[med-svn] r4940 - in trunk/packages/embassy-domainatrix/tags: . 0.1.0+20100115-1/debian 0.1.0+20100115-1/debian/manpages
Charles Plessy
plessy at alioth.debian.org
Sat Jun 26 08:52:38 UTC 2010
Author: plessy
Date: 2010-06-26 08:52:38 +0000 (Sat, 26 Jun 2010)
New Revision: 4940
Added:
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/changelog
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/control
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/embassy-domainatrix.manpages
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/cathparse.1e
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainnr.1e
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainreso.1e
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainseqs.1e
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainsse.1e
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/libscan.1e
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/libscanout.1e
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/scopparse.1e
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/ssematch.1e
Removed:
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/changelog
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/control
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/embassy-domainatrix.manpages
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/cathparse.1e
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainnr.1e
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainreso.1e
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainseqs.1e
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainsse.1e
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/libscan.1e
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/libscanout.1e
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/scopparse.1e
trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/ssematch.1e
Log:
[svn-buildpackage] Tagging embassy-domainatrix 0.1.0+20100115-1
Deleted: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/changelog
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/changelog 2010-06-26 01:48:38 UTC (rev 4938)
+++ trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/changelog 2010-06-26 08:52:38 UTC (rev 4940)
@@ -1,30 +0,0 @@
-embassy-domainatrix (0.1.0+20090715-1) unstable; urgency=low
-
- * New upstream release in which the version number was unchanged.
- * 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.
- * Refreshed and experimented on debian/copyright.
- * debian/*manpages* refreshed and moved to section 1e.
-
- -- Charles Plessy <plessy at debian.org> Mon, 03 Aug 2009 19:38:00 +0900
-
-embassy-domainatrix (0.1.0+20080715-1) unstable; urgency=low
-
- * New upstream release in which the version number was unchanged.
- * debian/control:
- - Updated my email address.
- - Build against EMBOSS 6.
- - Using debhelper 7.
- - Checked conformance with Policy 3.8.0 (no changes needed).
- - Corrected DM-Upload-Allowed.
- * debian/copyright updated to latest format.
-
- -- Charles Plessy <plessy at debian.org> Thu, 26 Feb 2009 09:57:33 +0900
-
-embassy-domainatrix (0.1.0-1) unstable; urgency=low
-
- * Initial release
-
- -- Charles Plessy <charles-debian-nospam at plessy.org> Tue, 25 Sep 2007 13:52:47 +0900
Copied: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/changelog (from rev 4939, trunk/packages/embassy-domainatrix/trunk/debian/changelog)
===================================================================
--- trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/changelog (rev 0)
+++ trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/changelog 2010-06-26 08:52:38 UTC (rev 4940)
@@ -0,0 +1,39 @@
+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.
+ * 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.
+ * Refreshed and experimented on debian/copyright.
+ * debian/*manpages* refreshed and moved to section 1e.
+
+ -- Charles Plessy <plessy at debian.org> Mon, 03 Aug 2009 19:38:00 +0900
+
+embassy-domainatrix (0.1.0+20080715-1) unstable; urgency=low
+
+ * New upstream release in which the version number was unchanged.
+ * debian/control:
+ - Updated my email address.
+ - Build against EMBOSS 6.
+ - Using debhelper 7.
+ - Checked conformance with Policy 3.8.0 (no changes needed).
+ - Corrected DM-Upload-Allowed.
+ * debian/copyright updated to latest format.
+
+ -- Charles Plessy <plessy at debian.org> Thu, 26 Feb 2009 09:57:33 +0900
+
+embassy-domainatrix (0.1.0-1) unstable; urgency=low
+
+ * Initial release
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Tue, 25 Sep 2007 13:52:47 +0900
Deleted: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/control
===================================================================
--- trunk/packages/embassy-domainatrix/trunk/debian/control 2010-06-26 01:48:38 UTC (rev 4938)
+++ trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/control 2010-06-26 08:52:38 UTC (rev 4940)
@@ -1,28 +0,0 @@
-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
-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
-Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMAINATRIX
-
-Package: embassy-domainatrix
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Recommends: emboss
-Suggests: embassy
-Description: Extra EMBOSS commands to handle domain classification file
- The DOMAINATRIX programs were developed by Jon Ison and colleagues at MRC HGMP
- for their protein domain research. They are included as an EMBASSY package as
- a work in progress.
- .
- Applications in the current domainatrix release are cathparse (generates DCF
- file from raw CATH files), domainnr (removes redundant domains from a DCF
- file), domainreso (removes low resolution domains from a DCF file), domainseqs
- (adds sequence records to a DCF file), domainsse (adds secondary structure
- records to a DCF file), scopparse (generates DCF file from raw SCOP files) and
- ssematch (searches a DCF file for secondary structure matches).
Copied: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/control (from rev 4939, trunk/packages/embassy-domainatrix/trunk/debian/control)
===================================================================
--- trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/control (rev 0)
+++ trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/control 2010-06-26 08:52:38 UTC (rev 4940)
@@ -0,0 +1,28 @@
+Source: embassy-domainatrix
+Section: science
+Priority: optional
+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: 3.8.4
+Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMAINATRIX
+
+Package: embassy-domainatrix
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Recommends: emboss
+Suggests: embassy
+Description: Extra EMBOSS commands to handle domain classification file
+ The DOMAINATRIX programs were developed by Jon Ison and colleagues at MRC HGMP
+ for their protein domain research. They are included as an EMBASSY package as
+ a work in progress.
+ .
+ Applications in the current domainatrix release are cathparse (generates DCF
+ file from raw CATH files), domainnr (removes redundant domains from a DCF
+ file), domainreso (removes low resolution domains from a DCF file), domainseqs
+ (adds sequence records to a DCF file), domainsse (adds secondary structure
+ records to a DCF file), scopparse (generates DCF file from raw SCOP files) and
+ ssematch (searches a DCF file for secondary structure matches).
Deleted: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/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/tags/0.1.0+20100115-1/debian/embassy-domainatrix.manpages 2010-06-26 08:52:38 UTC (rev 4940)
@@ -1,9 +0,0 @@
-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
Copied: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/embassy-domainatrix.manpages (from rev 4939, trunk/packages/embassy-domainatrix/trunk/debian/embassy-domainatrix.manpages)
===================================================================
--- trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/embassy-domainatrix.manpages (rev 0)
+++ trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/embassy-domainatrix.manpages 2010-06-26 08:52:38 UTC (rev 4940)
@@ -0,0 +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/domainsse.1e
+debian/manpages/scopparse.1e
+debian/manpages/libscan.1e
Deleted: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/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/tags/0.1.0+20100115-1/debian/manpages/cathparse.1e 2010-06-26 08:52:38 UTC (rev 4940)
@@ -1,78 +0,0 @@
-'\" 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
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20090715
-.\" Language: English
-.\"
-.TH "CATHPARSE" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
-.\" -----------------------------------------------------------------
-.\" * set default formatting
-.\" -----------------------------------------------------------------
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.\" -----------------------------------------------------------------
-.\" * MAIN CONTENT STARTS HERE *
-.\" -----------------------------------------------------------------
-.SH "NAME"
-cathparse \- Generates DCF file from raw CATH files\&.
-.SH "SYNOPSIS"
-.HP \w'\fBcathparse\fR\ 'u
-\fBcathparse\fR \fB\-listfile\ \fR\fB\fIinfile\fR\fR \fB\-domfile\ \fR\fB\fIinfile\fR\fR \fB\-namesfile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
-.HP \w'\fBcathparse\fR\ 'u
-\fBcathparse\fR \fB\-help\fR
-.SH "DESCRIPTION"
-.PP
-\fBcathparse\fR
-is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
-.SH "OPTIONS"
-.SS "Input section"
-.PP
-\fB\-listfile\fR \fIinfile\fR
-.RS 4
-This option specifies the name of raw CATH classification file (caths\&.list\&.vX\&.X) (input)\&. The raw CATH parsable files (classification and description files) available from ftp\&.biochem\&.ucl\&.ac\&.uk (/pub/cathdata/v2\&.4)\&. Default value: caths\&.list\&.v2\&.4
-.RE
-.PP
-\fB\-domfile\fR \fIinfile\fR
-.RS 4
-This option specifies the name of raw CATH classification file (domlist\&.vX\&.X) (input)\&. The raw CATH parsable files (classification and description files) available from ftp\&.biochem\&.ucl\&.ac\&.uk (/pub/cathdata/v2\&.4)\&. Default value: domlist\&.v2\&.4
-.RE
-.PP
-\fB\-namesfile\fR \fIinfile\fR
-.RS 4
-This option specifies the name of raw CATH classification file (CAT\&.names\&.all\&.vX\&.X) (input)\&. The raw CATH parsable files (classification and description files) available from ftp\&.biochem\&.ucl\&.ac\&.uk (/pub/cathdata/v2\&.4)\&. Default value: CAT\&.names\&.all\&.v2\&.4
-.RE
-.SS "Output section"
-.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
-.RE
-.PP
-\fB\-logfile\fR \fIoutfile\fR
-.RS 4
-This option specifies the name of the CATHPARSE log file\&. Default value: cathparse\&.log
-.RE
-.SH "BUGS"
-.PP
-Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
-.SH "SEE ALSO"
-.PP
-cathparse is fully documented via the
-\fBtfm\fR(1)
-system\&.
-.SH "AUTHOR"
-.PP
-\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
-.SH "COPYRIGHT"
-.br
-.PP
-This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
-.sp
Copied: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/cathparse.1e (from rev 4939, trunk/packages/embassy-domainatrix/trunk/debian/manpages/cathparse.1e)
===================================================================
--- trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/cathparse.1e (rev 0)
+++ trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/cathparse.1e 2010-06-26 08:52:38 UTC (rev 4940)
@@ -0,0 +1,87 @@
+'\" t
+.\" Title: CATHPARSE
+.\" 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+20100115
+.\" Language: English
+.\"
+.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
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+cathparse \- Generates DCF file from raw CATH files\&.
+.SH "SYNOPSIS"
+.HP \w'\fBcathparse\fR\ 'u
+\fBcathparse\fR \fB\-listfile\ \fR\fB\fIinfile\fR\fR \fB\-domfile\ \fR\fB\fIinfile\fR\fR \fB\-namesfile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBcathparse\fR\ 'u
+\fBcathparse\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBcathparse\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-listfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of raw CATH classification file (caths\&.list\&.vX\&.X) (input)\&. The raw CATH parsable files (classification and description files) available from ftp\&.biochem\&.ucl\&.ac\&.uk (/pub/cathdata/v2\&.4)\&. Default value: caths\&.list\&.v2\&.4
+.RE
+.PP
+\fB\-domfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of raw CATH classification file (domlist\&.vX\&.X) (input)\&. The raw CATH parsable files (classification and description files) available from ftp\&.biochem\&.ucl\&.ac\&.uk (/pub/cathdata/v2\&.4)\&. Default value: domlist\&.v2\&.4
+.RE
+.PP
+\fB\-namesfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of raw CATH classification file (CAT\&.names\&.all\&.vX\&.X) (input)\&. The raw CATH parsable files (classification and description files) available from ftp\&.biochem\&.ucl\&.ac\&.uk (/pub/cathdata/v2\&.4)\&. Default value: CAT\&.names\&.all\&.v2\&.4
+.RE
+.SS "Output section"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+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
+.RS 4
+This option specifies the name of the CATHPARSE log file\&. Default value: cathparse\&.log
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+cathparse is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\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
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Deleted: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/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/tags/0.1.0+20100115-1/debian/manpages/domainnr.1e 2010-06-26 08:52:38 UTC (rev 4940)
@@ -1,121 +0,0 @@
-'\" 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
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20090715
-.\" Language: English
-.\"
-.TH "DOMAINNR" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
-.\" -----------------------------------------------------------------
-.\" * set default formatting
-.\" -----------------------------------------------------------------
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.\" -----------------------------------------------------------------
-.\" * MAIN CONTENT STARTS HERE *
-.\" -----------------------------------------------------------------
-.SH "NAME"
-domainnr \- Removes redundant domains from a DCF file\&.
-.SH "SYNOPSIS"
-.HP \w'\fBdomainnr\fR\ 'u
-\fBdomainnr\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-retain\ \fR\fB\fItoggle\fR\fR \fB\-node\ \fR\fB\fIlist\fR\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-threshlow\ \fR\fB\fIfloat\fR\fR \fB\-threshup\ \fR\fB\fIfloat\fR\fR [\fB\-gapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextend\ \fR\fB\fIfloat\fR\fR] \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-redoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
-.HP \w'\fBdomainnr\fR\ 'u
-\fBdomainnr\fR \fB\-help\fR
-.SH "DESCRIPTION"
-.PP
-\fBdomainnr\fR
-is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
-.SH "OPTIONS"
-.SS "Input section"
-.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\&.
-.RE
-.PP
-\fB\-datafile\fR \fImatrixf\fR
-.RS 4
-This option specifies the residue substitution matrix\&. This is used for sequence comparison\&. Default value: EBLOSUM62
-.RE
-.PP
-\fB\-retain\fR \fItoggle\fR
-.RS 4
-This option specifies whether to write redundant domains to a separate file\&. If this option is selected, redundant domains are written to a separate output file\&. Default value: N
-.RE
-.SS "Required section"
-.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
-.RE
-.PP
-\fB\-mode\fR \fIlist\fR
-.RS 4
-This option specifies whether to remove redundancy at a single threshold % sequence similarity or remove redundancy outside a range of acceptable threshold % similarity\&. All permutations of pair\-wise sequence alignments are calculated for each domain family in turn using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm\&. Redundant sequences are removed in one of two modes as follows: (i) If a pair of proteins achieve greater than a threshold percentage sequence similarity (specified by the user) the shortest sequence is discarded\&. (ii) If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range (specified by the user) the shortest sequence is discarded\&. Default value: 1
-.RE
-.PP
-\fB\-threshold\fR \fIfloat\fR
-.RS 4
-This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation\&. If a pair of proteins achieve greater than this threshold the shortest sequence is discarded\&. Default value: 95\&.0
-.RE
-.PP
-\fB\-threshlow\fR \fIfloat\fR
-.RS 4
-This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation\&. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\&. Default value: 30\&.0
-.RE
-.PP
-\fB\-threshup\fR \fIfloat\fR
-.RS 4
-This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation\&. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\&. Default value: 90\&.0
-.RE
-.SS "Additional section"
-.PP
-\fB\-gapopen\fR \fIfloat\fR
-.RS 4
-This option specifies the gap insertion penalty\&. This is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10
-.RE
-.PP
-\fB\-gapextend\fR \fIfloat\fR
-.RS 4
-This option specifies the gap extension penalty\&. This is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. Default value: 0\&.5
-.RE
-.SS "Advanced section"
-.SS "Output section"
-.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
-.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\&.
-.RE
-.PP
-\fB\-logfile\fR \fIoutfile\fR
-.RS 4
-This option specifies the name of log file for the build\&. The log file contains messages about any errors arising while domainnr ran\&. Default value: domainnr\&.log
-.RE
-.SH "BUGS"
-.PP
-Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
-.SH "SEE ALSO"
-.PP
-domainnr is fully documented via the
-\fBtfm\fR(1)
-system\&.
-.SH "AUTHOR"
-.PP
-\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
-.SH "COPYRIGHT"
-.br
-.PP
-This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
-.sp
Copied: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainnr.1e (from rev 4939, trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainnr.1e)
===================================================================
--- trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainnr.1e (rev 0)
+++ trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainnr.1e 2010-06-26 08:52:38 UTC (rev 4940)
@@ -0,0 +1,130 @@
+'\" t
+.\" Title: DOMAINNR
+.\" 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+20100115
+.\" Language: English
+.\"
+.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
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+domainnr \- Removes redundant domains from a DCF file\&.
+.SH "SYNOPSIS"
+.HP \w'\fBdomainnr\fR\ 'u
+\fBdomainnr\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-retain\ \fR\fB\fItoggle\fR\fR \fB\-node\ \fR\fB\fIlist\fR\fR \fB\-mode\ \fR\fB\fIlist\fR\fR \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-threshlow\ \fR\fB\fIfloat\fR\fR \fB\-threshup\ \fR\fB\fIfloat\fR\fR [\fB\-gapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-gapextend\ \fR\fB\fIfloat\fR\fR] \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-redoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdomainnr\fR\ 'u
+\fBdomainnr\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdomainnr\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dcfinfile\fR \fIinfile\fR
+.RS 4
+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
+.RS 4
+This option specifies the residue substitution matrix\&. This is used for sequence comparison\&. Default value: EBLOSUM62
+.RE
+.PP
+\fB\-retain\fR \fItoggle\fR
+.RS 4
+This option specifies whether to write redundant domains to a separate file\&. If this option is selected, redundant domains are written to a separate output file\&. Default value: N
+.RE
+.SS "Required section"
+.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 \*(AqClass\*(Aq entries belonging to the same Class will be non\-redundant\&. Default value: 1
+.RE
+.PP
+\fB\-mode\fR \fIlist\fR
+.RS 4
+This option specifies whether to remove redundancy at a single threshold % sequence similarity or remove redundancy outside a range of acceptable threshold % similarity\&. All permutations of pair\-wise sequence alignments are calculated for each domain family in turn using the EMBOSS implementation of the Needleman and Wunsch global alignment algorithm\&. Redundant sequences are removed in one of two modes as follows: (i) If a pair of proteins achieve greater than a threshold percentage sequence similarity (specified by the user) the shortest sequence is discarded\&. (ii) If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range (specified by the user) the shortest sequence is discarded\&. Default value: 1
+.RE
+.PP
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation\&. If a pair of proteins achieve greater than this threshold the shortest sequence is discarded\&. Default value: 95\&.0
+.RE
+.PP
+\fB\-threshlow\fR \fIfloat\fR
+.RS 4
+This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation\&. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\&. Default value: 30\&.0
+.RE
+.PP
+\fB\-threshup\fR \fIfloat\fR
+.RS 4
+This option specifies the % sequence identity redundancy threshold, which determines the redundancy calculation\&. If a pair of proteins have a percentage sequence similarity that lies outside an acceptable range the shortest sequence is discarded\&. Default value: 90\&.0
+.RE
+.SS "Additional section"
+.PP
+\fB\-gapopen\fR \fIfloat\fR
+.RS 4
+This option specifies the gap insertion penalty\&. This is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10
+.RE
+.PP
+\fB\-gapextend\fR \fIfloat\fR
+.RS 4
+This option specifies the gap extension penalty\&. This is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. Default value: 0\&.5
+.RE
+.SS "Advanced section"
+.SS "Output section"
+.PP
+\fB\-dcfoutfile\fR \fIoutfile\fR
+.RS 4
+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 \*(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
+.RS 4
+This option specifies the name of log file for the build\&. The log file contains messages about any errors arising while domainnr ran\&. Default value: domainnr\&.log
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+domainnr is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\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
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Deleted: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/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/tags/0.1.0+20100115-1/debian/manpages/domainreso.1e 2010-06-26 08:52:38 UTC (rev 4940)
@@ -1,74 +0,0 @@
-'\" 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
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20090715
-.\" Language: English
-.\"
-.TH "DOMAINRESO" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
-.\" -----------------------------------------------------------------
-.\" * set default formatting
-.\" -----------------------------------------------------------------
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.\" -----------------------------------------------------------------
-.\" * MAIN CONTENT STARTS HERE *
-.\" -----------------------------------------------------------------
-.SH "NAME"
-domainreso \- Remove low resolution domains from a DCF file\&.
-.SH "SYNOPSIS"
-.HP \w'\fBdomainreso\fR\ 'u
-\fBdomainreso\fR \fB\-cpdbpath\ \fR\fB\fIdirlist\fR\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR
-.HP \w'\fBdomainreso\fR\ 'u
-\fBdomainreso\fR \fB\-help\fR
-.SH "DESCRIPTION"
-.PP
-\fBdomainreso\fR
-is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "PROTEIN:3D STRUCTURE" command group(s)\&.
-.SH "OPTIONS"
-.SS "Input section"
-.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: \&./
-.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\&.
-.RE
-.SS "Required section"
-.PP
-\fB\-threshold\fR \fIfloat\fR
-.RS 4
-This option specifies the threshold for inclusion (Angstroms)\&. Domains exceeding the threshold for inclusion (Angstroms) will not be given in the output file\&. Default value: 2\&.8
-.RE
-.SS "Output section"
-.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
-.RE
-.SH "BUGS"
-.PP
-Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
-.SH "SEE ALSO"
-.PP
-domainreso is fully documented via the
-\fBtfm\fR(1)
-system\&.
-.SH "AUTHOR"
-.PP
-\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
-.SH "COPYRIGHT"
-.br
-.PP
-This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
-.sp
Copied: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainreso.1e (from rev 4939, trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainreso.1e)
===================================================================
--- trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainreso.1e (rev 0)
+++ trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainreso.1e 2010-06-26 08:52:38 UTC (rev 4940)
@@ -0,0 +1,83 @@
+'\" t
+.\" Title: DOMAINRESO
+.\" 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+20100115
+.\" Language: English
+.\"
+.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
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+domainreso \- Remove low resolution domains from a DCF file\&.
+.SH "SYNOPSIS"
+.HP \w'\fBdomainreso\fR\ 'u
+\fBdomainreso\fR \fB\-cpdbpath\ \fR\fB\fIdirlist\fR\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-threshold\ \fR\fB\fIfloat\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdomainreso\fR\ 'u
+\fBdomainreso\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdomainreso\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "PROTEIN:3D STRUCTURE" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-cpdbpath\fR \fIdirlist\fR
+.RS 4
+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 \*(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
+\fB\-threshold\fR \fIfloat\fR
+.RS 4
+This option specifies the threshold for inclusion (Angstroms)\&. Domains exceeding the threshold for inclusion (Angstroms) will not be given in the output file\&. Default value: 2\&.8
+.RE
+.SS "Output section"
+.PP
+\fB\-dcfoutfile\fR \fIoutfile\fR
+.RS 4
+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
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+domainreso is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\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
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Deleted: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/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/tags/0.1.0+20100115-1/debian/manpages/domainseqs.1e 2010-06-26 08:52:38 UTC (rev 4940)
@@ -1,100 +0,0 @@
-'\" 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
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20090715
-.\" Language: English
-.\"
-.TH "DOMAINSEQS" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
-.\" -----------------------------------------------------------------
-.\" * set default formatting
-.\" -----------------------------------------------------------------
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.\" -----------------------------------------------------------------
-.\" * MAIN CONTENT STARTS HERE *
-.\" -----------------------------------------------------------------
-.SH "NAME"
-domainseqs \- Adds sequence records to a DCF file\&.
-.SH "SYNOPSIS"
-.HP \w'\fBdomainseqs\fR\ 'u
-\fBdomainseqs\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-dpdbdir\ \fR\fB\fIdirectory\fR\fR \fB\-getswiss\ \fR\fB\fItoggle\fR\fR \fB\-pdbtospfile\ \fR\fB\fIinfile\fR\fR \fB\-datafile\ \fR\fB\fImatrixf\fR\fR \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
-.HP \w'\fBdomainseqs\fR\ 'u
-\fBdomainseqs\fR \fB\-help\fR
-.SH "DESCRIPTION"
-.PP
-\fBdomainseqs\fR
-is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
-.SH "OPTIONS"
-.SS "Input section"
-.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\&.
-.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: \&./
-.RE
-.PP
-\fB\-getswiss\fR \fItoggle\fR
-.RS 4
-Default value: N
-.RE
-.PP
-\fB\-pdbtospfile\fR \fIinfile\fR
-.RS 4
-This option specifies the name of the pdbcodes to swissprot indexing file\&. The swissprot:PDB equivalence file is generated by PDBTOSP
-.RE
-.PP
-\fB\-datafile\fR \fImatrixf\fR
-.RS 4
-This option specifies the residue substitution matrix, which is used for sequence comparison\&. Default value: EBLOSUM62
-.RE
-.SS "Required section"
-.SS "Additional section"
-.PP
-\fB\-gapopen\fR \fIfloat\fR
-.RS 4
-This option specifies the gap insertion penalty\&. This is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10
-.RE
-.PP
-\fB\-gapextend\fR \fIfloat\fR
-.RS 4
-This option specifies the gap extension penalty\&. This is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. Default value: 0\&.5
-.RE
-.SS "Output section"
-.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
-.RE
-.PP
-\fB\-logfile\fR \fIoutfile\fR
-.RS 4
-This option specifies the name of log file for the build\&. The log file contains messages about any errors arising while domainseqs ran\&. Default value: domainseqs\&.log
-.RE
-.SH "BUGS"
-.PP
-Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
-.SH "SEE ALSO"
-.PP
-domainseqs is fully documented via the
-\fBtfm\fR(1)
-system\&.
-.SH "AUTHOR"
-.PP
-\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
-.SH "COPYRIGHT"
-.br
-.PP
-This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
-.sp
Copied: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainseqs.1e (from rev 4939, trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainseqs.1e)
===================================================================
--- trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainseqs.1e (rev 0)
+++ trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainseqs.1e 2010-06-26 08:52:38 UTC (rev 4940)
@@ -0,0 +1,109 @@
+'\" t
+.\" Title: DOMAINSEQS
+.\" 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+20100115
+.\" Language: English
+.\"
+.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
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+domainseqs \- Adds sequence records to a DCF file\&.
+.SH "SYNOPSIS"
+.HP \w'\fBdomainseqs\fR\ 'u
+\fBdomainseqs\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-dpdbdir\ \fR\fB\fIdirectory\fR\fR \fB\-getswiss\ \fR\fB\fItoggle\fR\fR \fB\-pdbtospfile\ \fR\fB\fIinfile\fR\fR \fB\-datafile\ \fR\fB\fImatrixf\fR\fR \fB\-gapopen\ \fR\fB\fIfloat\fR\fR \fB\-gapextend\ \fR\fB\fIfloat\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdomainseqs\fR\ 'u
+\fBdomainseqs\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdomainseqs\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dcfinfile\fR \fIinfile\fR
+.RS 4
+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 \*(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
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-pdbtospfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of the pdbcodes to swissprot indexing file\&. The swissprot:PDB equivalence file is generated by PDBTOSP
+.RE
+.PP
+\fB\-datafile\fR \fImatrixf\fR
+.RS 4
+This option specifies the residue substitution matrix, which is used for sequence comparison\&. Default value: EBLOSUM62
+.RE
+.SS "Required section"
+.SS "Additional section"
+.PP
+\fB\-gapopen\fR \fIfloat\fR
+.RS 4
+This option specifies the gap insertion penalty\&. This is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10
+.RE
+.PP
+\fB\-gapextend\fR \fIfloat\fR
+.RS 4
+This option specifies the gap extension penalty\&. This is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. Default value: 0\&.5
+.RE
+.SS "Output section"
+.PP
+\fB\-dcfoutfile\fR \fIoutfile\fR
+.RS 4
+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
+.RS 4
+This option specifies the name of log file for the build\&. The log file contains messages about any errors arising while domainseqs ran\&. Default value: domainseqs\&.log
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+domainseqs is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\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
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Deleted: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/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/tags/0.1.0+20100115-1/debian/manpages/domainsse.1e 2010-06-26 08:52:38 UTC (rev 4940)
@@ -1,75 +0,0 @@
-'\" 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
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20090715
-.\" Language: English
-.\"
-.TH "DOMAINSSE" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
-.\" -----------------------------------------------------------------
-.\" * set default formatting
-.\" -----------------------------------------------------------------
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.\" -----------------------------------------------------------------
-.\" * MAIN CONTENT STARTS HERE *
-.\" -----------------------------------------------------------------
-.SH "NAME"
-domainsse \- Add secondary structure records to a DCF file\&.
-.SH "SYNOPSIS"
-.HP \w'\fBdomainsse\fR\ 'u
-\fBdomainsse\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-dccfdir\ \fR\fB\fIdirectory\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
-.HP \w'\fBdomainsse\fR\ 'u
-\fBdomainsse\fR \fB\-help\fR
-.SH "DESCRIPTION"
-.PP
-\fBdomainsse\fR
-is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
-.SH "OPTIONS"
-.SS "Input section"
-.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\&.
-.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: \&./
-.RE
-.SS "Required section"
-.SS "Advanced section"
-.SS "Output section"
-.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\&.
-.RE
-.PP
-\fB\-logfile\fR \fIoutfile\fR
-.RS 4
-This option specifies the name of the DOMAINSSE log file\&. Default value: domainsse\&.log
-.RE
-.SH "BUGS"
-.PP
-Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
-.SH "SEE ALSO"
-.PP
-domainsse is fully documented via the
-\fBtfm\fR(1)
-system\&.
-.SH "AUTHOR"
-.PP
-\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
-.SH "COPYRIGHT"
-.br
-.PP
-This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
-.sp
Copied: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainsse.1e (from rev 4939, trunk/packages/embassy-domainatrix/trunk/debian/manpages/domainsse.1e)
===================================================================
--- trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainsse.1e (rev 0)
+++ trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/domainsse.1e 2010-06-26 08:52:38 UTC (rev 4940)
@@ -0,0 +1,84 @@
+'\" t
+.\" Title: DOMAINSSE
+.\" 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+20100115
+.\" Language: English
+.\"
+.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
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+domainsse \- Add secondary structure records to a DCF file\&.
+.SH "SYNOPSIS"
+.HP \w'\fBdomainsse\fR\ 'u
+\fBdomainsse\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR \fB\-dccfdir\ \fR\fB\fIdirectory\fR\fR \fB\-dcfoutfile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBdomainsse\fR\ 'u
+\fBdomainsse\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBdomainsse\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dcfinfile\fR \fIinfile\fR
+.RS 4
+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 \*(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"
+.SS "Output section"
+.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 \*(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
+.RS 4
+This option specifies the name of the DOMAINSSE log file\&. Default value: domainsse\&.log
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+domainsse is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\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
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Deleted: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/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/tags/0.1.0+20100115-1/debian/manpages/libscan.1e 2010-06-26 08:52:38 UTC (rev 4940)
@@ -1,271 +0,0 @@
-'\" 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
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20090715
-.\" Language: English
-.\"
-.TH "LIBSCAN" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
-.\" -----------------------------------------------------------------
-.\" * set default formatting
-.\" -----------------------------------------------------------------
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.\" -----------------------------------------------------------------
-.\" * MAIN CONTENT STARTS HERE *
-.\" -----------------------------------------------------------------
-.SH "NAME"
-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
-.HP \w'\fBlibscan\fR\ 'u
-\fBlibscan\fR \fB\-help\fR
-.SH "DESCRIPTION"
-.PP
-\fBlibscan\fR
-is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&.
-.SH "OPTIONS"
-.PP
-\fB\-mode\fR \fIlist\fR
-.RS 4
-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
-.RS 4
-Default value: N
-.RE
-.PP
-\fB\-henik\fR \fIbool\fR
-.RS 4
-Default value: N
-.RE
-.PP
-\fB\-hmm\fR \fIbool\fR
-.RS 4
-Default value: N
-.RE
-.PP
-\fB\-sam\fR \fIbool\fR
-.RS 4
-Default value: N
-.RE
-.PP
-\fB\-pssm\fR \fIbool\fR
-.RS 4
-Default value: Y
-.RE
-.PP
-\fB\-sig\fR \fIbool\fR
-.RS 4
-Default value: N
-.RE
-.PP
-\fB\-hmmpath\fR \fIstring\fR
-.RS 4
-Default value: \&./lib/
-.RE
-.PP
-\fB\-hmmextn\fR \fIstring\fR
-.RS 4
-Default value: \&.hmm
-.RE
-.PP
-\fB\-hmmoutpath\fR \fIstring\fR
-.RS 4
-Default value: \&./
-.RE
-.PP
-\fB\-hmmoutextn\fR \fIstring\fR
-.RS 4
-Default value: \&.hmmout
-.RE
-.PP
-\fB\-sampath\fR \fIstring\fR
-.RS 4
-Default value: \&./
-.RE
-.PP
-\fB\-samextn\fR \fIstring\fR
-.RS 4
-Default value: \&.mod
-.RE
-.PP
-\fB\-samoutpath\fR \fIstring\fR
-.RS 4
-Default value: \&./
-.RE
-.PP
-\fB\-samoutextn\fR \fIstring\fR
-.RS 4
-Default value: \&.samout
-.RE
-.PP
-\fB\-pssmpath\fR \fIstring\fR
-.RS 4
-Default value: /data/structure/lib/pssm/
-.RE
-.PP
-\fB\-pssmextn\fR \fIstring\fR
-.RS 4
-Default value: \&.chk
-.RE
-.PP
-\fB\-niter\fR \fIint\fR
-.RS 4
-Default value: 1
-.RE
-.PP
-\fB\-thresh\fR \fIfloat\fR
-.RS 4
-Default value: 100
-.RE
-.PP
-\fB\-maxhit\fR \fIint\fR
-.RS 4
-Default value: 1000
-.RE
-.PP
-\fB\-pssmoutpath\fR \fIstring\fR
-.RS 4
-Default value: \&./
-.RE
-.PP
-\fB\-pssmoutextn\fR \fIstring\fR
-.RS 4
-Default value: \&.pssmout
-.RE
-.PP
-\fB\-gbvpath\fR \fIstring\fR
-.RS 4
-Default value: \&./
-.RE
-.PP
-\fB\-gbvextn\fR \fIstring\fR
-.RS 4
-Default value: \&.grib
-.RE
-.PP
-\fB\-gbvgapo\fR \fIfloat\fR
-.RS 4
-Default value: 10\&.0
-.RE
-.PP
-\fB\-gbvgape\fR \fIfloat\fR
-.RS 4
-Default value: 0\&.5
-.RE
-.PP
-\fB\-gbvoutpath\fR \fIstring\fR
-.RS 4
-Default value: \&./
-.RE
-.PP
-\fB\-gbvoutextn\fR \fIstring\fR
-.RS 4
-Default value: \&.gribout
-.RE
-.PP
-\fB\-hnfpath\fR \fIstring\fR
-.RS 4
-Default value: \&./
-.RE
-.PP
-\fB\-hnfextn\fR \fIstring\fR
-.RS 4
-Default value: \&.henik
-.RE
-.PP
-\fB\-hnfgapo\fR \fIfloat\fR
-.RS 4
-Default value: 10\&.0
-.RE
-.PP
-\fB\-hnfgape\fR \fIfloat\fR
-.RS 4
-Default value: 0\&.5
-.RE
-.PP
-\fB\-hnfoutpath\fR \fIstring\fR
-.RS 4
-Default value: \&./
-.RE
-.PP
-\fB\-hnfoutextn\fR \fIstring\fR
-.RS 4
-Default value: \&.henikout
-.RE
-.PP
-\fB\-sigpath\fR \fIstring\fR
-.RS 4
-Default value: \&./
-.RE
-.PP
-\fB\-sigextn\fR \fIstring\fR
-.RS 4
-Default value: \&.sig
-.RE
-.PP
-\fB\-nterm\fR \fIlist\fR
-.RS 4
-Default value: 1
-.RE
-.PP
-\fB\-sub\fR \fImatrixf\fR
-.RS 4
-Default value: EBLOSUM62
-.RE
-.PP
-\fB\-siggapo\fR \fIfloat\fR
-.RS 4
-Default value: 10\&.0
-.RE
-.PP
-\fB\-siggape\fR \fIfloat\fR
-.RS 4
-Default value: 0\&.5
-.RE
-.PP
-\fB\-sigoutpath\fR \fIstring\fR
-.RS 4
-Default value: \&./
-.RE
-.PP
-\fB\-sigoutextn\fR \fIstring\fR
-.RS 4
-Default value: \&.sigout
-.RE
-.PP
-\fB\-db\fR \fIseqset\fR
-.RS 4
-In database search mode libscan scans each discriminating element against a sequence set\&. In library screen mode, libscan reads a sequence set and screens each sequence against the library (directories of disciminating elements) Default value: 49142\&.vdhf
-.RE
-.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
-.RE
-.SH "BUGS"
-.PP
-Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
-.SH "SEE ALSO"
-.PP
-libscan is fully documented via the
-\fBtfm\fR(1)
-system\&.
-.SH "AUTHOR"
-.PP
-\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
-.SH "COPYRIGHT"
-.br
-.PP
-This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
-.sp
Copied: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/libscan.1e (from rev 4939, trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscan.1e)
===================================================================
--- trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/libscan.1e (rev 0)
+++ trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/libscan.1e 2010-06-26 08:52:38 UTC (rev 4940)
@@ -0,0 +1,280 @@
+'\" t
+.\" Title: LIBSCAN
+.\" 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+20100115
+.\" Language: English
+.\"
+.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
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+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\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"
+.PP
+\fBlibscan\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&.
+.SH "OPTIONS"
+.PP
+\fB\-mode\fR \fIlist\fR
+.RS 4
+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 \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-henik\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-hmm\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-sam\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-pssm\fR \fIboolean\fR
+.RS 4
+Default value: Y
+.RE
+.PP
+\fB\-sig\fR \fIboolean\fR
+.RS 4
+Default value: N
+.RE
+.PP
+\fB\-hmmpath\fR \fIstring\fR
+.RS 4
+Default value: \&./lib/
+.RE
+.PP
+\fB\-hmmextn\fR \fIstring\fR
+.RS 4
+Default value: \&.hmm
+.RE
+.PP
+\fB\-hmmoutpath\fR \fIstring\fR
+.RS 4
+Default value: \&./
+.RE
+.PP
+\fB\-hmmoutextn\fR \fIstring\fR
+.RS 4
+Default value: \&.hmmout
+.RE
+.PP
+\fB\-sampath\fR \fIstring\fR
+.RS 4
+Default value: \&./
+.RE
+.PP
+\fB\-samextn\fR \fIstring\fR
+.RS 4
+Default value: \&.mod
+.RE
+.PP
+\fB\-samoutpath\fR \fIstring\fR
+.RS 4
+Default value: \&./
+.RE
+.PP
+\fB\-samoutextn\fR \fIstring\fR
+.RS 4
+Default value: \&.samout
+.RE
+.PP
+\fB\-pssmpath\fR \fIstring\fR
+.RS 4
+Default value: /data/structure/lib/pssm/
+.RE
+.PP
+\fB\-pssmextn\fR \fIstring\fR
+.RS 4
+Default value: \&.chk
+.RE
+.PP
+\fB\-niter\fR \fIinteger\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-thresh\fR \fIfloat\fR
+.RS 4
+Default value: 100
+.RE
+.PP
+\fB\-maxhit\fR \fIinteger\fR
+.RS 4
+Default value: 1000
+.RE
+.PP
+\fB\-pssmoutpath\fR \fIstring\fR
+.RS 4
+Default value: \&./
+.RE
+.PP
+\fB\-pssmoutextn\fR \fIstring\fR
+.RS 4
+Default value: \&.pssmout
+.RE
+.PP
+\fB\-gbvpath\fR \fIstring\fR
+.RS 4
+Default value: \&./
+.RE
+.PP
+\fB\-gbvextn\fR \fIstring\fR
+.RS 4
+Default value: \&.grib
+.RE
+.PP
+\fB\-gbvgapo\fR \fIfloat\fR
+.RS 4
+Default value: 10\&.0
+.RE
+.PP
+\fB\-gbvgape\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.5
+.RE
+.PP
+\fB\-gbvoutpath\fR \fIstring\fR
+.RS 4
+Default value: \&./
+.RE
+.PP
+\fB\-gbvoutextn\fR \fIstring\fR
+.RS 4
+Default value: \&.gribout
+.RE
+.PP
+\fB\-hnfpath\fR \fIstring\fR
+.RS 4
+Default value: \&./
+.RE
+.PP
+\fB\-hnfextn\fR \fIstring\fR
+.RS 4
+Default value: \&.henik
+.RE
+.PP
+\fB\-hnfgapo\fR \fIfloat\fR
+.RS 4
+Default value: 10\&.0
+.RE
+.PP
+\fB\-hnfgape\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.5
+.RE
+.PP
+\fB\-hnfoutpath\fR \fIstring\fR
+.RS 4
+Default value: \&./
+.RE
+.PP
+\fB\-hnfoutextn\fR \fIstring\fR
+.RS 4
+Default value: \&.henikout
+.RE
+.PP
+\fB\-sigpath\fR \fIstring\fR
+.RS 4
+Default value: \&./
+.RE
+.PP
+\fB\-sigextn\fR \fIstring\fR
+.RS 4
+Default value: \&.sig
+.RE
+.PP
+\fB\-nterm\fR \fIlist\fR
+.RS 4
+Default value: 1
+.RE
+.PP
+\fB\-sub\fR \fImatrixf\fR
+.RS 4
+Default value: EBLOSUM62
+.RE
+.PP
+\fB\-siggapo\fR \fIfloat\fR
+.RS 4
+Default value: 10\&.0
+.RE
+.PP
+\fB\-siggape\fR \fIfloat\fR
+.RS 4
+Default value: 0\&.5
+.RE
+.PP
+\fB\-sigoutpath\fR \fIstring\fR
+.RS 4
+Default value: \&./
+.RE
+.PP
+\fB\-sigoutextn\fR \fIstring\fR
+.RS 4
+Default value: \&.sigout
+.RE
+.PP
+\fB\-db\fR \fIseqset\fR
+.RS 4
+In database search mode libscan scans each discriminating element against a sequence set\&. In library screen mode, libscan reads a sequence set and screens each sequence against the library (directories of disciminating elements) Default value: 49142\&.vdhf
+.RE
+.PP
+\fB\-scopf\fR \fIinfile\fR
+.RS 4
+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
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+libscan is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\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
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Deleted: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/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/tags/0.1.0+20100115-1/debian/manpages/libscanout.1e 2010-06-26 08:52:38 UTC (rev 4940)
@@ -1,64 +0,0 @@
-'\" 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
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20090715
-.\" Language: English
-.\"
-.TH "LIBSCANOUT" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
-.\" -----------------------------------------------------------------
-.\" * set default formatting
-.\" -----------------------------------------------------------------
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.\" -----------------------------------------------------------------
-.\" * MAIN CONTENT STARTS HERE *
-.\" -----------------------------------------------------------------
-.SH "NAME"
-libscanout \- Reads a DHF file and writes a file of top\-scoring Classes, Folds and Superfamilies\&.
-.SH "SYNOPSIS"
-.HP \w'\fBlibscanout\fR\ 'u
-\fBlibscanout\fR \fB\-dhfinfile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
-.HP \w'\fBlibscanout\fR\ 'u
-\fBlibscanout\fR \fB\-help\fR
-.SH "DESCRIPTION"
-.PP
-\fBlibscanout\fR
-is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&.
-.SH "OPTIONS"
-.SS "Input section"
-.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\&.
-.RE
-.SS "Required section"
-.SS "Output section"
-.PP
-\fB\-outfile\fR \fIoutfile\fR
-.RS 4
-This option specifies the location of the summary file (output)\&. The summary file contains lists of domain Classes, Superfamilies and Families rank\-ordered on the basis of score (highest\-scoring first)\&.
-.RE
-.SH "BUGS"
-.PP
-Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
-.SH "SEE ALSO"
-.PP
-libscanout is fully documented via the
-\fBtfm\fR(1)
-system\&.
-.SH "AUTHOR"
-.PP
-\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
-.SH "COPYRIGHT"
-.br
-.PP
-This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
-.sp
Copied: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/libscanout.1e (from rev 4939, trunk/packages/embassy-domainatrix/trunk/debian/manpages/libscanout.1e)
===================================================================
--- trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/libscanout.1e (rev 0)
+++ trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/libscanout.1e 2010-06-26 08:52:38 UTC (rev 4940)
@@ -0,0 +1,73 @@
+'\" t
+.\" Title: LIBSCANOUT
+.\" 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+20100115
+.\" Language: English
+.\"
+.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
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+libscanout \- Reads a DHF file and writes a file of top\-scoring Classes, Folds and Superfamilies\&.
+.SH "SYNOPSIS"
+.HP \w'\fBlibscanout\fR\ 'u
+\fBlibscanout\fR \fB\-dhfinfile\ \fR\fB\fIinfile\fR\fR \fB\-outfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBlibscanout\fR\ 'u
+\fBlibscanout\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBlibscanout\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Protein:3D Structure" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-dhfinfile\fR \fIinfile\fR
+.RS 4
+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"
+.PP
+\fB\-outfile\fR \fIoutfile\fR
+.RS 4
+This option specifies the location of the summary file (output)\&. The summary file contains lists of domain Classes, Superfamilies and Families rank\-ordered on the basis of score (highest\-scoring first)\&.
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+libscanout is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\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
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Deleted: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/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/tags/0.1.0+20100115-1/debian/manpages/scopparse.1e 2010-06-26 08:52:38 UTC (rev 4940)
@@ -1,85 +0,0 @@
-'\" 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
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20090715
-.\" Language: English
-.\"
-.TH "SCOPPARSE" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
-.\" -----------------------------------------------------------------
-.\" * set default formatting
-.\" -----------------------------------------------------------------
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.\" -----------------------------------------------------------------
-.\" * MAIN CONTENT STARTS HERE *
-.\" -----------------------------------------------------------------
-.SH "NAME"
-scopparse \- Generate DCF file from raw SCOP files\&.
-.SH "SYNOPSIS"
-.HP \w'\fBscopparse\fR\ 'u
-\fBscopparse\fR \fB\-classfile\ \fR\fB\fIinfile\fR\fR \fB\-desinfile\ \fR\fB\fIinfile\fR\fR \fB\-nosegments\ \fR\fB\fIboolean\fR\fR \fB\-nomultichain\ \fR\fB\fIboolean\fR\fR [\fB\-nominor\ \fR\fB\fIboolean\fR\fR] \fB\-dcffile\ \fR\fB\fIoutfile\fR\fR
-.HP \w'\fBscopparse\fR\ 'u
-\fBscopparse\fR \fB\-help\fR
-.SH "DESCRIPTION"
-.PP
-\fBscopparse\fR
-is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
-.SH "OPTIONS"
-.SS "Input section"
-.PP
-\fB\-classfile\fR \fIinfile\fR
-.RS 4
-This option specifies the name of raw SCOP classification file dir\&.cla\&.scop\&.txt_X\&.XX (input)\&. This is the raw SCOP classification file available at http://scop\&.mrc\-lmb\&.cam\&.ac\&.uk/scop/parse/dir\&.cla\&.scop\&.txt_1\&.57\&.
-.RE
-.PP
-\fB\-desinfile\fR \fIinfile\fR
-.RS 4
-This option specifies the name of raw SCOP description file dir\&.des\&.scop\&.txt_X\&.XX (input)\&. This is the raw SCOP description file available at http://scop\&.mrc\-lmb\&.cam\&.ac\&.uk/scop/parse/dir\&.des\&.scop\&.txt_1\&.57\&.
-.RE
-.SS "Required section"
-.PP
-\fB\-nosegments\fR \fIboolean\fR
-.RS 4
-This option specifies whether to omit domains comprising of more than one segment\&. This is necessary if a continuous residue sequence is required\&. Default value: N
-.RE
-.PP
-\fB\-nomultichain\fR \fIboolean\fR
-.RS 4
-This option specifies whether to omit domains comprising segments from more than one chain\&. This is necessary if a continuous residue sequence is required\&. Default value: N
-.RE
-.SS "Additional section"
-.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
-.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
-.RE
-.SH "BUGS"
-.PP
-Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
-.SH "SEE ALSO"
-.PP
-scopparse is fully documented via the
-\fBtfm\fR(1)
-system\&.
-.SH "AUTHOR"
-.PP
-\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
-.SH "COPYRIGHT"
-.br
-.PP
-This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
-.sp
Copied: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/scopparse.1e (from rev 4939, trunk/packages/embassy-domainatrix/trunk/debian/manpages/scopparse.1e)
===================================================================
--- trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/scopparse.1e (rev 0)
+++ trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/scopparse.1e 2010-06-26 08:52:38 UTC (rev 4940)
@@ -0,0 +1,94 @@
+'\" t
+.\" Title: SCOPPARSE
+.\" 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+20100115
+.\" Language: English
+.\"
+.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
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+scopparse \- Generate DCF file from raw SCOP files\&.
+.SH "SYNOPSIS"
+.HP \w'\fBscopparse\fR\ 'u
+\fBscopparse\fR \fB\-classfile\ \fR\fB\fIinfile\fR\fR \fB\-desinfile\ \fR\fB\fIinfile\fR\fR \fB\-nosegments\ \fR\fB\fIboolean\fR\fR \fB\-nomultichain\ \fR\fB\fIboolean\fR\fR [\fB\-nominor\ \fR\fB\fIboolean\fR\fR] \fB\-dcffile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBscopparse\fR\ 'u
+\fBscopparse\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBscopparse\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-classfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of raw SCOP classification file dir\&.cla\&.scop\&.txt_X\&.XX (input)\&. This is the raw SCOP classification file available at http://scop\&.mrc\-lmb\&.cam\&.ac\&.uk/scop/parse/dir\&.cla\&.scop\&.txt_1\&.57\&.
+.RE
+.PP
+\fB\-desinfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of raw SCOP description file dir\&.des\&.scop\&.txt_X\&.XX (input)\&. This is the raw SCOP description file available at http://scop\&.mrc\-lmb\&.cam\&.ac\&.uk/scop/parse/dir\&.des\&.scop\&.txt_1\&.57\&.
+.RE
+.SS "Required section"
+.PP
+\fB\-nosegments\fR \fIboolean\fR
+.RS 4
+This option specifies whether to omit domains comprising of more than one segment\&. This is necessary if a continuous residue sequence is required\&. Default value: N
+.RE
+.PP
+\fB\-nomultichain\fR \fIboolean\fR
+.RS 4
+This option specifies whether to omit domains comprising segments from more than one chain\&. This is necessary if a continuous residue sequence is required\&. Default value: N
+.RE
+.SS "Additional section"
+.PP
+\fB\-nominor\fR \fIboolean\fR
+.RS 4
+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 \*(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
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+scopparse is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\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
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
Deleted: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/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/tags/0.1.0+20100115-1/debian/manpages/ssematch.1e 2010-06-26 08:52:38 UTC (rev 4940)
@@ -1,110 +0,0 @@
-'\" 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
-.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20090715
-.\" Language: English
-.\"
-.TH "SSEMATCH" "1e" "08/03/2009" "EMBOSS 0.1.0+20090715" "EMBOSS Manual for Debian"
-.\" -----------------------------------------------------------------
-.\" * set default formatting
-.\" -----------------------------------------------------------------
-.\" disable hyphenation
-.nh
-.\" disable justification (adjust text to left margin only)
-.ad l
-.\" -----------------------------------------------------------------
-.\" * MAIN CONTENT STARTS HERE *
-.\" -----------------------------------------------------------------
-.SH "NAME"
-ssematch \- Search a DCF file for secondary structure matches\&.
-.SH "SYNOPSIS"
-.HP \w'\fBssematch\fR\ 'u
-\fBssematch\fR \fB\-ssinfile\ \fR\fB\fIinfile\fR\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-maxhits\ \fR\fB\fIinteger\fR\fR [\fB\-rgapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-rgapextend\ \fR\fB\fIfloat\fR\fR] [\fB\-egapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-egapextend\ \fR\fB\fIfloat\fR\fR] \fB\-outssfile\ \fR\fB\fIoutfile\fR\fR \fB\-outsefile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
-.HP \w'\fBssematch\fR\ 'u
-\fBssematch\fR \fB\-help\fR
-.SH "DESCRIPTION"
-.PP
-\fBssematch\fR
-is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
-.SH "OPTIONS"
-.SS "Input section"
-.PP
-\fB\-ssinfile\fR \fIinfile\fR
-.RS 4
-This option specifies the name of the file of secondary structure (input)\&.
-.RE
-.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\&.
-.RE
-.PP
-\fB\-datafile\fR \fImatrixf\fR
-.RS 4
-This option specifies the secondary structure substitution matrix\&. Default value: SSSUB
-.RE
-.SS "Required section"
-.PP
-\fB\-maxhits\fR \fIinteger\fR
-.RS 4
-This option specifies the number of top\-scoring matches to report\&. Default value: 5
-.RE
-.SS "Additional section"
-.PP
-\fB\-rgapopen\fR \fIfloat\fR
-.RS 4
-This options specifies the gap insertion penalty for reside\-based alignment\&. The gap insertion penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10
-.RE
-.PP
-\fB\-rgapextend\fR \fIfloat\fR
-.RS 4
-This options specifies the gap extension penalty for residue\-based alignment\&. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. Default value: 0\&.5
-.RE
-.PP
-\fB\-egapopen\fR \fIfloat\fR
-.RS 4
-This options specifies the gap insertion penalty for element\-based alignment\&. The gap insertion penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10
-.RE
-.PP
-\fB\-egapextend\fR \fIfloat\fR
-.RS 4
-This options specifies the gap extension penalty for secondary structure element\-based alignment\&. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. Default value: 0\&.5
-.RE
-.SS "Output section"
-.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)\&.
-.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)\&.
-.RE
-.PP
-\fB\-logfile\fR \fIoutfile\fR
-.RS 4
-This option specifies the name of the ssematch log file (output)\&. Default value: ssematch\&.log
-.RE
-.SH "BUGS"
-.PP
-Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
-.SH "SEE ALSO"
-.PP
-ssematch is fully documented via the
-\fBtfm\fR(1)
-system\&.
-.SH "AUTHOR"
-.PP
-\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
-.SH "COPYRIGHT"
-.br
-.PP
-This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
-.sp
Copied: trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/ssematch.1e (from rev 4939, trunk/packages/embassy-domainatrix/trunk/debian/manpages/ssematch.1e)
===================================================================
--- trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/ssematch.1e (rev 0)
+++ trunk/packages/embassy-domainatrix/tags/0.1.0+20100115-1/debian/manpages/ssematch.1e 2010-06-26 08:52:38 UTC (rev 4940)
@@ -0,0 +1,119 @@
+'\" t
+.\" Title: SSEMATCH
+.\" 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+20100115
+.\" Language: English
+.\"
+.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
+.nh
+.\" disable justification (adjust text to left margin only)
+.ad l
+.\" -----------------------------------------------------------------
+.\" * MAIN CONTENT STARTS HERE *
+.\" -----------------------------------------------------------------
+.SH "NAME"
+ssematch \- Search a DCF file for secondary structure matches\&.
+.SH "SYNOPSIS"
+.HP \w'\fBssematch\fR\ 'u
+\fBssematch\fR \fB\-ssinfile\ \fR\fB\fIinfile\fR\fR \fB\-dcfinfile\ \fR\fB\fIinfile\fR\fR [\fB\-datafile\ \fR\fB\fImatrixf\fR\fR] \fB\-maxhits\ \fR\fB\fIinteger\fR\fR [\fB\-rgapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-rgapextend\ \fR\fB\fIfloat\fR\fR] [\fB\-egapopen\ \fR\fB\fIfloat\fR\fR] [\fB\-egapextend\ \fR\fB\fIfloat\fR\fR] \fB\-outssfile\ \fR\fB\fIoutfile\fR\fR \fB\-outsefile\ \fR\fB\fIoutfile\fR\fR \fB\-logfile\ \fR\fB\fIoutfile\fR\fR
+.HP \w'\fBssematch\fR\ 'u
+\fBssematch\fR \fB\-help\fR
+.SH "DESCRIPTION"
+.PP
+\fBssematch\fR
+is a command line program from EMBOSS (\(lqthe European Molecular Biology Open Software Suite\(rq)\&. It is part of the "Utils:Database creation" command group(s)\&.
+.SH "OPTIONS"
+.SS "Input section"
+.PP
+\fB\-ssinfile\fR \fIinfile\fR
+.RS 4
+This option specifies the name of the file of secondary structure (input)\&.
+.RE
+.PP
+\fB\-dcfinfile\fR \fIinfile\fR
+.RS 4
+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
+.RS 4
+This option specifies the secondary structure substitution matrix\&. Default value: SSSUB
+.RE
+.SS "Required section"
+.PP
+\fB\-maxhits\fR \fIinteger\fR
+.RS 4
+This option specifies the number of top\-scoring matches to report\&. Default value: 5
+.RE
+.SS "Additional section"
+.PP
+\fB\-rgapopen\fR \fIfloat\fR
+.RS 4
+This options specifies the gap insertion penalty for reside\-based alignment\&. The gap insertion penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10
+.RE
+.PP
+\fB\-rgapextend\fR \fIfloat\fR
+.RS 4
+This options specifies the gap extension penalty for residue\-based alignment\&. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. Default value: 0\&.5
+.RE
+.PP
+\fB\-egapopen\fR \fIfloat\fR
+.RS 4
+This options specifies the gap insertion penalty for element\-based alignment\&. The gap insertion penalty is the score taken away when a gap is created\&. The best value depends on the choice of comparison matrix\&. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAFULL matrix for nucleotide sequences\&. Default value: 10
+.RE
+.PP
+\fB\-egapextend\fR \fIfloat\fR
+.RS 4
+This options specifies the gap extension penalty for secondary structure element\-based alignment\&. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap\&. This is how long gaps are penalized\&. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty\&. Default value: 0\&.5
+.RE
+.SS "Output section"
+.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 \*(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 \*(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
+.RS 4
+This option specifies the name of the ssematch log file (output)\&. Default value: ssematch\&.log
+.RE
+.SH "BUGS"
+.PP
+Bugs can be reported to the Debian Bug Tracking system (http://bugs\&.debian\&.org/emboss), or directly to the EMBOSS developers (http://sourceforge\&.net/tracker/?group_id=93650&atid=605031)\&.
+.SH "SEE ALSO"
+.PP
+ssematch is fully documented via the
+\fBtfm\fR(1)
+system\&.
+.SH "AUTHOR"
+.PP
+\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
+.SH "COPYRIGHT"
+.br
+.PP
+This manual page was autogenerated from an Ajax Control Definition of the EMBOSS package\&. It can be redistributed under the same terms as EMBOSS itself\&.
+.sp
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