[med-svn] r146 - in trunk/packages/boxshade/trunk: . debian
Charles Plessy
charles-guest at costa.debian.org
Sat Oct 7 01:03:29 UTC 2006
Author: charles-guest
Date: 2006-10-07 01:03:29 +0000 (Sat, 07 Oct 2006)
New Revision: 146
Added:
trunk/packages/boxshade/trunk/boxshade.1
trunk/packages/boxshade/trunk/boxshade.sh
trunk/packages/boxshade/trunk/debian/
trunk/packages/boxshade/trunk/debian/README.Debian
trunk/packages/boxshade/trunk/debian/boxshade.xml
trunk/packages/boxshade/trunk/debian/changelog
trunk/packages/boxshade/trunk/debian/compat
trunk/packages/boxshade/trunk/debian/control
trunk/packages/boxshade/trunk/debian/copyright
trunk/packages/boxshade/trunk/debian/dirs
trunk/packages/boxshade/trunk/debian/manpages
trunk/packages/boxshade/trunk/debian/menu
trunk/packages/boxshade/trunk/debian/rules
Modified:
trunk/packages/boxshade/trunk/makefile.unx
Log:
Load boxshade-3.1.1 into trunk/packages/boxshade/trunk.
Added: trunk/packages/boxshade/trunk/boxshade.1
===================================================================
--- trunk/packages/boxshade/trunk/boxshade.1 (rev 0)
+++ trunk/packages/boxshade/trunk/boxshade.1 2006-10-07 01:03:29 UTC (rev 146)
@@ -0,0 +1,119 @@
+.\"Generated by db2man.xsl. Don't modify this, modify the source.
+.de Sh \" Subsection
+.br
+.if t .Sp
+.ne 5
+.PP
+\fB\\$1\fR
+.PP
+..
+.de Sp \" Vertical space (when we can't use .PP)
+.if t .sp .5v
+.if n .sp
+..
+.de Ip \" List item
+.br
+.ie \\n(.$>=3 .ne \\$3
+.el .ne 3
+.IP "\\$1" \\$2
+..
+.TH "BOXSHADE" 1 "February 26, 2004" "" ""
+.SH NAME
+boxshade \- Pretty-printing of multiple sequence alignments
+.SH "SYNOPSIS"
+.ad l
+.hy 0
+.HP 9
+\fBboxshade\fR
+.ad
+.hy
+
+.SH "DESCRIPTION"
+
+.PP
+\fBBOXSHADE\fR is a program for pretty\-printing multiple alignment output\&. The program itself doesn't do any alignment, you have to use a multiple alignment program like ClustalW or Pileup and use the output of these programs as input for BOXSHADE\&.
+
+.PP
+This manual page was written for the Debian™ distribution because the original program does not have a manual page\&. The presented information comes from the documentation of the Web Service of the 3\&.21 version that is not available as a Debian package\&.
+
+.PP
+BOXSHADE is a program for creating good looking printouts from multiple\-aligned protein or DNA sequences\&. The program does no alignment by itself, it has to take as input a file preprocessed by a multiple alignment program or a multiple file editor\&. See below for a list of supported input formats and output devices\&. In the standard BOXSHADE output, identical and similar residues in the multiple\-alignment chart are represented by different colors or shadings\&. There are some more options concerning the kind of shading to be applied, sequence numbering, consensus output and so on\&. The user interface is a bit clumsy at the moment, one has to answer a lot of questions in order to get the desired output\&. There is, however, the possibility to use default parameters from a standard parameter file or to supply the program with parameters from the command line\&. At the moment, the VMS and DOS versions of BOXSHADE have identical user interfaces\&.
+
+.PP
+\- Input formats \-
+
+.PP
+BOXSHADE 3\&.2 knows about the following input file formats: (some of the are generally used only for MSDOS or VMS systems) + CLUSTAL and CLUSTALV, multiple alignment program, DOS/VMS/MAC default extension \&.ALN + ESEE, multiple sequence editor, DOS default extension \&.ESE + PHYLIP, phylogenetic analysis package, DOS, VMS, UNIX default extension \&.PHY + PILEUP and PRETTY of the GCG sequence analysis package VMS/UNIX default extensions \&.MSF and \&.PRE NB!! you are strongly encouraged NOT to use the PRETTY format as input, it may be incompatible with the revised version of \&.MSF input\&. We can't actually think why anyone would use this format now, \&.MSF files are more useful generally\&. + MALIGNED, multiple sequence editor, VMS only default extension \&.MAL BOXSHADE tries to determine the file type from the extension but will work also if different extensions are used\&.
+
+.PP
+\- Output devices \-
+
+.PP
+POSTSCRIPT/EPS creates POSTSCRIPT(TM) files for printing on a Laserprinter or for further conversion with a POSTCRIPT interpreter (like GHOSTSCRIPT) + HPGL for export to various graphics programs or for conversion/printing with the shareware program PRINTGL\&. Plotting BOXSHADE output on a plotter is generally not recommended + RTF for export to various word\-processing and graphics programs + CRT, uses direct screen writes to the PC\-monitor\&. Possible options depend on the graphics adapter used\&. This output device is supported only in the MSDOS version\&. + ANSI\&. On a PC, this option uses an ANSI device driver (ANSI\&.SYS) that has to be loaded in CONFIG\&.SYS previously\&. Possible character renditions are reverse, bold,underlined, blinking etc\&. On non\-DOS systems, this option behaves more or less like the VT100 output mode\&. + VT100 for display on a VT100 compatible terminal or emulator\&. + ReGISterm for display on a ReGIS compatible graphics terminal or emulator\&. + ReGISfile for later conversion by the program RETOS (copyright DEC) in order to print on DIGITALs printer series\&. + LJ250 for printing on DIGITALS LJ250 color printer\&. + ASCII output showing either the conserved residues or the varying ones (others as '\-')\&. + FIG file for xfig 2\&.1\&. + PICT files for import to Mac and PC graphics progs\&. Some of the formats above offer the possibility of scaling the characters and of rotating the plot\&. Character size has to be entered in 'point' units\&. Normal output orientation is in portrait mode (PS/EPS/HPGL/PICT only), to obtain output in landscape orientation, 'rotate plot = y' has to be chosen\&. When creating multi\-page output, all pages are contained in a single output file\&. If one page per file is desired, one has to use the command line parameter /SPLIT\&. This is enforced when requesting EPSF or PICT file output, as multi\-page EPSFs are a contradiction of the purpose of an EPSF and large PICT files would probably be too big for most personal computers\&. While using the terminal as output device, the 'RETURN' key has to be pressed to obtain the next page of output\&.
+
+.PP
+\- Sequence numbering \-
+
+.PP
+Starting with version 2\&.2 there is the possibility to add numbering to the output files\&. The numbers are printed between the sequence names and the sequence itself\&. Since most of the input\-files either use no numbering or number the first position in the alignment always with a "1" (and that does not necessarily reflect the numbers within the original sequence), the user is asked to enter the starting position for each sequence\&. The command line flag /DEFNUM suppressed that question, a starting position of 1 is assumed for all sequences\&. Boxshade starts with the value entered for the leftmost position and continues numbering every valid symbol, skipping blanks, '\-','\&.' and stuff like that\&.
+
+.PP
+\- Default parameters \-
+
+.PP
+Several people using previous releases of BOXSHADE pointed me to the need of having default parameters for the various questions asked by the program\&. They argued that most sites only use one type of input files, one output device and one choice of colors for the output\&. I therefore added a management of default parameters allowing two levels of assistance to the user\&. 1) all default parameters are contained in an ASCII file that can be modified easily to accomodate the users taste\&. The format is roughly documented within the file\-header, it resembles the keyboard input one has to make if using the program interactively\&. There are two such files supplied with this release of BOXSHADE, BOX_DNA\&.PAR and BOX_PEP\&.PAR , holding some example parameters for peptide and dna\-comparisons\&. there are no big differences between these two, the major one is that when shading DNA\-comparisons one doesn't care of "similar" residues\&. 2) to run the program with minimal user interaction, I have added the possibility to use command line parameters\&. At the moment, you can use: /check : list all allowed command line paramters (this list) and allows parameters to be added\&. /def : program runs without questions, BOX_PEP\&.PAR is used as default /dna : makes the program use BOX_DNA\&.PAR as parameter file /pep : makes the program use BOX_PEP\&.PAR as parameter file /in=xxx : makes the program take xxx as input file /out=yyy : makes the program take yyy as output file (note1) /par=zzz : makes the program use zzz as a default parameter file /type=1 : makes the program assume an input file of type 1 (PRETTY/MSF) /dev=1 : makes the program assume and output device of type 1 (CRT) /numdef : use default numbering (all sequences starting with "1") /thr : threshold fraction of residues that must agree for a consensus /split : forces one page per file output, creates multiple output files\&. /cons : makes the program create an additional consensus line (see below) /symbcons=: influences the way the consensus line is displayed\&. (see below) /unix : writes output files in unix style (LF only) (note2) /dos : writes output files in DOS style (CR/LF) (note2) note1: on unix machines, use out=OUTPUT for terminal output on DOS machines, use out=con: on VMS machines, use out=tt: note2: if no mode is specified, the native style of the machine is used\&.
+
+.PP
+ATTENTION
+
+.PP
+on unix systems, the dash (\-) instead of the slash (/) has to be used as separation character for command line paramters\&. For example, a valid unix command line is: \fBboxshade \-def \-numdef \-cons \-symbcons=" \&.*" **************************************************************************\fR
+
+.PP
+\- Shading strategies (similarity to consensus or single sequence) \-
+
+.PP
+Starting with version 3, BOXSHADE has a new shading system\&. The first difference is the introduction of a threshold fraction of residues that must agree for there to be a consensus\&. Previously, the program assumed that SOME residue was always the consensus\&. If no two residues were the same, the first sequence provided the consensus residue\&. This threshold fraction can be any number between 0\&.0 and 1\&.0\&. The number of sequences that must agree for there to be a consensus is, as you might expect, this fraction times the total number of sequences in the alignment (fractions of a sequence count as one, e\&.g\&. 3\&.2 becomes 4)\&. The second difference is the idea of 'consensus by similarity'; this tries to take account of the situations where all the sequences may have (for example) R or K at a position, but neither in a majority\&. It would not be logical to shade one type of residue as 'identical' and the other as 'similar'; the threshold function might also eliminate both as being in too small numbers\&. Therefore, if there is not a single residue that is conserved (greater than the threshold) at a position, the program looks for a 'group' of amino acids that fulfills the requirements\&. 'Groups' are defined in the \&.grp files\&. Users can tailor these to their personal prejudices\&. Any amino acid not listed is assumed not to be in a group\&. All members of a group are considered to be mutually similar, unlike the \&.sim files, described below\&. If consensus by similarity is found, all the residues in the consensus are shaded using the 'similar' shading defined by the user\&. If the user does not select 'shading by similarity', only identity\-type consensus is looked at\&. If an identity\-type consensus is found, and similarity shading is in operation, the program looks to see if the remaining residues are similar to the consensus residue\&. Here the box_xxx\&.sim files are used\&. The main difference between relationships in these files and those in the \&.grp files is that, e\&.g\&. in a \&.grp file the line STA means that all three a\&.a\&.s are mutually similar\&. In a \&.sim file S TA means that both T and A are considered similar to S, where there is a conserved S residue in more than threshold number of sequences\&. However, it does NOT mean that T and A are similar to each other\&. Note that cases where two residues, or groups of residues, fulfill the threshold requirements (as could happen with values of the thr\&. fraction less than or equal to 0\&.5) are treated as having no consensus\&. This describes the main shading model 'shading according to a consensus'\&. The alternative model is called 'shading according to a master sequence'\&. In this case the user is prompted for a sequence of the alignment and consecutively that sequence is taken to be the 'consensus'\&. Only those residues become shaded that are identical or similar to the chosen sequence\&. Output obtained with this option tends to be less shaded and neglects similarities beween the other (non\-chosen) sequences\&. Starting in V2\&.7, this 'master sequence' can be hidden\&. Thus, it only influences the shading of the other sequences without being shown itself\&.
+
+.PP
+\- Consensus display \-
+
+.PP
+Starting with version 2\&.5, BOXSHADE offers the possibility to create an additional line holding a consensus symbol\&. This line can either be obtained by using the command line qualifier /CONS or interactively by answering the question ' create consensus? '\&. The way this consensus line is displayed can be modified by the command line parameter SYMBCONS=xyz, by editing the respecitve entry in the \&.PAR file or interactively\&. Since the SYMBCONS syntax is not intuitive, here a brief description: The SYMBCONS parameter consist of exactly three symbols: + the first one stands for 'normal' sequence residues that are not involved in any similar/identical relationship\&. + the second symbol represents positions that are similar in all sequences of the alignment\&. See the files BOX_PEP\&.SIM and BOX_DNA\&.SIM to see what residues are considered similar\&. + the third symbol represents positions that are identical in all sequences of the alignment\&. A SYMBCONS parameter string " \&.*" (blank/point/asterisc) means: label all positions in the alignment with totally identical residues by an asterisc, all positions with all similar residues by a point and do not mark the other positions\&. The letter 'B' can be used instead of the blank, this is necessary e\&.g\&. when using the command line option /SYMBCONS=B\&.* which gives the same result as the above example\&. The option /SYMBCONS= \&.* would result in an unexpected behaviour because MSDOS squeezes blanks out of the command line\&. Besides points, asteriscs and other symbols, there are two special characters when they appear in the SYMBCONS string: 'L' and 'U'\&. An 'L' means, that a lowercase representation of the most abundant residue at that position is to be used instead of a fixed consensus symbol while an 'U' means an uppercase character representation of that residue\&. A possible application would be the SYMBCONS string " LU" where similar residues are represented by lowercase characters and identical by uppercase characters\&.
+
+.PP
+\- shareware/PD programs useful in conjunction with BOXSHADE \-
+
+.PP
+multiple alignment files that to be used by BOXSHADE can be created, amongst others, by the following PD/freeware programs: + PHYLIP by Joe Felsenstein, available by ftp from anthro\&.utah\&.edu + ESEE by Eric Cabot, available from the same sources as BOXSHADE (see above) + CLUSTAL by Des Higgins, ditto for preview/conversion of POSTSCRIPT files, the program GHOSTSCRIPT from GNU software foundation is highly recommended\&. It is available from all major MSDOS ftp\-sites (e\&.g\&. SIMTEL or ftp\&.uni\-koeln\&.de) There is also a version tested for use with boxshade available at vax0\&.biomed\&.uni\-koeln\&.de although this might be not the most recent release\&. for Mac users, there is MacGhostscript, also available from the main archives (info\-mac, umich and their mirrors)\&. A *very* good tool for putting a preview image into an EPSF file, often a prerequisite for incorporating into a drawing package, is PS2EPS, by Peter Lerup\&. This can be found on info\-mac\&. for preview/conversion of HPGL files, the shareware program PRINTGL 1\&.18 by Cary Ravitz is highly recommended\&. It is available from many MSDOS ftp sites and from netserv at embl\-heidelberg\&.de \- output on dot printers \- Since PRINTGL offers a broad choice of printer types and is a nice program, I recommend its use for printing BOXSHADE output on non\-POSTSCRIPT printers\&. Use HPGL output with options 0F1N for normal residues 2F1N for identical residues 3F1N for similar residues 2F4N for conserved residues 8 for character size not rotated (these are the standard parameters in BOX_PEP\&.PAR) for creating a HPGL files\&. (lets call it TEST\&.PLT) Now use PRINTGL either interactively by calling PMI or use a command line like: PRINTGL /Fx/S0340/Waaac/Ptest\&.plt where test\&.plt is to be replaced by the filename to convert and the x in the expression /Fx is to be replaced by the letter of the printer you use\&. (See the PRINTGL documentation for further details)
+
+.SH "
+RESTRICTIONS
+"
+
+.PP
+The RTF output and PHYLIP input implementations are still experimental\&. Please tell me of your experiences with the program\&. + the current DOS version supports only 13 sequences with 2000 residues each\&. This parameters can be easily changed in the source code\&. If you cannot compile the sources because you are lacking a pascal compiler, contact the author for precompiled versions
+
+.SH "DISTRIBUTION POLICY"
+
+.PP
+BOXSHADE is completely public\-domain and may be passed around and modified without any notice to the author\&. If you have problems, suggestions or remarks, please contact either of us: Kay Hofmann, PhD Tel: +49 (221) 950 4814 Bioinformatics Group FAX: +49 (221) 950 4848 MEMOREC Stoffel GmbH Stoeckheimer Weg 1 D50829 Koeln/Germany E\-mail: Kay\&.Hofmann at memorec\&.com Michael D\&. Baron Institute for Animal Health Ash Road Pirbright Surrey GU24 0NF U\&.K\&. E\-mail: michael\&.baron at bbsrc\&.ac\&.uk
+
+.SH "SEE ALSO"
+
+.PP
+/etc/boxshade/*\&.par
+
+.PP
+seaview (1), clustalw (1)
+
+.SH "AUTHOR"
+
+.PP
+This manual page was written by Steffen Moeller <moeller at pzr\&.uni\-rostock\&.de> for the Debian™ system (but may be used by others)\&. Permission is granted to copy, distribute and/or modify this document under the terms of the GNU General Public License, Version 2 any later version published by the Free Software Foundation\&.
+
+.PP
+On Debian systems, the complete text of the GNU General Public License can be found in /usr/share/common\-licenses/GPL\&.
+
+.SH AUTHOR
+Steffen Möller.
Added: trunk/packages/boxshade/trunk/boxshade.sh
===================================================================
--- trunk/packages/boxshade/trunk/boxshade.sh (rev 0)
+++ trunk/packages/boxshade/trunk/boxshade.sh 2006-10-07 01:03:29 UTC (rev 146)
@@ -0,0 +1,3 @@
+#!/bin/bash
+export BOXDIR=/etc/boxshade
+/usr/lib/boxshade/boxshade $*
Added: trunk/packages/boxshade/trunk/debian/README.Debian
===================================================================
--- trunk/packages/boxshade/trunk/debian/README.Debian (rev 0)
+++ trunk/packages/boxshade/trunk/debian/README.Debian 2006-10-07 01:03:29 UTC (rev 146)
@@ -0,0 +1,11 @@
+boxshade for Debian
+-------------------
+
+The web interface for boxshare is available for download
+on ftp://www.isrec.isb-sib.ch/pub/software/unix/boxshade/www/box_www.tar.Z
+
+It is not yet debinanised, please request this package and
+explain your demand for it or use it on
+http://www.ch.embnet.org/software/BOX_form.html
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>, Sun, 29 Feb 2004 13:17:22 +0100
Added: trunk/packages/boxshade/trunk/debian/boxshade.xml
===================================================================
--- trunk/packages/boxshade/trunk/debian/boxshade.xml (rev 0)
+++ trunk/packages/boxshade/trunk/debian/boxshade.xml 2006-10-07 01:03:29 UTC (rev 146)
@@ -0,0 +1,358 @@
+<?xml version='1.0' encoding='ISO-8859-1'?>
+<!DOCTYPE refentry PUBLIC "-//OASIS//DTD DocBook XML V4.2//EN"
+"http://www.oasis-open.org/docbook/xml/4.2/docbookx.dtd" [
+
+<!--
+
+Process this file with an XSLT processor: `xsltproc \
+-''-nonet /usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
+manpages/docbook.xsl manpage.dbk'. A manual page
+<package>.<section> will be generated. You may view the
+manual page with: nroff -man <package>.<section> | less'. A
+typical entry in a Makefile or Makefile.am is:
+
+DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/\
+manpages/docbook.xsl
+XP=xsltproc -''-nonet
+
+manpage.1: manpage.dbk
+ $(XP) $(DB2MAN) $<
+
+The xsltproc binary is found in the xsltproc package. The
+XSL files are in docbook-xsl. Please remember that if you
+create the nroff version in one of the debian/rules file
+targets (such as build), you will need to include xsltproc
+and docbook-xsl in your Build-Depends control field.
+
+-->
+
+ <!-- Fill in your name for FIRSTNAME and SURNAME. -->
+ <!ENTITY dhfirstname "<firstname>Steffen</firstname>">
+ <!ENTITY dhsurname "<surname>Möller</surname>">
+ <!-- Please adjust the date whenever revising the manpage. -->
+ <!ENTITY dhdate "<date>February 26, 2004</date>">
+ <!-- SECTION should be 1-8, maybe w/ subsection other parameters are
+ allowed: see man(7), man(1). -->
+ <!ENTITY dhsection "<manvolnum>1</manvolnum>">
+ <!ENTITY dhemail "<email>moeller at pzr.uni-rostock.de</email>">
+ <!ENTITY dhusername "Steffen Moeller">
+ <!ENTITY dhucpackage "<refentrytitle>BOXSHADE</refentrytitle>">
+ <!ENTITY dhpackage "boxshade">
+
+ <!ENTITY debian "<productname>Debian</productname>">
+ <!ENTITY gnu "<acronym>GNU</acronym>">
+ <!ENTITY gpl "&gnu; <acronym>GPL</acronym>">
+]>
+
+<refentry>
+ <refentryinfo>
+ <address>
+ &dhemail;
+ </address>
+ <author>
+ &dhfirstname;
+ &dhsurname;
+ </author>
+ <copyright>
+ <year>2003</year>
+ <holder>&dhusername;</holder>
+ </copyright>
+ &dhdate;
+ </refentryinfo>
+ <refmeta>
+ &dhucpackage;
+
+ &dhsection;
+ </refmeta>
+ <refnamediv>
+ <refname>&dhpackage;</refname>
+
+ <refpurpose>Pretty-printing of multiple sequence alignments</refpurpose>
+ </refnamediv>
+ <refsynopsisdiv>
+ <cmdsynopsis>
+ <command>&dhpackage;</command>
+ </cmdsynopsis>
+ </refsynopsisdiv>
+ <refsect1>
+ <title>DESCRIPTION</title>
+ <para><command>BOXSHADE</command> is a program for pretty-printing multiple alignment output. The program itself doesn't do any alignment, you have to use a multiple alignment program like ClustalW or Pileup and use the output of these programs as input for BOXSHADE.</para>
+
+ <para>This manual page was written for the &debian; distribution
+ because the original program does not have a manual page. The presented information comes from the documentation of the Web Service of the 3.21 version that is not available as a Debian package.
+ </para>
+
+ <para>
+BOXSHADE is a program for creating good looking printouts from
+multiple-aligned protein or DNA sequences. The program does no alignment
+by itself, it has to take as input a file preprocessed by a multiple
+alignment program or a multiple file editor. See below for a list of
+supported input formats and output devices. In the standard BOXSHADE
+output, identical and similar residues in the multiple-alignment chart
+are represented by different colors or shadings. There are some more
+options concerning the kind of shading to be applied, sequence numbering,
+consensus output and so on. The user interface is a bit clumsy at
+the moment, one has to answer a lot of questions in order to get the
+desired output. There is, however, the possibility to use default
+parameters from a standard parameter file or to supply the program
+with parameters from the command line. At the moment, the VMS and DOS
+versions of BOXSHADE have identical user interfaces.
+</para>
+<para>- Input formats -</para>
+<para>
+BOXSHADE 3.2 knows about the following input file formats: (some of
+the are generally used only for MSDOS or VMS systems) + CLUSTAL and
+CLUSTALV, multiple alignment program, DOS/VMS/MAC default extension .ALN
++ ESEE, multiple sequence editor, DOS default extension .ESE + PHYLIP,
+phylogenetic analysis package, DOS, VMS, UNIX default extension .PHY +
+PILEUP and PRETTY of the GCG sequence analysis package VMS/UNIX default
+extensions .MSF and .PRE NB!! you are strongly encouraged NOT to use the
+PRETTY format as input, it may be incompatible with the revised version
+of .MSF input. We can't actually think why anyone would use this format
+now, .MSF files are more useful generally. + MALIGNED, multiple sequence
+editor, VMS only default extension .MAL BOXSHADE tries to determine the
+file type from the extension but will work also if different extensions
+are used.
+</para>
+<para> - Output devices - </para>
+<para>POSTSCRIPT/EPS creates POSTSCRIPT(TM) files for printing on
+a Laserprinter or for further conversion with a POSTCRIPT interpreter
+(like GHOSTSCRIPT) + HPGL for export to various graphics programs or
+for conversion/printing with the shareware program PRINTGL. Plotting
+BOXSHADE output on a plotter is generally not recommended + RTF for
+export to various word-processing and graphics programs + CRT, uses direct
+screen writes to the PC-monitor. Possible options depend on the graphics
+adapter used. This output device is supported only in the MSDOS version. +
+ANSI. On a PC, this option uses an ANSI device driver (ANSI.SYS) that has
+to be loaded in CONFIG.SYS previously. Possible character renditions are
+reverse, bold,underlined, blinking etc. On non-DOS systems, this option
+behaves more or less like the VT100 output mode. + VT100 for display on a
+VT100 compatible terminal or emulator. + ReGISterm for display on a ReGIS
+compatible graphics terminal or emulator. + ReGISfile for later conversion
+by the program RETOS (copyright DEC) in order to print on DIGITALs
+printer series. + LJ250 for printing on DIGITALS LJ250 color printer. +
+ASCII output showing either the conserved residues or the varying ones
+(others as '-'). + FIG file for xfig 2.1. + PICT files for import to Mac
+and PC graphics progs. Some of the formats above offer the possibility
+of scaling the characters and of rotating the plot. Character size has
+to be entered in 'point' units. Normal output orientation is in portrait
+mode (PS/EPS/HPGL/PICT only), to obtain output in landscape orientation,
+'rotate plot = y' has to be chosen. When creating multi-page output,
+all pages are contained in a single output file. If one page per file
+is desired, one has to use the command line parameter /SPLIT. This is
+enforced when requesting EPSF or PICT file output, as multi-page EPSFs
+are a contradiction of the purpose of an EPSF and large PICT files would
+probably be too big for most personal computers. While using the terminal
+as output device, the 'RETURN' key has to be pressed to obtain the next
+page of output.
+</para>
+<para>- Sequence numbering - </para>
+<para>Starting with version 2.2 there
+is the possibility to add numbering to the output files. The numbers are
+printed between the sequence names and the sequence itself. Since most of
+the input-files either use no numbering or number the first position in
+the alignment always with a "1" (and that does not necessarily reflect
+the numbers within the original sequence), the user is asked to enter
+the starting position for each sequence. The command line flag /DEFNUM
+suppressed that question, a starting position of 1 is assumed for all
+sequences. Boxshade starts with the value entered for the leftmost
+position and continues numbering every valid symbol, skipping blanks,
+'-','.' and stuff like that.
+</para>
+<para>- Default parameters -</para>
+<para>Several people using
+previous releases of BOXSHADE pointed me to the need of having default
+parameters for the various questions asked by the program. They argued
+that most sites only use one type of input files, one output device and
+one choice of colors for the output. I therefore added a management of
+default parameters allowing two levels of assistance to the user. 1) all
+default parameters are contained in an ASCII file that can be modified
+easily to accomodate the users taste. The format is roughly documented
+within the file-header, it resembles the keyboard input one has to make
+if using the program interactively. There are two such files supplied
+with this release of BOXSHADE, BOX_DNA.PAR and BOX_PEP.PAR , holding
+some example parameters for peptide and dna-comparisons. there are no
+big differences between these two, the major one is that when shading
+DNA-comparisons one doesn't care of "similar" residues. 2) to run the
+program with minimal user interaction, I have added the possibility to
+use command line parameters. At the moment, you can use: /check : list
+all allowed command line paramters (this list) and allows parameters to
+be added. /def : program runs without questions, BOX_PEP.PAR is used as
+default /dna : makes the program use BOX_DNA.PAR as parameter file /pep :
+makes the program use BOX_PEP.PAR as parameter file /in=xxx : makes the
+program take xxx as input file /out=yyy : makes the program take yyy as
+output file (note1) /par=zzz : makes the program use zzz as a default
+parameter file /type=1 : makes the program assume an input file of type
+1 (PRETTY/MSF) /dev=1 : makes the program assume and output device of
+type 1 (CRT) /numdef : use default numbering (all sequences starting
+with "1") /thr : threshold fraction of residues that must agree for a
+consensus /split : forces one page per file output, creates multiple
+output files. /cons : makes the program create an additional consensus
+line (see below) /symbcons=: influences the way the consensus line is
+displayed. (see below) /unix : writes output files in unix style (LF only)
+(note2) /dos : writes output files in DOS style (CR/LF) (note2) note1:
+on unix machines, use out=OUTPUT for terminal output on DOS machines,
+use out=con: on VMS machines, use out=tt: note2: if no mode is specified,
+the native style of the machine is used.
+ </para>
+<para>ATTENTION</para>
+<para>on unix systems, the dash (-) instead of the slash (/) has to be used as separation character for command line paramters. For example, a valid unix command line is: <command>boxshade -def -numdef -cons -symbcons=" .*" **************************************************************************</command>
+</para>
+<para>- Shading strategies (similarity to consensus or single sequence) -</para>
+<para>
+Starting with version 3, BOXSHADE has a new shading system. The first
+difference is the introduction of a threshold fraction of residues that
+must agree for there to be a consensus. Previously, the program assumed
+that SOME residue was always the consensus. If no two residues were the
+same, the first sequence provided the consensus residue. This threshold
+fraction can be any number between 0.0 and 1.0. The number of sequences
+that must agree for there to be a consensus is, as you might expect,
+this fraction times the total number of sequences in the alignment
+(fractions of a sequence count as one, e.g. 3.2 becomes 4). The second
+difference is the idea of 'consensus by similarity'; this tries to take
+account of the situations where all the sequences may have (for example)
+R or K at a position, but neither in a majority. It would not be logical
+to shade one type of residue as 'identical' and the other as 'similar';
+the threshold function might also eliminate both as being in too small
+numbers. Therefore, if there is not a single residue that is conserved
+(greater than the threshold) at a position, the program looks for a
+'group' of amino acids that fulfills the requirements. 'Groups' are
+defined in the .grp files. Users can tailor these to their personal
+prejudices. Any amino acid not listed is assumed not to be in a group. All
+members of a group are considered to be mutually similar, unlike the
+.sim files, described below. If consensus by similarity is found, all the
+residues in the consensus are shaded using the 'similar' shading defined
+by the user. If the user does not select 'shading by similarity', only
+identity-type consensus is looked at. If an identity-type consensus is
+found, and similarity shading is in operation, the program looks to see
+if the remaining residues are similar to the consensus residue. Here the
+box_xxx.sim files are used. The main difference between relationships
+in these files and those in the .grp files is that, e.g. in a .grp
+file the line STA means that all three a.a.s are mutually similar. In
+a .sim file S TA means that both T and A are considered similar to S,
+where there is a conserved S residue in more than threshold number of
+sequences. However, it does NOT mean that T and A are similar to each
+other. Note that cases where two residues, or groups of residues,
+fulfill the threshold requirements (as could happen with values of
+the thr. fraction less than or equal to 0.5) are treated as having no
+consensus. This describes the main shading model 'shading according to
+a consensus'. The alternative model is called 'shading according to
+a master sequence'. In this case the user is prompted for a sequence
+of the alignment and consecutively that sequence is taken to be the
+'consensus'. Only those residues become shaded that are identical or
+similar to the chosen sequence. Output obtained with this option tends
+to be less shaded and neglects similarities beween the other (non-chosen)
+sequences. Starting in V2.7, this 'master sequence' can be hidden. Thus,
+it only influences the shading of the other sequences without being
+shown itself.
+</para>
+<para>- Consensus display - </para>
+<para>Starting with version 2.5, BOXSHADE
+offers the possibility to create an additional line holding a consensus
+symbol. This line can either be obtained by using the command line
+qualifier /CONS or interactively by answering the question ' create
+consensus? '. The way this consensus line is displayed can be modified
+by the command line parameter SYMBCONS=xyz, by editing the respecitve
+entry in the .PAR file or interactively. Since the SYMBCONS syntax is
+not intuitive, here a brief description: The SYMBCONS parameter consist
+of exactly three symbols: + the first one stands for 'normal' sequence
+residues that are not involved in any similar/identical relationship. +
+the second symbol represents positions that are similar in all sequences
+of the alignment. See the files BOX_PEP.SIM and BOX_DNA.SIM to see
+what residues are considered similar. + the third symbol represents
+positions that are identical in all sequences of the alignment. A
+SYMBCONS parameter string " .*" (blank/point/asterisc) means: label
+all positions in the alignment with totally identical residues by an
+asterisc, all positions with all similar residues by a point and do not
+mark the other positions. The letter 'B' can be used instead of the blank,
+this is necessary e.g. when using the command line option /SYMBCONS=B.*
+which gives the same result as the above example. The option /SYMBCONS=
+.* would result in an unexpected behaviour because MSDOS squeezes blanks
+out of the command line. Besides points, asteriscs and other symbols,
+there are two special characters when they appear in the SYMBCONS string:
+'L' and 'U'. An 'L' means, that a lowercase representation of the
+most abundant residue at that position is to be used instead of a fixed
+consensus symbol while an 'U' means an uppercase character representation
+of that residue. A possible application would be the SYMBCONS string "
+LU" where similar residues are represented by lowercase characters and
+identical by uppercase characters.
+</para>
+<para>
+- shareware/PD programs useful in conjunction with BOXSHADE -
+</para>
+<para>
+multiple alignment files that to be used by BOXSHADE can be created,
+amongst others, by the following PD/freeware programs: + PHYLIP by Joe
+Felsenstein, available by ftp from anthro.utah.edu + ESEE by Eric Cabot,
+available from the same sources as BOXSHADE (see above) + CLUSTAL by Des
+Higgins, ditto for preview/conversion of POSTSCRIPT files, the program
+GHOSTSCRIPT from GNU software foundation is highly recommended. It is
+available from all major MSDOS ftp-sites (e.g. SIMTEL or ftp.uni-koeln.de)
+There is also a version tested for use with boxshade available at
+vax0.biomed.uni-koeln.de although this might be not the most recent
+release. for Mac users, there is MacGhostscript, also available from the
+main archives (info-mac, umich and their mirrors). A *very* good tool
+for putting a preview image into an EPSF file, often a prerequisite for
+incorporating into a drawing package, is PS2EPS, by Peter Lerup. This can
+be found on info-mac. for preview/conversion of HPGL files, the shareware
+program PRINTGL 1.18 by Cary Ravitz is highly recommended. It is available
+from many MSDOS ftp sites and from netserv at embl-heidelberg.de - output on
+dot printers - Since PRINTGL offers a broad choice of printer types and
+is a nice program, I recommend its use for printing BOXSHADE output on
+non-POSTSCRIPT printers. Use HPGL output with options 0F1N for normal
+residues 2F1N for identical residues 3F1N for similar residues 2F4N
+for conserved residues 8 for character size not rotated (these are the
+standard parameters in BOX_PEP.PAR) for creating a HPGL files. (lets call
+it TEST.PLT) Now use PRINTGL either interactively by calling PMI or use
+a command line like: PRINTGL /Fx/S0340/Waaac/Ptest.plt where test.plt is
+to be replaced by the filename to convert and the x in the expression
+/Fx is to be replaced by the letter of the printer you use. (See the
+PRINTGL documentation for further details)
+</para>
+</refsect1>
+<refsect1><title>
+RESTRICTIONS
+</title></refsect1>
+<para>
+The RTF output and PHYLIP input implementations are still
+experimental. Please tell me of your experiences with the program. +
+the current DOS version supports only 13 sequences with 2000 residues
+each. This parameters can be easily changed in the source code. If you
+cannot compile the sources because you are lacking a pascal compiler,
+contact the author for precompiled versions
+</para>
+<refsect1><title>DISTRIBUTION POLICY</title>
+<para>
+BOXSHADE is completely public-domain and may be passed around and modified without any notice to the author. If you have problems, suggestions or remarks, please contact either of us:
+Kay Hofmann, PhD Tel: +49 (221) 950 4814 Bioinformatics Group FAX: +49 (221) 950 4848
+MEMOREC Stoffel GmbH Stoeckheimer Weg 1 D50829 Koeln/Germany
+E-mail: Kay.Hofmann at memorec.com
+Michael D. Baron Institute for Animal Health Ash Road Pirbright Surrey GU24 0NF U.K.
+E-mail: michael.baron at bbsrc.ac.uk
+</para>
+</refsect1>
+ <refsect1>
+ <title>SEE ALSO</title>
+
+ <para>/etc/boxshade/*.par</para>
+ <para><application>seaview</application> (1),
+ <application>clustalw</application> (1)
+ </para>
+ </refsect1>
+ <refsect1>
+ <title>AUTHOR</title>
+
+ <para>This manual page was written by &dhusername; &dhemail; for
+ the &debian; system (but may be used by others). Permission is
+ granted to copy, distribute and/or modify this document under
+ the terms of the &gnu; General Public License, Version 2 any
+ later version published by the Free Software Foundation.
+ </para>
+ <para>
+ On Debian systems, the complete text of the GNU General Public
+ License can be found in /usr/share/common-licenses/GPL.
+ </para>
+
+ </refsect1>
+</refentry>
+
Added: trunk/packages/boxshade/trunk/debian/changelog
===================================================================
--- trunk/packages/boxshade/trunk/debian/changelog (rev 0)
+++ trunk/packages/boxshade/trunk/debian/changelog 2006-10-07 01:03:29 UTC (rev 146)
@@ -0,0 +1,6 @@
+boxshade (3.1.1-1) unstable; urgency=low
+
+ * Initial Release (Closes: #234923).
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de> Thu, 26 Feb 2004 13:17:22 +0100
+
Added: trunk/packages/boxshade/trunk/debian/compat
===================================================================
--- trunk/packages/boxshade/trunk/debian/compat (rev 0)
+++ trunk/packages/boxshade/trunk/debian/compat 2006-10-07 01:03:29 UTC (rev 146)
@@ -0,0 +1 @@
+4
Added: trunk/packages/boxshade/trunk/debian/control
===================================================================
--- trunk/packages/boxshade/trunk/debian/control (rev 0)
+++ trunk/packages/boxshade/trunk/debian/control 2006-10-07 01:03:29 UTC (rev 146)
@@ -0,0 +1,18 @@
+Source: boxshade
+Section: science
+Priority: extra
+Maintainer: Steffen Moeller <moeller at pzr.uni-rostock.de>
+Build-Depends: debhelper (>= 4.0.0), xsltproc, docbook-xsl, docbook-xml
+Standards-Version: 3.6.0
+
+Package: boxshade
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: seaview, clustalw, xfig
+Description: [Biology] Pretty-printing of multiple sequence alignments
+ Boxshade reads a sequence alignment as input (e.g. from ClustalW) and
+ outputs files that may be incorporated to text processing software
+ (TeX via xfig, Word and OpenOffice via RTF). The post script format
+ is also supported.
+ .
+ Homepage: http://www.ch.embnet.org/software/BOX_form.html
Added: trunk/packages/boxshade/trunk/debian/copyright
===================================================================
--- trunk/packages/boxshade/trunk/debian/copyright (rev 0)
+++ trunk/packages/boxshade/trunk/debian/copyright 2006-10-07 01:03:29 UTC (rev 146)
@@ -0,0 +1,12 @@
+This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
+Thu, 26 Feb 2004 13:17:22 +0100.
+
+It was downloaded from: ftp://www.isrec.isb-sib.ch/pub/software/unix/boxshade/
+
+Upstream Authors: Kay Hofmann (kay.hofmann at memorec.de), Michael Baron (michael.baron at bbsrc.ac.uk), Hartmut Schirmer
+
+Copyright:
+
+ No license restrictions. In a personal email from the 26th of February 2004 Kay Hofmann replied
+ "Das ganze Teil ist komplett public domain, Du kannst damit anstellen was immer du willst, ...".
+ that the software is completely public domain, allowing me to do with it whatever I want.
Added: trunk/packages/boxshade/trunk/debian/dirs
===================================================================
--- trunk/packages/boxshade/trunk/debian/dirs (rev 0)
+++ trunk/packages/boxshade/trunk/debian/dirs 2006-10-07 01:03:29 UTC (rev 146)
@@ -0,0 +1,2 @@
+usr/bin
+usr/sbin
Added: trunk/packages/boxshade/trunk/debian/manpages
===================================================================
--- trunk/packages/boxshade/trunk/debian/manpages (rev 0)
+++ trunk/packages/boxshade/trunk/debian/manpages 2006-10-07 01:03:29 UTC (rev 146)
@@ -0,0 +1 @@
+boxshade.1
Added: trunk/packages/boxshade/trunk/debian/menu
===================================================================
--- trunk/packages/boxshade/trunk/debian/menu (rev 0)
+++ trunk/packages/boxshade/trunk/debian/menu 2006-10-07 01:03:29 UTC (rev 146)
@@ -0,0 +1,6 @@
+?package(boxshade):\
+ needs="text"\
+ section="Apps/Science"\
+ title="Boxshade"\
+ command="/usr/bin/boxshade"
+
Added: trunk/packages/boxshade/trunk/debian/rules
===================================================================
--- trunk/packages/boxshade/trunk/debian/rules (rev 0)
+++ trunk/packages/boxshade/trunk/debian/rules 2006-10-07 01:03:29 UTC (rev 146)
@@ -0,0 +1,109 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+# Sample debian/rules that uses debhelper.
+# GNU copyright 1997 to 1999 by Joey Hess.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+
+
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+ CFLAGS += -O0
+else
+ CFLAGS += -O2
+endif
+ifeq (,$(findstring nostrip,$(DEB_BUILD_OPTIONS)))
+ INSTALL_PROGRAM += -s
+endif
+
+configure: configure-stamp
+configure-stamp:
+ dh_testdir
+ # Add here commands to configure the package.
+
+ touch configure-stamp
+
+
+build: build-stamp
+
+DB2MAN=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh/manpages/docbook.xsl
+XP=xsltproc -''-nonet
+
+boxshade.1: debian/boxshade.xml
+ $(XP) $(DB2MAN) $<
+
+
+build-stamp: configure-stamp boxshade.1
+ dh_testdir
+
+ # Add here commands to compile the package.
+ $(MAKE) -f makefile.unx
+ touch build-stamp
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp configure-stamp
+
+ # Add here commands to clean up after the build process.
+ -$(MAKE) -f makefile.unx clean
+
+ dh_clean
+
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+
+ # Add here commands to install the package into debian/boxshade.
+ mkdir -p $(CURDIR)/debian/boxshade/usr/bin \
+ $(CURDIR)/debian/boxshade/usr/lib/boxshade \
+ $(CURDIR)/debian/boxshade/etc/boxshade || true
+
+ cp boxshade.sh $(CURDIR)/debian/boxshade/usr/bin/boxshade
+ cp boxshade $(CURDIR)/debian/boxshade/usr/lib/boxshade
+ cp *.grp *.par *.sim $(CURDIR)/debian/boxshade/etc/boxshade
+
+
+# Build architecture-independent files here.
+binary-indep: build install
+# We have nothing to do by default.
+
+# Build architecture-dependent files here.
+binary-arch: build install
+ dh_testdir
+ dh_testroot
+ dh_installchangelogs
+ dh_installdocs
+# dh_installexamples
+# dh_install
+ dh_installmenu
+# dh_installdebconf
+# dh_installlogrotate
+# dh_installemacsen
+# dh_installpam
+# dh_installmime
+# dh_installinit
+# dh_installcron
+# dh_installinfo
+ dh_installman
+ dh_link
+ dh_strip
+ dh_compress
+ dh_fixperms
+# dh_perl
+# dh_python
+# dh_makeshlibs
+ dh_installdeb
+ dh_shlibdeps
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure
Property changes on: trunk/packages/boxshade/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Modified: trunk/packages/boxshade/trunk/makefile.unx
===================================================================
--- trunk/packages/boxshade/trunk/makefile.unx 2006-10-07 01:02:32 UTC (rev 145)
+++ trunk/packages/boxshade/trunk/makefile.unx 2006-10-07 01:03:29 UTC (rev 146)
@@ -40,3 +40,8 @@
dv_ps$(OBJ): dv_ps.c bx_types.h bx_read.h dv_all.h version.h
dv_regis$(OBJ): dv_regis.c bx_types.h bx_read.h dv_all.h
dv_rtf$(OBJ): dv_rtf.c bx_types.h bx_read.h dv_all.h
+
+.PHONY: clean
+
+clean:
+ rm -f $(OBJS) boxshade$(EXE)
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