[med-svn] r4939 - in trunk/packages/embassy-domainatrix/trunk/debian: . manpages
Charles Plessy
plessy at alioth.debian.org
Sat Jun 26 08:39:20 UTC 2010
Author: plessy
Date: 2010-06-26 08:39:19 +0000 (Sat, 26 Jun 2010)
New Revision: 4939
Modified:
trunk/packages/embassy-domainatrix/trunk/debian/changelog
trunk/packages/embassy-domainatrix/trunk/debian/control
trunk/packages/embassy-domainatrix/trunk/debian/embassy-domainatrix.manpages
trunk/packages/embassy-domainatrix/trunk/debian/manpages/cathparse.1e
trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainnr.1e
trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainreso.1e
trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainseqs.1e
trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainsse.1e
trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscan.1e
trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscanout.1e
trunk/packages/embassy-domainatrix/trunk/debian/manpages/scopparse.1e
trunk/packages/embassy-domainatrix/trunk/debian/manpages/ssematch.1e
Log:
New upstream release (last January).
Modified: trunk/packages/embassy-domainatrix/trunk/debian/changelog
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/changelog 2010-06-26 01:48:38 UTC (rev 4938)
+++ trunk/packages/embassy-domainatrix/trunk/debian/changelog 2010-06-26 08:39:19 UTC (rev 4939)
@@ -1,3 +1,12 @@
+embassy-domainatrix (0.1.0+20100115-1) unstable; urgency=low
+
+ * New upstream release in which the version number was unchanged.
+ * debian/control:
+ - Build against EMBOSS 6.2 (Closes: #587118)
+ - Checked conformance with Policy 3.8.4 (no changes needed).
+ * debian/*manpages* refreshed
+ -- Charles Plessy <plessy at debian.org> Sat, 26 Jun 2010 17:18:45 +0900
+
embassy-domainatrix (0.1.0+20090715-1) unstable; urgency=low
* New upstream release in which the version number was unchanged.
@@ -4,9 +13,9 @@
* debian/control:
- Build against EMBOSS 6.1
- Checked conformance with Policy 3.8.2 (no changes needed).
- * debian/watch: mangle Debian version to ignore the timestamp.
+ * debian/watch: mangle Debian version to ignore the timestamp.
* Refreshed and experimented on debian/copyright.
- * debian/*manpages* refreshed and moved to section 1e.
+ * debian/*manpages* refreshed and moved to section 1e.
-- Charles Plessy <plessy at debian.org> Mon, 03 Aug 2009 19:38:00 +0900
Modified: trunk/packages/embassy-domainatrix/trunk/debian/control
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/control 2010-06-26 01:48:38 UTC (rev 4938)
+++ trunk/packages/embassy-domainatrix/trunk/debian/control 2010-06-26 08:39:19 UTC (rev 4939)
@@ -1,13 +1,13 @@
Source: embassy-domainatrix
Section: science
Priority: optional
-Build-Depends: cdbs, debhelper (>= 7), libajax6-dev (>= 6.1), libnucleus6-dev (>= 6.1), emboss-lib, libx11-dev, libgd2-xpm-dev
+Build-Depends: cdbs, debhelper (>= 7), libajax6-dev (>= 6.2), libnucleus6-dev (>= 6.2), emboss-lib, libx11-dev, libgd2-xpm-dev
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Charles Plessy <plessy at debian.org>
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/embassy-domainatrix/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/embassy-domainatrix/trunk/
-Standards-Version: 3.8.2
+Standards-Version: 3.8.4
Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMAINATRIX
Package: embassy-domainatrix
Modified: trunk/packages/embassy-domainatrix/trunk/debian/embassy-domainatrix.manpages
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/embassy-domainatrix.manpages 2010-06-26 01:48:38 UTC (rev 4938)
+++ trunk/packages/embassy-domainatrix/trunk/debian/embassy-domainatrix.manpages 2010-06-26 08:39:19 UTC (rev 4939)
@@ -1,9 +1,9 @@
+debian/manpages/domainseqs.1e
+debian/manpages/domainreso.1e
+debian/manpages/libscanout.1e
+debian/manpages/domainnr.1e
+debian/manpages/ssematch.1e
debian/manpages/cathparse.1e
-debian/manpages/domainreso.1e
-debian/manpages/domainseqs.1e
debian/manpages/domainsse.1e
debian/manpages/scopparse.1e
-debian/manpages/ssematch.1e
-debian/manpages/libscanout.1e
-debian/manpages/domainnr.1e
debian/manpages/libscan.1e
Modified: trunk/packages/embassy-domainatrix/trunk/debian/manpages/cathparse.1e
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/cathparse.1e 2010-06-26 01:48:38 UTC (rev 4938)
+++ trunk/packages/embassy-domainatrix/trunk/debian/manpages/cathparse.1e 2010-06-26 08:39:19 UTC (rev 4939)
@@ -1,14 +1,23 @@
'\" t
.\" Title: CATHPARSE
-.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
-.\" Date: 08/03/2009
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 06/26/2010
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20090715
+.\" Source: EMBOSS 0.1.0+20100115
.\" Language: English
.\"
-.TH "CATHPARSE" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
+.TH "CATHPARSE" "1e" "06/26/2010" "EMBOSS 0.1.0+20100115" "EMBOSS Manual for Debian"
.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
.\" * set default formatting
.\" -----------------------------------------------------------------
.\" disable hyphenation
@@ -50,7 +59,7 @@
.PP
\fB\-outfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of CATH DCF file (domain classification file) (output)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: Ecath\&.dat
+This option specifies the name of CATH DCF file (domain classification file) (output)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: Ecath\&.dat
.RE
.PP
\fB\-logfile\fR \fIoutfile\fR
@@ -67,7 +76,7 @@
system\&.
.SH "AUTHOR"
.PP
-\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
Modified: trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainnr.1e
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainnr.1e 2010-06-26 01:48:38 UTC (rev 4938)
+++ trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainnr.1e 2010-06-26 08:39:19 UTC (rev 4939)
@@ -1,14 +1,23 @@
'\" t
.\" Title: DOMAINNR
-.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
-.\" Date: 08/03/2009
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 06/26/2010
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20090715
+.\" Source: EMBOSS 0.1.0+20100115
.\" Language: English
.\"
-.TH "DOMAINNR" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
+.TH "DOMAINNR" "1e" "06/26/2010" "EMBOSS 0.1.0+20100115" "EMBOSS Manual for Debian"
.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
.\" * set default formatting
.\" -----------------------------------------------------------------
.\" disable hyphenation
@@ -34,7 +43,7 @@
.PP
\fB\-dcfinfile\fR \fIinfile\fR
.RS 4
-This option specifies name of DCF file (domain classification file) (input)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
+This option specifies name of DCF file (domain classification file) (input)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
.RE
.PP
\fB\-datafile\fR \fImatrixf\fR
@@ -50,7 +59,7 @@
.PP
\fB\-node\fR \fIlist\fR
.RS 4
-This option specifies the node for redundancy removal\&. Redundancy can be removed at any specified node in the SCOP or CATH hierarchies\&. For example by selecting \'Class\' entries belonging to the same Class will be non\-redundant\&. Default value: 1
+This option specifies the node for redundancy removal\&. Redundancy can be removed at any specified node in the SCOP or CATH hierarchies\&. For example by selecting \*(AqClass\*(Aq entries belonging to the same Class will be non\-redundant\&. Default value: 1
.RE
.PP
\fB\-mode\fR \fIlist\fR
@@ -88,12 +97,12 @@
.PP
\fB\-dcfoutfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of non\-redundant DCF file (domain classification file) (output)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: test\&.scop
+This option specifies the name of non\-redundant DCF file (domain classification file) (output)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: test\&.scop
.RE
.PP
\fB\-redoutfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of DCF file (domain classification file) for redundant sequences (output)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
+This option specifies the name of DCF file (domain classification file) for redundant sequences (output)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
.RE
.PP
\fB\-logfile\fR \fIoutfile\fR
@@ -110,7 +119,7 @@
system\&.
.SH "AUTHOR"
.PP
-\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
Modified: trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainreso.1e
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainreso.1e 2010-06-26 01:48:38 UTC (rev 4938)
+++ trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainreso.1e 2010-06-26 08:39:19 UTC (rev 4939)
@@ -1,14 +1,23 @@
'\" t
.\" Title: DOMAINRESO
-.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
-.\" Date: 08/03/2009
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 06/26/2010
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20090715
+.\" Source: EMBOSS 0.1.0+20100115
.\" Language: English
.\"
-.TH "DOMAINRESO" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
+.TH "DOMAINRESO" "1e" "06/26/2010" "EMBOSS 0.1.0+20100115" "EMBOSS Manual for Debian"
.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
.\" * set default formatting
.\" -----------------------------------------------------------------
.\" disable hyphenation
@@ -34,12 +43,12 @@
.PP
\fB\-cpdbpath\fR \fIdirlist\fR
.RS 4
-This option specifies the location of domain CCF file (clean coordinate files) (input)\&. A \'clean cordinate file\' contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL\-like)\&. The files, generated by using PDBPARSE (pdb files) or DOMAINER (domains), contain \'cleaned\-up\' data that is self\-consistent and error\-corrected\&. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS\&. Default value: \&./
+This option specifies the location of domain CCF file (clean coordinate files) (input)\&. A \*(Aqclean cordinate file\*(Aq contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL\-like)\&. The files, generated by using PDBPARSE (pdb files) or DOMAINER (domains), contain \*(Aqcleaned\-up\*(Aq data that is self\-consistent and error\-corrected\&. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS\&. Default value: \&./
.RE
.PP
\fB\-dcfinfile\fR \fIinfile\fR
.RS 4
-This option specifies the name of DCF file (domain classification file) (input)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
+This option specifies the name of DCF file (domain classification file) (input)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
.RE
.SS "Required section"
.PP
@@ -51,7 +60,7 @@
.PP
\fB\-dcfoutfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of DCF file (domain classification file) (output)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: test\&.scop
+This option specifies the name of DCF file (domain classification file) (output)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: test\&.scop
.RE
.SH "BUGS"
.PP
@@ -63,7 +72,7 @@
system\&.
.SH "AUTHOR"
.PP
-\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
Modified: trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainseqs.1e
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainseqs.1e 2010-06-26 01:48:38 UTC (rev 4938)
+++ trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainseqs.1e 2010-06-26 08:39:19 UTC (rev 4939)
@@ -1,14 +1,23 @@
'\" t
.\" Title: DOMAINSEQS
-.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
-.\" Date: 08/03/2009
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 06/26/2010
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20090715
+.\" Source: EMBOSS 0.1.0+20100115
.\" Language: English
.\"
-.TH "DOMAINSEQS" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
+.TH "DOMAINSEQS" "1e" "06/26/2010" "EMBOSS 0.1.0+20100115" "EMBOSS Manual for Debian"
.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
.\" * set default formatting
.\" -----------------------------------------------------------------
.\" disable hyphenation
@@ -34,12 +43,12 @@
.PP
\fB\-dcfinfile\fR \fIinfile\fR
.RS 4
-This option specifies the name of DCF file (domain classification file) (input)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
+This option specifies the name of DCF file (domain classification file) (input)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
.RE
.PP
\fB\-dpdbdir\fR \fIdirectory\fR
.RS 4
-This option specifies the location of domain CCF file (clean coordinate files) (input)\&. A \'clean cordinate file\' contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL\-like)\&. The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain \'cleaned\-up\' data that is self\-consistent and error\-corrected\&. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS\&. Default value: \&./
+This option specifies the location of domain CCF file (clean coordinate files) (input)\&. A \*(Aqclean cordinate file\*(Aq contains coordinate and other data for a single PDB file or a single domain from SCOP or CATH, in CCF format (EMBL\-like)\&. The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain \*(Aqcleaned\-up\*(Aq data that is self\-consistent and error\-corrected\&. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS\&. Default value: \&./
.RE
.PP
\fB\-getswiss\fR \fItoggle\fR
@@ -72,7 +81,7 @@
.PP
\fB\-dcfoutfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of DCF file (domain classification file) (output)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: domainseqs\&.out
+This option specifies the name of DCF file (domain classification file) (output)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: domainseqs\&.out
.RE
.PP
\fB\-logfile\fR \fIoutfile\fR
@@ -89,7 +98,7 @@
system\&.
.SH "AUTHOR"
.PP
-\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
Modified: trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainsse.1e
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainsse.1e 2010-06-26 01:48:38 UTC (rev 4938)
+++ trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainsse.1e 2010-06-26 08:39:19 UTC (rev 4939)
@@ -1,14 +1,23 @@
'\" t
.\" Title: DOMAINSSE
-.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
-.\" Date: 08/03/2009
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 06/26/2010
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20090715
+.\" Source: EMBOSS 0.1.0+20100115
.\" Language: English
.\"
-.TH "DOMAINSSE" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
+.TH "DOMAINSSE" "1e" "06/26/2010" "EMBOSS 0.1.0+20100115" "EMBOSS Manual for Debian"
.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
.\" * set default formatting
.\" -----------------------------------------------------------------
.\" disable hyphenation
@@ -34,12 +43,12 @@
.PP
\fB\-dcfinfile\fR \fIinfile\fR
.RS 4
-This option specifies the name of the DCF file (domain classification file) (input)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
+This option specifies the name of the DCF file (domain classification file) (input)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
.RE
.PP
\fB\-dccfdir\fR \fIdirectory\fR
.RS 4
-This option specifies the location of the domain CCF file (clean coordinate files) (input)\&. A \'clean cordinate file\' contains protein coordinate and derived data for a single PDB file (\'protein clean coordinate file\') or a single domain from SCOP or CATH (\'domain clean coordinate file\'), in CCF format (EMBL\-like)\&. The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain \'cleaned\-up\' data that is self\-consistent and error\-corrected\&. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS\&. Default value: \&./
+This option specifies the location of the domain CCF file (clean coordinate files) (input)\&. A \*(Aqclean cordinate file\*(Aq contains protein coordinate and derived data for a single PDB file (\*(Aqprotein clean coordinate file\*(Aq) or a single domain from SCOP or CATH (\*(Aqdomain clean coordinate file\*(Aq), in CCF format (EMBL\-like)\&. The files, generated by using PDBPARSE (PDB files) or DOMAINER (domains), contain \*(Aqcleaned\-up\*(Aq data that is self\-consistent and error\-corrected\&. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS\&. Default value: \&./
.RE
.SS "Required section"
.SS "Advanced section"
@@ -47,7 +56,7 @@
.PP
\fB\-dcfoutfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of the DCF file (domain classification file) with secondary structure records (output)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
+This option specifies the name of the DCF file (domain classification file) with secondary structure records (output)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
.RE
.PP
\fB\-logfile\fR \fIoutfile\fR
@@ -64,7 +73,7 @@
system\&.
.SH "AUTHOR"
.PP
-\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
Modified: trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscan.1e
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscan.1e 2010-06-26 01:48:38 UTC (rev 4938)
+++ trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscan.1e 2010-06-26 08:39:19 UTC (rev 4939)
@@ -1,14 +1,23 @@
'\" t
.\" Title: LIBSCAN
-.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
-.\" Date: 08/03/2009
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 06/26/2010
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20090715
+.\" Source: EMBOSS 0.1.0+20100115
.\" Language: English
.\"
-.TH "LIBSCAN" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
+.TH "LIBSCAN" "1e" "06/26/2010" "EMBOSS 0.1.0+20100115" "EMBOSS Manual for Debian"
.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
.\" * set default formatting
.\" -----------------------------------------------------------------
.\" disable hyphenation
@@ -22,7 +31,7 @@
libscan \- Diagnostic searches for protein families\&.
.SH "SYNOPSIS"
.HP \w'\fBlibscan\fR\ 'u
-\fBlibscan\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-grib\ \fR\fB\fIbool\fR\fR \fB\-henik\ \fR\fB\fIbool\fR\fR \fB\-hmm\ \fR\fB\fIbool\fR\fR \fB\-sam\ \fR\fB\fIbool\fR\fR \fB\-pssm\ \fR\fB\fIbool\fR\fR \fB\-sig\ \fR\fB\fIbool\fR\fR \fB\-hmmpath\ \fR\fB\fIstring\fR\fR \fB\-hmmextn\ \fR\fB\fIstring\fR\fR \fB\-hmmoutpath\ \fR\fB\fIstring\fR\fR \fB\-hmmoutextn\ \fR\fB\fIstring\fR\fR \fB\-sampath\ \fR\fB\fIstring\fR\fR \fB\-samextn\ \fR\fB\fIstring\fR\fR \fB\-samoutpath\ \fR\fB\fIstring\fR\fR \fB\-samoutextn\ \fR\fB\fIstring\fR\fR \fB\-pssmpath\ \fR\fB\fIstring\fR\fR \fB\-pssmextn\ \fR\fB\fIstring\fR\fR \fB\-niter\ \fR\fB\fIint\fR\fR \fB\-thresh\ \fR\fB\fIfloat\fR\fR \fB\-maxhit\ \fR\fB\fIint\fR\fR \fB\-pssmoutpath\ \fR\fB\fIstring\fR\fR \fB\-pssmoutextn\ \fR\fB\fIstring\fR\fR \fB\-gbvpath\ \fR\fB\fIstring\fR\fR \fB\-gbvextn\ \fR\fB\fIstring\fR\fR \fB\-gbvgapo\ \fR\fB\fIfloat\fR\fR \fB\-gbvgape\ \fR\fB\fIfloat\fR\fR \fB\-gbvoutpath\ \fR\fB\fIstring\fR\fR \fB\-gbvoutextn\ \fR\fB\fIstring\fR\fR \fB\-hnfpath\ \fR\fB\fIstring\fR\fR \fB\-hnfextn\ \fR\fB\fIstring\fR\fR \fB\-hnfgapo\ \fR\fB\fIfloat\fR\fR \fB\-hnfgape\ \fR\fB\fIfloat\fR\fR \fB\-hnfoutpath\ \fR\fB\fIstring\fR\fR \fB\-hnfoutextn\ \fR\fB\fIstring\fR\fR \fB\-sigpath\ \fR\fB\fIstring\fR\fR \fB\-sigextn\ \fR\fB\fIstring\fR\fR \fB\-nterm\ \fR\fB\fIlist\fR\fR \fB\-sub\ \fR\fB\fImatrixf\fR\fR \fB\-siggapo\ \fR\fB\fIfloat\fR\fR \fB\-siggape\ \fR\fB\fIfloat\fR\fR \fB\-sigoutpath\ \fR\fB\fIstring\fR\fR \fB\-sigoutextn\ \fR\fB\fIstring\fR\fR \fB\-db\ \fR\fB\fIseqset\fR\fR \fB\-scopf\ \fR\fB\fIinfile\fR\fR
+\fBlibscan\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-grib\ \fR\fB\fIboolean\fR\fR \fB\-henik\ \fR\fB\fIboolean\fR\fR \fB\-hmm\ \fR\fB\fIboolean\fR\fR \fB\-sam\ \fR\fB\fIboolean\fR\fR \fB\-pssm\ \fR\fB\fIboolean\fR\fR \fB\-sig\ \fR\fB\fIboolean\fR\fR \fB\-hmmpath\ \fR\fB\fIstring\fR\fR \fB\-hmmextn\ \fR\fB\fIstring\fR\fR \fB\-hmmoutpath\ \fR\fB\fIstring\fR\fR \fB\-hmmoutextn\ \fR\fB\fIstring\fR\fR \fB\-sampath\ \fR\fB\fIstring\fR\fR \fB\-samextn\ \fR\fB\fIstring\fR\fR \fB\-samoutpath\ \fR\fB\fIstring\fR\fR \fB\-samoutextn\ \fR\fB\fIstring\fR\fR \fB\-pssmpath\ \fR\fB\fIstring\fR\fR \fB\-pssmextn\ \fR\fB\fIstring\fR\fR \fB\-niter\ \fR\fB\fIinteger\fR\fR \fB\-thresh\ \fR\fB\fIfloat\fR\fR \fB\-maxhit\ \fR\fB\fIinteger\fR\fR \fB\-pssmoutpath\ \fR\fB\fIstring\fR\fR \fB\-pssmoutextn\ \fR\fB\fIstring\fR\fR \fB\-gbvpath\ \fR\fB\fIstring\fR\fR \fB\-gbvextn\ \fR\fB\fIstring\fR\fR \fB\-gbvgapo\ \fR\fB\fIfloat\fR\fR \fB\-gbvgape\ \fR\fB\fIfloat\fR\fR \fB\-gbvoutpath\ \fR\fB\fIstring\fR\fR \fB\-gbvoutextn\ \fR\fB\fIstring\fR\fR \fB\-hnfpath\ \fR\fB\fIstring\fR\fR \fB\-hnfextn\ \fR\fB\fIstring\fR\fR \fB\-hnfgapo\ \fR\fB\fIfloat\fR\fR \fB\-hnfgape\ \fR\fB\fIfloat\fR\fR \fB\-hnfoutpath\ \fR\fB\fIstring\fR\fR \fB\-hnfoutextn\ \fR\fB\fIstring\fR\fR \fB\-sigpath\ \fR\fB\fIstring\fR\fR \fB\-sigextn\ \fR\fB\fIstring\fR\fR \fB\-nterm\ \fR\fB\fIlist\fR\fR \fB\-sub\ \fR\fB\fImatrixf\fR\fR \fB\-siggapo\ \fR\fB\fIfloat\fR\fR \fB\-siggape\ \fR\fB\fIfloat\fR\fR \fB\-sigoutpath\ \fR\fB\fIstring\fR\fR \fB\-sigoutextn\ \fR\fB\fIstring\fR\fR \fB\-db\ \fR\fB\fIseqset\fR\fR \fB\-scopf\ \fR\fB\fIinfile\fR\fR
.HP \w'\fBlibscan\fR\ 'u
\fBlibscan\fR \fB\-help\fR
.SH "DESCRIPTION"
@@ -36,32 +45,32 @@
libscan runs in one of two modes either (i) database search mode or (ii) library screen mode\&. In database search mode libscan reads one or more directories each containing a single type of discriminating element, the permitted types are sparse sequence signature, Gribskov profile, Henikoff profile or hidden Markov model\&. In library screen mode, libscan reads a sequence set, screens each sequence against the library (directories of discriminating elements) and writes a library scan file (of top\-scoring families) for each one\&. Default value: 2
.RE
.PP
-\fB\-grib\fR \fIbool\fR
+\fB\-grib\fR \fIboolean\fR
.RS 4
Default value: N
.RE
.PP
-\fB\-henik\fR \fIbool\fR
+\fB\-henik\fR \fIboolean\fR
.RS 4
Default value: N
.RE
.PP
-\fB\-hmm\fR \fIbool\fR
+\fB\-hmm\fR \fIboolean\fR
.RS 4
Default value: N
.RE
.PP
-\fB\-sam\fR \fIbool\fR
+\fB\-sam\fR \fIboolean\fR
.RS 4
Default value: N
.RE
.PP
-\fB\-pssm\fR \fIbool\fR
+\fB\-pssm\fR \fIboolean\fR
.RS 4
Default value: Y
.RE
.PP
-\fB\-sig\fR \fIbool\fR
+\fB\-sig\fR \fIboolean\fR
.RS 4
Default value: N
.RE
@@ -116,7 +125,7 @@
Default value: \&.chk
.RE
.PP
-\fB\-niter\fR \fIint\fR
+\fB\-niter\fR \fIinteger\fR
.RS 4
Default value: 1
.RE
@@ -126,7 +135,7 @@
Default value: 100
.RE
.PP
-\fB\-maxhit\fR \fIint\fR
+\fB\-maxhit\fR \fIinteger\fR
.RS 4
Default value: 1000
.RE
@@ -248,7 +257,7 @@
.PP
\fB\-scopf\fR \fIinfile\fR
.RS 4
-In either mode, a \'scop classification file\' is required as a source of family classification data\&. A scop classification file contains classification and other data for domains from the scop database\&. The file is in embl\-like format and is generated by scopparse\&. Domain sequence information can be added to the file by using scopseqs\&. Default value: /data/structure/dcf/scop_raw\&.dcf
+In either mode, a \*(Aqscop classification file\*(Aq is required as a source of family classification data\&. A scop classification file contains classification and other data for domains from the scop database\&. The file is in embl\-like format and is generated by scopparse\&. Domain sequence information can be added to the file by using scopseqs\&. Default value: /data/structure/dcf/scop_raw\&.dcf
.RE
.SH "BUGS"
.PP
@@ -260,7 +269,7 @@
system\&.
.SH "AUTHOR"
.PP
-\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
Modified: trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscanout.1e
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscanout.1e 2010-06-26 01:48:38 UTC (rev 4938)
+++ trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscanout.1e 2010-06-26 08:39:19 UTC (rev 4939)
@@ -1,14 +1,23 @@
'\" t
.\" Title: LIBSCANOUT
-.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
-.\" Date: 08/03/2009
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 06/26/2010
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20090715
+.\" Source: EMBOSS 0.1.0+20100115
.\" Language: English
.\"
-.TH "LIBSCANOUT" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
+.TH "LIBSCANOUT" "1e" "06/26/2010" "EMBOSS 0.1.0+20100115" "EMBOSS Manual for Debian"
.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
.\" * set default formatting
.\" -----------------------------------------------------------------
.\" disable hyphenation
@@ -34,7 +43,7 @@
.PP
\fB\-dhfinfile\fR \fIinfile\fR
.RS 4
-This option specifies the location of the DHF file (domain hits file) (input)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in FASTA or EMBL formats\&. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH\&.
+This option specifies the location of the DHF file (domain hits file) (input)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in FASTA or EMBL formats\&. The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH\&.
.RE
.SS "Required section"
.SS "Output section"
@@ -53,7 +62,7 @@
system\&.
.SH "AUTHOR"
.PP
-\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
Modified: trunk/packages/embassy-domainatrix/trunk/debian/manpages/scopparse.1e
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/scopparse.1e 2010-06-26 01:48:38 UTC (rev 4938)
+++ trunk/packages/embassy-domainatrix/trunk/debian/manpages/scopparse.1e 2010-06-26 08:39:19 UTC (rev 4939)
@@ -1,14 +1,23 @@
'\" t
.\" Title: SCOPPARSE
-.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
-.\" Date: 08/03/2009
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 06/26/2010
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20090715
+.\" Source: EMBOSS 0.1.0+20100115
.\" Language: English
.\"
-.TH "SCOPPARSE" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
+.TH "SCOPPARSE" "1e" "06/26/2010" "EMBOSS 0.1.0+20100115" "EMBOSS Manual for Debian"
.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
.\" * set default formatting
.\" -----------------------------------------------------------------
.\" disable hyphenation
@@ -56,13 +65,13 @@
.PP
\fB\-nominor\fR \fIboolean\fR
.RS 4
-This option specifies whether to omit domains from minor classes (defined as anything not in class \'All alpha proteins\', \'All beta proteins\', \'Alpha and beta proteins (a/b)\' or \'Alpha and beta proteins (a+b)\')\&. This is necessary or appropriate for many analyses\&. Default value: N
+This option specifies whether to omit domains from minor classes (defined as anything not in class \*(AqAll alpha proteins\*(Aq, \*(AqAll beta proteins\*(Aq, \*(AqAlpha and beta proteins (a/b)\*(Aq or \*(AqAlpha and beta proteins (a+b)\*(Aq)\&. This is necessary or appropriate for many analyses\&. Default value: N
.RE
.SS "Output section"
.PP
\fB\-dcffile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of SCOP DCF file (domain classification file) (output)\&. A \'domain classification file\' contains classification and other data for domains from the SCOP or CATH databases\&. The file is generated by using DOMAINER and is in DCF format (EMBL\-like)\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: test\&.scop
+This option specifies the name of SCOP DCF file (domain classification file) (output)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from the SCOP or CATH databases\&. The file is generated by using DOMAINER and is in DCF format (EMBL\-like)\&. Domain sequence information can be added to the file by using DOMAINSEQS\&. Default value: test\&.scop
.RE
.SH "BUGS"
.PP
@@ -74,7 +83,7 @@
system\&.
.SH "AUTHOR"
.PP
-\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
Modified: trunk/packages/embassy-domainatrix/trunk/debian/manpages/ssematch.1e
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/manpages/ssematch.1e 2010-06-26 01:48:38 UTC (rev 4938)
+++ trunk/packages/embassy-domainatrix/trunk/debian/manpages/ssematch.1e 2010-06-26 08:39:19 UTC (rev 4939)
@@ -1,14 +1,23 @@
'\" t
.\" Title: SSEMATCH
-.\" Author: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-.\" Generator: DocBook XSL Stylesheets v1.75.1 <http://docbook.sf.net/>
-.\" Date: 08/03/2009
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 06/26/2010
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20090715
+.\" Source: EMBOSS 0.1.0+20100115
.\" Language: English
.\"
-.TH "SSEMATCH" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
+.TH "SSEMATCH" "1e" "06/26/2010" "EMBOSS 0.1.0+20100115" "EMBOSS Manual for Debian"
.\" -----------------------------------------------------------------
+.\" * Define some portability stuff
+.\" -----------------------------------------------------------------
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.\" http://bugs.debian.org/507673
+.\" http://lists.gnu.org/archive/html/groff/2009-02/msg00013.html
+.\" ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+.ie \n(.g .ds Aq \(aq
+.el .ds Aq '
+.\" -----------------------------------------------------------------
.\" * set default formatting
.\" -----------------------------------------------------------------
.\" disable hyphenation
@@ -39,7 +48,7 @@
.PP
\fB\-dcfinfile\fR \fIinfile\fR
.RS 4
-This option specifies the name of the DCF file (domain classification file) (input)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
+This option specifies the name of the DCF file (domain classification file) (input)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&. The files are generated by using SCOPPARSE and CATHPARSE\&. Domain sequence information can be added to the file by using DOMAINSEQS\&.
.RE
.PP
\fB\-datafile\fR \fImatrixf\fR
@@ -77,12 +86,12 @@
.PP
\fB\-outssfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of the file containing top\-scoring domains for residue\-based alignment (output)\&.A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&.
+This option specifies the name of the file containing top\-scoring domains for residue\-based alignment (output)\&.A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&.
.RE
.PP
\fB\-outsefile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of the file containing top\-scoring domains for secondary structure element\-based alignment (output)\&. A \'domain classification file\' contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&.
+This option specifies the name of the file containing top\-scoring domains for secondary structure element\-based alignment (output)\&. A \*(Aqdomain classification file\*(Aq contains classification and other data for domains from SCOP or CATH, in DCF format (EMBL\-like)\&.
.RE
.PP
\fB\-logfile\fR \fIoutfile\fR
@@ -99,7 +108,7 @@
system\&.
.SH "AUTHOR"
.PP
-\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
More information about the debian-med-commit
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