[med-svn] r148 - in trunk/packages/boxshade/trunk: . debian
Charles Plessy
charles-guest at costa.debian.org
Sat Oct 21 01:56:33 UTC 2006
Author: charles-guest
Date: 2006-10-21 01:56:32 +0000 (Sat, 21 Oct 2006)
New Revision: 148
Added:
trunk/packages/boxshade/trunk/debian/boxshade.1.xml
trunk/packages/boxshade/trunk/debian/conffiles
trunk/packages/boxshade/trunk/debian/dirs
trunk/packages/boxshade/trunk/debian/install
Removed:
trunk/packages/boxshade/trunk/boxshade.1
trunk/packages/boxshade/trunk/debian/boxshade.xml
trunk/packages/boxshade/trunk/debian/dirs
trunk/packages/boxshade/trunk/debian/manpages
Modified:
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/rules
Log:
Upgrading version number and manpage, cleaning debian/rules.
Deleted: trunk/packages/boxshade/trunk/boxshade.1
===================================================================
--- trunk/packages/boxshade/trunk/boxshade.1 2006-10-14 12:23:15 UTC (rev 147)
+++ trunk/packages/boxshade/trunk/boxshade.1 2006-10-21 01:56:32 UTC (rev 148)
@@ -1,119 +0,0 @@
-.\"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/debian/boxshade.1.xml
===================================================================
--- trunk/packages/boxshade/trunk/debian/boxshade.1.xml (rev 0)
+++ trunk/packages/boxshade/trunk/debian/boxshade.1.xml 2006-10-21 01:56:32 UTC (rev 148)
@@ -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>
+
Deleted: trunk/packages/boxshade/trunk/debian/boxshade.xml
===================================================================
--- trunk/packages/boxshade/trunk/debian/boxshade.xml 2006-10-14 12:23:15 UTC (rev 147)
+++ trunk/packages/boxshade/trunk/debian/boxshade.xml 2006-10-21 01:56:32 UTC (rev 148)
@@ -1,358 +0,0 @@
-<?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>
-
Modified: trunk/packages/boxshade/trunk/debian/changelog
===================================================================
--- trunk/packages/boxshade/trunk/debian/changelog 2006-10-14 12:23:15 UTC (rev 147)
+++ trunk/packages/boxshade/trunk/debian/changelog 2006-10-21 01:56:32 UTC (rev 148)
@@ -1,3 +1,13 @@
+boxshade (3.3.1) unstable; urgency=low
+
+ * New version number, but upsteams' 3.3.1 was already packaged in Debian
+ under number 3.1.1
+ * Swiching to collaborative maintainance: Maintainer is a mailing-list,
+ Uploaders are real people.
+ * Using debhelper v5 and conforming to policy 3.7.2.
+
+ -- Charles Plessy <charles-debian-nospam at plessy.org> Wed, 18 Oct 2006 23:16:40 +0900
+
boxshade (3.1.1-1) unstable; urgency=low
* Initial Release (Closes: #234923).
Modified: trunk/packages/boxshade/trunk/debian/compat
===================================================================
--- trunk/packages/boxshade/trunk/debian/compat 2006-10-14 12:23:15 UTC (rev 147)
+++ trunk/packages/boxshade/trunk/debian/compat 2006-10-21 01:56:32 UTC (rev 148)
@@ -1 +1 @@
-4
+5
Added: trunk/packages/boxshade/trunk/debian/conffiles
===================================================================
Modified: trunk/packages/boxshade/trunk/debian/control
===================================================================
--- trunk/packages/boxshade/trunk/debian/control 2006-10-14 12:23:15 UTC (rev 147)
+++ trunk/packages/boxshade/trunk/debian/control 2006-10-21 01:56:32 UTC (rev 148)
@@ -1,18 +1,24 @@
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
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steffen Moeller <steffen_moeller at gmx.de>, Charles Plessy <charles-debian-nospam at plessy.org>
+Build-Depends: debhelper (>= 5), xsltproc, docbook-xsl, docbook-xml
+Standards-Version: 3.7.2
Package: boxshade
Architecture: any
Depends: ${shlibs:Depends}, ${misc:Depends}
-Suggests: seaview, clustalw, xfig
+Suggests: seaview, kalign, 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
+ 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 alignment editor. Boxshade reads multiple-aligned
+ sequences from either PILEUP-MSF, CLUSTAL-ALN, MALIGNED-data and ESEE-save
+ files (limited to a maximum of 150 sequences with up to 10000 elements each).
+ Various kinds of shading can be applied to identical/similar residues. Output
+ is written to screen or to a file in the following formats: ANSI/VT100,
+ PS/EPS, RTF, HPGL, ReGIS, LJ250-printer, ASCII, xFIG, PICT, HTML
+.
+ Homepage: http://www.ch.embnet.org/software/BOX_form.html
Modified: trunk/packages/boxshade/trunk/debian/copyright
===================================================================
--- trunk/packages/boxshade/trunk/debian/copyright 2006-10-14 12:23:15 UTC (rev 147)
+++ trunk/packages/boxshade/trunk/debian/copyright 2006-10-21 01:56:32 UTC (rev 148)
@@ -1,12 +1,34 @@
This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
-Thu, 26 Feb 2004 13:17:22 +0100.
+Thu, 26 Feb 2004 13:17:22 +0100. Starting from 2006, the packaging work is
+hereby placed in the public domain.
-It was downloaded from: ftp://www.isrec.isb-sib.ch/pub/software/unix/boxshade/
+It was downloaded from: ftp://www.isrec.isb-sib.ch/pub/software/unix/boxshade/3.3.1/
+(This is the C version)
-Upstream Authors: Kay Hofmann (kay.hofmann at memorec.de), Michael Baron (michael.baron at bbsrc.ac.uk), Hartmut Schirmer
+Boxshade is completely public-domain and may be
+passed around and modified without any notice to the author.
-Copyright:
+the authors addresses are:
- 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.
+ Kay Hofmann Michael D. Baron
+ Bioinformatics Group BBSRC Institute for Animal Health
+ ISREC Pirbright, Surrey GU24 0NF
+ CH-1066 Epalinges s/Lausanne U.K.
+ Switzerland
+
+C port by
+
+ Hartmut Schirmer
+ Technische Fakultaet
+ Kaiserstr. 2
+ D-24143 Kiel
+ Germany
+
+for any comments write an E-mail to
+ Kay: khofmann at isrec-sun1.unil.ch
+ Michael: baron at bbsrc.ac.uk (though kay wrote 99% of the program and is more
+ likely to be of help, especially with input and output problems)
+ Hartmut: hsc at techfak.uni-kiel.de (don't send Kay or Michael any questions
+ concerning the 'C' version of boxshade)
+
+(The comments after the email adresses are form the authors themselves.)
Deleted: trunk/packages/boxshade/trunk/debian/dirs
===================================================================
--- trunk/packages/boxshade/trunk/debian/dirs 2006-10-14 12:23:15 UTC (rev 147)
+++ trunk/packages/boxshade/trunk/debian/dirs 2006-10-21 01:56:32 UTC (rev 148)
@@ -1,2 +0,0 @@
-usr/bin
-usr/sbin
Added: trunk/packages/boxshade/trunk/debian/dirs
===================================================================
Added: trunk/packages/boxshade/trunk/debian/install
===================================================================
Deleted: trunk/packages/boxshade/trunk/debian/manpages
===================================================================
--- trunk/packages/boxshade/trunk/debian/manpages 2006-10-14 12:23:15 UTC (rev 147)
+++ trunk/packages/boxshade/trunk/debian/manpages 2006-10-21 01:56:32 UTC (rev 148)
@@ -1 +0,0 @@
-boxshade.1
Modified: trunk/packages/boxshade/trunk/debian/rules
===================================================================
--- trunk/packages/boxshade/trunk/debian/rules 2006-10-14 12:23:15 UTC (rev 147)
+++ trunk/packages/boxshade/trunk/debian/rules 2006-10-21 01:56:32 UTC (rev 148)
@@ -3,12 +3,6 @@
# 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)))
@@ -20,14 +14,7 @@
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
@@ -39,8 +26,6 @@
build-stamp: configure-stamp boxshade.1
dh_testdir
-
- # Add here commands to compile the package.
$(MAKE) -f makefile.unx
touch build-stamp
@@ -48,8 +33,6 @@
dh_testdir
dh_testroot
rm -f build-stamp configure-stamp
-
- # Add here commands to clean up after the build process.
-$(MAKE) -f makefile.unx clean
dh_clean
@@ -83,22 +66,11 @@
# 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_installman debian/boxshade.1
dh_link
dh_strip
dh_compress
dh_fixperms
-# dh_perl
-# dh_python
-# dh_makeshlibs
dh_installdeb
dh_shlibdeps
dh_gencontrol
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