[med-svn] r242 - trunk/packages/probcons/trunk/debian
Charles Plessy
charles-guest at alioth.debian.org
Wed Apr 4 00:57:32 UTC 2007
Author: charles-guest
Date: 2007-04-04 00:57:31 +0000 (Wed, 04 Apr 2007)
New Revision: 242
Modified:
trunk/packages/probcons/trunk/debian/changelog
trunk/packages/probcons/trunk/debian/pc-compare.1.xml
trunk/packages/probcons/trunk/debian/pc-makegnuplot.1.xml
trunk/packages/probcons/trunk/debian/pc-project.1.xml
trunk/packages/probcons/trunk/debian/probcons-RNA.1.xml
trunk/packages/probcons/trunk/debian/probcons.1.xml
trunk/packages/probcons/trunk/debian/rules
Log:
updated manpages
Modified: trunk/packages/probcons/trunk/debian/changelog
===================================================================
--- trunk/packages/probcons/trunk/debian/changelog 2007-04-04 00:12:17 UTC (rev 241)
+++ trunk/packages/probcons/trunk/debian/changelog 2007-04-04 00:57:31 UTC (rev 242)
@@ -3,8 +3,9 @@
* New upstream release, buildable with gcc 4.3 (Closes: #417482)
* Add Subversion repository URL to debian/control.
* Including /usr/share/dpatch/dpatch.make in debian/rules.
+ * Updated manpages using the template of docbook-xsl 1.71.0.dfsg.1-1.1.
- -- Charles Plessy <charles-debian-nospam at plessy.org> Wed, 4 Apr 2007 09:08:31 +0900
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Wed, 4 Apr 2007 09:56:46 +0900
probcons (1.11-1) unstable; urgency=low
Modified: trunk/packages/probcons/trunk/debian/pc-compare.1.xml
===================================================================
--- trunk/packages/probcons/trunk/debian/pc-compare.1.xml 2007-04-04 00:12:17 UTC (rev 241)
+++ trunk/packages/probcons/trunk/debian/pc-compare.1.xml 2007-04-04 00:57:31 UTC (rev 242)
@@ -1,15 +1,20 @@
<?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 V4.2//EN"
"/usr/share/xml/docbook/schema/dtd/4.4/docbookx.dtd" [
- <!ENTITY dhfirstname "<firstname>Plessy</firstname>">
- <!ENTITY dhsurname "<surname>Plessy</surname>">
- <!ENTITY dhdate "<date>mai 3, 2006</date>">
- <!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
- <!ENTITY dhusername "Charles Plessy">
- <!ENTITY dhucpackage "<refentrytitle>PROBCONS-EXTRA</refentrytitle>">
- <!ENTITY dhpackage "pc-compare">
+ <!ENTITY dhfirstname "Charles">
+ <!ENTITY dhsurname "Plessy">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
+ <!ENTITY dhdate "2007-04-04">
+ <!ENTITY dhsection "1">
+ <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhucpackage "PROBCONS">
+ <!ENTITY dhpackage "probcons">
+ <!ENTITY dhrelease "1.12">
+ <!ENTITY dhproduct "&dhpackage;">
+ <!ENTITY dhtitle "Probcons Manual">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
@@ -17,24 +22,50 @@
<refentry>
<refentryinfo>
- <address>
- &dhemail;
- </address>
-<!-- <author>
- &dhfirstname;
- &dhsurname;
- </author> -->
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <date>&dhdate;</date>
+ <authorgroup>
+ <author>
+ <firstname>Chuong</firstname>
+ <surname>Do</surname>
+ <contrib>Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.</contrib>
+ <address>
+ <email>chuongdo at cs.stanford.edu</email>
+ </address>
+ </author>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Wrote this manpage in DocBook XML for the Debian distribution.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <!--<copyright>
+ <year>2004</year>
+ <year>2005</year>
+ <year>2006</year>
+ <year>2007</year>
+ <holder>Chuong Do</holder>
+ </copyright>
<copyright>
- <year>2006</year>
- <holder>&dhusername;</holder>
- </copyright>
- &dhdate;
+ <year>2006</year>
+ <year>2007</year>
+ <holder>&dhusername;</holder>
+ </copyright>--><!-- Public domain: no copyright -->
+ <legalnotice>
+ <para>This program and its manpage are in the public domain.</para>
+ </legalnotice>
</refentryinfo>
+
<refmeta>
- &dhucpackage;
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
+ </refmeta>
- &dhsection;
- </refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
@@ -63,7 +94,23 @@
<refsect1>
<title>SEE ALSO</title>
- <para>pc-makegnuplot (1) and pc-project (1), from the probcons-extra package, and probcons (1) and probcons-RNA (1) from the probcons package.</para>
+ <para>
+ <citerefentry>
+ <refentrytitle>pc-makegnufile</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>,
+ <citerefentry>
+ <refentrytitle>pc-project</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>,from the probcons-extra package, and
+ <citerefentry>
+ <refentrytitle>probcons</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry> and
+ <citerefentry>
+ <refentrytitle>probcons-RNA</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry> from the probcons package.</para>
</refsect1>
<refsect1>
@@ -71,19 +118,4 @@
<para>Please cite Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340.</para>
</refsect1>
- <refsect1>
- <title>AUTHORS</title>
-
- <para>&dhpackage; was written by Chuong Do <email>chuongdo at cs.stanford.edu</email> in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.</para>
-
- <para>This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others).
- </para>
-
- </refsect1>
-
- <refsect1>
- <title>LICENCE</title>
- <para>This program and its manpage are in the public domain.</para>
- </refsect1>
-
</refentry>
Modified: trunk/packages/probcons/trunk/debian/pc-makegnuplot.1.xml
===================================================================
--- trunk/packages/probcons/trunk/debian/pc-makegnuplot.1.xml 2007-04-04 00:12:17 UTC (rev 241)
+++ trunk/packages/probcons/trunk/debian/pc-makegnuplot.1.xml 2007-04-04 00:57:31 UTC (rev 242)
@@ -1,15 +1,20 @@
<?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 V4.2//EN"
"/usr/share/xml/docbook/schema/dtd/4.4/docbookx.dtd" [
- <!ENTITY dhfirstname "<firstname>Plessy</firstname>">
- <!ENTITY dhsurname "<surname>Plessy</surname>">
- <!ENTITY dhdate "<date>mai 3, 2006</date>">
- <!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
- <!ENTITY dhusername "Charles Plessy">
- <!ENTITY dhucpackage "<refentrytitle>PROBCONS-EXTRA</refentrytitle>">
- <!ENTITY dhpackage "pc-makegnuplot">
+ <!ENTITY dhfirstname "Charles">
+ <!ENTITY dhsurname "Plessy">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
+ <!ENTITY dhdate "2007-04-04">
+ <!ENTITY dhsection "1">
+ <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhucpackage "PROBCONS">
+ <!ENTITY dhpackage "probcons">
+ <!ENTITY dhrelease "1.12">
+ <!ENTITY dhproduct "&dhpackage;">
+ <!ENTITY dhtitle "Probcons Manual">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
@@ -17,24 +22,50 @@
<refentry>
<refentryinfo>
- <address>
- &dhemail;
- </address>
-<!-- <author>
- &dhfirstname;
- &dhsurname;
- </author> -->
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <date>&dhdate;</date>
+ <authorgroup>
+ <author>
+ <firstname>Chuong</firstname>
+ <surname>Do</surname>
+ <contrib>Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.</contrib>
+ <address>
+ <email>chuongdo at cs.stanford.edu</email>
+ </address>
+ </author>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Wrote this manpage in DocBook XML for the Debian distribution.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <!--<copyright>
+ <year>2004</year>
+ <year>2005</year>
+ <year>2006</year>
+ <year>2007</year>
+ <holder>Chuong Do</holder>
+ </copyright>
<copyright>
- <year>2006</year>
- <holder>&dhusername;</holder>
- </copyright>
- &dhdate;
+ <year>2006</year>
+ <year>2007</year>
+ <holder>&dhusername;</holder>
+ </copyright>--><!-- Public domain: no copyright -->
+ <legalnotice>
+ <para>This program and its manpage are in the public domain.</para>
+ </legalnotice>
</refentryinfo>
+
<refmeta>
- &dhucpackage;
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
+ </refmeta>
- &dhsection;
- </refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
@@ -54,7 +85,23 @@
<refsect1>
<title>SEE ALSO</title>
- <para>pc-compare (1) and pc-project (1), from the probcons-extra package, and probcons (1) and probcons-RNA (1) from the probcons package.</para>
+ <para>
+ <citerefentry>
+ <refentrytitle>pc-compare</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>,
+ <citerefentry>
+ <refentrytitle>pc-project</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>,from the probcons-extra package, and
+ <citerefentry>
+ <refentrytitle>probcons</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry> and
+ <citerefentry>
+ <refentrytitle>probcons-RNA</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry> from the probcons package.</para>
</refsect1>
<refsect1>
@@ -62,19 +109,4 @@
<para>Please cite Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340.</para>
</refsect1>
- <refsect1>
- <title>AUTHORS</title>
-
- <para>&dhpackage; was written by Chuong Do <email>chuongdo at cs.stanford.edu</email> in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.</para>
-
- <para>This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others).
- </para>
-
- </refsect1>
-
- <refsect1>
- <title>LICENCE</title>
- <para>This program and its manpage are in the public domain.</para>
- </refsect1>
-
</refentry>
Modified: trunk/packages/probcons/trunk/debian/pc-project.1.xml
===================================================================
--- trunk/packages/probcons/trunk/debian/pc-project.1.xml 2007-04-04 00:12:17 UTC (rev 241)
+++ trunk/packages/probcons/trunk/debian/pc-project.1.xml 2007-04-04 00:57:31 UTC (rev 242)
@@ -1,15 +1,20 @@
<?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 V4.2//EN"
"/usr/share/xml/docbook/schema/dtd/4.4/docbookx.dtd" [
- <!ENTITY dhfirstname "<firstname>Plessy</firstname>">
- <!ENTITY dhsurname "<surname>Plessy</surname>">
- <!ENTITY dhdate "<date>mai 3, 2006</date>">
- <!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
- <!ENTITY dhusername "Charles Plessy">
- <!ENTITY dhucpackage "<refentrytitle>PROBCONS-EXTRA</refentrytitle>">
- <!ENTITY dhpackage "pc-project">
+ <!ENTITY dhfirstname "Charles">
+ <!ENTITY dhsurname "Plessy">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
+ <!ENTITY dhdate "2007-04-04">
+ <!ENTITY dhsection "1">
+ <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhucpackage "PROBCONS">
+ <!ENTITY dhpackage "probcons">
+ <!ENTITY dhrelease "1.12">
+ <!ENTITY dhproduct "&dhpackage;">
+ <!ENTITY dhtitle "Probcons Manual">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
@@ -17,24 +22,50 @@
<refentry>
<refentryinfo>
- <address>
- &dhemail;
- </address>
-<!-- <author>
- &dhfirstname;
- &dhsurname;
- </author> -->
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <date>&dhdate;</date>
+ <authorgroup>
+ <author>
+ <firstname>Chuong</firstname>
+ <surname>Do</surname>
+ <contrib>Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.</contrib>
+ <address>
+ <email>chuongdo at cs.stanford.edu</email>
+ </address>
+ </author>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Wrote this manpage in DocBook XML for the Debian distribution.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <!--<copyright>
+ <year>2004</year>
+ <year>2005</year>
+ <year>2006</year>
+ <year>2007</year>
+ <holder>Chuong Do</holder>
+ </copyright>
<copyright>
- <year>2006</year>
- <holder>&dhusername;</holder>
- </copyright>
- &dhdate;
+ <year>2006</year>
+ <year>2007</year>
+ <holder>&dhusername;</holder>
+ </copyright>--><!-- Public domain: no copyright -->
+ <legalnotice>
+ <para>This program and its manpage are in the public domain.</para>
+ </legalnotice>
</refentryinfo>
+
<refmeta>
- &dhucpackage;
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
+ </refmeta>
- &dhsection;
- </refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
@@ -54,30 +85,29 @@
<para>&dhpackage; is named <filename>project</filename> in the original sources, but has been remamed to avoid collision with other program names.</para>
</refsect1>
-
<refsect1>
<title>SEE ALSO</title>
- <para>pc-compare (1) and pc-makegnuplot (1), from the probcons-extra package, and probcons (1) and probcons-RNA (1) from the probcons package.</para>
+ <para>
+ <citerefentry>
+ <refentrytitle>pc-makegnufile</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>,
+ <citerefentry>
+ <refentrytitle>pc-compare</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>,from the probcons-extra package, and
+ <citerefentry>
+ <refentrytitle>probcons</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry> and
+ <citerefentry>
+ <refentrytitle>probcons-RNA</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry> from the probcons package.</para>
</refsect1>
<refsect1>
<title>REFERENCE</title>
<para>Please cite Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340.</para>
</refsect1>
-
- <refsect1>
- <title>AUTHORS</title>
-
- <para>&dhpackage; was written by Chuong Do <email>chuongdo at cs.stanford.edu</email> in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.</para>
-
- <para>This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others).
- </para>
-
- </refsect1>
-
- <refsect1>
- <title>LICENCE</title>
- <para>This program and its manpage are in the public domain.</para>
- </refsect1>
-
</refentry>
Modified: trunk/packages/probcons/trunk/debian/probcons-RNA.1.xml
===================================================================
--- trunk/packages/probcons/trunk/debian/probcons-RNA.1.xml 2007-04-04 00:12:17 UTC (rev 241)
+++ trunk/packages/probcons/trunk/debian/probcons-RNA.1.xml 2007-04-04 00:57:31 UTC (rev 242)
@@ -1,15 +1,20 @@
<?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 V4.2//EN"
"/usr/share/xml/docbook/schema/dtd/4.4/docbookx.dtd" [
- <!ENTITY dhfirstname "<firstname>Plessy</firstname>">
- <!ENTITY dhsurname "<surname>Plessy</surname>">
- <!ENTITY dhdate "<date>mai 3, 2006</date>">
- <!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
- <!ENTITY dhusername "Charles Plessy">
- <!ENTITY dhucpackage "<refentrytitle>PROBCONS</refentrytitle>">
- <!ENTITY dhpackage "probcons-RNA">
+ <!ENTITY dhfirstname "Charles">
+ <!ENTITY dhsurname "Plessy">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
+ <!ENTITY dhdate "2007-04-04">
+ <!ENTITY dhsection "1">
+ <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhucpackage "PROBCONS">
+ <!ENTITY dhpackage "probcons">
+ <!ENTITY dhrelease "1.12">
+ <!ENTITY dhproduct "&dhpackage;">
+ <!ENTITY dhtitle "Probcons Manual">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
@@ -17,47 +22,86 @@
<refentry>
<refentryinfo>
- <address>
- &dhemail;
- </address>
-<!-- <author>
- &dhfirstname;
- &dhsurname;
- </author> -->
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <date>&dhdate;</date>
+ <authorgroup>
+ <author>
+ <firstname>Chuong</firstname>
+ <surname>Do</surname>
+ <contrib>Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.</contrib>
+ <address>
+ <email>chuongdo at cs.stanford.edu</email>
+ </address>
+ </author>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Wrote this manpage in DocBook XML for the Debian distribution.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <!--<copyright>
+ <year>2004</year>
+ <year>2005</year>
+ <year>2006</year>
+ <year>2007</year>
+ <holder>Chuong Do</holder>
+ </copyright>
<copyright>
- <year>2006</year>
- <holder>&dhusername;</holder>
- </copyright>
- &dhdate;
+ <year>2006</year>
+ <year>2007</year>
+ <holder>&dhusername;</holder>
+ </copyright>--><!-- Public domain: no copyright -->
+ <legalnotice>
+ <para>This program and its manpage are in the public domain.</para>
+ </legalnotice>
</refentryinfo>
+
<refmeta>
- &dhucpackage;
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
+ </refmeta>
- &dhsection;
- </refmeta>
<refnamediv>
<refname>&dhpackage;</refname>
<refpurpose>An experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE.</refpurpose>
</refnamediv>
+
<refsect1>
<title>DESCRIPTION</title>
- <para>See the manpage of probcons (1) for the command-line arguments, and <filename>/usr/share/doc/README.Debian</filename> for more informations about how probcons-RNA has been built.</para>
+ <para>See the manpage of <citerefentry><refentrytitle>probcons</refentrytitle><manvolnum>1</manvolnum></citerefentry> for the command-line arguments, and <filename>/usr/share/doc/README.Debian</filename> for more informations about how probcons-RNA has been built.</para>
</refsect1>
- <refsect1>
- <title>AUTHORS</title>
+ <refsect1>
+ <title>SEE ALSO</title>
+ <itemizedlist>
+ <listitem><para>You can find more information in the manual of ProbCons, which is located in <filename>/usr/share/doc/probcons/manual.pdf</filename> in Debian systems.</para></listitem>
- <para>&dhpackage; was written by Chuong Do <email>chuongdo at cs.stanford.edu</email> in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.</para>
-
- <para>This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others).
- </para>
-
+ <listitem>
+ <para>
+ <citerefentry>
+ <refentrytitle>probcons</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>,
+ <citerefentry>
+ <refentrytitle>pc-makegnufile</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>,
+ <citerefentry>
+ <refentrytitle>pc-compare</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>,
+ <citerefentry>
+ <refentrytitle>pc-project</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>,
+ which are distributed separately in the probcons-extra package.</para></listitem>
+ </itemizedlist>
</refsect1>
- <refsect1>
- <title>LICENCE</title>
- <para>This program and its manpage are in the public domain.</para>
- </refsect1>
-
</refentry>
Modified: trunk/packages/probcons/trunk/debian/probcons.1.xml
===================================================================
--- trunk/packages/probcons/trunk/debian/probcons.1.xml 2007-04-04 00:12:17 UTC (rev 241)
+++ trunk/packages/probcons/trunk/debian/probcons.1.xml 2007-04-04 00:57:31 UTC (rev 242)
@@ -1,15 +1,20 @@
<?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 V4.2//EN"
"/usr/share/xml/docbook/schema/dtd/4.4/docbookx.dtd" [
- <!ENTITY dhfirstname "<firstname>Plessy</firstname>">
- <!ENTITY dhsurname "<surname>Plessy</surname>">
- <!ENTITY dhdate "<date>mai 3, 2006</date>">
- <!ENTITY dhsection "<manvolnum>1</manvolnum>">
- <!ENTITY dhemail "<email>charles-debian-nospam at plessy.org</email>">
- <!ENTITY dhusername "Charles Plessy">
- <!ENTITY dhucpackage "<refentrytitle>PROBCONS</refentrytitle>">
+ <!ENTITY dhfirstname "Charles">
+ <!ENTITY dhsurname "Plessy">
+ <!ENTITY dhusername "&dhfirstname; &dhsurname;">
+ <!ENTITY dhdate "2007-04-04">
+ <!ENTITY dhsection "1">
+ <!ENTITY dhemail "charles-debian-nospam at plessy.org">
+ <!ENTITY dhucpackage "PROBCONS">
<!ENTITY dhpackage "probcons">
+ <!ENTITY dhrelease "1.12">
+ <!ENTITY dhproduct "&dhpackage;">
+ <!ENTITY dhtitle "Probcons Manual">
<!ENTITY debian "<productname>Debian</productname>">
<!ENTITY gnu "<acronym>GNU</acronym>">
<!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
@@ -17,27 +22,53 @@
<refentry>
<refentryinfo>
- <address>
- &dhemail;
- </address>
-<!-- <author>
- &dhfirstname;
- &dhsurname;
- </author> -->
+ <title>&dhtitle;</title>
+ <productname>&dhpackage;</productname>
+ <releaseinfo role="version">&dhrelease;</releaseinfo>
+ <date>&dhdate;</date>
+ <authorgroup>
+ <author>
+ <firstname>Chuong</firstname>
+ <surname>Do</surname>
+ <contrib>Wrote probcons in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.</contrib>
+ <address>
+ <email>chuongdo at cs.stanford.edu</email>
+ </address>
+ </author>
+ <author>
+ <firstname>&dhfirstname;</firstname>
+ <surname>&dhsurname;</surname>
+ <contrib>Wrote this manpage in DocBook XML for the Debian distribution.</contrib>
+ <address>
+ <email>&dhemail;</email>
+ </address>
+ </author>
+ </authorgroup>
+ <!--<copyright>
+ <year>2004</year>
+ <year>2005</year>
+ <year>2006</year>
+ <year>2007</year>
+ <holder>Chuong Do</holder>
+ </copyright>
<copyright>
- <year>2006</year>
- <holder>&dhusername;</holder>
- </copyright>
- &dhdate;
+ <year>2006</year>
+ <year>2007</year>
+ <holder>&dhusername;</holder>
+ </copyright>--><!-- Public domain: no copyright -->
+ <legalnotice>
+ <para>This program and its manpage are in the public domain.</para>
+ </legalnotice>
</refentryinfo>
+
<refmeta>
- &dhucpackage;
-
- &dhsection;
+ <refentrytitle>&dhucpackage;</refentrytitle>
+ <manvolnum>&dhsection;</manvolnum>
</refmeta>
+
<refnamediv>
<refname>&dhpackage;</refname>
-
+
<refpurpose>align multiple protein sequences and print to standard output</refpurpose>
</refnamediv>
<refsynopsisdiv>
@@ -174,9 +205,23 @@
<itemizedlist>
<listitem><para>You can find more information in the manual of ProbCons, which is located in <filename>/usr/share/doc/probcons/manual.pdf</filename> in Debian systems.</para></listitem>
- <listitem><para>An experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE, probcons-RNA (1), is also distributed in the ProbCons Debian package.</para></listitem>
+ <listitem><para>An experimental version of ProbCons compiled with parameters estimated via unsupervised training on BRAliBASE, <citerefentry><refentrytitle>probcons-RNA</refentrytitle><manvolnum>1</manvolnum></citerefentry>, is also distributed in the ProbCons Debian package.</para></listitem>
- <listitem><para>pc-makegnufile (1), pc-compare (1), pc-project (1), which are distributed separately in the probcons-extra package.</para></listitem>
+ <listitem>
+ <para>
+ <citerefentry>
+ <refentrytitle>pc-makegnufile</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>,
+ <citerefentry>
+ <refentrytitle>pc-compare</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>,
+ <citerefentry>
+ <refentrytitle>pc-project</refentrytitle>
+ <manvolnum>1</manvolnum>
+ </citerefentry>,
+ which are distributed separately in the probcons-extra package.</para></listitem>
</itemizedlist>
</refsect1>
@@ -185,20 +230,4 @@
<para>Please cite Do, C.B., Mahabhashyam, M.S.P., Brudno, M., and Batzoglou, S. 2005. PROBCONS: Probabilistic Consistency-based Multiple Sequence Alignment. Genome Research 15: 330-340.</para>
</refsect1>
- <refsect1>
- <title>AUTHORS</title>
-
- <para>&dhpackage; was written by Chuong Do <email>chuongdo at cs.stanford.edu</email> in collaboration with Michael Brudno in the research group of Serafim Batzoglou, Department of Computer Science, Stanford University.</para>
-
- <para>This manual page was written by &dhusername; &dhemail; for the &debian; system (but may be used by others).
- </para>
-
- </refsect1>
-
- <refsect1>
- <title>LICENCE</title>
- <para>This program and its manpage are in the public domain.</para>
- </refsect1>
-
-
</refentry>
Modified: trunk/packages/probcons/trunk/debian/rules
===================================================================
--- trunk/packages/probcons/trunk/debian/rules 2007-04-04 00:12:17 UTC (rev 241)
+++ trunk/packages/probcons/trunk/debian/rules 2007-04-04 00:57:31 UTC (rev 242)
@@ -5,17 +5,19 @@
# As a special exception, when this file is copied by dh-make into a
# dh-make output file, you may use that output file without restriction.
# This special exception was added by Craig Small in version 0.37 of dh-make.
-# Modifications by Charles Plessy during the year 2006 can also
+# Modifications by Charles Plessy during the years 2006 and 2007can also
# be used without restriction.
-CFLAGS = -Wall -g
-
BINARIES = probcons probcons-RNA project pc-compare makegnuplot
-
MANPAGES = debian/probcons.1 debian/probcons-RNA.1 debian/pc-compare.1 debian/pc-project.1 debian/pc-makegnuplot.1
-DB2MAN = "/usr/share/xml/docbook/stylesheet/nwalsh/manpages/docbook.xsl"
-XP = xsltproc -o debian/ -''-nonet
+XP = xsltproc \
+ -''-nonet \
+ -''-param man.charmap.use.subset "0" \
+ -''-param make.year.ranges "1" \
+ -''-param make.single.year.ranges "1"
+CFLAGS = -Wall -g
+
ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
CFLAGS += -O0
else
@@ -32,11 +34,11 @@
touch build-stamp
manpages: debian/probcons.1.xml debian/probcons-RNA.1.xml debian/pc-project.1.xml debian/pc-compare.1.xml debian/pc-makegnuplot.1.xml
- $(XP) $(DB2MAN) debian/probcons.1.xml
- $(XP) $(DB2MAN) debian/probcons-RNA.1.xml
- $(XP) $(DB2MAN) debian/pc-project.1.xml
- $(XP) $(DB2MAN) debian/pc-compare.1.xml
- $(XP) $(DB2MAN) debian/pc-makegnuplot.1.xml
+ $(XP) debian/probcons.1.xml
+ $(XP) debian/probcons-RNA.1.xml
+ $(XP) debian/pc-project.1.xml
+ $(XP) debian/pc-compare.1.xml
+ $(XP) debian/pc-makegnuplot.1.xml
clean: unpatch
dh_testdir
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