@
+ }
+
+
+- @Override
+ public Map<String, Object> getProperty(String arg0) {
+ // TODO Auto-generated method stub
+ return null;
Deleted: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_itext_class_updates
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/fix_itext_class_updates 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_itext_class_updates 2016-12-20 10:42:49 UTC (rev 23335)
@@ -1,18 +0,0 @@
-Subject: iText move a class to an other package
-Description: one of the class from iText moved to an other package.
- Upstream code needs to refer to this new package and depends on
- newer release if iText5
-Author: Olivier Sallou <osallou at debian.org>
-Last-Updated: 2013-06-18
-Forwarded: no
---- a/biojava-forester/src/main/java/org/forester/archaeopteryx/PdfExporter.java
-+++ b/biojava-forester/src/main/java/org/forester/archaeopteryx/PdfExporter.java
-@@ -39,7 +39,7 @@
- import com.itextpdf.text.DocumentException;
- import com.itextpdf.text.FontFactory;
- import com.itextpdf.text.Rectangle;
--import com.itextpdf.text.pdf.DefaultFontMapper;
-+import com.itextpdf.awt.DefaultFontMapper;
- import com.itextpdf.text.pdf.PdfContentByte;
- import com.itextpdf.text.pdf.PdfWriter;
-
Copied: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_itext_class_updates (from rev 23275, trunk/packages/biojava4-live/trunk/debian/patches/fix_itext_class_updates)
===================================================================
--- trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_itext_class_updates (rev 0)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/fix_itext_class_updates 2016-12-20 10:42:49 UTC (rev 23335)
@@ -0,0 +1,18 @@
+Subject: iText move a class to an other package
+Description: one of the class from iText moved to an other package.
+ Upstream code needs to refer to this new package and depends on
+ newer release if iText5
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2013-06-18
+Forwarded: no
+--- a/biojava-forester/src/main/java/org/forester/archaeopteryx/PdfExporter.java
++++ b/biojava-forester/src/main/java/org/forester/archaeopteryx/PdfExporter.java
+@@ -40,7 +40,7 @@
+ import com.itextpdf.text.DocumentException;
+ import com.itextpdf.text.FontFactory;
+ import com.itextpdf.text.Rectangle;
+-import com.itextpdf.text.pdf.DefaultFontMapper;
++import com.itextpdf.awt.DefaultFontMapper;
+ import com.itextpdf.text.pdf.PdfContentByte;
+ import com.itextpdf.text.pdf.PdfWriter;
+
Copied: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/ignore_fake_tests (from rev 23276, trunk/packages/biojava4-live/trunk/debian/patches/ignore_fake_tests)
===================================================================
--- trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/ignore_fake_tests (rev 0)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/ignore_fake_tests 2016-12-20 10:42:49 UTC (rev 23335)
@@ -0,0 +1,48 @@
+Subject: ignore some test classes
+Description: some class tests do not have tests inside, but junit tries to execute them.
+ Simple skip those classes with no real test to avoid errors during build.
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2016-12-09
+Forwarded: no
+--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/profeat/CookBookTest.java
++++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/profeat/CookBookTest.java
+@@ -25,7 +25,7 @@
+ import org.biojava.nbio.aaproperties.profeat.IProfeatProperties.GROUPING;
+ import org.biojava.nbio.aaproperties.profeat.IProfeatProperties.TRANSITION;
+ import org.biojava.nbio.aaproperties.profeat.ProfeatProperties;
+-//import org.junit.Test;
++import org.junit.Test;
+ import org.slf4j.Logger;
+ import org.slf4j.LoggerFactory;
+
+@@ -37,6 +37,9 @@
+
+ // TODO there's no assertions here, i.e. this is not a test! must fix! For the moment removed test tags - JD 2016-03-08
+
++ at Test
++public void testFakeTest(){}
++
+ public void shortExample1() throws Exception{
+ /*
+ * Composition
+--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/GenerateJavaCodesFromTextTest.java
++++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/GenerateJavaCodesFromTextTest.java
+@@ -20,7 +20,7 @@
+ */
+ package org.biojava.nbio.aaproperties.xml;
+
+-//import org.junit.Test;
++import org.junit.Test;
+ import org.slf4j.Logger;
+ import org.slf4j.LoggerFactory;
+
+@@ -36,6 +36,9 @@
+
+ private final static Logger logger = LoggerFactory.getLogger(GenerateJavaCodesFromTextTest.class);
+
++ at Test
++public void testFake(){}
++
+ /*
+ * Generate java codes from two text files; Symbol2Name.txt and Symbol2Weight.txt
+ */
Copied: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/remove_openchart_use (from rev 23275, trunk/packages/biojava4-live/trunk/debian/patches/remove_openchart_use)
===================================================================
--- trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/remove_openchart_use (rev 0)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/remove_openchart_use 2016-12-20 10:42:49 UTC (rev 23335)
@@ -0,0 +1,231 @@
+Subject: forester needs openchart library
+Description: biojava makes use of a limited set of forester
+ As openchart is not available in Debian, remove openchart related calls
+ to make forester compilation OK in biojava context
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2016-12-09
+Forwarded: no
+--- a/biojava-forester/src/main/java/org/forester/msa_compactor/Chart.java
++++ b/biojava-forester/src/main/java/org/forester/msa_compactor/Chart.java
+@@ -40,47 +40,22 @@
+
+ import org.forester.util.ForesterUtil;
+
+-import com.approximatrix.charting.coordsystem.BoxCoordSystem;
+-import com.approximatrix.charting.model.MultiScatterDataModel;
+-import com.approximatrix.charting.render.MultiScatterChartRenderer;
+-import com.approximatrix.charting.swing.ChartPanel;
+
+ public final class Chart extends JDialog implements ActionListener {
+
+ final private static NumberFormat NF_1 = new DecimalFormat( "0.##" );
+ private static final long serialVersionUID = -5292420246132943515L;
+- private ChartPanel _chart_panel = null;
+- private final int _initial_number_of_seqs;
++ private final int _initial_number_of_seqs=0;
+ private final JMenuItem _m_exit = new JMenuItem();
+- private final List<MsaProperties> _msa_props;
+- private final boolean _show_msa_qual;
+- private final String _title;
++ private final List<MsaProperties> _msa_props=null;
++ private final boolean _show_msa_qual=false;
++ private final String _title=null;
+
+ private Chart( final List<MsaProperties> msa_props,
+ final int initial_number_of_seqs,
+ final boolean show_msa_qual,
+ final String title ) {
+ super();
+- _msa_props = msa_props;
+- _title = title;
+- _initial_number_of_seqs = initial_number_of_seqs;
+- _show_msa_qual = show_msa_qual;
+- setTitle( "msa compactor" );
+- setSize( 600, 500 );
+- setResizable( true );
+- final JPanel content_pane = new JPanel();
+- content_pane.setLayout( new BorderLayout() );
+- setContentPane( content_pane );
+- final JMenuBar menu_bar = new JMenuBar();
+- final JMenu file_menu = new JMenu();
+- file_menu.setText( "File" );
+- _m_exit.setText( "Exit" );
+- file_menu.add( _m_exit );
+- menu_bar.add( file_menu );
+- setJMenuBar( menu_bar );
+- setDefaultCloseOperation( WindowConstants.DISPOSE_ON_CLOSE );
+- _m_exit.addActionListener( this );
+- content_pane.add( obtainChartPanel(), BorderLayout.CENTER );
+ }
+
+ @Override
+@@ -90,150 +65,4 @@
+ }
+ }
+
+- private ChartPanel obtainChartPanel() {
+- if ( _chart_panel == null ) {
+- final MultiScatterDataModel model = new MultiScatterDataModel();
+- final double[][] seqs_length = new double[ _msa_props.size() ][ 2 ];
+- int max_length = -1;
+- int min_length = Integer.MAX_VALUE;
+- double max_gap_ratio = -1;
+- double min_gap_ratio = Double.MAX_VALUE;
+- double max_avg_gap_count = -1;
+- double min_avg_gap_count = Double.MAX_VALUE;
+- for( int i = 0; i < _msa_props.size(); ++i ) {
+- seqs_length[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
+- //
+- final int length = _msa_props.get( i ).getLength();
+- seqs_length[ i ][ 1 ] = length;
+- if ( length > max_length ) {
+- max_length = length;
+- }
+- if ( length < min_length ) {
+- min_length = length;
+- }
+- //
+- final double gap_ratio = _msa_props.get( i ).getGapRatio();
+- if ( gap_ratio > max_gap_ratio ) {
+- max_gap_ratio = gap_ratio;
+- }
+- if ( gap_ratio < min_gap_ratio ) {
+- min_gap_ratio = gap_ratio;
+- }
+- //
+- final double avg_gap_count = _msa_props.get( i ).getAvgNumberOfGaps();
+- if ( avg_gap_count > max_avg_gap_count ) {
+- max_avg_gap_count = avg_gap_count;
+- }
+- if ( avg_gap_count < min_avg_gap_count ) {
+- min_avg_gap_count = avg_gap_count;
+- }
+- }
+- model.addData( seqs_length, "Length" + " (" + minMaxToString( min_length, max_length ) + ")" );
+- model.setSeriesLine( "Series " + "Length", true );
+- model.setSeriesMarker( "Series " + "Length", false );
+- final double[][] seqs_gaps = new double[ _msa_props.size() ][ 2 ];
+- double max_ent7 = -1;
+- double max_ent21 = -1;
+- double min_ent7 = Double.MAX_VALUE;
+- double min_ent21 = Double.MAX_VALUE;
+- if ( _show_msa_qual ) {
+- for( int i = 0; i < _msa_props.size(); ++i ) {
+- final double ent7 = _msa_props.get( i ).getEntropy7();
+- if ( ent7 > max_ent7 ) {
+- max_ent7 = ent7;
+- }
+- if ( ent7 < max_ent7 ) {
+- min_ent7 = ent7;
+- }
+- final double ent21 = _msa_props.get( i ).getEntropy21();
+- if ( ent21 > min_ent21 ) {
+- max_ent21 = ent21;
+- }
+- if ( ent21 < min_ent21 ) {
+- min_ent21 = ent21;
+- }
+- }
+- }
+- final double gap_ratio_factor = ( max_length / 2.0 ) / max_gap_ratio;
+- final double avg_gaps_counts_factor = ( max_length / 2.0 ) / max_avg_gap_count;
+- final double ent7_factor = ( max_length / 2.0 ) / max_ent7;
+- final double ent21_factor = ( max_length / 2.0 ) / max_ent21;
+- for( int i = 0; i < _msa_props.size(); ++i ) {
+- seqs_gaps[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
+- seqs_gaps[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getGapRatio() * gap_ratio_factor );
+- }
+- model.addData( seqs_gaps, "Gap Ratio" + " (" + minMaxToString( min_gap_ratio, max_gap_ratio ) + ")" );
+- model.setSeriesLine( "Series " + "Gap Ratio", true );
+- model.setSeriesMarker( "Series " + "Gap Ratio", false );
+- final double[][] gap_counts = new double[ _msa_props.size() ][ 2 ];
+- for( int i = 0; i < _msa_props.size(); ++i ) {
+- gap_counts[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
+- gap_counts[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getAvgNumberOfGaps()
+- * avg_gaps_counts_factor );
+- }
+- model.addData( gap_counts, "Mean Gap Count" + " (" + minMaxToString( min_avg_gap_count, max_avg_gap_count )
+- + ")" );
+- model.setSeriesLine( "Series " + "Mean Gap Count", true );
+- model.setSeriesMarker( "Series " + "Mean Gap Count", false );
+- if ( _show_msa_qual ) {
+- final double[][] entropy7 = new double[ _msa_props.size() ][ 2 ];
+- for( int i = 0; i < _msa_props.size(); ++i ) {
+- entropy7[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
+- entropy7[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getEntropy7() * ent7_factor );
+- }
+- model.addData( entropy7, "Entropy norm 7" + " (" + minMaxToString( min_ent7, max_ent7 ) + ")" );
+- model.setSeriesLine( "Series " + "Entropy norm 7", true );
+- model.setSeriesMarker( "Series " + "Entropy norm 7", false );
+- //
+- final double[][] entropy21 = new double[ _msa_props.size() ][ 2 ];
+- for( int i = 0; i < _msa_props.size(); ++i ) {
+- entropy21[ i ][ 0 ] = _initial_number_of_seqs - _msa_props.get( i ).getNumberOfSequences();
+- entropy21[ i ][ 1 ] = ForesterUtil.roundToInt( _msa_props.get( i ).getEntropy21() * ent21_factor );
+- }
+- model.addData( entropy21, "Entropy norm 21" + " (" + minMaxToString( min_ent21, max_ent21 ) + ")" );
+- model.setSeriesLine( "Series " + "Entropy norm 21", true );
+- model.setSeriesMarker( "Series " + "Entropy norm 21", false );
+- }
+- final BoxCoordSystem coord = new BoxCoordSystem( model );
+- coord.setUnitFont( coord.getUnitFont().deriveFont( 16.0f ) );
+- coord.setXAxisUnit( "Number of Removed Sequences" );
+- coord.setPaintGrid( true );
+- coord.setYAxisUnit( "MSA Length" );
+- _chart_panel = new ChartPanel( model, _title );
+- _chart_panel.setCoordSystem( coord );
+- final MultiScatterChartRenderer renderer = new MultiScatterChartRenderer( coord, model );
+- renderer.setAllowBuffer( false );
+- _chart_panel.addChartRenderer( renderer, 0 );
+- }
+- return _chart_panel;
+- }
+-
+- private final static String minMaxToString( final double min, final double max ) {
+- return NF_1.format( min ) + "-" + NF_1.format( max );
+- }
+-
+- public static void display( final List<MsaProperties> msa_props,
+- final int initial_number_of_seqs,
+- final boolean show_msa_qual,
+- final String title ) {
+- try {
+- UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
+- }
+- catch ( final Exception e ) {
+- e.printStackTrace();
+- }
+- final Chart chart = new Chart( msa_props, initial_number_of_seqs, show_msa_qual, title );
+- chart.setVisible( true );
+- }
+-
+- public static void main( final String[] args ) {
+- try {
+- UIManager.setLookAndFeel( UIManager.getSystemLookAndFeelClassName() );
+- }
+- catch ( final Exception e ) {
+- e.printStackTrace();
+- }
+- final Chart temp = new Chart( null, 0, true, "title" );
+- temp.setVisible( true );
+- }
+ }
+--- a/biojava-forester/src/main/java/org/forester/application/msa_compactor.java
++++ b/biojava-forester/src/main/java/org/forester/application/msa_compactor.java
+@@ -39,7 +39,6 @@
+ import org.forester.msa.Msa.MSA_FORMAT;
+ import org.forester.msa.MsaInferrer;
+ import org.forester.msa.MsaMethods;
+-import org.forester.msa_compactor.Chart;
+ import org.forester.msa_compactor.MsaCompactor;
+ import org.forester.msa_compactor.MsaProperties;
+ import org.forester.util.CommandLineArguments;
+@@ -396,7 +395,7 @@
+ else {
+ msa_props = mc.chart( step, realign, normalize_for_effective_seq_length );
+ }
+- Chart.display( msa_props, initial_number_of_seqs, report_entropy, in.getName() );
++ //Chart.display( msa_props, initial_number_of_seqs, report_entropy, in.getName() );
+ System.out.println();
+ System.out.println( "Final MSA properties" );
+ printMsaInfo( msa, MsaMethods.calculateEffectiveLengthStatistics( msa ));
Deleted: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/series
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/series 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/series 2016-12-20 10:42:49 UTC (rev 23335)
@@ -1,6 +0,0 @@
-fix_itext_class_updates
-use_simple_json
-fix_import
-faketest
-fix_ascii_characters_mapping
-skip_network_related_tests
Copied: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/series (from rev 23275, trunk/packages/biojava4-live/trunk/debian/patches/series)
===================================================================
--- trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/series (rev 0)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/series 2016-12-20 10:42:49 UTC (rev 23335)
@@ -0,0 +1,8 @@
+fix_itext_class_updates
+use_simple_json
+fix_import
+faketest
+fix_ascii_characters_mapping
+skip_network_related_tests
+remove_openchart_use
+ignore_fake_tests
Deleted: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/skip_network_related_tests
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/skip_network_related_tests 2016-12-20 10:42:49 UTC (rev 23335)
@@ -1,143 +0,0 @@
-Author: Olivier Sallou <osallou at debian/org>
-Last-Updated: 2015-01-31
-Subject: Some tests use network access
-Description: Remove tests requiring external
- network access
-Forwarded: yes
-Bug: https://redmine.open-bio.org/issues/3402
---- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
-+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
-@@ -75,18 +75,7 @@
- /*
- * Method 1: With the GenbankProxySequenceReader
- */
-- //Try with the GenbankProxySequenceReader
-- GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
-- = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"), "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
-- ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
-- genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
-- logger.info("Sequence({},{}) = {}...", proteinSequence.getAccession(), proteinSequence.getLength(), proteinSequence.getSequenceAsString().substring(0, 10));
--
-- GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader
-- = new GenbankProxySequenceReader<NucleotideCompound>(System.getProperty("java.io.tmpdir"), "NM_001126", DNACompoundSet.getDNACompoundSet());
-- DNASequence dnaSequence = new DNASequence(genbankDNAReader);
-- genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
-- logger.info("Sequence({},{}) = {}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
-+
- /*
- * Method 2: With the GenbankReaderHelper
- */
---- a/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
-+++ b/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
-@@ -67,20 +67,6 @@
-
- private void testUniprot(String uniprotID) throws CompoundNotFoundException, IOException {
-
-- ProteinSequence seq = getUniprot(uniprotID);
--
-- AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
--
--/* for (AminoAcidCompound compound : seq) {
-- System.out.println(compound.getShortName() + " " + compound.getLongName() + " " + compound.getDescription() + " | " + compoundSet.getEquivalentCompounds(compound) + " " + compound.getMolecularWeight() + " " + compound.getBase());
-- }
-- */
-- assertTrue(compoundSet.isValidSequence(seq));
--
--
--
-- Jronn.getDisorderScores(seq);
--
-
- }
-
---- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
-+++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
-@@ -75,88 +75,10 @@
-
- @Test
- public void testFeatures() throws IOException, InterruptedException, CompoundNotFoundException {
-- logger.info("run test for protein: {}", gi);
-- GenbankProxySequenceReader<AminoAcidCompound> genbankReader
-- = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"),
-- this.gi,
-- AminoAcidCompoundSet.getAminoAcidCompoundSet());
--
-- // why only tests on protein sequences?
-- ProteinSequence seq = new ProteinSequence(genbankReader);
--
-- Assert.assertNotNull("protein sequence is null", seq);
--
-- /*
-- parse description from header. There is no separate interface/abstract class for method getHeader()
-- so it should be done here (manualy).
-- */
-- genbankReader.getHeaderParser().parseHeader(genbankReader.getHeader(), seq);
--
-- // test description
-- Assert.assertTrue(seq.getDescription() != null);
--
-- // test accession Id
-- logger.info("accession id: {}", seq.getAccession().getID());
-- Assert.assertNotNull(seq.getAccession().getID());
-- // test GID number
-- Assert.assertEquals(gi, seq.getAccession().getIdentifier());
-- logger.info("found identifier '{}'", seq.getAccession().getIdentifier());
--
-- // test taxonomy id
-- logger.info("taxonomy id: {}", seq.getTaxonomy().getID());
-- Assert.assertNotNull(seq.getTaxonomy().getID());
-- Assert.assertNotNull(Integer.decode(seq.getTaxonomy().getID().split(":")[1]));
--
-- // test taxonomy name
-- String taxonName = seq.getFeaturesByType("source").get(0).getQualifiers().get("organism").getValue();
-- logger.info("taxonomy name '{}'", taxonName);
-- Assert.assertNotNull(taxonName);
--
-- if (seq.getFeaturesByType("CDS").size() > 0) {
-- FeatureInterface<AbstractSequence<AminoAcidCompound>, AminoAcidCompound> CDS = seq.getFeaturesByType("CDS").get(0);
-- logger.info("CDS: {}", CDS);
-- String codedBy = CDS.getQualifiers().get("coded_by").getValue();
-- Assert.assertNotNull(codedBy);
-- Assert.assertTrue(!codedBy.isEmpty());
-- logger.info("\t\tcoded_by: {}", codedBy);
-- }
- }
-
- @Test
- public void testProteinSequenceFactoring() throws Exception {
- logger.info("create protein sequence test for target {}", gi);
--
-- GenbankProxySequenceReader<AminoAcidCompound> genbankReader
-- = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"),
-- this.gi,
-- AminoAcidCompoundSet.getAminoAcidCompoundSet());
--
-- ProteinSequence seq = new ProteinSequence(genbankReader);
--
-- // if target protein contain CDS/coded_by than it should contain parent nucleotide seq
-- ArrayList<AbstractFeature> CDSs = genbankReader.getFeatures().get("CDS");
--
-- if (CDSs != null) {
-- if (CDSs.size() == 1) {
-- Qualifier codedBy = (Qualifier) CDSs.get(0).getQualifiers().get("coded_by");
-- if (codedBy != null) {
--
-- AbstractSequence<?> parentSeq = seq.getParentSequence();
-- Assert.assertNotNull(parentSeq);
--
-- /*
-- Sometimes protein might have many 'parents' with different accessions
-- so accession is not set.
--
-- That test is always failed
-- */
-- //Assert.assertTrue(parentSeq.getAccession());
-- Assert.assertTrue(!parentSeq.getSequenceAsString().isEmpty());
-- }
-- }
-- } else {
-- logger.info("target {} has no CDS", gi);
-- }
--
- }
- }
Copied: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/skip_network_related_tests (from rev 23277, trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests)
===================================================================
--- trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/skip_network_related_tests (rev 0)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/skip_network_related_tests 2016-12-20 10:42:49 UTC (rev 23335)
@@ -0,0 +1,144 @@
+Subject: remove tests needing network
+Description: debian builds expects to run with no network
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2016-12-09
+Forwarded: no
+--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
++++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/GenbankCookbookTest.java
+@@ -67,21 +67,6 @@
+ @Test
+ public void testProcess() throws Throwable {
+ /*
+- * Method 1: With the GenbankProxySequenceReader
+- */
+- //Try with the GenbankProxySequenceReader
+- GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
+- = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"), "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
+- ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
+- genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
+- logger.info("Sequence({},{}) = {}...", proteinSequence.getAccession(), proteinSequence.getLength(), proteinSequence.getSequenceAsString().substring(0, 10));
+-
+- GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader
+- = new GenbankProxySequenceReader<NucleotideCompound>(System.getProperty("java.io.tmpdir"), "NM_001126", DNACompoundSet.getDNACompoundSet());
+- DNASequence dnaSequence = new DNASequence(genbankDNAReader);
+- genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
+- logger.info("Sequence({},{}) = {}...", dnaSequence.getAccession(), dnaSequence.getLength(), dnaSequence.getSequenceAsString().substring(0, 10));
+- /*
+ * Method 2: With the GenbankReaderHelper
+ */
+ //Try with the GenbankReaderHelper
+--- a/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
++++ b/biojava-protein-disorder/src/test/java/org/biojava/nbio/ronn/NonstandardProteinCompoundTest.java
+@@ -67,20 +67,6 @@
+
+ private void testUniprot(String uniprotID) throws CompoundNotFoundException, IOException {
+
+- ProteinSequence seq = getUniprot(uniprotID);
+-
+- AminoAcidCompoundSet compoundSet = AminoAcidCompoundSet.getAminoAcidCompoundSet();
+-
+-/* for (AminoAcidCompound compound : seq) {
+- System.out.println(compound.getShortName() + " " + compound.getLongName() + " " + compound.getDescription() + " | " + compoundSet.getEquivalentCompounds(compound) + " " + compound.getMolecularWeight() + " " + compound.getBase());
+- }
+- */
+- assertTrue(compoundSet.isValidSequence(seq));
+-
+-
+-
+- Jronn.getDisorderScores(seq);
+-
+
+ }
+
+--- a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
++++ b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/loader/GenbankProxySequenceReaderTest.java
+@@ -75,89 +75,9 @@
+
+ @Test
+ public void testFeatures() throws IOException, InterruptedException, CompoundNotFoundException {
+- logger.info("run test for protein: {}", gi);
+- GenbankProxySequenceReader<AminoAcidCompound> genbankReader
+- = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"),
+- this.gi,
+- AminoAcidCompoundSet.getAminoAcidCompoundSet());
+-
+- // why only tests on protein sequences?
+- ProteinSequence seq = new ProteinSequence(genbankReader);
+-
+- Assert.assertNotNull("protein sequence is null", seq);
+-
+- /*
+- parse description from header. There is no separate interface/abstract class for method getHeader()
+- so it should be done here (manualy).
+- */
+- genbankReader.getHeaderParser().parseHeader(genbankReader.getHeader(), seq);
+-
+- // test description
+- Assert.assertTrue(seq.getDescription() != null);
+-
+- // test accession Id
+- logger.info("accession id: {}", seq.getAccession().getID());
+- Assert.assertNotNull(seq.getAccession().getID());
+- // test GID number
+- Assert.assertEquals(gi, seq.getAccession().getIdentifier());
+- logger.info("found identifier '{}'", seq.getAccession().getIdentifier());
+-
+- // test taxonomy id
+- logger.info("taxonomy id: {}", seq.getTaxonomy().getID());
+- Assert.assertNotNull(seq.getTaxonomy().getID());
+- Assert.assertNotNull(Integer.decode(seq.getTaxonomy().getID().split(":")[1]));
+-
+- // test taxonomy name
+- String taxonName = seq.getFeaturesByType("source").get(0).getQualifiers().get("organism").get(0).getValue();
+- logger.info("taxonomy name '{}'", taxonName);
+- Assert.assertNotNull(taxonName);
+-
+- if (seq.getFeaturesByType("CDS").size() > 0) {
+- FeatureInterface<AbstractSequence<AminoAcidCompound>, AminoAcidCompound> CDS = seq.getFeaturesByType("CDS").get(0);
+- logger.info("CDS: {}", CDS);
+- String codedBy = CDS.getQualifiers().get("coded_by").get(0).getValue();
+- Assert.assertNotNull(codedBy);
+- Assert.assertTrue(!codedBy.isEmpty());
+- logger.info("\t\tcoded_by: {}", codedBy);
+- }
+ }
+
+ @Test
+ public void testProteinSequenceFactoring() throws Exception {
+- logger.info("create protein sequence test for target {}", gi);
+-
+- GenbankProxySequenceReader<AminoAcidCompound> genbankReader
+- = new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"),
+- this.gi,
+- AminoAcidCompoundSet.getAminoAcidCompoundSet());
+-
+- ProteinSequence seq = new ProteinSequence(genbankReader);
+-
+- // if target protein contain CDS/coded_by than it should contain parent nucleotide seq
+- ArrayList<AbstractFeature> CDSs = genbankReader.getFeatures().get("CDS");
+-
+- if (CDSs != null) {
+- if (CDSs.size() == 1) {
+- ArrayList<Qualifier> qualifiers = (ArrayList)CDSs.get(0).getQualifiers().get("coded_by");
+- Qualifier codedBy = qualifiers.get(0);
+- if (codedBy != null) {
+-
+- AbstractSequence<?> parentSeq = seq.getParentSequence();
+- Assert.assertNotNull(parentSeq);
+-
+- /*
+- Sometimes protein might have many 'parents' with different accessions
+- so accession is not set.
+-
+- That test is always failed
+- */
+- //Assert.assertTrue(parentSeq.getAccession());
+- Assert.assertTrue(!parentSeq.getSequenceAsString().isEmpty());
+- }
+- }
+- } else {
+- logger.info("target {} has no CDS", gi);
+- }
+-
+ }
+ }
Deleted: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/use_simple_json
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/use_simple_json 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/use_simple_json 2016-12-20 10:42:49 UTC (rev 23335)
@@ -1,55 +0,0 @@
-Subject: use simple_json library
-Author: Olivier Sallou <osallou at debian.org>
-Description: json.org library is not "free", use simple_json
- library and update according to API
-Last-Updated: 2012-12-02
-
---- a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
-+++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
-@@ -20,8 +20,10 @@
- */
- package org.biojava.nbio.ws.hmmer;
-
--import net.sf.json.JSONArray;
--import net.sf.json.JSONObject;
-+import org.json.simple.JSONArray;
-+import org.json.simple.JSONObject;
-+import org.json.simple.JSONValue;
-+
- import org.biojava.nbio.core.sequence.ProteinSequence;
-
- import java.io.*;
-@@ -133,15 +135,13 @@
-
- SortedSet<HmmerResult> results = new TreeSet<HmmerResult>();
- try {
-- JSONObject json = JSONObject.fromObject(result.toString());
--
-- JSONObject hmresults = json.getJSONObject("results");
--
-+ JSONObject json= (JSONObject) JSONValue.parse(result.toString());
-+ JSONObject hmresults = (JSONObject) json.get("results");
-
-- JSONArray hits = hmresults.getJSONArray("hits");
-+ JSONArray hits = (JSONArray) hmresults.get("hits");
-
- for(int i =0 ; i < hits.size() ; i++){
-- JSONObject hit = hits.getJSONObject(i);
-+ JSONObject hit = (JSONObject) hits.get(i);
- //System.out.println("hit: "+ hit);
-
- HmmerResult hmmResult = new HmmerResult();
-@@ -166,11 +166,11 @@
- hmmResult.setPvalue((Double)hit.get("pvalue"));
- hmmResult.setScore(Float.parseFloat((String)hit.get("score")));
-
-- JSONArray hmmdomains = hit.getJSONArray("domains");
-+ JSONArray hmmdomains = (JSONArray) hit.get("domains");
-
- SortedSet<HmmerDomain> domains = new TreeSet<HmmerDomain>();
- for ( int j= 0 ; j < hmmdomains.size() ; j++){
-- JSONObject d = hmmdomains.getJSONObject(j);
-+ JSONObject d = (JSONObject) hmmdomains.get(j);
- //System.out.println(d);
- Integer is_included = getInteger(d.get("is_included"));
- if ( is_included == 0) {
Copied: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/use_simple_json (from rev 23275, trunk/packages/biojava4-live/trunk/debian/patches/use_simple_json)
===================================================================
--- trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/use_simple_json (rev 0)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/patches/use_simple_json 2016-12-20 10:42:49 UTC (rev 23335)
@@ -0,0 +1,55 @@
+Subject: use simple_json library
+Author: Olivier Sallou <osallou at debian.org>
+Description: json.org library is not "free", use simple_json
+ library and update according to API
+Last-Updated: 2012-12-02
+
+--- a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
++++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java
+@@ -20,8 +20,10 @@
+ */
+ package org.biojava.nbio.ws.hmmer;
+
+-import net.sf.json.JSONArray;
+-import net.sf.json.JSONObject;
++import org.json.simple.JSONArray;
++import org.json.simple.JSONObject;
++import org.json.simple.JSONValue;
++
+ import org.biojava.nbio.core.sequence.ProteinSequence;
+
+ import java.io.*;
+@@ -132,15 +134,13 @@
+
+ SortedSet<HmmerResult> results = new TreeSet<HmmerResult>();
+ try {
+- JSONObject json = JSONObject.fromObject(result.toString());
+-
+- JSONObject hmresults = json.getJSONObject("results");
+-
++ JSONObject json= (JSONObject) JSONValue.parse(result.toString());
++ JSONObject hmresults = (JSONObject) json.get("results");
+
+- JSONArray hits = hmresults.getJSONArray("hits");
++ JSONArray hits = (JSONArray) hmresults.get("hits");
+
+ for(int i =0 ; i < hits.size() ; i++){
+- JSONObject hit = hits.getJSONObject(i);
++ JSONObject hit = (JSONObject) hits.get(i);
+ //System.out.println("hit: "+ hit);
+
+ HmmerResult hmmResult = new HmmerResult();
+@@ -165,11 +165,11 @@
+ hmmResult.setPvalue((Double)hit.get("pvalue"));
+ hmmResult.setScore(Float.parseFloat((String)hit.get("score")));
+
+- JSONArray hmmdomains = hit.getJSONArray("domains");
++ JSONArray hmmdomains = (JSONArray) hit.get("domains");
+
+ SortedSet<HmmerDomain> domains = new TreeSet<HmmerDomain>();
+ for ( int j= 0 ; j < hmmdomains.size() ; j++){
+- JSONObject d = hmmdomains.getJSONObject(j);
++ JSONObject d = (JSONObject) hmmdomains.get(j);
+ //System.out.println(d);
+ Integer is_included = getInteger(d.get("is_included"));
+ if ( is_included == 0) {
Deleted: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/watch
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/watch 2016-12-09 10:01:25 UTC (rev 23274)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/watch 2016-12-20 10:42:49 UTC (rev 23335)
@@ -1,6 +0,0 @@
-version=3
-
-#opts=filenamemangle=s/.+\/biojava-?(\d\S*)\.tar\.gz/biojava-$1.tar.gz/ \
-opts=dversionmangle=s/\+(repack|dfsg)// \
- https://github.com/biojava/biojava/tags .*/biojava-?([.\d]+)\.tar\.gz
-
Copied: trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/watch (from rev 23275, trunk/packages/biojava4-live/trunk/debian/watch)
===================================================================
--- trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/watch (rev 0)
+++ trunk/packages/biojava4-live/tags/4.2.4+dfsg-2/debian/watch 2016-12-20 10:42:49 UTC (rev 23335)
@@ -0,0 +1,6 @@
+version=3
+
+#opts=filenamemangle=s/.+\/biojava-?(\d\S*)\.tar\.gz/biojava-$1.tar.gz/ \
+opts=dversionmangle=s/\+(repack|dfsg)// \
+ https://github.com/biojava/biojava/tags .*/biojava-?(4\S*)\.tar\.gz
+
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