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debian/alter-sequence-alignment.jlibs
View file @ a3644dc3
alter-lib/dist/*
alter-lib/target/alter-*.jar
debian/alter-sequence-alignment.poms
View file @ a3644dc3
......@@ -27,4 +27,3 @@
#
pom.xml --has-package-version
alter-lib/pom.xml --has-package-version
alter-web/pom.xml --has-package-version
debian/changelog
View file @ a3644dc3
alter-sequence-alignment (1.3.4-1) UNRELEASED; urgency=medium
alter-sequence-alignment (1.3.4-1) unstable; urgency=medium
* New upstream version
* d/watch: Source moved to Github
* Update copyright
* Standards-Version: 4.1.4
* Point VCS fields to Salsa
* debhelper 11
-- Andreas Tille <tille@debian.org> Wed, 04 Jul 2018 09:05:14 +0200
-- Andreas Tille <tille@debian.org> Wed, 04 Jul 2018 14:25:09 +0200
alter-sequence-alignment (1.3.3+dfsg-1) unstable; urgency=low
......
debian/control
View file @ a3644dc3
......@@ -3,7 +3,7 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
Uploaders: Andreas Tille <tille@debian.org>
Section: java
Priority: optional
Build-Depends: debhelper (>= 9),
Build-Depends: debhelper (>= 11~),
javahelper,
maven-debian-helper,
libproperties-maven-plugin-java,
......@@ -11,10 +11,11 @@ Build-Depends: debhelper (>= 9),
libjavacc-maven-plugin-java,
libmaven-assembly-plugin-java,
libargs4j-java,
libmaven-war-plugin-java
Standards-Version: 3.9.6
Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/alter-sequence-alignment.git
Vcs-Git: git://anonscm.debian.org/debian-med/alter-sequence-alignment.git
rename,
python-markdown
Standards-Version: 4.1.4
Vcs-Browser: https://salsa.debian.org/med-team/alter-sequence-alignment
Vcs-Git: https://salsa.debian.org/med-team/alter-sequence-alignment.git
Homepage: http://sing.ei.uvigo.es/ALTER/
Package: alter-sequence-alignment
......
debian/copyright
View file @ a3644dc3
......@@ -8,12 +8,12 @@ Copyright: 2009-2016 David Posada <dposada@uvigo.es>,
Florentino Fdez-Riverola <riverola@uvigo.es>
License: LGPL-3+
Files: alter-lib/src/cmdLine/*.java
alter-lib/src/converter/*.java
alter-lib/src/gui/*.java
alter-lib/src/reader/*
alter-lib/src/types/*
alter-lib/src/writer/*
Files: alter-lib/src/main/java/es/uvigo/ei/sing/alter/cmdLine/*.java
alter-lib/src/main/java/es/uvigo/ei/sing/alter/converter/*.java
alter-lib/src/main/java/es/uvigo/ei/sing/alter/gui/*.java
alter-lib/src/main/java/es/uvigo/ei/sing/alter/reader/*
alter-lib/src/main/java/es/uvigo/ei/sing/alter/types/*
alter-lib/src/main/java/es/uvigo/ei/sing/alter/writer/*
Copyright: 2009-2016 David Posada <dposada@uvigo.es>,
Florentino Fdez-Riverola <riverola@uvigo.es>
License: GPL-3+
......
debian/maven.rules
View file @ a3644dc3
es.uvigo.ei.sing alter-lib jar s/.*/debian/ * *
es.uvigo.ei.sing alter-project pom s/.*/debian/ * *
es.uvigo.ei.sing alter-web war s/.*/debian/ * *
debian/patches/fix_unmappable_characters.patch deleted 100644 → 0
View file @ 4a5b42fc
Author: Andreas Tille <tille@debian.org>
Last-Update: Sat, 05 Sep 2015 07:13:34 +0200
Description: Build has problems with non-ASCII characters in comments
--- a/alter-lib/src/converter/ProgramOptions.java
+++ b/alter-lib/src/converter/ProgramOptions.java
@@ -22,7 +22,7 @@ import java.util.*;
/**
* Provides methods to check the supported programs and formats, as well as
* the possible options for each one of them.
- * @author Daniel Gonzalez Peña
+ * @author Daniel Gonzalez Pena
*/
public class ProgramOptions{
--- a/alter-lib/src/reader/ReaderUtils.java
+++ b/alter-lib/src/reader/ReaderUtils.java
@@ -38,7 +38,7 @@ public class ReaderUtils
public static void replaceMatch(Sequence seq, Sequence first) throws ParseException
{
if (seq.getData().contains("."))
- //Lanzar excepción si el caracter está en la primera secuencia
+ //Lanzar excepcion si el caracter esta en la primera secuencia
if (seq == first)
throw new ParseException("Match character \".\" in first sequence of MSA.");
else
--- a/alter-lib/src/writer/Writer.java
+++ b/alter-lib/src/writer/Writer.java
@@ -20,7 +20,7 @@ package writer;
import types.MSA;
/**
- * Define los métodos que deben implementar todos los escritores.
+ * Define los metodos que deben implementar todos los escritores.
* @author Daniel Gomez Blanco
* @version 1.1
*/
--- a/alter-lib/src/writer/FastaWriter.java
+++ b/alter-lib/src/writer/FastaWriter.java
@@ -145,7 +145,7 @@ public class FastaWriter implements Writ
//Mientras queden caracteres por escribir
while(!data.isEmpty())
{
- //Si hay caracteres para hacer una línea
+ //Si hay caracteres para hacer una linea
if (data.length() > 60)
{
outb.append(data.substring(0, 60));
--- a/alter-lib/src/writer/NexusWriter.java
+++ b/alter-lib/src/writer/NexusWriter.java
@@ -343,7 +343,7 @@ public class NexusWriter implements Writ
outb.append(id + WriterUtils.align(id.length(),longestId)
+ WriterUtils.align(longestId, 10) + " ");
- //Escribir una línea si es posible
+ //Escribir una linea si es posible
if (data[index].length() > 50)
{
outb.append(data[index].substring(0, 50));
--- a/alter-lib/src/writer/PhylipCodABCWriter.java
+++ b/alter-lib/src/writer/PhylipCodABCWriter.java
@@ -25,7 +25,7 @@ import types.Typeable;
/**
* Extends class PhylipWriter to adapt the output to CodABC.
- * @author Daniel Glez-Peña
+ * @author Daniel Glez-Pena
* @version 1.0
*/
--- a/alter-lib/src/writer/PirDnaSPWriter.java
+++ b/alter-lib/src/writer/PirDnaSPWriter.java
@@ -34,7 +34,7 @@ public class PirDnaSPWriter extends PirW
/**
* Constructor de la clase. Llama al constructor de la superclase.
* @param os Sistema operativo de salida.
- * @param lowerCase Salida en letras minúsculas.
+ * @param lowerCase Salida en letras minusculas.
* @param match Salida codificada con caracteres match.
* @param logger Nombre del logger a instanciar.
*/
@@ -45,7 +45,7 @@ public class PirDnaSPWriter extends PirW
/**
* Escribe un MSA en formato PIR adaptado a dnaSP. Para ello
- * comprueba que el MSA no sea de proteínas. Luego llama al método de la superclase.
+ * comprueba que el MSA no sea de proteinas. Luego llama al metodo de la superclase.
* @param msa MSA de entrada.
* @return Cadena con la el MSA en formato PIR.
*/
--- a/alter-lib/src/writer/PirWriter.java
+++ b/alter-lib/src/writer/PirWriter.java
@@ -114,10 +114,10 @@ public class PirWriter implements Writer
/**
* Devuelve una cadena con el identificador de la secuencia. En caso de
- * que el identificador de secuencia esté repetido se renombra.
+ * que el identificador de secuencia este repetido se renombra.
* @param seq Secuencia de la cual se desea obtener el identificador.
* @param ids Secuencias copiadas hasta el momento.
- * @return Identificador de secuencia único.
+ * @return Identificador de secuencia unico.
*/
protected String getId(Sequence seq, LinkedHashSet<String> ids)
{
debian/patches/lower_case_jar.patch deleted 100644 → 0
View file @ 4a5b42fc
Author: Andreas Tille <tille@debian.org>
Last-Update: Sat, 05 Sep 2015 07:13:34 +0200
Description: Resulting JAR should have lower case name
--- a/alter-lib/build.xml
+++ b/alter-lib/build.xml
@@ -49,7 +49,7 @@
</target>
<target name="buildjar" depends="clean, build">
<mkdir dir="${dist}"/>
- <jar destfile="${dist}/ALTER.jar"
+ <jar destfile="${dist}/alter.jar"
basedir="${build}" manifest="${ALTERLIB.basedir}/MANIFEST.MF"/>
</target>
</project>
debian/patches/series
View file @ a3644dc3
#suppress_build_web_interface.patch
#use_debian_packaged_jar.patch
#fix_unmappable_characters.patch
#lower_case_jar.patch
suppress_build_web_interface.patch
update_doc.patch
debian/patches/suppress_build_web_interface.patch
View file @ a3644dc3
Author: Andreas Tille <tille@debian.org>
Last-Update: Sat, 05 Sep 2015 07:13:34 +0200
Last-Update: Wed, 04 Jul 2018 09:05:14 +0200
Description: Currently only the library is packaged while the web interface is ignored
The rationale is that libalter-java is packaged as a dependency for
other packages. There was no explicite request to package the
other packages. There was no explicit request to package the
web interface which involves a lot of third party JARs and thus
makes it complex to package.
--- a/build.xml
+++ b/build.xml
@@ -1,9 +1,8 @@
<?xml version="1.0" encoding="UTF-8"?>
-<project name="ALTER" default="buildall" basedir=".">
+<project name="ALTER" default="buildlib" basedir=".">
--- a/pom.xml
+++ b/pom.xml
@@ -32,7 +32,6 @@
<target name="buildlib">
<ant antfile="build.xml" dir="./alter-lib" inheritAll="false"/>
- <copy file="./alter-lib/dist/ALTER.jar" tofile="./web/ALTER.jar"/>
</target>
<target name="buildall" depends="clean, buildlib">
@@ -11,8 +10,6 @@
</target>
<target name="clean">
<ant antfile="build.xml" dir="./alter-lib" target="clean" inheritAll="false"/>
- <ant antfile="build.xml" dir="./web" target="clean" inheritAll="false"/>
- <delete file="./web/ALTER.jar"/>
</target>
</project>
<modules>
<module>alter-lib</module>
- <module>alter-web</module>
</modules>
<build>
debian/patches/update_doc.patch 0 → 100644
View file @ a3644dc3
Author: Andreas Tille <tille@debian.org>
Last-Update: Wed, 04 Jul 2018 09:05:14 +0200
Description: Remove non-applicable parts of the doc, adapt doc to Debian installation
--- a/README.md
+++ b/README.md
@@ -14,41 +14,16 @@ ALTER contains a set of components:
3. A desktop graphical user interface (GUI).
4. A web interface (a running instance is here: [http://sing.ei.uvigo.es/alter](http://sing.ei.uvigo.es/alter)).
-# Building ALTER and running from source
-
-## Build
-Before starting, you have to download and install:
-
-1. Git tool for cloning the last version
-2. A Java Compiler and tool
-3. The Maven tool
-
-And now, you can download and build it by performing:
-
-```
-git clone https://github.com/sing-group/ALTER.git
-cd ALTER
-mvn package
-```
## Running the desktop graphical user interface
```
-java -jar alter-lib/target/ALTER-1.3.4-jar-with-dependencies.jar
+alter-sequence-alignment
```
## Running the command line user interface
```
-java -jar alter-lib/target/ALTER-1.3.4-jar-with-dependencies.jar help
-```
-
-## Running the web user interface in your own machine
-1. Download a jetty-runner.jar, which is a server of Java Web applications. For example, download the 9.4.0RC1 version from here [here](http://central.maven.org/maven2/org/eclipse/jetty/jetty-runner/9.4.0.RC1/jetty-runner-9.4.0.RC1.jar)
-2. Place the jetty-runner-9.4.0.RC1.jar inside your ALTER folder, and the run:
+alter-sequence-alignment help
```
-java -jar jetty-runner-9.4.0.RC1.jar alter-web/target/alter-web-1.3.4.war
-```
-
-Once the server has started, surf to [http://localhost:8080](http://localhost:8080/)
# Use the core library in your projects
@@ -84,7 +59,7 @@ Import our repository into your pom.xml
### Include the .jar inside your classpath
-You have to include the alter-lib/target/ALTER-1.3.4-jar-with-dependencies.jar file in your classpath
+You have to include the /usr/share/java/alter.jar file in your classpath
## Make a sequence conversion inside your Java code
Here it is an example to convert a NEXUS file to ALN.
debian/patches/use_debian_packaged_jar.patch deleted 100644 → 0
View file @ 4a5b42fc
Author: Andreas Tille <tille@debian.org>
Last-Update: Sat, 05 Sep 2015 07:13:34 +0200
Description: Use Debian packaged JARs
--- a/alter-lib/build.xml
+++ b/alter-lib/build.xml
@@ -5,13 +5,13 @@
<property name="build" location="${ALTERLIB.basedir}/build"/>
<property name="src" location="${ALTERLIB.basedir}/src"/>
<property name="dist" location="${ALTERLIB.basedir}/dist"/>
- <property name="javacchome" location="${ALTERLIB.basedir}/javacc-5.0"/>
+ <property name="javacchome" location="/usr/share/java/"/>
<property name="grammars" location="${src}/parser"/>
<property name="javaversion" value="1.6" />
<taskdef resource="net/sf/antcontrib/antcontrib.properties">
<classpath>
- <pathelement location="${ALTERLIB.basedir}/ant-contrib/ant-contrib-1.0b3.jar"/>
+ <pathelement location="/usr/share/ant/lib/ant-contrib.jar"/>
</classpath>
</taskdef>
debian/rules
View file @ a3644dc3
......@@ -5,5 +5,10 @@ JAVA_HOME=/usr/lib/jvm/default-java
%:
dh $@ --with javahelper
get-orig-source:
uscan --verbose --force-download --repack --compression xz
override_dh_auto_build:
dh_auto_build
markdown_py -f README.html README.md
override_jh_installlibs:
file-rename 's/ALTER-([\d.]+)-jar-with-dependencies.jar/alter-\1.jar/' alter-lib/target/ALTER-1.3.4-jar-with-dependencies.jar
jh_installlibs