[med-svn] r1960 - trunk/packages/dialign-t/trunk/debian
plessy at alioth.debian.org
plessy at alioth.debian.org
Tue Jun 3 11:42:02 UTC 2008
Author: plessy
Date: 2008-06-03 11:42:00 +0000 (Tue, 03 Jun 2008)
New Revision: 1960
Modified:
trunk/packages/dialign-t/trunk/debian/changelog
trunk/packages/dialign-t/trunk/debian/control
trunk/packages/dialign-t/trunk/debian/copyright
trunk/packages/dialign-t/trunk/debian/dialign-tx.1
trunk/packages/dialign-t/trunk/debian/dialign-tx.1.xml
Log:
Minor upstream release.
Modified: trunk/packages/dialign-t/trunk/debian/changelog
===================================================================
--- trunk/packages/dialign-t/trunk/debian/changelog 2008-06-03 02:04:57 UTC (rev 1959)
+++ trunk/packages/dialign-t/trunk/debian/changelog 2008-06-03 11:42:00 UTC (rev 1960)
@@ -1,3 +1,15 @@
+dialign-t (1.0.1-1) unstable; urgency=low
+
+ * New upstream release updating bibliographic reference.
+ * debian/copyright: cosmetic changes.
+ * debian/dialign.1*:
+ - Converted DiAlign to DIALIGN;
+ - updated reference;
+ - incremented copyright year and version number.
+ * debian/control: updated reference.
+
+ -- Charles Plessy <plessy at debian.org> Tue, 03 Jun 2008 19:58:50 +0900
+
dialign-t (1.0.0-1) unstable; urgency=low
[ David Paleino ]
Modified: trunk/packages/dialign-t/trunk/debian/control
===================================================================
--- trunk/packages/dialign-t/trunk/debian/control 2008-06-03 02:04:57 UTC (rev 1959)
+++ trunk/packages/dialign-t/trunk/debian/control 2008-06-03 11:42:00 UTC (rev 1960)
@@ -29,8 +29,8 @@
.
DIALIGN-TX has been published in Amarendran R. Subramanian, Michael Kaufmann,
Burkhard Morgenstern: Improvement of the segment-based approach for multiple
- sequence alignment by combining greedy and progressive alignment strategies.
- Submission in Progress, 2008.
+ sequence alignment by combining greedy and progressive alignment strategies,
+ Algorithms for Molecular Biology 3:6, 2008
Package: dialign-tx-data
Architecture: all
Modified: trunk/packages/dialign-t/trunk/debian/copyright
===================================================================
--- trunk/packages/dialign-t/trunk/debian/copyright 2008-06-03 02:04:57 UTC (rev 1959)
+++ trunk/packages/dialign-t/trunk/debian/copyright 2008-06-03 11:42:00 UTC (rev 1960)
@@ -1,25 +1,13 @@
-X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
-X-Debianized-By: Charles Plessy <plessy at debian.org>
-X-Debianized-Date: Tue, 9 Oct 2007 23:17:04 +0900
-X-Source-Downloaded-From: http://dialign-tx.gobics.de/DIALIGN-TX_1.0.0.tar.gz
-X-Upstream-Author: Amarendran R. Subramanian <subraman at informatik.uni-tuebingen.de>
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=129
+Upstream-Author: Amarendran R. Subramanian <subraman at informatik.uni-tuebingen.de>
+Packaged-By: Charles Plessy <plessy at debian.org>
+Packaged-Date: Tue, 9 Oct 2007 23:17:04 +0900
+Original-Source-Location: http://dialign-tx.gobics.de/DIALIGN-TX_1.0.1.tar.gz
-
-Files: debian/*
-
-Copyright: © 2007-2008 Charles Plessy <plessy at debian.org>
- © 2008 David Paleino <d.paleino at gmail.com>
-
-License: LGPL-2.1+
- The Debian packaging is licensed under the same terms as DIALIGN-TX itself.
-
-
Files: *
-
-Copyright: © 2004-2007 Amarendran R. Subramanian
+Copyright: © 2004-2008 Amarendran R. Subramanian
© 2004 Volker Menrad
© 2004 Dorothea Emig
-
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
@@ -34,6 +22,11 @@
You should have received a copy of the GNU Lesser General Public
License along with this package; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-
X-Comment: On Debian systems, the complete text of the GNU Lesser General
Public License can be found in `/usr/share/common-licenses/LGPL'.
+
+Files: debian/*
+Copyright: © 2007-2008 Charles Plessy <plessy at debian.org>
+ © 2008 David Paleino <d.paleino at gmail.com>
+License: LGPL-2.1+
+ The Debian packaging is licensed under the same terms as DIALIGN-TX itself.
Modified: trunk/packages/dialign-t/trunk/debian/dialign-tx.1
===================================================================
--- trunk/packages/dialign-t/trunk/debian/dialign-tx.1 2008-06-03 02:04:57 UTC (rev 1959)
+++ trunk/packages/dialign-t/trunk/debian/dialign-tx.1 2008-06-03 11:42:00 UTC (rev 1960)
@@ -1,23 +1,23 @@
.\" Title: DIALIGN-TX
.\" Author: Amarendran R. Subramanian <subraman at informatik.uni-tuebingen.de>
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 04/30/2008
-.\" Manual: DiAlign-TX: Parameters
-.\" Source: dialign-tx 1.0.0
+.\" Date: 06/03/2008
+.\" Manual: DIALIGN-TX: Parameters
+.\" Source: dialign-tx 1.0.1
.\"
-.TH "DIALIGN\-TX" "1" "04/30/2008" "dialign-tx 1.0.0" "DiAlign-TX: Parameters"
+.TH "DIALIGN\-TX" "1" "06/03/2008" "dialign-tx 1.0.1" "DIALIGN-TX: Parameters"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-dialign-tx - Segment-based multiple sequence alignment
+dialign-tx \- Segment-based multiple sequence alignment
.SH "SYNOPSIS"
.HP 11
\fBdialign\-tx\fR [\fBOPTIONS\fR] {\fIconf\-directory\fR} {\fIfasta\-file\fR} [\fIfasta\-out\-file\fR]
.SH "DESCRIPTION"
.PP
-DIALIGN\-TX is an improved algorithm for segment\-based multiple protein alignments\. DIALIGN\-TX is a complete reimplementation of the segment\-base approach including several new improvements and heuristics that significantly enhance the quality of the output alignments compared to DIALIGN 2\.2\. This significant superiority has been observed on local as well on global alignment benchmarks\.
+DIALIGN\-TX is an improved algorithm for segment\-based multiple protein alignments\&. DIALIGN\-TX is a complete reimplementation of the segment\-base approach including several new improvements and heuristics that significantly enhance the quality of the output alignments compared to DIALIGN 2\&.2\&. This significant superiority has been observed on local as well on global alignment benchmarks\&.
.SH "OPTIONS"
.PP
\fB\-d\fR
@@ -35,17 +35,17 @@
.PP
\fB\-s\fR
.RS 4
-Maximum amount of input sequences [DEFAULT 5000]\.
+Maximum amount of input sequences [DEFAULT 5000]\&.
.RE
.PP
\fB\-a\fR
.RS 4
-Maximum number of characters per line in a FASTA file [DEFAULT 100]\.
+Maximum number of characters per line in a FASTA file [DEFAULT 100]\&.
.RE
.PP
\fB\-c\fR
.RS 4
-Maximum amount of characters per line when printing a sequence [DEFAULT 80]\.
+Maximum amount of characters per line when printing a sequence [DEFAULT 80]\&.
.RE
.PP
\fB\-l\fR
@@ -61,59 +61,59 @@
.PP
\fB\-m\fR
.RS 4
-Score matrix file name (in the configuration directory) [DEFAULT PROTEIN: BLOSUM\.scr] / [DEFAULT DNA: dna_matrix\.scr]\.
+Score matrix file name (in the configuration directory) [DEFAULT PROTEIN: BLOSUM\&.scr] / [DEFAULT DNA: dna_matrix\&.scr]\&.
.RE
.PP
\fB\-w\fR
.RS 4
-Defines the minimum weight when the weight formula is changed to 1\-pow(1\-prob, factor) [DEFAULT 0\.000000065]\.
+Defines the minimum weight when the weight formula is changed to 1\-pow(1\-prob, factor) [DEFAULT 0\&.000000065]\&.
.RE
.PP
\fB\-p\fR
.RS 4
-Probability distribution file name (in the configuration directory) [DEFAULT PROTEIN: BLOSUM\.diag_prob_t10] / [DEFAULT DNA: dna_diag_prob_100_exp_550000]\.
+Probability distribution file name (in the configuration directory) [DEFAULT PROTEIN: BLOSUM\&.diag_prob_t10] / [DEFAULT DNA: dna_diag_prob_100_exp_550000]\&.
.RE
.PP
\fB\-v\fR
.RS 4
-Add to each score (to prevent negative values) [DEFAULT 0]\.
+Add to each score (to prevent negative values) [DEFAULT 0]\&.
.RE
.PP
\fB\-t\fR
.RS 4
\(lqEven\(rq
-threshold for low score for sequences alignment [DEFAULT PROTEIN: 4] / [DEFAULT DNA: 0]\.
+threshold for low score for sequences alignment [DEFAULT PROTEIN: 4] / [DEFAULT DNA: 0]\&.
.RE
.PP
\fB\-n\fR
.RS 4
-Maximum number of consecutive positions for window containing low scoring positions [DEFAULT PROTEIN: 4] / [DEFAULT DNA: 1]\.
+Maximum number of consecutive positions for window containing low scoring positions [DEFAULT PROTEIN: 4] / [DEFAULT DNA: 1]\&.
.RE
.PP
\fB\-g\fR
.RS 4
-Global minimum fragment length for stop criterion [DEFAULT PROTEIN: 40] / [DEFAULT DNA: 1]\.
+Global minimum fragment length for stop criterion [DEFAULT PROTEIN: 40] / [DEFAULT DNA: 1]\&.
.RE
.PP
\fB\-m\fR
.RS 4
-Minimal allowed average score in frag window containing low scoring positions [DEFAULT PROTEIN: 4\.0] / [DEFAULT DNA: 0\.9]\.
+Minimal allowed average score in frag window containing low scoring positions [DEFAULT PROTEIN: 4\&.0] / [DEFAULT DNA: 0\&.9]\&.
.RE
.PP
\fB\-o\fR
.RS 4
-Wether overlap weights are calculated or not [DEFAULT 0]\.
+Wether overlap weights are calculated or not [DEFAULT 0]\&.
.RE
.PP
\fB\-f\fR
.RS 4
-Minimum fragment length [DEFAULT 1]\.
+Minimum fragment length [DEFAULT 1]\&.
.RE
.PP
\fB\-r\fR
.RS 4
-Threshold weight to consider the fragment at all [DEFAULT 0\.0]\.
+Threshold weight to consider the fragment at all [DEFAULT 0\&.0]\&.
.RE
.PP
\fB\-u\fR
@@ -121,22 +121,22 @@
[DEFAULT 0]
.IP "" 4
- 1: Only use a sqrt(amount_of_seqs) stripe of neighbour sequences to calculate pairwise alignments (increase performance)\.
+ 1: Only use a sqrt(amount_of_seqs) stripe of neighbour sequences to calculate pairwise alignments (increase performance)\&.
.IP "" 4
- 0: All pairwise alignments will be calculated\.
+ 0: All pairwise alignments will be calculated\&.
.RE
.PP
\fB\-D\fR
.RS 4
-Input is DNA\-sequence\.
+Input is DNA\-sequence\&.
.RE
.PP
\fB\-T\fR
.RS 4
-Translate DNA into aminoacids from begin to end (length will be cut to mod 3 = 0)\.
+Translate DNA into aminoacids from begin to end (length will be cut to mod 3 = 0)\&.
.sp
.it 1 an-trap
.nr an-no-space-flag 1
@@ -145,13 +145,13 @@
Warning
Do not use
\fB\-D\fR
-with this option (Default values for PROTEIN input will be loaded)\.
+with this option (Default values for PROTEIN input will be loaded)\&.
.RE
.PP
\fB\-L\fR
.RS 4
-Compare only longest Open Reading Frame\.
+Compare only longest Open Reading Frame\&.
.sp
.it 1 an-trap
.nr an-no-space-flag 1
@@ -160,13 +160,13 @@
Warning
Do not use
\fB\-D\fR
-with this option (Default values for PROTEIN input will be loaded)\.
+with this option (Default values for PROTEIN input will be loaded)\&.
.RE
.PP
\fB\-O\fR
.RS 4
-Translate DNA to aminoacids, reading frame for each sequence calculated due to its longest ORF\.
+Translate DNA to aminoacids, reading frame for each sequence calculated due to its longest ORF\&.
.sp
.it 1 an-trap
.nr an-no-space-flag 1
@@ -175,28 +175,28 @@
Warning
Do not use
\fB\-D\fR
-with this option (Default values for PROTEIN input will be loaded)\.
+with this option (Default values for PROTEIN input will be loaded)\&.
.RE
.PP
\fB\-P\fR
.RS 4
-Output in aminoacids, no retranslation of DNA sequences [DEFAULT: input = output]\.
+Output in aminoacids, no retranslation of DNA sequences [DEFAULT: input = output]\&.
.RE
.PP
\fB\-F\fR
.RS 4
-Fast mode (implies \-l0, since it already significantly reduces sensitivity)\.
+Fast mode (implies \-l0, since it already significantly reduces sensitivity)\&.
.RE
.PP
\fB\-C\fR
.RS 4
-Generate probability table saved in /usr/share/dialign\-tx/prob_table and exit\.
+Generate probability table saved in /usr/share/dialign\-tx/prob_table and exit\&.
.RE
.PP
\fB\-H\fR, \fB\-h\fR
.RS 4
-Print this message\.
+Print this message\&.
.RE
.SH "FILES"
.PP
@@ -204,22 +204,22 @@
.RS 4
This is the default conf\-directory that
\fBdialign\-tx\fR
-expects as its first argument, as supplied in the upstream sources\.
+expects as its first argument, as supplied in the upstream sources\&.
.RE
.SH "SEE ALSO"
.PP
DIALIGN\-TX is a re\-implementation of
-\fBdialign2-2\fR(1)\. (See http://dialign\.gobics\.de/ for more information about DIALIGN2)\.
+\fBdialign2-2\fR(1)\&. (See http://dialign\&.gobics\&.de/ for more information about DIALIGN2)\&.
.PP
-The website of DIALIGN\-TX is http://dialign\-tx\.gobics\.de/
+The website of DIALIGN\-TX is http://dialign\-tx\&.gobics\&.de/
.SH "REFERENCES"
.PP
-Amarendran R\. Subramanian, Michael Kaufmann, Burkhard Morgenstern: DIALIGN\-TX: improvement of the segment\-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies\. In Progress, 2008\.
+Amarendran R\&. Subramanian, Michael Kaufmann, Burkhard Morgenstern: DIALIGN\-TX: improvement of the segment\-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies, Algorithms for Molecular Biology 3:6, 2008\&.
.PP
-Amarendran R\. Subramanian, Jan Weyer\-Menkhoff, Michael Kaufmann, Burkhard Morgenstern: DIALIGN\-T: An improved algorithm for segment\-based multiple sequence alignment\. BMC Bioinformatics 2005, 6:66\.
+Amarendran R\&. Subramanian, Jan Weyer\-Menkhoff, Michael Kaufmann, Burkhard Morgenstern: DIALIGN\-T: An improved algorithm for segment\-based multiple sequence alignment\&. BMC Bioinformatics 2005, 6:66\&.
.SH "AUTHORS"
.PP
-\fBAmarendran R\. Subramanian\fR <\&subraman at informatik\.uni\-tuebingen\.de\&>
+\fBAmarendran R\&. Subramanian\fR <\&subraman at informatik\&.uni\-tuebingen\&.de\&>
.sp -1n
.IP "" 4
Author of dialign\-tx
@@ -234,28 +234,28 @@
.IP "" 4
Co\-author of dialign\-tx
.PP
-\fBCharles Plessy\fR <\&plessy at debian\.org\&>
+\fBCharles Plessy\fR <\&plessy at debian\&.org\&>
.sp -1n
.IP "" 4
-Converted this guide in DocBook XML for the Debian distribution\.
+Converted this guide in DocBook XML for the Debian distribution\&.
.SH "COPYRIGHT"
-Copyright \(co 2004, 2005, 2006, 2007 Amarendran R. Subramanian (DiAlign-TX)
+Copyright \(co 2004, 2005, 2006, 2007, 2008 Amarendran R. Subramanian (DIALIGN-TX)
.br
-Copyright \(co 2004 Volker Menrad (DiAlign-TX)
+Copyright \(co 2004 Volker Menrad (DIALIGN-TX)
.br
-Copyright \(co 2004 Dorothea Emig (DiAlign-TX)
+Copyright \(co 2004 Dorothea Emig (DIALIGN-TX)
.br
-Copyright \(co 2007 Charles Plessy (This document and its XML source.)
+Copyright \(co 2007, 2008 Charles Plessy (This document and its XML source.)
.br
.PP
-DiAlign\-TX 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\.
+DIALIGN\-TX 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\&.
.PP
-DiAlign\-TX 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 Lesser General Public License for more details\.
+DIALIGN\-TX 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 Lesser General Public License for more details\&.
.PP
-You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc\., 51 Franklin St, Fifth Floor, Boston, MA 02110\-1301 USA
+You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc\&., 51 Franklin St, Fifth Floor, Boston, MA 02110\-1301 USA
.PP
On Debian system, a copy of the GNU Lesser General Public License is available in
-\fI/usr/share/common\-licences\fR\.
+\fI/usr/share/common\-licences\fR\&.
.PP
-This documentation and its XML source file can be used, modified and redistributed under the same terms as DiAlign\-TX itself\.
+This documentation and its XML source file can be used, modified and redistributed under the same terms as DIALIGN\-TX itself\&.
.sp
Modified: trunk/packages/dialign-t/trunk/debian/dialign-tx.1.xml
===================================================================
--- trunk/packages/dialign-t/trunk/debian/dialign-tx.1.xml 2008-06-03 02:04:57 UTC (rev 1959)
+++ trunk/packages/dialign-t/trunk/debian/dialign-tx.1.xml 2008-06-03 11:42:00 UTC (rev 1960)
@@ -1,8 +1,8 @@
<?xml version='1.0' encoding='ISO-8859-1'?>
<?xml-stylesheet type="text/xsl"
href="http://docbook.sourceforge.net/release/xsl/current/manpages/docbook.xsl"?>
-<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.4//EN"
- "http://www.oasis-open.org/docbook/xml/4.4/docbookx.dtd" [
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.5//EN"
+ "http://www.oasis-open.org/docbook/xml/4.5/docbookx.dtd" [
<!-- Process this file with an XSLT processor, e.g. xsltproc: -->
<!-- `xsltproc \
@@ -18,8 +18,8 @@
<!ENTITY dhsurname "Plessy">
<!ENTITY dhemail "plessy at debian.org">
<!ENTITY dhusername "&dhfirstname; &dhsurname;">
- <!ENTITY dhrelease "1.0.0">
- <!ENTITY dhtitle "DiAlign-TX: Parameters">
+ <!ENTITY dhrelease "1.0.1">
+ <!ENTITY dhtitle "DIALIGN-TX: Parameters">
<!ENTITY dhucpackage "DIALIGN-TX">
<!ENTITY dhpackage "dialign-tx">
<!ENTITY dhproduct "&dhpackage;">
@@ -71,31 +71,33 @@
<year>2004</year>
<year>2005</year>
<year>2006</year>
- <year>2007</year>
- <holder>Amarendran R. Subramanian (DiAlign-TX)</holder>
+ <year>2007</year>
+ <year>2008</year>
+ <holder>Amarendran R. Subramanian (DIALIGN-TX)</holder>
</copyright>
<copyright>
<year>2004</year>
- <holder>Volker Menrad (DiAlign-TX)</holder>
+ <holder>Volker Menrad (DIALIGN-TX)</holder>
</copyright>
<copyright>
<year>2004</year>
- <holder>Dorothea Emig (DiAlign-TX)</holder>
+ <holder>Dorothea Emig (DIALIGN-TX)</holder>
</copyright>
<copyright>
<year>2007</year>
+ <year>2008</year>
<holder>&dhusername; (This document and its XML source.)</holder>
</copyright>
<legalnotice>
<para>
- DiAlign-TX 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.
+ DIALIGN-TX 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.
</para>
<para>
- DiAlign-TX 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 Lesser General Public License for more details.
+ DIALIGN-TX 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 Lesser General Public License for more details.
</para>
<para>
You should have received a copy of the GNU Lesser General Public License along with this library; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
@@ -104,7 +106,7 @@
On Debian system, a copy of the GNU Lesser General Public License is available in <filename class="directory">/usr/share/common-licences</filename>.
</para>
<para>
- This documentation and its XML source file can be used, modified and redistributed under the same terms as DiAlign-TX itself.
+ This documentation and its XML source file can be used, modified and redistributed under the same terms as DIALIGN-TX itself.
</para>
</legalnotice>
</refentryinfo>
@@ -395,7 +397,7 @@
<refsect1 id="reference">
<title>REFERENCES</title>
<para>
- Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern: DIALIGN-TX: improvement of the segment-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies. In Progress, 2008.
+ Amarendran R. Subramanian, Michael Kaufmann, Burkhard Morgenstern: DIALIGN-TX: improvement of the segment-based approach for multiple sequence alignment by combining greedy and progressive alignment strategies, Algorithms for Molecular Biology 3:6, 2008.
</para>
<para>
Amarendran R. Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann, Burkhard Morgenstern: DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment. BMC Bioinformatics 2005, 6:66.
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