diff --git a/README.md b/README.md
index 944963819332272c08db5a77685e10a03d274613..1a9c39aeceb7a63cabb054a9628fa18b6129c4f0 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
# Concatenate
-_Concatenate_ is a command line program written in [Java](https://docs.oracle.com/javase/8/docs/technotes/guides/language/index.html) that allows building a supermatrix of characters from a set of multiple sequence alignments (MSA).
+_Concatenate_ is a command line program written in [Java](https://docs.oracle.com/javase/8/docs/technotes/guides/language/index.html) to build a supermatrix of characters from a set of multiple sequence alignments (MSA) in FASTA or PHYLIP format.
## Compilation and execution
@@ -8,6 +8,10 @@ The source code of _Concatenate_ is inside the _src_ directory and could be comp
#### Building an executable jar file
+Clone this repository with the following command line:
+```bash
+git clone https://gitlab.pasteur.fr/GIPhy/Concatenate.git
+```
On computers with [Oracle JDK](http://www.oracle.com/technetwork/java/javase/downloads/index.html) (6 or higher) installed, a Java executable jar file could be created. In a command-line window, go to the _src_ directory and type:
```bash
javac Concatenate.java
@@ -15,37 +19,51 @@ echo Main-Class: Concatenate > MANIFEST.MF
jar -cmvf MANIFEST.MF Concatenate.jar Concatenate.class
rm MANIFEST.MF Concatenate.class
```
-This will create the executable jar file `Concatenate.jar` that could be launched with the following command line model:
+This will create the executable jar file `Concatenate.jar` that could be run with the following command line model:
```bash
java -jar Concatenate.jar [options]
```
#### Building a native code binary
-On computers with the [GNU compiler GCJ](https://gcc.gnu.org/onlinedocs/gcc-4.2.4/gcj/) installed, a binary could also be built. In a command-line window, go to the _src_ directory, and type:
+Clone this repository with the following command line:
```bash
-make
+git clone https://gitlab.pasteur.fr/GIPhy/Concatenate.git
+```
+On computers with [GraalVM](hhttps://www.graalvm.org/downloads/) installed, a native executable can be built. In a command-line window, go to the _src_ directory, and type:
+```bash
+javac Concatenate.java
+native-image Concatenate Concatenate
+rm Concatenate.class
```
-This will create the executable binary file `concatenate` that could be launched with the following command line model:
+This will create the native executable `Conctenate` that can be run with the following command line model:
```bash
-./concatenate [options]
+./Concatenate [options]
```
+
## Usage
Launch _Concatenate_ without option to read the following documentation:
```
--i <infile> To indicate the input file that contains containing every MSA file name (one
- per line). If the character % is set before a file name, the corresponding
- MSA will be not used to build the supermatrix of characters. Each MSA file
- should contain one MSA (DNA, RNA, amino acid, O1, ...) in either FASTA or
- PHYLIP format. Relative/absolute path is allowed for each MSA file (default:
- datafiles.txt).
--o <outfile> To set the output file name (default: supermatrix.phy or supermatrix.fasta)
--f To write the supermatrix of characters in FASTA format (default: PHYLIP)
--l <integer> To set the maximum length of the written sequences (default: infinity); when
- option -f is not set, this option leads to a PHYLIP-interleaved ouput file
+ Concatenate
+
+ USAGE: Concatenate [-i <infile>] [-o <outfile>] [-f] [-l <integer>]
+
+ where options are:
+
+ -i <infile> to indicate the input file that contains containing every MSA file name (one
+ per line). If the character % is set before a file name, the corresponding
+ MSA will be not used to build the supermatrix of characters. Each MSA file
+ should contain one MSA (DNA, RNA, amino acid, O1, ...) in either FASTA or
+ PHYLIP format. Relative/absolute path is allowed for each MSA file (default:
+ datafiles.txt).
+ -o <outfile> To set the output file name (default: supermatrix.phy or supermatrix.fasta)
+ -f To write the supermatrix of characters in FASTA format (default: PHYLIP)
+ -l <integer> To set the maximum length of the written sequences (default: infinity); when
+ option -f is not set, this option leads to a PHYLIP-interleaved ouput file
+
```
## Notes
diff --git a/src/Concatenate.java b/src/Concatenate.java
index 8300d000775309211b2ae91519f9b28793a11fa9..856b1b7a1c575ede0850af95d044a7298fcff7e1 100644
--- a/src/Concatenate.java
+++ b/src/Concatenate.java
@@ -1,31 +1,30 @@
/*
- ####################################################################
- Concatenate: building a supermatrix of characters by concatenating
- a set of multiple sequence alignment
+ ########################################################################################################
- Copyright (C) 2018 Alexis Criscuolo
-
- This program 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 3 of the License, or
+ Concatenate: building a supermatrix of characters by concatenating a set of multiple sequence alignment
+
+ Copyright (C) 2018-2020 Institut Pasteur
+
+ This program 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 3 of the License, or
(at your option) any later version.
- This program 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.
+ This program 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/>.
-
- Contact:
- Institut Pasteur
- Bioinformatics and Biostatistics Hub
- C3BI, USR 3756 IP CNRS
- Paris, FRANCE
+ You should have received a copy of the GNU General Public License along with this program. If not, see
+ <http://www.gnu.org/licenses/>.
+
+ Contact:
+ Alexis Criscuolo alexis.criscuolo@pasteur.fr
+ Genome Informatics & Phylogenetics (GIPhy) giphy.pasteur.fr
+ Bioinformatics and Biostatistics Hub research.pasteur.fr/team/hub-giphy
+ USR 3756 IP CNRS research.pasteur.fr/team/bioinformatics-and-biostatistics-hub
+ Dpt. Biologie Computationnelle research.pasteur.fr/department/computational-biology
+ Institut Pasteur, Paris, FRANCE research.pasteur.fr
- alexis.criscuolo@pasteur.fr
- ####################################################################
+ ########################################################################################################
*/
import java.io.*;
@@ -34,8 +33,9 @@ import java.util.*;
public class Concatenate {
// constants
+ final static String VERSION = "0.1b.201024ac";
final static String MISSING = "????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????????"; // one thousand unknown character states
- final static String BLANK = " "; // one thousand blank characters
+ final static String BLANK = " "; // one thousand blank characters
final static String NO_FILE = "n.o.f.i.l.e";
// options
@@ -70,11 +70,13 @@ public class Concatenate {
// ###########################
if ( args.length < 2 ) {
System.out.println("");
- System.out.println(" USAGE: Concatenate [options]");
+ System.out.println(" Concatenate v." + VERSION + " Copyright (C) 2019-2020 Institut Pasteur");
+ System.out.println("");
+ System.out.println(" USAGE: Concatenate [-i <infile>] [-o <outfile>] [-f] [-l <integer>]");
System.out.println("");
System.out.println(" where options are:");
System.out.println("");
- System.out.println(" -i <infile> To indicate the input file that contains containing every MSA file name (one ");
+ System.out.println(" -i <infile> to indicate the input file that contains containing every MSA file name (one");
System.out.println(" per line). If the character % is set before a file name, the corresponding");
System.out.println(" MSA will be not used to build the supermatrix of characters. Each MSA file");
System.out.println(" should contain one MSA (DNA, RNA, amino acid, O1, ...) in either FASTA or");
diff --git a/src/Makefile b/src/Makefile
deleted file mode 100644
index 5f1dc3945706c60deef43737cc3dd2d82ebdbbff..0000000000000000000000000000000000000000
--- a/src/Makefile
+++ /dev/null
@@ -1,8 +0,0 @@
-GCJ=gcj
-GCJFLAGS=-fsource=1.6 -march=native -msse2 -O3 -minline-all-stringops -fomit-frame-pointer -momit-leaf-frame-pointer -fstrict-aliasing -fno-store-check -fno-bounds-check -funroll-all-loops -Wall
-OTHERFLAGS=-funsafe-math-optimizations -ffast-math
-MAIN=Concatenate
-EXEC=concatenate
-
-Concatenate: Concatenate.java
- $(GCJ) $(GCJFLAGS) --main=$(MAIN) $(MAIN).java -o $(EXEC)