[med-svn] r1839 - trunk/packages/primer3/trunk/debian
plessy at alioth.debian.org
plessy at alioth.debian.org
Fri May 9 04:09:38 UTC 2008
Author: plessy
Date: 2008-05-09 04:09:37 +0000 (Fri, 09 May 2008)
New Revision: 1839
Modified:
trunk/packages/primer3/trunk/debian/changelog
trunk/packages/primer3/trunk/debian/copyright
trunk/packages/primer3/trunk/debian/ntdpal.1
trunk/packages/primer3/trunk/debian/ntdpal.1.xml
trunk/packages/primer3/trunk/debian/oligotm.1
trunk/packages/primer3/trunk/debian/oligotm.1.xml
trunk/packages/primer3/trunk/debian/primer3_core.1
trunk/packages/primer3/trunk/debian/primer3_core.1.xml
Log:
New upstream release
Modified: trunk/packages/primer3/trunk/debian/changelog
===================================================================
--- trunk/packages/primer3/trunk/debian/changelog 2008-05-09 00:55:07 UTC (rev 1838)
+++ trunk/packages/primer3/trunk/debian/changelog 2008-05-09 04:09:37 UTC (rev 1839)
@@ -1,8 +1,12 @@
-primer3 (1.1.3-2) UNRELEASED; urgency=low
+primer3 (1.1.4-1) unstable; urgency=low
- * Updated my email address.
+ * New upstream release (No changes on Linux systems).
+ * Updated my email address (debian/control, debian/copyright, manpages).
+ * Updated the manpages:
+ - using DocBook 4.5
+ - incremented Primer3 version to 1.1.4
- -- Charles Plessy <plessy at debian.org> Sun, 27 Apr 2008 17:02:01 +0900
+ -- Charles Plessy <plessy at debian.org> Fri, 09 May 2008 12:54:28 +0900
primer3 (1.1.3-1) unstable; urgency=low
Modified: trunk/packages/primer3/trunk/debian/copyright
===================================================================
--- trunk/packages/primer3/trunk/debian/copyright 2008-05-09 00:55:07 UTC (rev 1838)
+++ trunk/packages/primer3/trunk/debian/copyright 2008-05-09 04:09:37 UTC (rev 1839)
@@ -1,41 +1,9 @@
-X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
-X-Debianized-By: Steffen Möller <moeller at debian.org>
-X-Debianized-Date: Wed, 31 Mar 2004 15:07:10 +0200
-X-Source-Downloaded-From: http://sourceforge.net/projects/primer3/
-X-Upstream-Authors: Steve Rozen and Helen Skaletsky
+Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=103
+Debianized-By: Steffen Möller <moeller at debian.org>
+Debianized-Date: Wed, 31 Mar 2004 15:07:10 +0200
+Original-Source-Location: http://downloads.sourceforge.net/primer3/primer3-1.1.4.tar.gz
+Upstream-Author: Steve Rozen and Helen Skaletsky
-Files: debian/*
-Copyright: © 2004 Steffen Möller <moeller at debian.org>
- © 2006-2008 Charles Plessy <charles-debian-nospam at plessy.org>
- © 2008 David Paleino <d.paleino at gmail.com>
-License: PD
- The packaging work is hereby released in the public domain unless stated
- otherwise.
-
-
-Files: src/oligotm*, tst/oligotm_test.pl
-Copyright: © 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008
- Whitehead Institute for Biomedical Research,
- Steve Rozen (http://jura.wi.mit.edu/rozen),
- Helen Skaletsky
-License: GPL-2+
- The oligotm library 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.
- .
- The oligotm library 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 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 General
-Public License can be found in `/usr/share/common-licenses/GPL'.
-
-
Files: *
Copyright: © 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008
Whitehead Institute for Biomedical Research,
@@ -67,3 +35,33 @@
THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Files: src/oligotm*, tst/oligotm_test.pl
+Copyright: © 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008
+ Whitehead Institute for Biomedical Research,
+ Steve Rozen (http://jura.wi.mit.edu/rozen),
+ Helen Skaletsky
+License: GPL-2+
+ The oligotm library 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.
+ .
+ The oligotm library 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 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 General
+Public License can be found in `/usr/share/common-licenses/GPL'.
+
+Files: debian/*
+Copyright: © 2004 Steffen Möller <moeller at debian.org>
+ © 2006-2008 Charles Plessy <plessy at debian.org>
+ © 2008 David Paleino <d.paleino at gmail.com>
+License: PD
+ The packaging work is hereby released in the public domain unless stated
+ otherwise.
Modified: trunk/packages/primer3/trunk/debian/ntdpal.1
===================================================================
--- trunk/packages/primer3/trunk/debian/ntdpal.1 2008-05-09 00:55:07 UTC (rev 1838)
+++ trunk/packages/primer3/trunk/debian/ntdpal.1 2008-05-09 04:09:37 UTC (rev 1839)
@@ -1,78 +1,78 @@
.\" Title: NTDPAL
.\" Author:
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 02/22/2008
+.\" Date: 05/09/2008
.\" Manual: Primer3 User Manuals
-.\" Source: ntdpal 1.1.3
+.\" Source: ntdpal 1.1.4
.\"
-.TH "NTDPAL" "1" "02/22/2008" "ntdpal 1.1.3" "Primer3 User Manuals"
+.TH "NTDPAL" "1" "05/09/2008" "ntdpal 1.1.4" "Primer3 User Manuals"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-ntdpal - Provides Primer3's alignment functionality
+ntdpal \- Provides Primer3's alignment functionality
.SH "SYNOPSIS"
.HP 7
\fBntdpal\fR [\-g\ \fIgval\fR] [\-l\ \fIlval\fR] [\-m\ \fImval\fR] [\-f1,\ f2,\ f3] [\-p] [\-s] [\-e] {\fIseq1\fR} {\fIseq2\fR} {\fImode\fR}
.SH "DESCRIPTION"
.PP
-Ntdpal (NucleoTide Dynamic Programming ALignment) is a stand\-alone program that provides Primer3\'s alignment functionality (local, a\.k\.a\. Smith\-Waterman, global, a\.k\.a\. Needleman\-Wunsch, plus "half global")\.
+Ntdpal (NucleoTide Dynamic Programming ALignment) is a stand\-alone program that provides Primer3\'s alignment functionality (local, a\&.k\&.a\&. Smith\-Waterman, global, a\&.k\&.a\&. Needleman\-Wunsch, plus "half global")\&.
.SH "OPTIONS"
.PP
\fB\-g\fR \fIgval\fR
.RS 4
\fIgval\fR
-is a (positive) float (\.01 precision) specifying penaltiy for creating a gap respectively (the penalties are subtracted from the output score)
+is a (positive) float (\&.01 precision) specifying penaltiy for creating a gap respectively (the penalties are subtracted from the output score)
.RE
.PP
\fB\-l\fR \fIval\fR
.RS 4
\fIlval\fR
-is a (positive) float (\.01 precision) specifying penaltiy for lengthening a gap respectively (the penalties are subtracted from the output score)
+is a (positive) float (\&.01 precision) specifying penaltiy for lengthening a gap respectively (the penalties are subtracted from the output score)
.RE
.PP
\fB\-a\fR
.RS 4
-Causes the scoring matrix to be modified by dpal_set_ambiguity_codes\.
+Causes the scoring matrix to be modified by dpal_set_ambiguity_codes\&.
.RE
.PP
\fB\-e\fR
.RS 4
-Causes the end postion of the alignment in both sequences to be printed\. Do not confuse with the \'e\'
-\fImode\fR\.
+Causes the end postion of the alignment in both sequences to be printed\&. Do not confuse with the \'e\'
+\fImode\fR\&.
.RE
.PP
\fB\-f1, \-f2, \-f3\fR
.RS 4
-Force specific implementations\. \-f2 forces use an implementation that might provide more informative error messages, possibly at the expense of some speed\.
+Force specific implementations\&. \-f2 forces use an implementation that might provide more informative error messages, possibly at the expense of some speed\&.
.RE
.PP
\fB\-h\fR
.RS 4
-Use a different scoring matrix: G and C matches = 3, A and T = 2, and mismatches = \-0\.5\. (The default scoring matrix assigns 1 to a match, and \-1 to a mismatch\.)
+Use a different scoring matrix: G and C matches = 3, A and T = 2, and mismatches = \-0\&.5\&. (The default scoring matrix assigns 1 to a match, and \-1 to a mismatch\&.)
.RE
.PP
\fB\-p\fR
.RS 4
-Causes the alignment to be displayed on stderr\.
+Causes the alignment to be displayed on stderr\&.
.RE
.PP
\fB\-s\fR
.RS 4
causes
\fIonly\fR
-the score to printed\.
+the score to printed\&.
.RE
.PP
\fB\-m\fR \fImval\fR
.RS 4
-is the maximum allowed gap (default is 3)\.
+is the maximum allowed gap (default is 3)\&.
.RE
.PP
\fIseq1\fR and \fIseq2\fR
.RS 4
-are the sequences to be aligned\.
+are the sequences to be aligned\&.
.RE
.PP
\fImode\fR
@@ -82,14 +82,14 @@
\fIG\fR,
\fIl\fR, or
\fIL\fR
-specifying a global, global end\-anchored, local, or local end\-achored alignment respectively\. For backward compatibility
+specifying a global, global end\-anchored, local, or local end\-achored alignment respectively\&. For backward compatibility
\fIe\fR
is equivalent to
-\fIG\fR\.
+\fIG\fR\&.
.RE
.SH "REFERENCE"
.PP
-Please cite Rozen, S\., Skaletsky, H\. "Primer3 on the WWW for general users and for biologist programmers\." In S\. Krawetz and S\. Misener, eds\. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology\. Humana Press, Totowa, NJ, 2000, pages 365\-386\.
+Please cite Rozen, S\&., Skaletsky, H\&. "Primer3 on the WWW for general users and for biologist programmers\&." In S\&. Krawetz and S\&. Misener, eds\&. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology\&. Humana Press, Totowa, NJ, 2000, pages 365\-386\&.
.SH "SEE ALSO"
.PP
@@ -99,14 +99,14 @@
Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky
.br
.PP
-All rights reserved\. On Debian\-based systems, please consult
+All rights reserved\&. On Debian\-based systems, please consult
\fI/usr/share/doc/primer3/copyright\fR
-to read the licence of ntdpal\.
+to read the licence of ntdpal\&.
.PP
This manual page was written by Charles Plessy
-<charles\-debian\-nospam at plessy\.org>
+<plessy at debian\&.org>
for the
Debian(TM)
-system (but may be used by others)\. Permission is granted to copy, distribute and/or modify this document under the same terms as oligotm itself\.
+system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the same terms as oligotm itself\&.
.sp
Modified: trunk/packages/primer3/trunk/debian/ntdpal.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/ntdpal.1.xml 2008-05-09 00:55:07 UTC (rev 1838)
+++ trunk/packages/primer3/trunk/debian/ntdpal.1.xml 2008-05-09 04:09:37 UTC (rev 1839)
@@ -1,17 +1,17 @@
<?xml version='1.0' encoding='UTF-8'?>
<?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" [
<!ENTITY dhfirstname "<firstname>Charles</firstname>">
<!ENTITY dhsurname "<surname>Plessy</surname>">
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
+ <!ENTITY dhemail "<email>plessy at debian.org</email>">
<!ENTITY dhusername "Charles Plessy">
<!ENTITY dhtitle "Primer3 User Manuals">
<!ENTITY dhucpackage "<refentrytitle>NTDPAL</refentrytitle>">
<!ENTITY dhpackage "ntdpal">
- <!ENTITY dhrelease "1.1.3">
+ <!ENTITY dhrelease "1.1.4">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
Modified: trunk/packages/primer3/trunk/debian/oligotm.1
===================================================================
--- trunk/packages/primer3/trunk/debian/oligotm.1 2008-05-09 00:55:07 UTC (rev 1838)
+++ trunk/packages/primer3/trunk/debian/oligotm.1 2008-05-09 04:09:37 UTC (rev 1839)
@@ -1,17 +1,17 @@
.\" Title: OLIGOTM
.\" Author:
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 02/22/2008
+.\" Date: 05/09/2008
.\" Manual: Primer3 User Manuals
-.\" Source: oligotm 1.1.3
+.\" Source: oligotm 1.1.4
.\"
-.TH "OLIGOTM" "1" "02/22/2008" "oligotm 1.1.3" "Primer3 User Manuals"
+.TH "OLIGOTM" "1" "05/09/2008" "oligotm 1.1.4" "Primer3 User Manuals"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-oligotm - Prints oligo's melting temperature on stdout
+oligotm \- Prints oligo's melting temperature on stdout
.SH "SYNOPSIS"
.HP 8
\fBoligotm\fR [OPTIONS] {oligo}
@@ -21,27 +21,27 @@
.PP
\fBoligotm\fR
-prints the melting temperature of a given desoxyribooligonucleotide on the standard output\. It is part of the oligotm library\.
+prints the melting temperature of a given desoxyribooligonucleotide on the standard output\&. It is part of the oligotm library\&.
.SH "OPTIONS"
.PP
\fB\-mv\fR \fImonovalent_conc\fR
.RS 4
-Concentration of monovalent cations in mM, by default 50\ mM\.
+Concentration of monovalent cations in mM, by default 50\ \&mM\&.
.RE
.PP
\fB\-dv\fR \fIdivalent_conc\fR
.RS 4
-Concentration of divalent cations in mM, by default 0\ mM\.
+Concentration of divalent cations in mM, by default 0\ \&mM\&.
.RE
.PP
\fB\-n\fR \fIdNTP_conc\fR
.RS 4
-Concentration of deoxynycleotide triphosphate in mM, by default 0\ mM\.
+Concentration of deoxynycleotide triphosphate in mM, by default 0\ \&mM\&.
.RE
.PP
\fB\-d\fR \fIdna_conc\fR
.RS 4
-Concentration of DNA strands in nM, by default 50\ nM\.
+Concentration of DNA strands in nM, by default 50\ \&nM\&.
.RE
.PP
\fB\-tp\fR \fI[0|1]\fR
@@ -50,48 +50,48 @@
.sp
.RS 4
\h'-04'\(bu\h'+03'\fI0\fR
-Breslauer et al\., 1986 and Rychlik et al\., 1990 (used by primer3 up to and including release 1\.1\.0)\. This is the default, but
+Breslauer et al\&., 1986 and Rychlik et al\&., 1990 (used by primer3 up to and including release 1\&.1\&.0)\&. This is the default, but
\fInot\fR
-the recommended value\.
+the recommended value\&.
.RE
.sp
.RS 4
\h'-04'\(bu\h'+03'\fI1\fR
-Use nearest neighbor parameter from SantaLucia 1998\.
-\fIThis is the recommended value\fR\.
+Use nearest neighbor parameter from SantaLucia 1998\&.
+\fIThis is the recommended value\fR\&.
.RE
.RE
.PP
-\fB\-sc\fR \fI[0\.\.2]\fR
+\fB\-sc\fR \fI[0\&.\&.2]\fR
.RS 4
Specifies salt correction formula for the melting temperature calculation:
.sp
.RS 4
\h'-04'\(bu\h'+03'\fI0\fR
-Schildkraut and Lifson 1965, used by primer3 up to and including release 1\.1\.0\. This is the default, but
+Schildkraut and Lifson 1965, used by primer3 up to and including release 1\&.1\&.0\&. This is the default, but
\fInot\fR
-the recommended value\.
+the recommended value\&.
.RE
.sp
.RS 4
\h'-04'\(bu\h'+03'\fI1\fR
-SantaLucia 1998\.
-\fIThis is the recommended value\fR\.
+SantaLucia 1998\&.
+\fIThis is the recommended value\fR\&.
.RE
.sp
.RS 4
\h'-04'\(bu\h'+03'\fI1\fR
-Owczarzy et al\., 2004\.
+Owczarzy et al\&., 2004\&.
.RE
.RE
.PP
\fB\-i\fR
.RS 4
-prints references to publications which were used for thermodynamic calculations\.
+prints references to publications which were used for thermodynamic calculations\&.
.RE
.SH "REFERENCE"
.PP
-Please cite Rozen, S\., Skaletsky, H\. "Primer3 on the WWW for general users and for biologist programmers\." In S\. Krawetz and S\. Misener, eds\. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology\. Humana Press, Totowa, NJ, 2000, pages 365\-386\.
+Please cite Rozen, S\&., Skaletsky, H\&. "Primer3 on the WWW for general users and for biologist programmers\&." In S\&. Krawetz and S\&. Misener, eds\&. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology\&. Humana Press, Totowa, NJ, 2000, pages 365\-386\&.
.SH "SEE ALSO"
.PP
@@ -101,14 +101,14 @@
Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky
.br
.PP
-All rights reserved\. On Debian\-based systems, please consult
+All rights reserved\&. On Debian\-based systems, please consult
\fI/usr/share/doc/primer3/copyright\fR
-to read the licence of oligotm\.
+to read the licence of oligotm\&.
.PP
This manual page was written by Charles Plessy
-<charles\-debian\-nospam at plessy\.org>
+<plessy at debian\&.org>
for the
Debian(TM)
-system (but may be used by others)\. Permission is granted to copy, distribute and/or modify this document under the same terms as oligotm itself\.
+system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the same terms as oligotm itself\&.
.sp
Modified: trunk/packages/primer3/trunk/debian/oligotm.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/oligotm.1.xml 2008-05-09 00:55:07 UTC (rev 1838)
+++ trunk/packages/primer3/trunk/debian/oligotm.1.xml 2008-05-09 04:09:37 UTC (rev 1839)
@@ -1,17 +1,17 @@
<?xml version='1.0' encoding='UTF-8'?>
<?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" [
<!ENTITY dhfirstname "<firstname>Charles</firstname>">
<!ENTITY dhsurname "<surname>Plessy</surname>">
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
+ <!ENTITY dhemail "<email>plessy at debian.org</email>">
<!ENTITY dhusername "Charles Plessy">
<!ENTITY dhucpackage "<refentrytitle>OLIGOTM</refentrytitle>">
<!ENTITY dhtitle "Primer3 User Manuals">
<!ENTITY dhpackage "oligotm">
- <!ENTITY dhrelease "1.1.3">
+ <!ENTITY dhrelease "1.1.4">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
Modified: trunk/packages/primer3/trunk/debian/primer3_core.1
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3_core.1 2008-05-09 00:55:07 UTC (rev 1838)
+++ trunk/packages/primer3/trunk/debian/primer3_core.1 2008-05-09 04:09:37 UTC (rev 1839)
@@ -1,40 +1,40 @@
.\" Title: PRIMER3_CORE
.\" Author:
.\" Generator: DocBook XSL Stylesheets v1.73.2 <http://docbook.sf.net/>
-.\" Date: 02/22/2008
+.\" Date: 05/09/2008
.\" Manual: Primer3 User Manuals
-.\" Source: primer3_core 1.1.3
+.\" Source: primer3_core 1.1.4
.\"
-.TH "PRIMER3_CORE" "1" "02/22/2008" "primer3_core 1.1.3" "Primer3 User Manuals"
+.TH "PRIMER3_CORE" "1" "05/09/2008" "primer3_core 1.1.4" "Primer3 User Manuals"
.\" disable hyphenation
.nh
.\" disable justification (adjust text to left margin only)
.ad l
.SH "NAME"
-primer3_core - Designs primers for PCR
+primer3_core \- Designs primers for PCR
.SH "SYNOPSIS"
.HP 13
\fBprimer3_core\fR [\-format_output] [\-strict_tags] [<\ \fIinput_file\fR]
.SH "DESCRIPTION"
.PP
-primer3_core picks primers for PCR reactions, considering as criteria oligonucleotide melting temperature, size, GC content and primer\-dimer possibilities, PCR product size, positional constraints within the source sequence, and miscellaneous other constraints\.
+primer3_core picks primers for PCR reactions, considering as criteria oligonucleotide melting temperature, size, GC content and primer\-dimer possibilities, PCR product size, positional constraints within the source sequence, and miscellaneous other constraints\&.
.PP
-By default, primer3_core accepts input and produces output in Boulder\-io format, a pre\-XML text\-based input/output format for program\-to\-program data interchange format\. The Boulder\-io format and the commands that primer3_core understands are described in the
+By default, primer3_core accepts input and produces output in Boulder\-io format, a pre\-XML text\-based input/output format for program\-to\-program data interchange format\&. The Boulder\-io format and the commands that primer3_core understands are described in the
\fIREADME\fR
file, which on Debian systems can be found in
-\fI/usr/share/doc/primer3/\fR\.
+\fI/usr/share/doc/primer3/\fR\&.
.SH "OPTIONS"
.PP
\fB\-format_output\fR
.RS 4
-Prints a more user\-oriented report for each sequence\.
+Prints a more user\-oriented report for each sequence\&.
.RE
.PP
\fB\-strict_tags\fR
.RS 4
primer3_core echoes and ignores any tags it does not recognize, unless the
\fB\-strict_tags\fR
-flag is set on the command line, in which case primer3_core prints an error in the PRIMER_ERROR output tag, and prints additional information on stdout; this option can be useful for debugging systems that incorporate primer\.
+flag is set on the command line, in which case primer3_core prints an error in the PRIMER_ERROR output tag, and prints additional information on stdout; this option can be useful for debugging systems that incorporate primer\&.
.RE
.sp
.it 1 an-trap
@@ -43,31 +43,31 @@
.br
Note
.PP
-The old flag \-2x_compat is no longer supported\.
+The old flag \-2x_compat is no longer supported\&.
.SH "EXIT STATUS CODES"
.sp
.RS 4
-\h'-04'\(bu\h'+03'0 on normal operation\.
+\h'-04'\(bu\h'+03'0 on normal operation\&.
.RE
.sp
.RS 4
-\h'-04'\(bu\h'+03'\-1 under the following conditions: illegal command\-line arguments, unable to fflush stdout, unable to open (for writing and creating) a \.for, \.rev or \.int file (probably due to a protection problem)\.
+\h'-04'\(bu\h'+03'\-1 under the following conditions: illegal command\-line arguments, unable to fflush stdout, unable to open (for writing and creating) a \&.for, \&.rev or \&.int file (probably due to a protection problem)\&.
.RE
.sp
.RS 4
-\h'-04'\(bu\h'+03'\-2 on out\-of\-memory\.
+\h'-04'\(bu\h'+03'\-2 on out\-of\-memory\&.
.RE
.sp
.RS 4
-\h'-04'\(bu\h'+03'\-3 empty input\.
+\h'-04'\(bu\h'+03'\-3 empty input\&.
.RE
.sp
.RS 4
-\h'-04'\(bu\h'+03'\-4 error in a "Global" input tag (message in PRIMER_ERROR)\.
+\h'-04'\(bu\h'+03'\-4 error in a "Global" input tag (message in PRIMER_ERROR)\&.
.RE
.SH "REFERENCE"
.PP
-Please cite Rozen, S\., Skaletsky, H\. "Primer3 on the WWW for general users and for biologist programmers\." In S\. Krawetz and S\. Misener, eds\. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology\. Humana Press, Totowa, NJ, 2000, pages 365\-386\.
+Please cite Rozen, S\&., Skaletsky, H\&. "Primer3 on the WWW for general users and for biologist programmers\&." In S\&. Krawetz and S\&. Misener, eds\&. Bioinformatics Methods and Protocols in the series Methods in Molecular Biology\&. Humana Press, Totowa, NJ, 2000, pages 365\-386\&.
.SH "SEE ALSO"
.PP
@@ -77,14 +77,14 @@
Copyright \(co 1996,1997,1998,1999,2000,2001,2004,2006,2007,2008 Whitehead Institute for Biomedical Research, Steve Rozen (http://jura.wi.mit.edu/rozen), Helen Skaletsky
.br
.PP
-All rights reserved\. On Debian\-based systems, please consult
+All rights reserved\&. On Debian\-based systems, please consult
\fI/usr/share/doc/primer3/copyright\fR
-to read the licence of primer3_core\.
+to read the licence of primer3_core\&.
.PP
This manual page was written by Steffen Moeller
-<steffen_moeller at gmx\.de>
+<moeller at debian\&.org>
for the
Debian(TM)
-system (but may be used by others)\. Permission is granted to copy, distribute and/or modify this document under the same terms as primer3_core itself\.
+system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the same terms as primer3_core itself\&.
.sp
Modified: trunk/packages/primer3/trunk/debian/primer3_core.1.xml
===================================================================
--- trunk/packages/primer3/trunk/debian/primer3_core.1.xml 2008-05-09 00:55:07 UTC (rev 1838)
+++ trunk/packages/primer3/trunk/debian/primer3_core.1.xml 2008-05-09 04:09:37 UTC (rev 1839)
@@ -1,18 +1,18 @@
<?xml version='1.0' encoding='UTF-8'?>
<?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" [
<!ENTITY dhfirstname "<firstname>Steffen</firstname>">
<!ENTITY dhsurname "<surname>Moeller</surname>">
<!-- Please adjust the date whenever revising the manpage. -->
<!ENTITY dhtitle "Primer3 User Manuals">
<!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>steffen_moeller at gmx.de</email>">
+ <!ENTITY dhemail "<email>moeller at debian.org</email>">
<!ENTITY dhusername "Steffen Moeller">
<!ENTITY dhucpackage "<refentrytitle>PRIMER3_CORE</refentrytitle>">
<!ENTITY dhpackage "primer3_core">
- <!ENTITY dhrelease "1.1.3">
+ <!ENTITY dhrelease "1.1.4">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
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