[med-svn] r4943 - in trunk/packages/embassy-domsearch/trunk/debian: . manpages
Charles Plessy
plessy at alioth.debian.org
Sat Jun 26 14:22:54 UTC 2010
Author: plessy
Date: 2010-06-26 14:22:52 +0000 (Sat, 26 Jun 2010)
New Revision: 4943
Modified:
trunk/packages/embassy-domsearch/trunk/debian/changelog
trunk/packages/embassy-domsearch/trunk/debian/control
trunk/packages/embassy-domsearch/trunk/debian/embassy-domsearch.manpages
trunk/packages/embassy-domsearch/trunk/debian/manpages/seqfraggle.1e
trunk/packages/embassy-domsearch/trunk/debian/manpages/seqnr.1e
trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsearch.1e
trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsort.1e
trunk/packages/embassy-domsearch/trunk/debian/manpages/seqwords.1e
Log:
New upstream release (last January).
Modified: trunk/packages/embassy-domsearch/trunk/debian/changelog
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/changelog 2010-06-26 09:56:01 UTC (rev 4942)
+++ trunk/packages/embassy-domsearch/trunk/debian/changelog 2010-06-26 14:22:52 UTC (rev 4943)
@@ -1,3 +1,15 @@
+embassy-domsearch (0.1.0++20100115-1) unstable; urgency=low
+
+ * New upstream release in which the version number was unchanged.
+ (I chose a strange version number to avoid an epoch because of
+ the typo in the previous number).
+ * debian/control:
+ - Build against EMBOSS 6.2 (Closes: #587119).
+ - Checked conformance with Policy 3.8.4 (no changes needed).
+ * debian/*manpages* refreshed.
+
+ -- Charles Plessy <plessy at debian.org> Sat, 26 Jun 2010 22:58:36 +0900
+
embassy-domsearch (0.1.0+20980715-1) unstable; urgency=low
* Initial release (Closes: #537204).
Modified: trunk/packages/embassy-domsearch/trunk/debian/control
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/control 2010-06-26 09:56:01 UTC (rev 4942)
+++ trunk/packages/embassy-domsearch/trunk/debian/control 2010-06-26 14:22:52 UTC (rev 4943)
@@ -1,13 +1,13 @@
Source: embassy-domsearch
Section: science
Priority: optional
-Build-Depends: cdbs, debhelper (>= 7), libajax6-dev, libnucleus6-dev, emboss-lib, libx11-dev, libgd2-xpm-dev
+Build-Depends: cdbs, debhelper (>= 7), libajax6-dev (>= 6.2), libnucleus6-dev (>= 6.2), emboss-lib (>= 6.2), 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-domsearch/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/embassy-domsearch/trunk/
-Standards-Version: 3.8.2
+Standards-Version: 3.8.4
Homepage: http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMSEARCH
Package: embassy-domsearch
Modified: trunk/packages/embassy-domsearch/trunk/debian/embassy-domsearch.manpages
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/embassy-domsearch.manpages 2010-06-26 09:56:01 UTC (rev 4942)
+++ trunk/packages/embassy-domsearch/trunk/debian/embassy-domsearch.manpages 2010-06-26 14:22:52 UTC (rev 4943)
@@ -1,5 +1,5 @@
+debian/manpages/seqsort.1e
+debian/manpages/seqsearch.1e
+debian/manpages/seqwords.1e
debian/manpages/seqfraggle.1e
debian/manpages/seqnr.1e
-debian/manpages/seqsearch.1e
-debian/manpages/seqsort.1e
-debian/manpages/seqwords.1e
Modified: trunk/packages/embassy-domsearch/trunk/debian/manpages/seqfraggle.1e
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqfraggle.1e 2010-06-26 09:56:01 UTC (rev 4942)
+++ trunk/packages/embassy-domsearch/trunk/debian/manpages/seqfraggle.1e 2010-06-26 14:22:52 UTC (rev 4943)
@@ -1,14 +1,23 @@
'\" t
.\" Title: SEQFRAGGLE
-.\" 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: 07/16/2009
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 06/26/2010
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20980715
+.\" Source: EMBOSS 0.1.0++20100115
.\" Language: English
.\"
-.TH "SEQFRAGGLE" "1e" "07/16/2009" "EMBOSS 0.1.0+20980715" "EMBOSS Manual for Debian"
+.TH "SEQFRAGGLE" "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\-dhfinpath\fR \fIdirlist\fR
.RS 4
-This option specifies the location of DHF files (domain hits files) or other sequence files (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\&. Alternatively, SEQFRAGGLE will accept sequence or sequence sets in any of the common formats\&. Default value: \&./
+This option specifies the location of DHF files (domain hits files) or other sequence files (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\&. Alternatively, SEQFRAGGLE will accept sequence or sequence sets in any of the common formats\&. Default value: \&./
.RE
.SS "Required section"
.PP
@@ -46,7 +55,7 @@
.PP
\fB\-dhfoutdir\fR \fIoutdir\fR
.RS 4
-This option specifies the location of DHF files (domain hits files) (output)\&. 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\&. Alternatively, SEQFRAGGLE will write output files in any of the common formats\&. Default value: \&./
+This option specifies the location of DHF files (domain hits files) (output)\&. 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\&. Alternatively, SEQFRAGGLE will write output files in any of the common formats\&. Default value: \&./
.RE
.SH "BUGS"
.PP
@@ -58,7 +67,7 @@
system\&.
.SH "AUTHOR"
.PP
-\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
Modified: trunk/packages/embassy-domsearch/trunk/debian/manpages/seqnr.1e
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqnr.1e 2010-06-26 09:56:01 UTC (rev 4942)
+++ trunk/packages/embassy-domsearch/trunk/debian/manpages/seqnr.1e 2010-06-26 14:22:52 UTC (rev 4943)
@@ -1,14 +1,23 @@
'\" t
.\" Title: SEQNR
-.\" 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: 07/16/2009
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 06/26/2010
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20980715
+.\" Source: EMBOSS 0.1.0++20100115
.\" Language: English
.\"
-.TH "SEQNR" "1e" "07/16/2009" "EMBOSS 0.1.0+20980715" "EMBOSS Manual for Debian"
+.TH "SEQNR" "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\-dhfinpath\fR \fIdirlist\fR
.RS 4
-This option specifies the location of DHF files (domain hits files) (input)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
+This option specifies the location of DHF files (domain hits files) (input)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
.RE
.PP
\fB\-dosing\fR \fItoggle\fR
@@ -44,7 +53,7 @@
.PP
\fB\-singletsdir\fR \fIdirectory\fR
.RS 4
-This option specifies the location of singlet filter sequences (e\&.g\&. DHF files) (input)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
+This option specifies the location of singlet filter sequences (e\&.g\&. DHF files) (input)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
.RE
.PP
\fB\-dosets\fR \fItoggle\fR
@@ -54,7 +63,7 @@
.PP
\fB\-insetsdir\fR \fIdirectory\fR
.RS 4
-This option specifies location of sets of filter sequences (e\&.g\&. DAF files) (input)\&. A \'domain alignment file\' contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The file is in clustal format annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./
+This option specifies location of sets of filter sequences (e\&.g\&. DAF files) (input)\&. A \*(Aqdomain alignment file\*(Aq contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The file is in clustal format annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./
.RE
.PP
\fB\-matrix\fR \fImatrixf\fR
@@ -97,7 +106,7 @@
.PP
\fB\-dhfoutdir\fR \fIoutdir\fR
.RS 4
-This option specifies the location of DHF files (domain hits files) of non\-redundant sequences (output)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
+This option specifies the location of DHF files (domain hits files) of non\-redundant sequences (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
.RE
.PP
\fB\-dored\fR \fItoggle\fR
@@ -107,7 +116,7 @@
.PP
\fB\-redoutdir\fR \fIoutdir\fR
.RS 4
-This option specifies the location of DHF files (domain hits files) of redundant sequences (output)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
+This option specifies the location of DHF files (domain hits files) of redundant sequences (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
.RE
.PP
\fB\-logfile\fR \fIoutfile\fR
@@ -124,7 +133,7 @@
system\&.
.SH "AUTHOR"
.PP
-\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
Modified: trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsearch.1e
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsearch.1e 2010-06-26 09:56:01 UTC (rev 4942)
+++ trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsearch.1e 2010-06-26 14:22:52 UTC (rev 4943)
@@ -1,14 +1,23 @@
'\" t
.\" Title: SEQSEARCH
-.\" 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: 07/16/2009
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 06/26/2010
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20980715
+.\" Source: EMBOSS 0.1.0++20100115
.\" Language: English
.\"
-.TH "SEQSEARCH" "1e" "07/16/2009" "EMBOSS 0.1.0+20980715" "EMBOSS Manual for Debian"
+.TH "SEQSEARCH" "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\-inseqspath\fR \fIdirlist\fR
.RS 4
-This option specifies the location of sequences, e\&.g\&. DAF files (domain alignment files) (input)\&. SEQSEARCH takes as input a database of either i\&. single sequences, ii\&. sets of unaligned sequences or iii\&. sets of aligned sequences, e\&.g\&. a domain alignment file\&. A \'domain alignment file\' contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The file is in clustal format annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./
+This option specifies the location of sequences, e\&.g\&. DAF files (domain alignment files) (input)\&. SEQSEARCH takes as input a database of either i\&. single sequences, ii\&. sets of unaligned sequences or iii\&. sets of aligned sequences, e\&.g\&. a domain alignment file\&. A \*(Aqdomain alignment file\*(Aq contains a sequence alignment of domains belonging to the same SCOP or CATH family\&. The file is in clustal format annotated with domain family classification information\&. The files generated by using SCOPALIGN will contain a structure\-based sequence alignment of domains of known structure only\&. Such alignments can be extended with sequence relatives (of unknown structure) by using SEQALIGN\&. Default value: \&./
.RE
.PP
\fB\-database\fR \fIstring\fR
@@ -66,7 +75,7 @@
.PP
\fB\-dhfoutdir\fR \fIoutdir\fR
.RS 4
-This option specifies the location of DHF files (domain hits files) (output)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in FASTA format\&. 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\&. Default value: \&./
+This option specifies the location of DHF files (domain hits files) (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in FASTA format\&. 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\&. Default value: \&./
.RE
.PP
\fB\-logfile\fR \fIoutfile\fR
@@ -83,7 +92,7 @@
system\&.
.SH "AUTHOR"
.PP
-\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
Modified: trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsort.1e
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsort.1e 2010-06-26 09:56:01 UTC (rev 4942)
+++ trunk/packages/embassy-domsearch/trunk/debian/manpages/seqsort.1e 2010-06-26 14:22:52 UTC (rev 4943)
@@ -1,14 +1,23 @@
'\" t
.\" Title: SEQSORT
-.\" 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: 07/16/2009
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 06/26/2010
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20980715
+.\" Source: EMBOSS 0.1.0++20100115
.\" Language: English
.\"
-.TH "SEQSORT" "1e" "07/16/2009" "EMBOSS 0.1.0+20980715" "EMBOSS Manual for Debian"
+.TH "SEQSORT" "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\-dhfindir\fR \fIdirectory\fR
.RS 4
-This option specifies the location of DHF files (domain hits files) (input)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
+This option specifies the location of DHF files (domain hits files) (input)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
.RE
.SS "Required section"
.PP
@@ -56,17 +65,17 @@
.PP
\fB\-dhfoutdir\fR \fIoutdir\fR
.RS 4
-This option specifies the location of DHF files (domain hits files) (output)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
+This option specifies the location of DHF files (domain hits files) (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA or EMBL\-like)\&. 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\&. Default value: \&./
.RE
.PP
\fB\-hitsfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of domain families file (output)\&. A \'domain families file\' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e\&.g\&. by using SEQSEARCH (psiblast)\&. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included\&. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a \'domain ambiguities file\'\&. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file)\&. Default value: fam\&.dhf
+This option specifies the name of domain families file (output)\&. A \*(Aqdomain families file\*(Aq contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e\&.g\&. by using SEQSEARCH (psiblast)\&. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included\&. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a \*(Aqdomain ambiguities file\*(Aq\&. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file)\&. Default value: fam\&.dhf
.RE
.PP
\fB\-ambigfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of domain ambiguities file (output)\&. A \'domain families file\' contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e\&.g\&. by using SEQSEARCH (psiblast)\&. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included\&. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a \'domain ambiguities file\'\&. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file)\&. Default value: oth\&.dhf
+This option specifies the name of domain ambiguities file (output)\&. A \*(Aqdomain families file\*(Aq contains sequence relatives (hits) for each of a number of different SCOP or CATH families found from searching a sequence database, e\&.g\&. by using SEQSEARCH (psiblast)\&. The file contains the collated search results for the indvidual families; only those hits of unambiguous family assignment are included\&. Hits of ambiguous family assignment are assigned as relatives to a SCOP or CATH superfamily or fold instead and are collated into a \*(Aqdomain ambiguities file\*(Aq\&. The domain families and ambiguities files are generated by using SEQSORT and use the same format as a DHF file (domain hits file)\&. Default value: oth\&.dhf
.RE
.SH "BUGS"
.PP
@@ -78,7 +87,7 @@
system\&.
.SH "AUTHOR"
.PP
-\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
Modified: trunk/packages/embassy-domsearch/trunk/debian/manpages/seqwords.1e
===================================================================
--- trunk/packages/embassy-domsearch/trunk/debian/manpages/seqwords.1e 2010-06-26 09:56:01 UTC (rev 4942)
+++ trunk/packages/embassy-domsearch/trunk/debian/manpages/seqwords.1e 2010-06-26 14:22:52 UTC (rev 4943)
@@ -1,14 +1,23 @@
'\" t
.\" Title: SEQWORDS
-.\" 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: 07/16/2009
+.\" Author: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+.\" Generator: DocBook XSL Stylesheets v1.75.2 <http://docbook.sf.net/>
+.\" Date: 06/26/2010
.\" Manual: EMBOSS Manual for Debian
-.\" Source: EMBOSS 0.1.0+20980715
+.\" Source: EMBOSS 0.1.0++20100115
.\" Language: English
.\"
-.TH "SEQWORDS" "1e" "07/16/2009" "EMBOSS 0.1.0+20980715" "EMBOSS Manual for Debian"
+.TH "SEQWORDS" "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
@@ -45,7 +54,7 @@
.PP
\fB\-outfile\fR \fIoutfile\fR
.RS 4
-This option specifies the name of the DHF file (domain hits file) (output)\&. A \'domain hits file\' contains database hits (sequences) with domain classification information, in the DHF format (FASTA\-like)\&. The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH, hits retrieved by a sparse protein signatare by using SIGSCAN or various types of HMM and profile by using LIBSCAN\&. Default value: test\&.hits
+This option specifies the name of the DHF file (domain hits file) (output)\&. A \*(Aqdomain hits file\*(Aq contains database hits (sequences) with domain classification information, in the DHF format (FASTA\-like)\&. The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a sequence database\&. Files containing hits retrieved by PSIBLAST are generated by using SEQSEARCH, hits retrieved by a sparse protein signatare by using SIGSCAN or various types of HMM and profile by using LIBSCAN\&. Default value: test\&.hits
.RE
.SH "BUGS"
.PP
@@ -57,7 +66,7 @@
system\&.
.SH "AUTHOR"
.PP
-\fBDebian\-Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
+\fBDebian Med Packaging Team\fR <\&debian\-med\-packaging at lists\&.alioth\&.debian\&.org\&>
.RS 4
Wrote the script used to autogenerate this manual page\&.
.RE
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