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