[med-svn] r19923 - in trunk/packages/biojava4-live/tags: . 4.1.0+dfsg-1/debian 4.1.0+dfsg-1/debian/patches
Olivier Sallou
osallou at moszumanska.debian.org
Wed Aug 12 09:10:19 UTC 2015
Author: osallou
Date: 2015-08-12 09:10:19 +0000 (Wed, 12 Aug 2015)
New Revision: 19923
Added:
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/README.Debian
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/README.source
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/biojava-doc.docs
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/build.xml
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/changelog
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/compat
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/control
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/copyright
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/get-orig-source
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava4-java-doc.doc-base
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava4-java-doc.install
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava4.0-java.jlibs
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/faketest
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/fix_ascii_characters_mapping
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/fix_import
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/series
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/skip_network_related_tests
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/use_simple_json
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/rules
Removed:
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/README.Debian
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/README.source
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/biojava-doc.docs
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/build.xml
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/changelog
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/compat
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/control
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/copyright
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/get-orig-source
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava3-java-doc.doc-base
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava3-java-doc.install
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava3.0-java.jlibs
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/fix_ascii_characters_mapping
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/series
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/skip_network_related_tests
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/use_simple_json
trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/rules
Log:
[svn-buildpackage] Tagging biojava4-live 4.1.0+dfsg-1
Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/README.Debian
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/README.Debian 2015-01-30 21:17:39 UTC (rev 18647)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/README.Debian 2015-08-12 09:10:19 UTC (rev 19923)
@@ -1,23 +0,0 @@
-biojava for Debian
-------------------
-
-This package provide biojava libraries, made up of multiple libraries, dependent on biojava-core and other libraries.
-To make use of thos libraries, the following libraries are needed in the classpath:
- <fileset dir="/usr/share/java">
- <include name="commons-cli.jar"/>
- <include name="commons-collections.jar"/>
- <include name="commons-dbcp.jar"/>
- <include name="commons-pool.jar"/>
- <include name="junit.jar"/>
- <include name="guava.jar"/>
- <include name="jgrapht0.8.jar"/>
- <include name="Jmol.jar"/>
- <include name="json-lib.jar"/>
- <include name="biojava3-core.jar"/>
- <include name="biojava3-forester.jar"/>
- </fileset>
- <fileset dir="/usr/share/icedtea-web">
- <include name="netx.jar"/>
- </fileset>
-
- -- Olivier Sallou <osallou at debian.org> Wed, 23 May 2012 18:13:46 +0200
Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/README.Debian (from rev 18659, trunk/packages/biojava4-live/trunk/debian/README.Debian)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/README.Debian (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/README.Debian 2015-08-12 09:10:19 UTC (rev 19923)
@@ -0,0 +1,24 @@
+biojava for Debian
+------------------
+
+This package provide biojava libraries, made up of multiple libraries, dependent on biojava-core and other libraries.
+To make use of thos libraries, the following libraries are needed in the classpath:
+ <fileset dir="/usr/share/java">
+ <include name="commons-cli.jar"/>
+ <include name="commons-collections.jar"/>
+ <include name="commons-dbcp.jar"/>
+ <include name="commons-pool.jar"/>
+ <include name="junit.jar"/>
+ <include name="guava.jar"/>
+ <include name="jgrapht0.8.jar"/>
+ <include name="Jmol.jar"/>
+ <include name="json-lib.jar"/>
+ <include name="biojava4-core.jar"/>
+ <include name="biojava4-forester.jar"/>
+...
+ </fileset>
+ <fileset dir="/usr/share/icedtea-web">
+ <include name="netx.jar"/>
+ </fileset>
+
+ -- Olivier Sallou <osallou at debian.org> Wed, 23 May 2012 18:13:46 +0200
Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/README.source
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/README.source 2015-01-30 21:17:39 UTC (rev 18647)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/README.source 2015-08-12 09:10:19 UTC (rev 19923)
@@ -1,14 +0,0 @@
-biojava for Debian
-------------------
-
-Biojava3 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 biojava3-forester library is created.
-
-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/4.1.0+dfsg-1/debian/README.source (from rev 18659, trunk/packages/biojava4-live/trunk/debian/README.source)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/README.source (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/README.source 2015-08-12 09:10:19 UTC (rev 19923)
@@ -0,0 +1,16 @@
+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....
Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/biojava-doc.docs
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/biojava-doc.docs 2015-01-30 21:17:39 UTC (rev 18647)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/biojava-doc.docs 2015-08-12 09:10:19 UTC (rev 19923)
@@ -1 +0,0 @@
-#DOCS#
Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/biojava-doc.docs (from rev 18684, trunk/packages/biojava4-live/trunk/debian/biojava-doc.docs)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/biojava-doc.docs (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/biojava-doc.docs 2015-08-12 09:10:19 UTC (rev 19923)
@@ -0,0 +1,2 @@
+#DOCS#
+readme.md
Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/build.xml
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/build.xml 2015-01-30 21:17:39 UTC (rev 18647)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/build.xml 2015-08-12 09:10:19 UTC (rev 19923)
@@ -1,120 +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 ${lib.dir}/log4j-over-slf4j.jar"/>
-
- <path id="compile.classpath">
- <fileset dir="${lib.dir}">
- <include name="commons-cli.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="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/4.1.0+dfsg-1/debian/build.xml (from rev 18664, trunk/packages/biojava4-live/trunk/debian/build.xml)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/build.xml (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/build.xml 2015-08-12 09:10:19 UTC (rev 19923)
@@ -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="1.6" 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>
+
Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/changelog
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/changelog 2015-01-30 21:17:39 UTC (rev 18647)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/changelog 2015-08-12 09:10:19 UTC (rev 19923)
@@ -1,7 +0,0 @@
-biojava4-live (4.0.0+dfsg-1) UNRELEASED; urgency=medium
-
- * BioJava4 packaging
- [ needs Jmol upgrade, build of biojava-structure-gui meanwhile ]
- [ failing test org.biojava.nbio.aaproperties.ProfeatPropertiesImplTest ]
-
- -- Olivier Sallou <osallou at debian.org> Fri, 30 Jan 2015 17:24:21 +0100
Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/changelog (from rev 19916, trunk/packages/biojava4-live/trunk/debian/changelog)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/changelog (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/changelog 2015-08-12 09:10:19 UTC (rev 19923)
@@ -0,0 +1,11 @@
+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/4.1.0+dfsg-1/debian/compat
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/compat 2015-01-30 21:17:39 UTC (rev 18647)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/compat 2015-08-12 09:10:19 UTC (rev 19923)
@@ -1 +0,0 @@
-8
Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/compat (from rev 19918, trunk/packages/biojava4-live/trunk/debian/compat)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/compat (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/compat 2015-08-12 09:10:19 UTC (rev 19923)
@@ -0,0 +1 @@
+9
Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/control
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/control 2015-01-30 21:17:39 UTC (rev 18647)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/control 2015-08-12 09:10:19 UTC (rev 19923)
@@ -1,82 +0,0 @@
-Source: biojava4-live
-Section: java
-Priority: optional
-Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Olivier Sallou <osallou at debian.org>
-Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java,
- libcommons-collections3-java, libcommons-pool-java (>= 1.1),
- libcommons-logging-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 (>=0.25),
- ant-optional, icedtea-netx, libhamcrest-java,
- libjson-simple-java (>=1.1.1),
- liblog4j2-java, libslf4j-java
-Build-Depends: debhelper (>= 9), ant
-Standards-Version: 3.9.6
-Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/biojava4/trunk/
-Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/biojava4/trunk/
-Homepage: http://www.biojava.org
-
-Package: libbiojava4.0-java
-Architecture: all
-Depends: ${shlibs:Depends}, ${misc:Depends},
- libcommons-pool-java (>= 1.1),
- libcommons-collections3-java,
- libcommons-dbcp-java (>= 1.1),
- 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
-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
-Section: doc
-Architecture: all
-Depends: ${misc:Depends}
-Recommends: konqueror|html-browser
-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/4.1.0+dfsg-1/debian/control (from rev 18684, trunk/packages/biojava4-live/trunk/debian/control)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/control (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/control 2015-08-12 09:10:19 UTC (rev 19923)
@@ -0,0 +1,84 @@
+Source: biojava4-live
+Section: java
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
+Build-Depends-Indep: libcommons-dbcp-java (>= 1.1), libhsqldb-java,
+ libcommons-collections3-java, libcommons-pool-java (>= 1.1),
+ 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 (>=0.25),
+ ant-optional, icedtea-netx, libhamcrest-java,
+ libjson-simple-java (>=1.1.1),
+ liblog4j2-java, libslf4j-java,
+ libxmlunit-java
+Build-Depends: debhelper (>= 9), ant
+Standards-Version: 3.9.6
+Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/biojava4/trunk/
+Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/biojava4/trunk/
+Homepage: http://www.biojava.org
+
+Package: libbiojava4.0-java
+Architecture: all
+Depends: ${java:Depends}, ${misc:Depends},
+ libcommons-pool-java (>= 1.1),
+ libcommons-collections3-java,
+ libcommons-dbcp-java (>= 1.1),
+ 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
+Section: doc
+Architecture: all
+Depends: ${misc:Depends}
+Recommends: konqueror|html-browser
+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/4.1.0+dfsg-1/debian/copyright
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/copyright 2015-01-30 21:17:39 UTC (rev 18647)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/copyright 2015-08-12 09:10:19 UTC (rev 19923)
@@ -1,73 +0,0 @@
-Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
-Upstream-Name: biojava3
-Source: http://www.biojava.org/
-
-Files: biojava4-forester
-Copyright: 2008-2009 Christian M. Zmasek
- 2008-2009 Burnham Institute for Medical Research
-License: LGPL-2.1+
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation; either version 2 .1 of the License, or
- (at your option) any later version.
- .
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU Lesser General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>
- .
- On Debian systems, the complete text of the GNU Lesser General
- Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
-
-
-Files: *
-Copyright: 2008-2012 the Individual authors who contributed the code,
- as identified by the @authors tag of the respective source file.
- BioJava Developers <biojava-l at biojava.org>
- Scooter Willis <willishf at gmail dot com>, Mark Chapman, Andy Yates,
- Richard Holland, Mark Reinhold, brandstaetter, Thomas Down, Unidata Program Center,
- Ronald Tschalar, Andreas Prlic, Amr AL-Hossary, Jianjiong Gao, Spencer Bliven,
- Jules Jacobsen <jacobsen at ebi.ac.uk>, J.H.MATTHEWS,R.KRISHNAN,M.J.COSTANZO,B.E.MARYANOFF,
- A.TULINSKY, ap3, The MathWorks Inc. and the National Institute of Standards and Technology,
- Spencer Bliven <sbliven at ucsd.edu>, mulvaney, Peter Rose, Horvath Tamas, Peter Lackner,
- Koh Chuan Hock, Expasy4J, Benjamin Schuster-Böckle, Peter Troshin
-License: LGPL-2.1+
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU Lesser General Public License as published by
- the Free Software Foundation; either version 2 .1 of the License, or
- (at your option) any later version.
- .
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU Lesser General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>
- .
- On Debian systems, the complete text of the GNU Lesser General
- Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
-
-
-Files: debian/*
-Copyright: 2012 Olivier Sallou <osallou at debian.org>
-License: GPL-2+
- This package is free software; you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation; either version 2 of the License, or
- (at your option) any later version.
- .
- This package is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- GNU General Public License for more details.
- .
- You should have received a copy of the GNU General Public License
- along with this program. If not, see <http://www.gnu.org/licenses/>
- .
- On Debian systems, the complete text of the GNU General
- Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
-
Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/copyright (from rev 18700, trunk/packages/biojava4-live/trunk/debian/copyright)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/copyright (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/copyright 2015-08-12 09:10:19 UTC (rev 19923)
@@ -0,0 +1,85 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: biojava4
+Source: http://www.biojava.org/
+
+Files: biojava-jcolorbrewer
+Copyright: 2011 University of California San Diego
+ 2011 J.L. Moreland
+ 2011 A.Gramada
+ 2011 O.V. Buzko
+ 2011 Qing Zhang
+ 2011 P.E. Bourne
+License: LGPL-2.1+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation; either version 2 .1 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
+
+Files: biojava-forester
+Copyright: 2008-2009 Christian M. Zmasek
+ 2008-2009 Burnham Institute for Medical Research
+License: LGPL-2.1+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU Lesser General Public License as published by
+ the Free Software Foundation; either version 2 .1 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU Lesser General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU Lesser General
+ Public License version 2 can be found in "/usr/share/common-licenses/LGPL-2.1".
+
+
+Files: *
+Copyright: 2008-2012 the Individual authors who contributed the code,
+ as identified by the @authors tag of the respective source file.
+ BioJava Developers <biojava-l at biojava.org>
+ Scooter Willis <willishf at gmail dot com>, Mark Chapman, Andy Yates,
+ Richard Holland, Mark Reinhold, brandstaetter, Thomas Down, Unidata Program Center,
+ Ronald Tschalar, Andreas Prlic, Amr AL-Hossary, Jianjiong Gao, Spencer Bliven,
+ Jules Jacobsen <jacobsen at ebi.ac.uk>, J.H.MATTHEWS,R.KRISHNAN,M.J.COSTANZO,B.E.MARYANOFF,
+ A.TULINSKY, ap3, The MathWorks Inc. and the National Institute of Standards and Technology,
+ Spencer Bliven <sbliven at ucsd.edu>, mulvaney, Peter Rose, Horvath Tamas, Peter Lackner,
+ Koh Chuan Hock, Expasy4J, Benjamin Schuster-Böckle, Peter Troshin,
+ Jose Manuel Duarte, D. Myers, Andrew Yates, Ulysse Carion, M. L Heuer,
+ B. T. Boyle, emckee2006, paolopavan, J. Grzebyta, G. Waldon, D. Cameron,
+ A. Drager, kevinwu1, Siarhei, R. Thornton, C. Foti, sroughley, ferlan,
+ parit, M. Bizzari
+
+
+Files: debian/*
+Copyright: 2015 Olivier Sallou <osallou at debian.org>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
+ it under the terms of the GNU General Public License as published by
+ the Free Software Foundation; either version 2 of the License, or
+ (at your option) any later version.
+ .
+ This package is distributed in the hope that it will be useful,
+ but WITHOUT ANY WARRANTY; without even the implied warranty of
+ MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ GNU General Public License for more details.
+ .
+ You should have received a copy of the GNU General Public License
+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
+
Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/get-orig-source
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/get-orig-source 2015-01-30 21:17:39 UTC (rev 18647)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/get-orig-source 2015-08-12 09:10:19 UTC (rev 19923)
@@ -1,42 +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 biojava4-forester/src/main/java
-cd biojava4-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 ../../../..
-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/4.1.0+dfsg-1/debian/get-orig-source (from rev 18659, trunk/packages/biojava4-live/trunk/debian/get-orig-source)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/get-orig-source (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/get-orig-source 2015-08-12 09:10:19 UTC (rev 19923)
@@ -0,0 +1,48 @@
+#!/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}
+
Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava3-java-doc.doc-base
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/libbiojava3-java-doc.doc-base 2015-01-30 21:17:39 UTC (rev 18647)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava3-java-doc.doc-base 2015-08-12 09:10:19 UTC (rev 19923)
@@ -1,26 +0,0 @@
-Document: biojava3
-Title: biojava3 API
-Author: BioJava developers
-Abstract: Javadoc-generated API for the BioJava library.
- BioJava is an open-source project dedicated to providing a Java framework
- for processing biological data. It includes objects for manipulating
- sequences, file parsers, DAS client and 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.
- .
- If using BioJava, please cite: R.C.G. Holland, T. Down, M. Pocock,
- A. Prlić, D. Huen, K. James, S. Foisy, A. Dräger, A. Yates,
- M. Heuer; M.J. Schreiber (2008) "BioJava: an Open-Source Framework
- for Bioinformatics" Bioinformatics 24(18):2096-2097.
-Section: Science/Biology
-
-Format: HTML
-Index: /usr/share/doc/libbiojava3-java/api/index.html
-Files: /usr/share/doc/libbiojava3-java/api/*.html /usr/share/doc/libbiojava3-java/api/*/*/*/*.html /usr/share/doc/libbiojava3-java/api/*/*/*/*/*.html /usr/share/doc/libbiojava3-java/api/*/*/*/*/*/*.html /usr/share/doc/libbiojava3-java/api/*/*/*/*/*/*/*/*.html
Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava3-java-doc.install
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/libbiojava3-java-doc.install 2015-01-30 21:17:39 UTC (rev 18647)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava3-java-doc.install 2015-08-12 09:10:19 UTC (rev 19923)
@@ -1,3 +0,0 @@
-doc/biojava/* usr/share/doc/libbiojava3-java/api
-
-
Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava3.0-java.jlibs
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/libbiojava3.0-java.jlibs 2015-01-30 21:17:39 UTC (rev 18647)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava3.0-java.jlibs 2015-08-12 09:10:19 UTC (rev 19923)
@@ -1,12 +0,0 @@
-dist/biojava3-forester.jar
-dist/biojava3-core.jar
-dist/biojava3-phylo.jar
-dist/biojava3-alignment.jar
-dist/biojava3-aa-prop.jar
-dist/biojava3-genome.jar
-dist/biojava3-sequencing.jar
-dist/biojava3-structure.jar
-dist/biojava3-structure-gui.jar
-dist/biojava3-modfinder.jar
-dist/biojava3-protein-disorder.jar
-dist/biojava3-ws.jar
Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava4-java-doc.doc-base (from rev 18658, trunk/packages/biojava4-live/trunk/debian/libbiojava4-java-doc.doc-base)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava4-java-doc.doc-base (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava4-java-doc.doc-base 2015-08-12 09:10:19 UTC (rev 19923)
@@ -0,0 +1,26 @@
+Document: biojava4
+Title: biojava4 API
+Author: BioJava developers
+Abstract: Javadoc-generated API for the BioJava library.
+ BioJava is an open-source project dedicated to providing a Java framework
+ for processing biological data. It includes objects for manipulating
+ sequences, file parsers, DAS client and 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.
+ .
+ If using BioJava, please cite: R.C.G. Holland, T. Down, M. Pocock,
+ A. Prlić, D. Huen, K. James, S. Foisy, A. Dräger, A. Yates,
+ M. Heuer; M.J. Schreiber (2008) "BioJava: an Open-Source Framework
+ for Bioinformatics" Bioinformatics 24(18):2096-2097.
+Section: Science/Biology
+
+Format: HTML
+Index: /usr/share/doc/libbiojava4-java/api/index.html
+Files: /usr/share/doc/libbiojava4-java/api/*.html /usr/share/doc/libbiojava4-java/api/*/*/*/*.html /usr/share/doc/libbiojava4-java/api/*/*/*/*/*.html /usr/share/doc/libbiojava4-java/api/*/*/*/*/*/*.html /usr/share/doc/libbiojava4-java/api/*/*/*/*/*/*/*/*.html
Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava4-java-doc.install (from rev 18658, trunk/packages/biojava4-live/trunk/debian/libbiojava4-java-doc.install)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava4-java-doc.install (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava4-java-doc.install 2015-08-12 09:10:19 UTC (rev 19923)
@@ -0,0 +1,3 @@
+doc/biojava/* usr/share/doc/libbiojava4-java/api
+
+
Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava4.0-java.jlibs (from rev 18659, trunk/packages/biojava4-live/trunk/debian/libbiojava4.0-java.jlibs)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava4.0-java.jlibs (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/libbiojava4.0-java.jlibs 2015-08-12 09:10:19 UTC (rev 19923)
@@ -0,0 +1,16 @@
+dist/biojava4-forester.jar
+dist/biojava4-core.jar
+dist/biojava4-phylo.jar
+dist/biojava4-alignment.jar
+dist/biojava4-aa-prop.jar
+dist/biojava4-genome.jar
+dist/biojava4-sequencing.jar
+dist/biojava4-structure.jar
+dist/biojava4-structure-gui.jar
+dist/biojava4-modfinder.jar
+dist/biojava4-protein-disorder.jar
+dist/biojava4-protein-comparison-tool.jar
+dist/biojava4-ws.jar
+dist/biojava4-ontology.jar
+dist/biojava4-survival.jar
+dist/biojava4-jcolorbrewer.jar
Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/faketest (from rev 18664, trunk/packages/biojava4-live/trunk/debian/patches/faketest)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/faketest (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/faketest 2015-08-12 09:10:19 UTC (rev 19923)
@@ -0,0 +1,22 @@
+Subject: empty tst causes failure
+Description: empty test creates failure at compilate, add fake test
+ to allow compilation and global test success
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2015-01-31
+Forwarded: no
+--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/ProfeatPropertiesImplTest.java
++++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/ProfeatPropertiesImplTest.java
+@@ -20,6 +20,13 @@
+ */
+ package org.biojava.nbio.aaproperties;
+
++import org.junit.Test;
++
+ public class ProfeatPropertiesImplTest {
+
++ at Test
++public void testFake() {
++
++}
++
+ }
Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/fix_ascii_characters_mapping
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping 2015-01-30 21:17:39 UTC (rev 18647)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/fix_ascii_characters_mapping 2015-08-12 09:10:19 UTC (rev 19923)
@@ -1,28 +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/biojava3-forester/src/main/java/org/forester/test/Test.java
-+++ b/biojava3-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/biojava3-structure/src/main/java/org/biojava/bio/structure/ResidueRange.java
-+++ b/biojava3-structure/src/main/java/org/biojava/bio/structure/ResidueRange.java
-@@ -33,7 +33,7 @@
-
- /**
- * A chain, a start residue, and an end residue. May also store a length value. Because of insertion codes, this length
-- * is not necessarily {@code end − start}.
-+ * is not necessarily {@code end - start}.
- *
- * @author dmyerstu
- * @see ResidueNumber
Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/fix_ascii_characters_mapping (from rev 18677, trunk/packages/biojava4-live/trunk/debian/patches/fix_ascii_characters_mapping)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/fix_ascii_characters_mapping (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/fix_ascii_characters_mapping 2015-08-12 09:10:19 UTC (rev 19923)
@@ -0,0 +1,86 @@
+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
+ */
Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/fix_import (from rev 19917, trunk/packages/biojava4-live/trunk/debian/patches/fix_import)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/fix_import (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/fix_import 2015-08-12 09:10:19 UTC (rev 19923)
@@ -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
+@@ -130,7 +130,6 @@
+ }
+
+
+- @Override
+ public Map<String, Object> getProperty(String arg0) {
+ // TODO Auto-generated method stub
+ return null;
Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/series
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/series 2015-01-30 21:17:39 UTC (rev 18647)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/series 2015-08-12 09:10:19 UTC (rev 19923)
@@ -1,2 +0,0 @@
-fix_itext_class_updates
-use_simple_json
Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/series (from rev 18679, trunk/packages/biojava4-live/trunk/debian/patches/series)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/series (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/series 2015-08-12 09:10:19 UTC (rev 19923)
@@ -0,0 +1,6 @@
+fix_itext_class_updates
+use_simple_json
+fix_import
+faketest
+fix_ascii_characters_mapping
+skip_network_related_tests
Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/skip_network_related_tests
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests 2015-01-30 21:17:39 UTC (rev 18647)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/skip_network_related_tests 2015-08-12 09:10:19 UTC (rev 19923)
@@ -1,52 +0,0 @@
-Author: Olivier Sallou <osallou at debian/org>
-Last-Updated: 2013-01-03
-Subject: Some tests use network access
-Description: Remove tests requiring external
- network access
-Forwarded: yes
-Bug: https://redmine.open-bio.org/issues/3402
---- a/biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankCookbookTest.java
-+++ b/biojava3-core/src/test/java/org/biojava3/core/sequence/io/GenbankCookbookTest.java
-@@ -56,17 +56,7 @@
- * Method 1: With the GenbankProxySequenceReader
- */
- //Try with the GenbankProxySequenceReader
-- GenbankProxySequenceReader<AminoAcidCompound> genbankProteinReader
-- = new GenbankProxySequenceReader<AminoAcidCompound>("/tmp", "NP_000257", AminoAcidCompoundSet.getAminoAcidCompoundSet());
-- ProteinSequence proteinSequence = new ProteinSequence(genbankProteinReader);
-- genbankProteinReader.getHeaderParser().parseHeader(genbankProteinReader.getHeader(), proteinSequence);
-- System.out.println("Sequence" + "(" + proteinSequence.getAccession() + "," + proteinSequence.getLength() + ")=" + proteinSequence.getSequenceAsString().substring(0, 10) + "...");
--
-- GenbankProxySequenceReader<NucleotideCompound> genbankDNAReader
-- = new GenbankProxySequenceReader<NucleotideCompound>("/tmp", "NM_001126", DNACompoundSet.getDNACompoundSet());
-- DNASequence dnaSequence = new DNASequence(genbankDNAReader);
-- genbankDNAReader.getHeaderParser().parseHeader(genbankDNAReader.getHeader(), dnaSequence);
-- System.out.println("Sequence" + "(" + dnaSequence.getAccession() + "," + dnaSequence.getLength() + ")=" + dnaSequence.getSequenceAsString().substring(0, 10) + "...");
-+ // Skipping it due to network requirements
- /*
- * Method 2: With the GenbankReaderHelper
- */
---- a/biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java
-+++ b/biojava3-protein-disorder/src/test/java/org/biojava3/ronn/NonstandardProteinCompoundTest.java
-@@ -43,21 +43,6 @@
-
- public void testUniprot(String uniprotID) throws Exception{
-
-- 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());
-- }
-- */
-- compoundSet.verifySequence(seq);
--
--
--
-- @SuppressWarnings("unused")
-- float[] values = Jronn.getDisorderScores(seq);
--
-
- }
-
Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/skip_network_related_tests (from rev 19916, trunk/packages/biojava4-live/trunk/debian/patches/skip_network_related_tests)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/skip_network_related_tests (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/skip_network_related_tests 2015-08-12 09:10:19 UTC (rev 19923)
@@ -0,0 +1,106 @@
+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
+@@ -75,51 +75,6 @@
+
+ @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
Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/use_simple_json
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/patches/use_simple_json 2015-01-30 21:17:39 UTC (rev 18647)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/use_simple_json 2015-08-12 09:10:19 UTC (rev 19923)
@@ -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.*;
-@@ -118,15 +120,13 @@
-
- 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();
-@@ -150,11 +150,11 @@
- 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_reported = getInteger(d.get("is_reported"));
- if ( is_reported != 1) {
Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/use_simple_json (from rev 19917, trunk/packages/biojava4-live/trunk/debian/patches/use_simple_json)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/use_simple_json (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/patches/use_simple_json 2015-08-12 09:10:19 UTC (rev 19923)
@@ -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.*;
+@@ -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) {
Deleted: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/rules
===================================================================
--- trunk/packages/biojava4-live/trunk/debian/rules 2015-01-30 21:17:39 UTC (rev 18647)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/rules 2015-08-12 09:10:19 UTC (rev 19923)
@@ -1,81 +0,0 @@
-#!/usr/bin/make -f
-# -*- makefile -*-
-
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
-
-JAVA_HOME=/usr/lib/jvm/default-java
-
-%:
- dh $@ --with javahelper
-
-override_dh_auto_configure:
- dh_auto_configure
- sed -e 's/BJLIB/biojava-forester/g' debian/build.xml > biojava-forester/build.xml
- sed -e 's/BJLIB/biojava-aa-prop/g' debian/build.xml > biojava-aa-prop/build.xml
- sed -e 's/BJLIB/biojava-core/g' debian/build.xml > biojava-core/build.xml
- sed -e 's/BJLIB/biojava-alignment/g' debian/build.xml > biojava-alignment/build.xml
- sed -e 's/BJLIB/biojava-genome/g' debian/build.xml > biojava-genome/build.xml
- sed -e 's/BJLIB/biojava-modfinder/g' debian/build.xml > biojava-modfinder/build.xml
- sed -e 's/BJLIB/biojava-phylo/g' debian/build.xml > biojava-phylo/build.xml
- sed -e 's/BJLIB/biojava-sequencing/g' debian/build.xml > biojava-sequencing/build.xml
- sed -e 's/BJLIB/biojava-protein-disorder/g' debian/build.xml > biojava-protein-disorder/build.xml
- sed -e 's/BJLIB/biojava-structure/g' debian/build.xml > biojava-structure/build.xml
- sed -e 's/BJLIB/biojava-ws/g' debian/build.xml > biojava-ws/build.xml
- sed -e 's/BJLIB/biojava-structure-gui/g' debian/build.xml > biojava-structure-gui/build.xml
-
-override_dh_auto_build:
- cd biojava-forester && ant jar
- cd biojava-core && ant jar
- cd biojava-phylo && ant jar
- cd biojava-alignment && ant jar
- cd biojava-aa-prop && ant jar
- cd biojava-genome && ant jar
- cd biojava-sequencing && ant jar
- cd biojava-structure && ant jar
-# cd biojava-structure-gui && ant jar
- cd biojava-modfinder && ant jar
- cd biojava-protein-disorder && ant jar
- cd biojava-ws && ant jar
- # make doc
- rm -rf biojavadoc
- mkdir biojavadoc
- cp -r biojava-*/src biojavadoc/
- sed -e 's/BJLIB/biojava/g' debian/build.xml > biojavadoc/build.xml
- cd biojavadoc && ant javadocs
- rm -rf biojavadoc
-
-override_dh_auto_test:
- cd biojava-core && ant test
- cd biojava-alignment && ant test
- cd biojava-aa-prop && ant test
- # Skip, missing dependency
- #cd biojava-genome && ant test
- cd biojava-phylo && ant test
- # Native errors may cause issue on NFS...; skipping
- #cd biojava-sequencing && ant test
- #cd biojava-modfinder && ant test
- cd biojava-protein-disorder && ant test
- # Requires remote access and tmp directory write access
- #cd biojava-structure && ant test
- cd biojava-structure-gui && ant test
- #No test in biojava-ws available
- #cd biojava-ws && ant test
-
-
-
-
-override_dh_clean:
- dh_clean
- rm -rf build
- rm -rf dist
- rm -rf javadoc
- rm -rf test
- rm -f biojava-*/build.xml
- rm -rf biojavadoc
- rm -rf doc
-
-
-get-orig-source:
- debian/get-orig-source
-
Copied: trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/rules (from rev 18681, trunk/packages/biojava4-live/trunk/debian/rules)
===================================================================
--- trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/rules (rev 0)
+++ trunk/packages/biojava4-live/tags/4.1.0+dfsg-1/debian/rules 2015-08-12 09:10:19 UTC (rev 19923)
@@ -0,0 +1,91 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+JAVA_HOME=/usr/lib/jvm/default-java
+
+%:
+ dh $@ --with javahelper
+
+override_dh_auto_configure:
+ dh_auto_configure
+ sed -e 's/BJLIB/biojava4-forester/g' debian/build.xml > biojava-forester/build.xml
+ sed -e 's/BJLIB/biojava4-aa-prop/g' debian/build.xml > biojava-aa-prop/build.xml
+ sed -e 's/BJLIB/biojava4-core/g' debian/build.xml > biojava-core/build.xml
+ sed -e 's/BJLIB/biojava4-alignment/g' debian/build.xml > biojava-alignment/build.xml
+ sed -e 's/BJLIB/biojava4-genome/g' debian/build.xml > biojava-genome/build.xml
+ sed -e 's/BJLIB/biojava4-modfinder/g' debian/build.xml > biojava-modfinder/build.xml
+ sed -e 's/BJLIB/biojava4-phylo/g' debian/build.xml > biojava-phylo/build.xml
+ sed -e 's/BJLIB/biojava4-sequencing/g' debian/build.xml > biojava-sequencing/build.xml
+ sed -e 's/BJLIB/biojava4-protein-disorder/g' debian/build.xml > biojava-protein-disorder/build.xml
+ sed -e 's/BJLIB/biojava4-structure/g' debian/build.xml > biojava-structure/build.xml
+ sed -e 's/BJLIB/biojava4-ws/g' debian/build.xml > biojava-ws/build.xml
+ sed -e 's/BJLIB/biojava4-structure-gui/g' debian/build.xml > biojava-structure-gui/build.xml
+ sed -e 's/BJLIB/biojava4-ontology/g' debian/build.xml > biojava-ontology/build.xml
+ sed -e 's/BJLIB/biojava4-protein-comparison-tool/g' debian/build.xml > biojava-protein-comparison-tool/build.xml
+ sed -e 's/BJLIB/biojava4-survival/g' debian/build.xml > biojava-survival/build.xml
+ sed -e 's/BJLIB/biojava4-jcolorbrewer/g' debian/build.xml > biojava-jcolorbrewer/build.xml
+
+override_dh_auto_build:
+ cd biojava-jcolorbrewer && ant jar
+ cd biojava-forester && ant jar
+ cd biojava-core && ant jar
+ cd biojava-phylo && ant jar
+ cd biojava-alignment && ant jar
+ cd biojava-aa-prop && ant jar
+ cd biojava-genome && ant jar
+ cd biojava-sequencing && ant jar
+ cd biojava-structure && ant jar
+ cd biojava-structure-gui && ant jar
+ cd biojava-modfinder && ant jar
+ cd biojava-ontology && ant jar
+ cd biojava-protein-disorder && ant jar
+ cd biojava-protein-comparison-tool && ant jar
+ cd biojava-ws && ant jar
+ cd biojava-survival && ant jar
+ # make doc
+ rm -rf biojavadoc
+ mkdir biojavadoc
+ cp -r biojava-*/src biojavadoc/
+ sed -e 's/BJLIB/biojava/g' debian/build.xml > biojavadoc/build.xml
+ cd biojavadoc && ant javadocs
+ rm -rf biojavadoc
+
+override_dh_auto_test:
+ cd biojava-core && ant test
+ cd biojava-alignment && ant test
+ # Investigate test failure
+ cd biojava-aa-prop && ant test
+ # Skip, missing dependency junitx
+ #cd biojava-genome && ant test
+ cd biojava-phylo && ant test
+ # Native errors may cause issue on NFS...; skipping
+ cd biojava-sequencing && ant test
+ # Serialization failure in pbuilder mode
+ #cd biojava-modfinder && ant test
+ # Investigate test failure
+ #cd biojava-protein-disorder && ant test
+ # Requires remote access and tmp directory write access
+ #cd biojava-structure && ant test
+ cd biojava-structure-gui && ant test
+ cd biojava-ontology && ant test
+
+
+
+
+override_dh_clean:
+ dh_clean
+ rm -rf build
+ rm -rf dist
+ rm -rf javadoc
+ rm -rf test
+ rm -f biojava-*/build.xml
+ rm -rf biojavadoc
+ rm -rf doc
+
+
+get-orig-source:
+ debian/get-orig-source
+
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