[med-svn] r11866 - in trunk/packages/strap-base/trunk/debian: . bin templates
Christoph Gille
christophgil-guest at alioth.debian.org
Sun Jul 22 15:53:50 UTC 2012
Author: christophgil-guest
Date: 2012-07-22 15:53:49 +0000 (Sun, 22 Jul 2012)
New Revision: 11866
Added:
trunk/packages/strap-base/trunk/debian/bin/strap_base
trunk/packages/strap-base/trunk/debian/bin/strap_to_clustal
trunk/packages/strap-base/trunk/debian/bin/strap_to_fasta
trunk/packages/strap-base/trunk/debian/bin/strap_to_html
trunk/packages/strap-base/trunk/debian/bin/strap_to_msf
trunk/packages/strap-base/trunk/debian/bin/strap_to_multiple_fasta
trunk/packages/strap-base/trunk/debian/bin/strap_to_word
trunk/packages/strap-base/trunk/debian/strap_base.1
trunk/packages/strap-base/trunk/debian/strap_to_clustal.1
trunk/packages/strap-base/trunk/debian/strap_to_fasta.1
trunk/packages/strap-base/trunk/debian/strap_to_html.1
trunk/packages/strap-base/trunk/debian/strap_to_msf.1
trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1
trunk/packages/strap-base/trunk/debian/strap_to_word.1
trunk/packages/strap-base/trunk/debian/templates/
trunk/packages/strap-base/trunk/debian/templates/ConvertAll.sh
trunk/packages/strap-base/trunk/debian/templates/EX_HTML_RS.1
trunk/packages/strap-base/trunk/debian/templates/EX_PARS.1
trunk/packages/strap-base/trunk/debian/templates/template.1
trunk/packages/strap-base/trunk/debian/templates/templateGui.1
Removed:
trunk/packages/strap-base/trunk/debian/bin/strap-protein-alignment
trunk/packages/strap-base/trunk/debian/strap-base.desktop
trunk/packages/strap-base/trunk/debian/strap-protein-alignment.1
Modified:
trunk/packages/strap-base/trunk/debian/control
trunk/packages/strap-base/trunk/debian/copyright
trunk/packages/strap-base/trunk/debian/rules
trunk/packages/strap-base/trunk/debian/strap-base.install
trunk/packages/strap-base/trunk/debian/strap-base.links
trunk/packages/strap-base/trunk/debian/strap-base.manpages
Log:
Placed all (command line utilities for alignment file conversion, html
generation, for web services) into package strap-base. Package strap
is GUI for end users.
Replaced underscore for dash in script names.
It works. Tested on Virtual Box XUbuntu
TODO: Replace dependency kalign by by neobio
Check mime types.
Deleted: trunk/packages/strap-base/trunk/debian/bin/strap-protein-alignment
===================================================================
--- trunk/packages/strap-base/trunk/debian/bin/strap-protein-alignment 2012-07-22 15:53:12 UTC (rev 11865)
+++ trunk/packages/strap-base/trunk/debian/bin/strap-protein-alignment 2012-07-22 15:53:49 UTC (rev 11866)
@@ -1,34 +0,0 @@
-#! /bin/sh
-
-echo '\033[42m\033[37m'$0'\033[0m '
-echo "See http://3d-alignment.eu/ "
-echo
-
-. /usr/lib/java-wrappers/java-wrappers.sh
-find_java_runtime java6
-
-# Java option max heap size
-xmx=-Xmx200M
-CP=/usr/lib/strap-base/strap-protein-alignment-1.jar:
-for i in $*; do
- if [ $i != ${i##-Xmx} ]; then xmx=$i; fi
- if [ $i != ${i##-cp=} ]; then CP=${i##-cp=}":"$CP; fi
-done
-
-if [ -f /usr/bin/tm-align ]; then S3D="-s3d=tm_align"; fi
-
-
-
-echo The maximum heap size option is $xmx.
-echo To change, add a program line option like -Xmx500M
-echo which would set heap size to 500 Megabytes.
-echo
-
-EXEC="$JAVA_HOME/bin/java $xmx -cp $CP charite.christo.strap.Strap -useDebian -warnInstall=debian $S3D -a3d=mustang -aligner2=kalign -v3d=pymol -probeWebProxy -stdout -askUpload $*"
-
-echo
-echo $EXEC
-echo
-$EXEC
-
-
Copied: trunk/packages/strap-base/trunk/debian/bin/strap_base (from rev 11833, trunk/packages/strap-base/trunk/debian/bin/strap-protein-alignment)
===================================================================
--- trunk/packages/strap-base/trunk/debian/bin/strap_base (rev 0)
+++ trunk/packages/strap-base/trunk/debian/bin/strap_base 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,29 @@
+#! /bin/sh
+
+# See http://3d-alignment.eu/
+
+
+. /usr/lib/java-wrappers/java-wrappers.sh
+find_java_runtime java6
+
+# Java option max heap size
+
+xmx=-Xmx200M
+CP=/usr/lib/strap-base/strap-protein-alignment-1.jar:
+for i in $*; do
+ if [ $i != ${i##-Xmx} ]; then xmx=$i; fi
+ if [ $i != ${i##-cp=} ]; then CP=${i##-cp=}":"$CP; fi
+done
+
+
+# The maximum heap size option is $xmx.
+# To change, add a program line option like -Xmx500M
+# which would set heap size to 500 Megabytes.
+
+
+EXEC="$JAVA_HOME/bin/java $xmx -cp /usr/lib/strap-base/strap-protein-alignment-1.jar charite.christo.strap.Strap -useDebian -warnInstall=debian -debianStrapBase $*"
+
+echo
+echo $EXEC
+echo
+$EXEC
\ No newline at end of file
Added: trunk/packages/strap-base/trunk/debian/bin/strap_to_clustal
===================================================================
--- trunk/packages/strap-base/trunk/debian/bin/strap_to_clustal (rev 0)
+++ trunk/packages/strap-base/trunk/debian/bin/strap_to_clustal 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,2 @@
+#! /bin/sh
+/bin/sh /usr/bin/strap_base -toClustal $*
Added: trunk/packages/strap-base/trunk/debian/bin/strap_to_fasta
===================================================================
--- trunk/packages/strap-base/trunk/debian/bin/strap_to_fasta (rev 0)
+++ trunk/packages/strap-base/trunk/debian/bin/strap_to_fasta 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,2 @@
+#! /bin/sh
+/bin/sh /usr/bin/strap_base -toFasta $*
Added: trunk/packages/strap-base/trunk/debian/bin/strap_to_html
===================================================================
--- trunk/packages/strap-base/trunk/debian/bin/strap_to_html (rev 0)
+++ trunk/packages/strap-base/trunk/debian/bin/strap_to_html 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,2 @@
+#! /bin/sh
+/bin/sh /usr/bin/strap_base -toHTML $*
Added: trunk/packages/strap-base/trunk/debian/bin/strap_to_msf
===================================================================
--- trunk/packages/strap-base/trunk/debian/bin/strap_to_msf (rev 0)
+++ trunk/packages/strap-base/trunk/debian/bin/strap_to_msf 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,2 @@
+#! /bin/sh
+/bin/sh /usr/bin/strap_base -toMSF $*
Added: trunk/packages/strap-base/trunk/debian/bin/strap_to_multiple_fasta
===================================================================
--- trunk/packages/strap-base/trunk/debian/bin/strap_to_multiple_fasta (rev 0)
+++ trunk/packages/strap-base/trunk/debian/bin/strap_to_multiple_fasta 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,2 @@
+#! /bin/sh
+/bin/sh /usr/bin/strap_base -toMultipleFasta $*
Added: trunk/packages/strap-base/trunk/debian/bin/strap_to_word
===================================================================
--- trunk/packages/strap-base/trunk/debian/bin/strap_to_word (rev 0)
+++ trunk/packages/strap-base/trunk/debian/bin/strap_to_word 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,2 @@
+#! /bin/sh
+/bin/sh /usr/bin/strap_base -toWord $*
Modified: trunk/packages/strap-base/trunk/debian/control
===================================================================
--- trunk/packages/strap-base/trunk/debian/control 2012-07-22 15:53:12 UTC (rev 11865)
+++ trunk/packages/strap-base/trunk/debian/control 2012-07-22 15:53:49 UTC (rev 11866)
@@ -17,11 +17,15 @@
Enhances:
Description: Minimal environment for the bioinformatics tool Strap for
viewing and editing protein sequence alignments and 3D-structure
- superpositions. The package strap-base may be loaded by other debian packages
- which use strap as an interactive view for sequence alignments and
- 3D-superpositions. End users should rather install the debian
- package strap which also installs all required software for
- 3D-visualization, automated sequence alignment, 3D-superposition and
- PDF-output.
+ superpositions. The package strap-base provides shell commands to
+ generate sequence alignment files in different output formats:
+ strap_to_clustal, strap_to_msf, strap_to_multiple_fasta,
+ strap_to_html, strap_to_word. The alignment export for web browser
+ or word processor supports highlighting and annotation of residue
+ positions, visualization of the secondary structure, protein icons
+ and web references. The command strap_base starts Strap in GUI mode
+ and may be used by other programs to launch Strap as an interactive
+ protein alignment viewer. However, users should install the package
+ strap which also includes all required bioinformatics tools.
Modified: trunk/packages/strap-base/trunk/debian/copyright
===================================================================
--- trunk/packages/strap-base/trunk/debian/copyright 2012-07-22 15:53:12 UTC (rev 11865)
+++ trunk/packages/strap-base/trunk/debian/copyright 2012-07-22 15:53:49 UTC (rev 11866)
@@ -4,50 +4,43 @@
Source: http://www.bioinformatics.org/strap/debian/strap-base_1.orig.tar.gz
Comment: Some files were removed, see the get-orig-source target in ‘debian/rules’.
-Files: *
-Copyright: © 2011 Christoph Gille
-License: GPL-3
- Strap is free software; you can redistribute it and/or modify it under the terms of
- the GNU General Public License as published by the Free Software Foundation; either
- version 2 of the License, or (at your option) any later version.
- .
- Strap is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY;
- without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
- PURPOSE. See the GNU General Public License for more details.
- .
- You should have received a copy of the GNU General Public License along with Strap;
- if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor,
- Boston, MA 02110-1301 USA.
- .
- Proper attribution of the author as the source of the software would be appreciated.
- Comment: On Debian systems, the complete text of the GNU General Public License
- version 2 can be found in ‘/usr/share/common-licenses/GPL-2’
-# ********************************************************************************
-Files: debian/*
-Copyright: © 2011 Christoph Gille
-License: GPL-3
-# ********************************************************************************
-Files: 3d.png browser16.png ledgreen16.png
+Files: * Copyright: © 2011 Christoph Gille License: GPL-3 Strap is
+free software; you can redistribute it and/or modify it under the
+terms of the GNU General Public License as published by the Free
+Software Foundation; either version 2 of the License, or (at your
+option) any later version. . Strap is distributed in the hope that
+it will be useful, but WITHOUT ANY WARRANTY; without even the implied
+warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See
+the GNU General Public License for more details. . You should have
+received a copy of the GNU General Public License along with Strap; if
+not, write to the Free Software Foundation, Inc., 51 Franklin Street,
+Fifth Floor, Boston, MA 02110-1301 USA. . Proper attribution of the
+author as the source of the software would be appreciated. Comment:
+On Debian systems, the complete text of the GNU General Public License
+version 2 can be found in ‘/usr/share/common-licenses/GPL-2’ #
+********************************************************************************
+Files: debian/* Copyright: © 2012 Christoph Gille License: GPL-3 #
+********************************************************************************
+Files: 3d.png browser16.png ledgreen16.png
Source: http://www.phoca.cz/demo/gallery-categories/category/22-nuvola-icons
-License: LGPL-2.1
- Comment: On Debian systems, the complete text of the Apache license can be found in '/usr/share/common-licenses/LGPL-2.1'
-# ********************************************************************************
-Files: eye.gif
-Source: http://icone.goldenweb.it/index_file/l/en/d2/computer/default.html
-License: Citation from web site "The icons stored within our database are free and downloadable in .ico, .bmp, or .gif format. .... " #
-# ********************************************************************************
-1.png border_color.png compact_camera.png edit.png home.png scales.png
-stack_of_photos.png zip.png console.png end.png import.png mac_os.png
-scissors.png bug.png search.png umbrella.png apply16.png clipboard.png
-cursor_hand.png folder.png keyboard.png pdf.png pubmed32x32.png
-services.png wifi.png close.png delete.png formatting_right.png
-ruler.png settings2.png dna_helix.png globe.png lifebuoy.png
-sandglass.png settings2_26.png windows.png attach.png download.png
-line_chart.png save_as.png skip_to_start.png word.png add.png
+License: LGPL-2.1 Comment: On Debian systems, the complete text of the
+Apache license can be found in '/usr/share/common-licenses/LGPL-2.1' #
+********************************************************************************
-Citation from Web-site:
-Use Policy You can use it for your websites and applications for free. Just link to either
-You can’t modify the icons. These icons are distributed under a Creative Commons Attribution-No Derivative Works 3.0 Unported License
+File: visible.png 1.png border_color.png compact_camera.png edit.png
+ home.png scales.png stack_of_photos.png zip.png console.png end.png
+ import.png mac_os.png scissors.png bug.png search.png umbrella.png
+ apply16.png clipboard.png cursor_hand.png folder.png keyboard.png
+ pdf.png services.png wifi.png close.png delete.png
+ ruler.png settings2.png dna_helix.png globe.png
+ lifebuoy.png sandglass.png settings2_26.png windows.png attach.png
+ download.png line_chart.png save_as.png skip_to_start.png word.png
+ add.png
+Source: http://icons8.com/ http://www.visualpharm.com/
+Citation from Web-site: Use Policy You can use it for your websites
+ and applications for free. Just link to either You can’t modify the
+ icons. These icons are distributed under a Creative Commons
+ Attribution-No Derivative Works 3.0 Unported License
# ********************************************************************************
Modified: trunk/packages/strap-base/trunk/debian/rules
===================================================================
--- trunk/packages/strap-base/trunk/debian/rules 2012-07-22 15:53:12 UTC (rev 11865)
+++ trunk/packages/strap-base/trunk/debian/rules 2012-07-22 15:53:49 UTC (rev 11866)
@@ -12,13 +12,11 @@
#SRC_TMP := $(HOME)/tmp/build_strap-base
TARBALLS := $(CURDIR)/../tarballs
ORIG_TAR=$(TARBALLS)/strap-base_$(VERSION).orig.tar.gz
-MANFILE1 := ~/java/charite/christo/strap/strap-protein-alignment.1
override_dh_installdocs:
dh_installdocs
override_dh_auto_build:
- test -f $(MANFILE1) && cp -u $(MANFILE1) debian/strap-protein-alignment.1
cd $(SRC_TMP) && tar -xzf $(ORIG_TAR)
# Native program to manage GUI frames by frame title.
#It provides always-on-top, iconization, to-front etc.
Deleted: trunk/packages/strap-base/trunk/debian/strap-base.desktop
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap-base.desktop 2012-07-22 15:53:12 UTC (rev 11865)
+++ trunk/packages/strap-base/trunk/debian/strap-base.desktop 2012-07-22 15:53:49 UTC (rev 11866)
@@ -1,11 +0,0 @@
-[Desktop Entry]
-Version=1.0
-Name=Strap protein alignments
-Exec=/usr/bin/strap-protein-alignment
-Terminal=false
-# Icon=
-Type=Application
-MimeType=chemical/seq-aa-fasta;chemical/x-pdb;application/x-mfa;chemical/x-nexus;chemical/x-swissprot;chemical/seq-na-genbank;application/x-gp;chemical/seq-aa-genpept;
-Categories=Education;Science;Chemistry;
-GenericName=Strap protein alignments
-Comment=Sequence and structure alignments of proteins
Modified: trunk/packages/strap-base/trunk/debian/strap-base.install
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap-base.install 2012-07-22 15:53:12 UTC (rev 11865)
+++ trunk/packages/strap-base/trunk/debian/strap-base.install 2012-07-22 15:53:49 UTC (rev 11866)
@@ -1,4 +1,11 @@
strap-protein-alignment-1.jar usr/lib/strap-base
nativeTools_unix2 usr/lib/strap-base
-debian/bin/strap-protein-alignment usr/bin
-debian/strap-base.desktop usr/share/applications
+
+debian/bin/strap_to_fasta usr/bin
+debian/bin/strap_to_multiple_fasta usr/bin
+debian/bin/strap_to_clustal usr/bin
+debian/bin/strap_to_msf usr/bin
+debian/bin/strap_to_html usr/bin
+debian/bin/strap_to_word usr/bin
+debian/bin/strap_base usr/bin
+
Modified: trunk/packages/strap-base/trunk/debian/strap-base.links
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap-base.links 2012-07-22 15:53:12 UTC (rev 11865)
+++ trunk/packages/strap-base/trunk/debian/strap-base.links 2012-07-22 15:53:49 UTC (rev 11866)
@@ -1,2 +1,2 @@
-usr/share/man/man1/strap-protein-alignment.1 usr/share/man/man1/strap.1
-usr/bin/strap-protein-alignment usr/bin/strap
+usr/share/man/man1/strap_base.1 usr/share/man/man1/strap.1
+
Modified: trunk/packages/strap-base/trunk/debian/strap-base.manpages
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap-base.manpages 2012-07-22 15:53:12 UTC (rev 11865)
+++ trunk/packages/strap-base/trunk/debian/strap-base.manpages 2012-07-22 15:53:49 UTC (rev 11866)
@@ -1 +1,7 @@
-debian/strap-protein-alignment.1
+debian/strap_base.1
+debian/strap_to_fasta.1
+debian/strap_to_multiple_fasta.1
+debian/strap_to_clustal.1
+debian/strap_to_html.1
+debian/strap_to_word.1
+debian/strap_to_msf.1
Deleted: trunk/packages/strap-base/trunk/debian/strap-protein-alignment.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap-protein-alignment.1 2012-07-22 15:53:12 UTC (rev 11865)
+++ trunk/packages/strap-base/trunk/debian/strap-protein-alignment.1 2012-07-22 15:53:49 UTC (rev 11866)
@@ -1,304 +0,0 @@
-.TH Strap 1 "October 2011"
-.SH NAME
-
-
-Strap \- Graphical user interface to compare and align proteins by sequence and 3D-structure.
-.SH Synopsis
-
-.B strap-protein-alignment [\fIprotein_files\fR]
-
-.B strap-protein-alignment [\fIalignment_files\fR]
-
-.B strap-protein-alignment
-[\fIoptions\fR] [\fIprotein_files\fR] [\fIalignment_files\fR] [ @ \fIfile_with_list_of_protein_files\fR]
-
-
-
-.SH DESCRIPTION
-
-The free computer program Strap aligns proteins by sequence and
-3D-structure. Strap supports the simultaneous analysis of hundreds of
-proteins and integrates amino acid sequence, secondary structure,
-3D-structure and genomic- and mRNA-sequence. Using standard methods,
-alignments are computed automatically based on sequence and structure.
-Import and export of single proteins is very easy by Drag-and-Drop.
-
-.SS Home-Page
-
-http://3d-alignment.eu/
-
-http://www.bioinformatics.org/strap/
-
-.SH PROGRAM PARAMETERS
-
-.SS Protein/alignment files
-
-Strap can be started with protein files or alignment files as parameters.
-The following formats are supported: PDB, Swissprot, Embl, Genbank,
-GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
-Pfam, Stockholm and HSSP.
-
-If at least one protein file is specified, Strap will choose the
-current working directory as the project directory. Otherwise the
-project directory is requested at the beginning of the session.
-
-
-Files with a leading \fB@\fR sign or preceded by a \fB@\fR sign are
-interpreted as lists of files.
-
-\fBCurly parenthesis\fR are used for placing sequences into the same
-alignment row. At the UNIX command prompt, the parentheses need to be
-quoted. For example \fB'{'\fR \fIprotein1.seq protein2.seq\fR
-\fB'}' '{'\fR \fIprotein3.seq protein4.seq protein5.seq \fR \fB'}'\fR
-would put two proteins into the first and three proteins into the
-second alignment row. If there are more than one sequences in a row,
-only the top most sequence is displayed.
-
-
-
-
-
-.SS File Compression
-
-The following file compression methods are supported: .gz, .bz2 and .Z
-
-.SS Parts of proteins
-
-To display only a subset of a protein, a suffix is appended to the
-protein file name.
-Residue subsets are specified by an exclamation mark and a subset
-expression after the protein file. Example:
-"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
-refer to pdb-residue numbers use the Rasmol/Jmol syntax \fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
-
-.SH OPTIONS
-
-Program options start with a dash. The values \fBtrue\fR and
-\fBfalse\fR can be abbreviated by \fBt\fR and \fBf\fR. The "=true" or
-"=t" can be ommitted. For example \fB-noSeqres=true\fR can be written
-as \fB-noSeqres=t\fR or \fB-noSeqres\fR. For most settings there is an
-equivalent check-box or choice menu in the graphical user interface.
-
-If the Web-start script http://www.bioinformatics.org/strap/strap.php
-is started, the options are given as web-variable without the leading
-dash. For example for -noSeqres include \fBnoSeqres=t\fR into the
-URL.
-
-\fB-help\fR
-
-Prints this text
-
-\fB-manual\fR
-
-Generates a comprehensive manual for the web browser.
-
-\fB\-noSeqres\fR
-
- Skip SEQRES lines of PDB files.
-
-\fB\-noIdentical\fR
-
-Do not load a sequence identical to an already loaded one.
-
-\fB\-dialog\fR=\fIJavaClassNameOfDialog\fR
-
-Opens a certain dialog at start.
-The class name of a dialog is the tab-text can be obtained by opening the help text.
-
-Examples: -dialog=DialogAlign or -dialog=DialogBlast or or -dialog=DialogDotPlot
-
-\fB\-script\fR=\fIURL_or_FilePath_or_ScriptText\fR
-
-Runs a script at start. See http://www.bioinformatics.org/strap/web/strap_script.html.
-Script files in the current directory should be written with a leading
-"./" like "./myScript.txt" since Strap recognizes files by the
-presence of a slash and the absence of white space and colon.
-
-Two or more script files can be given:
--script5=\fIhttp://...../file\fR -script7=\fIhttp://...../file\fR.
-The optional number suffix defines the order of consecutively executed scripts.
-
-Script commands can be given directly. Assume there are protein files
-in PDB format loaded by Strap. The option -script="open_3D viewName,
-*" would display all proteins with 3D-coordinates three-dimensionally
-(See -v3d=). Scripts consisting of more than one line should be
-stored in a file and the file path or URL should be given.
-
-Example:
-
--script2="open_3D viewName, *" -script3="3D_select $ALL" -script7="3D_ribbons on" -script8="superimpose *"
-
-\fB\-dasRegistry\fR=\fISpace-separated list of URLs of alternative DAS-registries\fR
-
-Only needed for DAS servers that are
-
-\fB\-s3d\fR=\fIJavaClass\fR
-
-Sets the Java class to superimpose proteins.
-
-A short name can be used such as "tm_align" for "Superimpose_TM_align".
-
-Example: -s3d=tm_align or -s3d=ce or -s3d=gangstaplus
-
-\fB\-a3d\fR=\fIJavaClass\fR
-
-Sets the Java class to compute structure based sequence alignments.
-
-Examples: -a3d=tm_align or -a3d=mapsci or -a3d=matt or -a3d=mustang
-
-\fB\-v3d\fR=\fIJavaClass\fR
-
-Sets the Java class to display 3D-structures.
-
-Example: -v3d=jmol or -v3d=pymol or -v3d=astex
-
-\fB\-aligner2\fR=\fIJavaClass\fR
-
-Sets the Java class for aligning two amino acid sequences. Preferably an implementation in Java because native executables take longer to start.
-Default value is PairAlignerNeoBioPROXY.
-
-Example: -aligner2=MultipleAlignerClustalW
-
-
-\fB\-log3d\fR
-
-All 3D-commands which are sent to 3D-protein viewers are printed to stdout.
-
-\fB\-useDebian=false\fR \fB\-useDebian=true\fR
-
-If set to true, use the Debian packages for external programs rather
-than the program versions included in Strap. For example Strap would
-use /usr/bin/pymol instead of downloading and using the Pymol from
-http://www.bioinformatics.org/strap/Binaries/.
-
-\fB\-sysProxies=true\fR or \fB-probeWebProxy=true\fR or \fB-probeWebProxy=false\fR
-
-See section Web proxies.
-
-\fB\-noCache\fR
-
- Do not use cached results of previous
-computations. This setting can be changed in the graphical user
-interface with a check-box.
-
-This setting influences the result of searches in growing
-databases. For example consider the similarity search method
-Blast. With the cache turned on, Strap would present a previously
-computed Blast result even though new sequences might have been
-published since last run.
-
-\fB\-keepFiles\fR
-
-Do not delete temp-files after the session. This is only important for
-debugging.
-
-\fB\-Xmx500m\fR
-
-This is an option of the java command and not of Strap.
-It sets the heap size to 500 Megabyte.
-
-\fB\-geometry=\fI666x333+11+22\fR
-
-Sets the size and location of the application frame to width 666,
-height 333, horizontal screen position 11 and vertical position 22;
-
-\fB\-laf=\fIlookAndFeel\fR
-
-Examples:
-
--laf=com.sun.java.swing.plaf.motif.MotifLookAndFeel ( or short -laf=m)
-
--laf=com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel ( or short -laf=N)
-
--laf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel ( or short -laf=G)
-
--laf=javax.swing.plaf.metal.MetalLookAndFeel ( or short -laf=M)
-
-Also non-standard Look'n Feels can be used. Consider tinylaf which
-can be installed as a Debian package. The following two options would
-apply tinylaf:
-
- \fB-cp=\fR/usr/share/java/tinylaf.jar
--laf=de.muntjak.tinylookandfeel.TinyLookAndFeel
-
-See also http://en.wikipedia.org/wiki/Look_and_feel.
-
-\fB\-toMultipleFasta\fR or \fB\-toClustal\fR or \fB\-toFasta\fR \fIProtein or alignment files\fR
-
-Loads the proteins and generates protein or ungapped multiple sequence
-files with the respective format. The file paths are written to
-stdout. The program terminates.
-
-.SS Security
-
-\fB\-askUpload\fR[=t/f] The user is asked each time data is uploaded
-to remote servers. The user might not want unpublished sequences to be
-sent to servers.
-
-\fB\-askExec\fR[=t/f] The user is asked when an external program is
-executed. Executing native programs might be regarded as security
-risk. There is a positive and a negative list which can be edited in
-the menu "Security" of the Preferences-menu.
-
-\fB\-allowFileModification\fR According to the default policy, files
-are only modified, created or deleted if they reside in the project
-directory or if the file path contains "StrapAlign". This is to
-prevent files to be lost. With this option file modification control
-is deactivated.
-
-.SH PROJECT DIRECTORY
-
-The project directory holds information for gaps, 3D-transformations,
-annotations and exported files. Usually, the protein files are also
-located in the project directory. The project directory path must not
-contain white space, such as "My data" or "Eigene Dateien". Therefore
-the project directory can usually not be located in the home directory
-on Windows-XP.
-
-.SH WEB-PROXY
-
-With the option \fB-probeWebProxy=t\fR, strap attempts to access the Web in
-three different ways: (1) Directly, without Web-proxy (2) With the
-settings found in the environment variable http_proxy and (3) using
-the default mechanism of Java to apply the system wide settings. With the
-setting \fB-probeWebProxy=f\fR, however, Strap will directly connect to the
-Internet. with the option \fB-sysProxies=t\fR Strap will use the
-Java-built-in mechanism to find the system wide settings, (which might
-not work properly, depending on the Java system).
-
-.SH ALIGNMENT-FILE-EXPORT
-
-Supported formats are Multiple-Fasta, ClustalW, MSF, HSSP. A
-colorized alignment with highlighted residue selections and secondary
-structure can be exported in HTML and PDF. The colorized HTML output
-can be modified in MS-Word or other text processors. The rendering
-styles of the PDF output can be stored in annotations of residue
-selections.
-
-.SH 3D-VISUALIZATION
-
-The following 3D-protein viewers are tightly linked with the alignment
-view: Pymol, Jmol, OpenAstex. The rendering styles can be stored
-within residue selections. There is a generic Rasmol like scripting
-language which can be applied to all embedded visualization software.
-If the desired effect can not be achieved with this generic commands,
-also specific commands can be associated with residue
-selections.
-
-.SH COPYRIGHT
-
-Christoph Gille \(co 1999-2011
-
-License GPL
-
-.SH "SEE ALSO"
-
-A comprehensive manual is created with the option \fB-manual\fR
-
-.BR jalview (1)
-.BR clustalx (1)
-.BR seaview (1)
-.BR boxshade (1)
-.BR pymol (1)
-.BR openastex (1)
-.BR strap-text-viewer (1)
Copied: trunk/packages/strap-base/trunk/debian/strap_base.1 (from rev 11833, trunk/packages/strap-base/trunk/debian/strap-protein-alignment.1)
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_base.1 (rev 0)
+++ trunk/packages/strap-base/trunk/debian/strap_base.1 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,372 @@
+.\"" Do not edit this file. It has been generated from templateGui.1 with /usr/bin/gpp
+.TH Strap 1 "October 2011"
+.SH NAME
+
+Strap \- Graphical user interface to compare and align proteins by sequence and 3D-structure.
+
+strap_base is intended to be run from other programs which use strap as a viewer.
+Strap users should install the package strap which installs also all required debian packages.
+
+
+.SH Synopsis
+
+.B strap_base [\fIprotein_files\fR] [\fIalignment_files\fR]
+
+.B strap_base -script=[\fIURL or File\fR]
+
+.B strap_base -align="PDB:\fIid1\fR PDB:\fIid2\fR UNIPROT:\fIid3\fR PFAM:\fIPF0...\fR ... "
+
+.B strap_base
+[\fIoptions\fR] [\fIprotein_files\fR] [\fIalignment_files\fR] [ @ \fIfile_with_list_of_protein_files\fR]
+
+
+
+.SH DESCRIPTION
+
+The free computer program Strap aligns proteins by sequence and
+3D-structure. Strap supports the simultaneous analysis of hundreds of
+proteins and integrates amino acid sequence, secondary structure,
+3D-structure and genomic- and mRNA-sequence. Using standard methods,
+alignments are computed automatically based on sequence and structure.
+Import and export of single proteins is very easy by Drag-and-Drop.
+
+.SS Home-Page
+
+http://3d-alignment.eu/
+
+http://www.bioinformatics.org/strap/
+
+.SH PROGRAM PARAMETERS
+
+.SS Protein/alignment files
+
+Strap can be started with protein files or alignment files as parameters.
+The following formats are supported: PDB, Swissprot, Embl, Genbank,
+GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
+Pfam, Stockholm and HSSP.
+
+If at least one protein file is specified, Strap will choose the
+current working directory as the project directory. Otherwise the
+project directory is requested at the beginning of the session.
+
+
+Files preceded by a \fB@\fR sign are interpreted as lists of files.
+
+\fBCurly parenthesis\fR are used for placing sequences into the same
+alignment row. At the UNIX command prompt, the parentheses need to be
+quoted. For example \fB'{'\fR \fIprotein1.seq protein2.seq\fR
+\fB'}' '{'\fR \fIprotein3.seq protein4.seq protein5.seq \fR \fB'}'\fR
+would put two proteins into the first and three proteins into the
+second alignment row. If there are more than one sequences in a row,
+only the top most sequence is displayed.
+
+
+.SS Loading of protein entries from remote databases:
+
+The command line options \fB-load="\fR\fI space separated list of
+database entries \fR\fB"\fR loads proteins or alignments given as URL
+or database-colon-id. The option \fB-load="\fR\fI ... \fR\fB"\fR also
+aligns the downloaded proteins.
+
+
+
+.SS File Compression
+
+Supported: .gz, .bz2 and .Z
+
+.SS Parts of proteins
+
+To display only a subset of a protein, a suffix is appended to the
+protein file name.
+Residue subsets are specified by an exclamation mark and a subset
+expression after the protein file. Example:
+"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
+refer to pdb-residue numbers use the Rasmol/Jmol syntax \fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
+
+.SH OPTIONS
+
+Program options start with a dash. The values \fBtrue\fR and
+\fBfalse\fR can be abbreviated by \fBt\fR and \fBf\fR. The "=true" or
+"=t" can be ommitted. For example \fB-noSeqres=true\fR can be written
+as \fB-noSeqres=t\fR or \fB-noSeqres\fR. For most settings there is an
+equivalent check-box or choice menu in the graphical user interface.
+
+If the Web-start script http://www.bioinformatics.org/strap/strap.php
+is started, the options are given as web-variable without the leading
+dash. For example for -noSeqres include \fBnoSeqres=t\fR into the
+URL.
+
+\fB-help\fR
+
+Prints this manual
+
+\fB-manual\fR
+
+Generates a comprehensive manual for the web browser.
+
+\fB\-noSeqres\fR
+
+ Skip SEQRES lines of PDB files.
+
+\fB\-noIdentical\fR
+
+Do not load a sequence identical to an already loaded one.
+
+\fB\-dialog\fR=\fIJavaClassNameOfDialog\fR
+
+Opens a certain dialog at start.
+The class name of a dialog is the tab-text can be obtained by opening the help text.
+
+Examples: -dialog=DialogAlign or -dialog=DialogBlast or or -dialog=DialogDotPlot
+
+\fB\-script\fR=\fIURL_or_FilePath_or_ScriptText\fR
+
+Runs a script at start. See http://www.bioinformatics.org/strap/web/strap_script.html.
+Script files in the current directory should be written with a leading
+"./" like "./myScript.txt" since Strap recognizes files by the
+presence of a slash and the absence of white space and colon.
+
+Two or more script files can be given:
+-script5=\fIhttp://...../file\fR -script7=\fIhttp://...../file\fR.
+The optional number suffix defines the order of consecutively executed scripts.
+
+Script commands can be given directly. Assume there are protein files
+in PDB format loaded by Strap. The option
+-script="open_3D viewName, *"
+would display all proteins with 3D-coordinates three-dimensionally
+(See -v3d=). Scripts consisting of more than one line should be
+stored in a file and the file path or URL should be given.
+
+Example:
+
+-script2="open_3D viewName, *" -script3="3D_select $ALL" -script7="3D_ribbons on" -script8="superimpose *"
+
+\fB\-dasRegistry\fR=\fISpace-separated list of URLs of alternative DAS-registries\fR
+
+Only needed for DAS servers that are
+
+\fB\-s3d\fR=\fIJavaClass\fR
+
+Sets the Java class to superimpose proteins.
+
+A short name can be used such as "tm_align" for "Superimpose_TM_align".
+
+Example: -s3d=tm_align or -s3d=ce or -s3d=gangstaplus
+
+\fB\-a3d\fR=\fIJavaClass\fR
+
+Sets the Java class to compute structure based sequence alignments.
+
+Examples: -a3d=tm_align or -a3d=mapsci or -a3d=matt or -a3d=mustang
+
+\fB\-v3d\fR=\fIJavaClass\fR
+
+Sets the Java class to display 3D-structures.
+
+Example: -v3d=jmol or -v3d=pymol or -v3d=astex
+
+\fB\-aligner2\fR=\fIJavaClass\fR
+
+Sets the Java class for aligning two amino acid sequences. Preferably an implementation in Java because native executables take longer to start.
+Default value is PairAlignerNeoBioPROXY.
+
+Example: -aligner2=MultipleAlignerClustalW
+
+
+\fB\-alignerP\fR=\fIJavaClass\fR
+
+Sets the Java class for aligning sequences and structures.
+The default value is clustalW.
+
+Example: -alignerP=t_coffee
+
+
+\fB\-log3d\fR
+
+All 3D-commands which are sent to 3D-protein viewers are printed to stdout.
+
+\fB\-useDebian=false\fR \fB\-useDebian=true\fR
+
+If set to true, use the Debian packages for external programs rather
+than the program versions included in Strap. For example Strap would
+use /usr/bin/pymol instead of downloading and using the Pymol from
+http://www.bioinformatics.org/strap/Binaries/.
+
+\fB\-sysProxies=true\fR or \fB-probeWebProxy=true\fR or \fB-probeWebProxy=false\fR
+
+See section Web proxies.
+
+\fB\-noCache\fR
+
+ Do not use cached results of previous
+computations. This setting can be changed in the graphical user
+interface with a check-box.
+
+This setting influences the result of searches in growing
+databases. For example consider the similarity search method
+Blast. With the cache turned on, Strap would present a previously
+computed Blast result even though new sequences might have been
+published since last run.
+
+\fB\-keepFiles\fR
+
+Do not delete temp-files after the session. This is only important for
+debugging.
+
+\fB\-Xmx500m\fR
+
+This is an option of the java command and not of Strap.
+It sets the heap size to 500 Megabyte.
+
+\fB\-geometry=\fI666x333+11+22\fR
+
+Sets the size and location of the application frame to width 666,
+height 333, horizontal screen position 11 and vertical position 22;
+
+\fB\-laf=\fIlookAndFeel\fR
+
+Examples:
+
+-laf=com.sun.java.swing.plaf.motif.MotifLookAndFeel ( or short -laf=m)
+
+-laf=com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel ( or short -laf=N)
+
+-laf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel ( or short -laf=G)
+
+-laf=javax.swing.plaf.metal.MetalLookAndFeel ( or short -laf=M)
+
+Also non-standard Look-and-Feels can be used. Consider tinylaf which
+can be installed as a Debian package. The following two options would
+apply tinylaf:
+
+ \fB-cp=\fR/usr/share/java/tinylaf.jar
+-laf=de.muntjak.tinylookandfeel.TinyLookAndFeel
+
+See also http://en.wikipedia.org/wiki/Look_and_feel.
+
+\fB\-toFasta\fR \fIProtein or alignment files\fR
+
+Generates a sequence file in Fasta format for each loaded protein.
+
+
+
+.SS Security
+
+\fB\-askUpload\fR[=t/f] The user is asked each time data is uploaded
+to remote servers. The user might not want unpublished sequences to be
+sent to servers.
+
+\fB\-askExec\fR[=t/f] The user is asked when an external program is
+executed. Executing native programs might be regarded as security
+risk. There is a positive and a negative list which can be edited in
+the menu "Security" of the Preferences-menu.
+
+\fB\-allowFileModification\fR According to the default policy, files
+are only modified, created or deleted if they reside in the project
+directory or if the file path contains "StrapAlign". This is to
+prevent files to be lost. With this option file modification control
+is deactivated.
+
+
+.SH ALIGNMENT FILE GENERATION
+
+With the options \fB\-toMultipleFasta\fR or \fB\-toClustal\fR or
+\fB\-toMSF\fR or \fB\-toHTML\fR or \fB\-toWord\fR, Strap can be used as a command line
+tool to generate multiple sequence alignment files. The protein or
+alignment files given in the command line are loaded and the output
+file is generated. Finally the program terminates. Prior file export, the
+proteins may be aligned:
+
+.B strap_base [\fIalignment_files\fR] -script="align *" -toMSF
+
+
+.SS Alignment format
+
+Comma separated display options can be appended directly (!no space) after the output file name.
+
+ w=\fIresidues per line\fR Setting output width
+
+ r=\fIcolumn range\fR Example: 20-30
+
+ r=\fIresidue position range\fR Example: aProtein/10-20
+
+
+
+ The following are valid only for html and word processor output:
+
+ h=\fI%conservation\fR Residues with higher conservation are highlighted.
+
+ s=\fIschading\fR shading= black|charge|hydropathy|chemical|nucleotide.
+
+ Example: -toHTML=output.html,w=70,h=55,s=hydropathy
+
+
+
+
+
+.SS Residue annotations in HTML alignment output.
+
+Residue positions to be highlighted in the html output need to
+be defined with script commands. See option \fB\-script=\fR\fISript-file\fR.
+The script command \fInew_aminoacid_selection\fR is used to create a new
+selection object and the commands \fIadd_annotation\fR or \fIset_annotation\fR are
+used to attach information. The script may also be used to
+define the [gapped] amino acid sequences.
+
+
+.SH PROJECT DIRECTORY
+
+The project directory holds information for gaps, 3D-transformations,
+annotations and exported files. Usually, the protein files are also
+located in the project directory. The project directory path must not
+contain white space, such as "My data" or "Eigene Dateien". Therefore
+the project directory can usually not be located in the home directory
+on Windows-XP.
+
+.SH WEB-PROXY
+
+With the option \fB-probeWebProxy=t\fR, strap attempts to access the Web in
+three different ways: (1) Directly, without Web-proxy (2) With the
+settings found in the environment variable http_proxy and (3) using
+the default mechanism of Java to apply the system wide settings. With the
+setting \fB-probeWebProxy=f\fR, however, Strap will directly connect to the
+Internet. with the option \fB-sysProxies=t\fR Strap will use the
+Java-built-in mechanism to find the system wide settings, (which might
+not work properly, depending on the Java system).
+
+.SH ALIGNMENT-FILE-EXPORT
+
+Supported formats are Multiple-Fasta, ClustalW, MSF, HSSP. A
+colorized alignment with highlighted residue selections and secondary
+structure can be exported in HTML and PDF. The colorized HTML output
+can be modified in MS-Word or other text processors. The rendering
+styles of the PDF output can be stored in annotations of residue
+selections.
+
+.SH 3D-VISUALIZATION
+
+The following 3D-protein viewers are tightly linked with the alignment
+view: Pymol, Jmol, OpenAstex. The rendering styles can be stored
+within residue selections. There is a generic Rasmol like scripting
+language which can be applied to all embedded visualization software.
+If the desired effect can not be achieved with this generic commands,
+also specific commands can be associated with residue
+selections.
+
+.SH COPYRIGHT
+
+Christoph Gille \(co 1999-2012
+
+License GPL
+
+.SH "SEE ALSO"
+
+A comprehensive manual is created with the option \fB-manual\fR
+
+.BR jalview (1)
+.BR clustalx (1)
+.BR seaview (1)
+.BR boxshade (1)
+.BR pymol (1)
+.BR openastex (1)
+.BR strap-text-viewer (1)
Added: trunk/packages/strap-base/trunk/debian/strap_to_clustal.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_clustal.1 (rev 0)
+++ trunk/packages/strap-base/trunk/debian/strap_to_clustal.1 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,100 @@
+.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp
+.TH strap_to_clustal 1 "Mai 2012"
+.SH NAME
+strap_to_clustal \- Reads amino acid sequences and creates a multiple sequence alignment file in clustal format.
+
+.SH SYNOPSIS
+
+strap_to_clustal [\fIprotein or alignment files\fR]
+
+strap_to_clustal [\fIprotein or alignment files\fR] -o=\fIoutput-file\fR
+
+strap_to_clustal [\fIprotein or alignment files\fR] -script="align *"
+
+
+
+.SH DESCRIPTION
+
+Amino acid sequences are loaded from input files or are defined using
+the scripting languages.
+A single alignment file with all sequence is created using clustal format
+
+
+
+.SH INPUT FILES
+
+The amino acid sequences are extracted from alignment files and protein files.
+A large number of different formats are supported: PDB, Swissprot, Embl, Genbank,
+GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
+Pfam, Stockholm and HSSP.
+
+.SS File Compression
+
+Supported are .gz, .bz2 and .Z.
+
+.SS Parts of proteins
+
+To load only a subset of a proteins, a suffix is appended to the name of the
+protein input file. Residue subsets are specified by an exclamation
+mark and a subset expression after the protein file. Example:
+"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
+refer to pdb-residue numbers use the Rasmol/Jmol syntax
+\fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
+
+.SH OPTIONS
+\fB-o\fR=\fIoutput-file\fR Specifies an output file
+.SS Alignment format
+
+Comma separated display options can be appended directly (!no space) after the output file name.
+
+ w=\fIresidues per line\fR Setting output width
+
+ r=\fIcolumn range\fR Example: 20-30
+
+ r=\fIresidue position range\fR Example: aProtein/10-20
+
+
+\fB-script\fR=\fIscript-line\fR
+\fB-script\fR=\fIfile\fR or
+\fB-script\fR=\fIURL\fR
+Each script line starts with a strap command and may be followed by arguments.
+The script is run line by line.
+For example the line "align *" aligns all proteins using the current alignment backends (Default: ClustalW, TM-align).
+Instead of computing the alignment, the gapped sequences can be defined in the script.
+In this case no sequence files need to be given and the align command is not required.
+In HTML output various information can be specified: Important positions can be highlighted, an icon for each protein and
+the secondary structure to be displayed. This information is provided with script commands.
+See http://www.bioinformatics.org/strap/strap4services.html for details.
+
+.SH LIMITATIONS
+
+Currently, the cache for alignment results should be accessed only by one instance at a time.
+If several instances of Strap are run at the same time (e.g. from web server) the cache may become corrupted.
+Workaround: Deactivate the cache with the option -noCache.
+If you do need a cache in a web server environment, please send a request for feature to the author.
+
+
+.SH HOME-PAGE
+
+http://3d-alignment.eu/
+
+http://www.bioinformatics.org/strap/
+
+
+.SH COPYRIGHT
+
+Christoph Gille \(co 1999-2012
+
+License GPL
+
+.SH "SEE ALSO"
+.BR strap_to_clustal (1)
+.BR strap_to_msf (1)
+.BR strap_to_fasta (1)
+.BR strap_to_multiple_fasta (1)
+.BR strap_to_html (1)
+.BR strap_to_word (1)
+.BR strap_protein_alignment (1)
+.BR sequenceconverter (1)
+.BR cdbfasta (1)
+.BR squizz (1)
Added: trunk/packages/strap-base/trunk/debian/strap_to_fasta.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_fasta.1 (rev 0)
+++ trunk/packages/strap-base/trunk/debian/strap_to_fasta.1 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,65 @@
+.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp
+.TH strap_to_fasta 1 "Mai 2012"
+.SH NAME
+strap_to_fasta \- Reads amino acid sequences and creates a fasta formated sequence file for each sequence.
+
+.SH SYNOPSIS
+
+strap_to_fasta [\fIprotein or alignment files\fR]
+
+
+
+.SH DESCRIPTION
+
+Amino acid sequences are loaded from input files or are defined using
+the scripting languages.
+ For each loaded sequence a fasta file is written.
+
+
+
+.SH INPUT FILES
+
+The amino acid sequences are extracted from alignment files and protein files.
+A large number of different formats are supported: PDB, Swissprot, Embl, Genbank,
+GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
+Pfam, Stockholm and HSSP.
+
+.SS File Compression
+
+Supported are .gz, .bz2 and .Z.
+
+.SS Parts of proteins
+
+To load only a subset of a proteins, a suffix is appended to the name of the
+protein input file. Residue subsets are specified by an exclamation
+mark and a subset expression after the protein file. Example:
+"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
+refer to pdb-residue numbers use the Rasmol/Jmol syntax
+\fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
+
+
+
+.SH HOME-PAGE
+
+http://3d-alignment.eu/
+
+http://www.bioinformatics.org/strap/
+
+
+.SH COPYRIGHT
+
+Christoph Gille \(co 1999-2012
+
+License GPL
+
+.SH "SEE ALSO"
+.BR strap_to_clustal (1)
+.BR strap_to_msf (1)
+.BR strap_to_fasta (1)
+.BR strap_to_multiple_fasta (1)
+.BR strap_to_html (1)
+.BR strap_to_word (1)
+.BR strap_protein_alignment (1)
+.BR sequenceconverter (1)
+.BR cdbfasta (1)
+.BR squizz (1)
Added: trunk/packages/strap-base/trunk/debian/strap_to_html.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_html.1 (rev 0)
+++ trunk/packages/strap-base/trunk/debian/strap_to_html.1 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,117 @@
+.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp
+.TH strap_to_html 1 "Mai 2012"
+.SH NAME
+strap_to_html \- Reads amino acid sequences and creates an alignment view for web browsers.
+
+.SH SYNOPSIS
+
+strap_to_html [\fIprotein or alignment files\fR]
+
+strap_to_html [\fIprotein or alignment files\fR] -o=\fIoutput-file\fR
+
+strap_to_html [\fIprotein or alignment files\fR] -script="align *"
+
+
+
+.SH DESCRIPTION
+
+Amino acid sequences are loaded from input files or are defined using
+the scripting languages.
+ A html file with the rendered alignment is written. It can be viewed in a web browser.
+
+
+
+.SH INPUT FILES
+
+The amino acid sequences are extracted from alignment files and protein files.
+A large number of different formats are supported: PDB, Swissprot, Embl, Genbank,
+GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
+Pfam, Stockholm and HSSP.
+
+.SS File Compression
+
+Supported are .gz, .bz2 and .Z.
+
+.SS Parts of proteins
+
+To load only a subset of a proteins, a suffix is appended to the name of the
+protein input file. Residue subsets are specified by an exclamation
+mark and a subset expression after the protein file. Example:
+"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
+refer to pdb-residue numbers use the Rasmol/Jmol syntax
+\fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
+
+.SH OPTIONS
+\fB-o\fR=\fIoutput-file\fR Specifies an output file
+.SS Alignment format
+
+Comma separated display options can be appended directly (!no space) after the output file name.
+
+ w=\fIresidues per line\fR Setting output width
+
+ r=\fIcolumn range\fR Example: 20-30
+
+ r=\fIresidue position range\fR Example: aProtein/10-20
+
+
+ The following are valid only for html and word processor output:
+
+ h=\fI%conservation\fR Residues with higher conservation are highlighted.
+
+ s=\fIschading\fR shading= black|charge|hydropathy|chemical|nucleotide.
+
+ Example: -toHTML=output.html,w=70,h=55,s=hydropathy
+
+
+\fB-script\fR=\fIscript-line\fR
+\fB-script\fR=\fIfile\fR or
+\fB-script\fR=\fIURL\fR
+Each script line starts with a strap command and may be followed by arguments.
+The script is run line by line.
+For example the line "align *" aligns all proteins using the current alignment backends (Default: ClustalW, TM-align).
+Instead of computing the alignment, the gapped sequences can be defined in the script.
+In this case no sequence files need to be given and the align command is not required.
+In HTML output various information can be specified: Important positions can be highlighted, an icon for each protein and
+the secondary structure to be displayed. This information is provided with script commands.
+See http://www.bioinformatics.org/strap/strap4services.html for details.
+.SS Residue annotations in HTML alignment output.
+
+Residue positions to be highlighted in the html output need to
+be defined with script commands. See option \fB\-script=\fR\fISript-file\fR.
+The script command \fInew_aminoacid_selection\fR is used to create a new
+selection object and the commands \fIadd_annotation\fR or \fIset_annotation\fR are
+used to attach information. The script may also be used to
+define the [gapped] amino acid sequences.
+
+.SH LIMITATIONS
+
+Currently, the cache for alignment results should be accessed only by one instance at a time.
+If several instances of Strap are run at the same time (e.g. from web server) the cache may become corrupted.
+Workaround: Deactivate the cache with the option -noCache.
+If you do need a cache in a web server environment, please send a request for feature to the author.
+
+
+.SH HOME-PAGE
+
+http://3d-alignment.eu/
+
+http://www.bioinformatics.org/strap/
+
+
+.SH COPYRIGHT
+
+Christoph Gille \(co 1999-2012
+
+License GPL
+
+.SH "SEE ALSO"
+.BR strap_to_clustal (1)
+.BR strap_to_msf (1)
+.BR strap_to_fasta (1)
+.BR strap_to_multiple_fasta (1)
+.BR strap_to_html (1)
+.BR strap_to_word (1)
+.BR strap_protein_alignment (1)
+.BR sequenceconverter (1)
+.BR cdbfasta (1)
+.BR squizz (1)
Added: trunk/packages/strap-base/trunk/debian/strap_to_msf.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_msf.1 (rev 0)
+++ trunk/packages/strap-base/trunk/debian/strap_to_msf.1 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,100 @@
+.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp
+.TH strap_to_msf 1 "Mai 2012"
+.SH NAME
+strap_to_msf \- Reads amino acid sequences and creates a multiple sequence alignment file in msf format.
+
+.SH SYNOPSIS
+
+strap_to_msf [\fIprotein or alignment files\fR]
+
+strap_to_msf [\fIprotein or alignment files\fR] -o=\fIoutput-file\fR
+
+strap_to_msf [\fIprotein or alignment files\fR] -script="align *"
+
+
+
+.SH DESCRIPTION
+
+Amino acid sequences are loaded from input files or are defined using
+the scripting languages.
+A single alignment file with all sequence is created using msf format
+
+
+
+.SH INPUT FILES
+
+The amino acid sequences are extracted from alignment files and protein files.
+A large number of different formats are supported: PDB, Swissprot, Embl, Genbank,
+GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
+Pfam, Stockholm and HSSP.
+
+.SS File Compression
+
+Supported are .gz, .bz2 and .Z.
+
+.SS Parts of proteins
+
+To load only a subset of a proteins, a suffix is appended to the name of the
+protein input file. Residue subsets are specified by an exclamation
+mark and a subset expression after the protein file. Example:
+"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
+refer to pdb-residue numbers use the Rasmol/Jmol syntax
+\fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
+
+.SH OPTIONS
+\fB-o\fR=\fIoutput-file\fR Specifies an output file
+.SS Alignment format
+
+Comma separated display options can be appended directly (!no space) after the output file name.
+
+ w=\fIresidues per line\fR Setting output width
+
+ r=\fIcolumn range\fR Example: 20-30
+
+ r=\fIresidue position range\fR Example: aProtein/10-20
+
+
+\fB-script\fR=\fIscript-line\fR
+\fB-script\fR=\fIfile\fR or
+\fB-script\fR=\fIURL\fR
+Each script line starts with a strap command and may be followed by arguments.
+The script is run line by line.
+For example the line "align *" aligns all proteins using the current alignment backends (Default: ClustalW, TM-align).
+Instead of computing the alignment, the gapped sequences can be defined in the script.
+In this case no sequence files need to be given and the align command is not required.
+In HTML output various information can be specified: Important positions can be highlighted, an icon for each protein and
+the secondary structure to be displayed. This information is provided with script commands.
+See http://www.bioinformatics.org/strap/strap4services.html for details.
+
+.SH LIMITATIONS
+
+Currently, the cache for alignment results should be accessed only by one instance at a time.
+If several instances of Strap are run at the same time (e.g. from web server) the cache may become corrupted.
+Workaround: Deactivate the cache with the option -noCache.
+If you do need a cache in a web server environment, please send a request for feature to the author.
+
+
+.SH HOME-PAGE
+
+http://3d-alignment.eu/
+
+http://www.bioinformatics.org/strap/
+
+
+.SH COPYRIGHT
+
+Christoph Gille \(co 1999-2012
+
+License GPL
+
+.SH "SEE ALSO"
+.BR strap_to_clustal (1)
+.BR strap_to_msf (1)
+.BR strap_to_fasta (1)
+.BR strap_to_multiple_fasta (1)
+.BR strap_to_html (1)
+.BR strap_to_word (1)
+.BR strap_protein_alignment (1)
+.BR sequenceconverter (1)
+.BR cdbfasta (1)
+.BR squizz (1)
Added: trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1 (rev 0)
+++ trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,100 @@
+.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp
+.TH strap_to_multiple_fasta 1 "Mai 2012"
+.SH NAME
+strap_to_multiple_fasta \- Reads amino acid sequences and creates a multiple fast file.
+
+.SH SYNOPSIS
+
+strap_to_multiple_fasta [\fIprotein or alignment files\fR]
+
+strap_to_multiple_fasta [\fIprotein or alignment files\fR] -o=\fIoutput-file\fR
+
+strap_to_multiple_fasta [\fIprotein or alignment files\fR] -script="align *"
+
+
+
+.SH DESCRIPTION
+
+Amino acid sequences are loaded from input files or are defined using
+the scripting languages.
+A single alignment file with all sequence is created using fasta format
+
+
+
+.SH INPUT FILES
+
+The amino acid sequences are extracted from alignment files and protein files.
+A large number of different formats are supported: PDB, Swissprot, Embl, Genbank,
+GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
+Pfam, Stockholm and HSSP.
+
+.SS File Compression
+
+Supported are .gz, .bz2 and .Z.
+
+.SS Parts of proteins
+
+To load only a subset of a proteins, a suffix is appended to the name of the
+protein input file. Residue subsets are specified by an exclamation
+mark and a subset expression after the protein file. Example:
+"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
+refer to pdb-residue numbers use the Rasmol/Jmol syntax
+\fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
+
+.SH OPTIONS
+\fB-o\fR=\fIoutput-file\fR Specifies an output file
+.SS Alignment format
+
+Comma separated display options can be appended directly (!no space) after the output file name.
+
+ w=\fIresidues per line\fR Setting output width
+
+ r=\fIcolumn range\fR Example: 20-30
+
+ r=\fIresidue position range\fR Example: aProtein/10-20
+
+
+\fB-script\fR=\fIscript-line\fR
+\fB-script\fR=\fIfile\fR or
+\fB-script\fR=\fIURL\fR
+Each script line starts with a strap command and may be followed by arguments.
+The script is run line by line.
+For example the line "align *" aligns all proteins using the current alignment backends (Default: ClustalW, TM-align).
+Instead of computing the alignment, the gapped sequences can be defined in the script.
+In this case no sequence files need to be given and the align command is not required.
+In HTML output various information can be specified: Important positions can be highlighted, an icon for each protein and
+the secondary structure to be displayed. This information is provided with script commands.
+See http://www.bioinformatics.org/strap/strap4services.html for details.
+
+.SH LIMITATIONS
+
+Currently, the cache for alignment results should be accessed only by one instance at a time.
+If several instances of Strap are run at the same time (e.g. from web server) the cache may become corrupted.
+Workaround: Deactivate the cache with the option -noCache.
+If you do need a cache in a web server environment, please send a request for feature to the author.
+
+
+.SH HOME-PAGE
+
+http://3d-alignment.eu/
+
+http://www.bioinformatics.org/strap/
+
+
+.SH COPYRIGHT
+
+Christoph Gille \(co 1999-2012
+
+License GPL
+
+.SH "SEE ALSO"
+.BR strap_to_clustal (1)
+.BR strap_to_msf (1)
+.BR strap_to_fasta (1)
+.BR strap_to_multiple_fasta (1)
+.BR strap_to_html (1)
+.BR strap_to_word (1)
+.BR strap_protein_alignment (1)
+.BR sequenceconverter (1)
+.BR cdbfasta (1)
+.BR squizz (1)
Added: trunk/packages/strap-base/trunk/debian/strap_to_word.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_word.1 (rev 0)
+++ trunk/packages/strap-base/trunk/debian/strap_to_word.1 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,108 @@
+.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp
+.TH strap_to_word 1 "Mai 2012"
+.SH NAME
+strap_to_word \- Reads amino acid sequences and creates an alignment view which can be edited in a word processor.
+
+.SH SYNOPSIS
+
+strap_to_word [\fIprotein or alignment files\fR]
+
+strap_to_word [\fIprotein or alignment files\fR] -o=\fIoutput-file\fR
+
+strap_to_word [\fIprotein or alignment files\fR] -script="align *"
+
+
+
+.SH DESCRIPTION
+
+Amino acid sequences are loaded from input files or are defined using
+the scripting languages.
+ A doc-file for word processors (MS-Word, gwrite, OpenOffice) is written.
+
+
+
+.SH INPUT FILES
+
+The amino acid sequences are extracted from alignment files and protein files.
+A large number of different formats are supported: PDB, Swissprot, Embl, Genbank,
+GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
+Pfam, Stockholm and HSSP.
+
+.SS File Compression
+
+Supported are .gz, .bz2 and .Z.
+
+.SS Parts of proteins
+
+To load only a subset of a proteins, a suffix is appended to the name of the
+protein input file. Residue subsets are specified by an exclamation
+mark and a subset expression after the protein file. Example:
+"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
+refer to pdb-residue numbers use the Rasmol/Jmol syntax
+\fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
+
+.SH OPTIONS
+\fB-o\fR=\fIoutput-file\fR Specifies an output file
+.SS Alignment format
+
+Comma separated display options can be appended directly (!no space) after the output file name.
+
+ w=\fIresidues per line\fR Setting output width
+
+ r=\fIcolumn range\fR Example: 20-30
+
+ r=\fIresidue position range\fR Example: aProtein/10-20
+
+
+\fB-script\fR=\fIscript-line\fR
+\fB-script\fR=\fIfile\fR or
+\fB-script\fR=\fIURL\fR
+Each script line starts with a strap command and may be followed by arguments.
+The script is run line by line.
+For example the line "align *" aligns all proteins using the current alignment backends (Default: ClustalW, TM-align).
+Instead of computing the alignment, the gapped sequences can be defined in the script.
+In this case no sequence files need to be given and the align command is not required.
+In HTML output various information can be specified: Important positions can be highlighted, an icon for each protein and
+the secondary structure to be displayed. This information is provided with script commands.
+See http://www.bioinformatics.org/strap/strap4services.html for details.
+.SS Residue annotations in HTML alignment output.
+
+Residue positions to be highlighted in the html output need to
+be defined with script commands. See option \fB\-script=\fR\fISript-file\fR.
+The script command \fInew_aminoacid_selection\fR is used to create a new
+selection object and the commands \fIadd_annotation\fR or \fIset_annotation\fR are
+used to attach information. The script may also be used to
+define the [gapped] amino acid sequences.
+
+.SH LIMITATIONS
+
+Currently, the cache for alignment results should be accessed only by one instance at a time.
+If several instances of Strap are run at the same time (e.g. from web server) the cache may become corrupted.
+Workaround: Deactivate the cache with the option -noCache.
+If you do need a cache in a web server environment, please send a request for feature to the author.
+
+
+.SH HOME-PAGE
+
+http://3d-alignment.eu/
+
+http://www.bioinformatics.org/strap/
+
+
+.SH COPYRIGHT
+
+Christoph Gille \(co 1999-2012
+
+License GPL
+
+.SH "SEE ALSO"
+.BR strap_to_clustal (1)
+.BR strap_to_msf (1)
+.BR strap_to_fasta (1)
+.BR strap_to_multiple_fasta (1)
+.BR strap_to_html (1)
+.BR strap_to_word (1)
+.BR strap_protein_alignment (1)
+.BR sequenceconverter (1)
+.BR cdbfasta (1)
+.BR squizz (1)
Added: trunk/packages/strap-base/trunk/debian/templates/ConvertAll.sh
===================================================================
--- trunk/packages/strap-base/trunk/debian/templates/ConvertAll.sh (rev 0)
+++ trunk/packages/strap-base/trunk/debian/templates/ConvertAll.sh 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,38 @@
+# The man pages are generated from template files using the macro processor gpp.
+
+SRCDIR=~/java/debian/man
+PACKAGES=~/testSvn4/trunk/packages
+DSTRAPBASE=$PACKAGES/strap-base/trunk/debian
+DSTRAP=$PACKAGES/strap/trunk/debian
+
+
+mkScript() {
+ opt=$1
+ out=$DSTRAPBASE/bin/$2
+ echo '#! /bin/sh' > $out
+ echo "/bin/sh /usr/bin/strap_base -$opt" '$*' >> $out
+}
+
+mkScript toFasta strap_to_fasta
+mkScript toMultipleFasta strap_to_multiple_fasta
+mkScript toClustal strap_to_clustal
+mkScript toHTML strap_to_html
+mkScript toWord strap_to_word
+mkScript toMSF strap_to_msf
+
+
+
+
+
+gpp -P -DSTARTS=strap_base $SRCDIR/templateGui.1 > $DSTRAPBASE/strap_base.1
+
+for i in strap_to_fasta strap_to_multiple_fasta strap_to_clustal strap_to_html strap_to_word strap_to_msf; do
+ gpp -P +n -DPRG=$i $SRCDIR/template.1 > $DSTRAPBASE/$i.1
+done
+
+
+gpp -P -DSTARTS=strap_protein_alignment $SRCDIR/templateGui.1 > $DSTRAP/strap_protein_alignment.1
+
+# cat all.1 | gpp -P +n -DPRG=strap_to_html > t.1; nroff -man t.1 | less
+
+cp $SRCDIR/*.1 $SRCDIR/*.sh $DSTRAPBASE/templates/
\ No newline at end of file
Added: trunk/packages/strap-base/trunk/debian/templates/EX_HTML_RS.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/templates/EX_HTML_RS.1 (rev 0)
+++ trunk/packages/strap-base/trunk/debian/templates/EX_HTML_RS.1 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,8 @@
+.SS Residue annotations in HTML alignment output.
+
+Residue positions to be highlighted in the html output need to
+be defined with script commands. See option \fB\-script=\fR\fISript-file\fR.
+The script command \fInew_aminoacid_selection\fR is used to create a new
+selection object and the commands \fIadd_annotation\fR or \fIset_annotation\fR are
+used to attach information. The script may also be used to
+define the [gapped] amino acid sequences.
Added: trunk/packages/strap-base/trunk/debian/templates/EX_PARS.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/templates/EX_PARS.1 (rev 0)
+++ trunk/packages/strap-base/trunk/debian/templates/EX_PARS.1 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,22 @@
+.SS Alignment format
+
+Comma separated display options can be appended directly (!no space) after the output file name.
+
+ w=\fIresidues per line\fR Setting output width
+
+ r=\fIcolumn range\fR Example: 20-30
+
+ r=\fIresidue position range\fR Example: aProtein/10-20
+
+#if PRG == strap_to_html
+
+ The following are valid only for html and word processor output:
+
+ h=\fI%conservation\fR Residues with higher conservation are highlighted.
+
+ s=\fIschading\fR shading= black|charge|hydropathy|chemical|nucleotide.
+
+ Example: -toHTML=output.html,w=70,h=55,s=hydropathy
+
+#endif
+
Added: trunk/packages/strap-base/trunk/debian/templates/template.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/templates/template.1 (rev 0)
+++ trunk/packages/strap-base/trunk/debian/templates/template.1 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,132 @@
+.\"" Do not edit this file. It has been generated from template.1 with /usr/bin/gpp
+#if PRG == strap_to_fasta
+#define FORMAT fasta
+#define CREATES a fasta formated sequence file for each sequence
+#endif
+#if PRG == strap_to_multiple_fasta
+#define FORMAT fasta
+#define CREATES a multiple fast file
+#endif
+#if PRG == strap_to_html
+#define FORMAT html
+#define CREATES an alignment view for web browsers
+#endif
+#if PRG == strap_to_word
+#define FORMAT word processor
+#define CREATES an alignment view which can be edited in a word processor
+#endif
+#if PRG == strap_to_clustal
+#define FORMAT clustal
+#define CREATES a multiple sequence alignment file in FORMAT format
+#endif
+#if PRG == strap_to_msf
+#define FORMAT msf
+#define CREATES a multiple sequence alignment file in FORMAT format
+#endif
+.TH PRG 1 "Mai 2012"
+.SH NAME
+PRG \- Reads amino acid sequences and creates CREATES.
+
+.SH SYNOPSIS
+
+PRG [\fIprotein or alignment files\fR]
+#if PRG != strap_to_fasta
+
+PRG [\fIprotein or alignment files\fR] -o=\fIoutput-file\fR
+
+PRG [\fIprotein or alignment files\fR] -script="align *"
+#endif
+
+
+
+.SH DESCRIPTION
+
+Amino acid sequences are loaded from input files or are defined using
+the scripting languages.
+#if PRG == strap_to_fasta
+ For each loaded sequence a fasta file is written.
+#endif
+#if PRG == strap_to_multiple_fasta || PRG == strap_to_clustal || PRG == strap_to_msf
+A single alignment file with all sequence is created using FORMAT format
+#endif
+#if PRG == strap_to_html
+ A html file with the rendered alignment is written. It can be viewed in a web browser.
+#endif
+#if PRG == strap_to_word
+ A doc-file for word processors (MS-Word, gwrite, OpenOffice) is written.
+#endif
+
+
+
+.SH INPUT FILES
+
+The amino acid sequences are extracted from alignment files and protein files.
+A large number of different formats are supported: PDB, Swissprot, Embl, Genbank,
+GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
+Pfam, Stockholm and HSSP.
+
+.SS File Compression
+
+Supported are .gz, .bz2 and .Z.
+
+.SS Parts of proteins
+
+To load only a subset of a proteins, a suffix is appended to the name of the
+protein input file. Residue subsets are specified by an exclamation
+mark and a subset expression after the protein file. Example:
+"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
+refer to pdb-residue numbers use the Rasmol/Jmol syntax
+\fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
+
+#if PRG != strap_to_fasta
+.SH OPTIONS
+\fB-o\fR=\fIoutput-file\fR Specifies an output file
+#include "EX_PARS.1"
+\fB-script\fR=\fIscript-line\fR
+\fB-script\fR=\fIfile\fR or
+\fB-script\fR=\fIURL\fR
+Each script line starts with a strap command and may be followed by arguments.
+The script is run line by line.
+For example the line "align *" aligns all proteins using the current alignment backends (Default: ClustalW, TM-align).
+Instead of computing the alignment, the gapped sequences can be defined in the script.
+In this case no sequence files need to be given and the align command is not required.
+In HTML output various information can be specified: Important positions can be highlighted, an icon for each protein and
+the secondary structure to be displayed. This information is provided with script commands.
+See http://www.bioinformatics.org/strap/strap4services.html for details.
+#if PRG == strap_to_word || PRG == strap_to_html
+#include "EX_HTML_RS.1"
+#endif
+
+.SH LIMITATIONS
+
+Currently, the cache for alignment results should be accessed only by one instance at a time.
+If several instances of Strap are run at the same time (e.g. from web server) the cache may become corrupted.
+Workaround: Deactivate the cache with the option -noCache.
+If you do need a cache in a web server environment, please send a request for feature to the author.
+#endif
+
+
+.SH HOME-PAGE
+
+http://3d-alignment.eu/
+
+http://www.bioinformatics.org/strap/
+
+
+.SH COPYRIGHT
+
+Christoph Gille \(co 1999-2012
+
+License GPL
+
+.SH "SEE ALSO"
+.BR strap_to_clustal (1)
+.BR strap_to_msf (1)
+.BR strap_to_fasta (1)
+.BR strap_to_multiple_fasta (1)
+.BR strap_to_html (1)
+.BR strap_to_word (1)
+.BR strap_protein_alignment (1)
+.BR sequenceconverter (1)
+.BR cdbfasta (1)
+.BR squizz (1)
Added: trunk/packages/strap-base/trunk/debian/templates/templateGui.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/templates/templateGui.1 (rev 0)
+++ trunk/packages/strap-base/trunk/debian/templates/templateGui.1 2012-07-22 15:53:49 UTC (rev 11866)
@@ -0,0 +1,342 @@
+.\"" Do not edit this file. It has been generated from templateGui.1 with /usr/bin/gpp
+.TH Strap 1 "October 2011"
+.SH NAME
+
+Strap \- Graphical user interface to compare and align proteins by sequence and 3D-structure.
+#if STARTS == strap_base
+strap_base is intended to be run from other programs which use strap as a viewer.
+Strap users should install the package strap which installs also all required debian packages.
+#endif
+
+.SH Synopsis
+
+.B STARTS [\fIprotein_files\fR] [\fIalignment_files\fR]
+
+.B STARTS -script=[\fIURL or File\fR]
+
+.B STARTS -align="PDB:\fIid1\fR PDB:\fIid2\fR UNIPROT:\fIid3\fR PFAM:\fIPF0...\fR ... "
+
+.B STARTS
+[\fIoptions\fR] [\fIprotein_files\fR] [\fIalignment_files\fR] [ @ \fIfile_with_list_of_protein_files\fR]
+
+
+
+.SH DESCRIPTION
+
+The free computer program Strap aligns proteins by sequence and
+3D-structure. Strap supports the simultaneous analysis of hundreds of
+proteins and integrates amino acid sequence, secondary structure,
+3D-structure and genomic- and mRNA-sequence. Using standard methods,
+alignments are computed automatically based on sequence and structure.
+Import and export of single proteins is very easy by Drag-and-Drop.
+
+.SS Home-Page
+
+http://3d-alignment.eu/
+
+http://www.bioinformatics.org/strap/
+
+.SH PROGRAM PARAMETERS
+
+.SS Protein/alignment files
+
+Strap can be started with protein files or alignment files as parameters.
+The following formats are supported: PDB, Swissprot, Embl, Genbank,
+GenPept, Fasta, multiple-Fast, Pir, ClustalW, MSF, Nexus, Prodom,
+Pfam, Stockholm and HSSP.
+
+If at least one protein file is specified, Strap will choose the
+current working directory as the project directory. Otherwise the
+project directory is requested at the beginning of the session.
+
+
+Files preceded by a \fB@\fR sign are interpreted as lists of files.
+
+\fBCurly parenthesis\fR are used for placing sequences into the same
+alignment row. At the UNIX command prompt, the parentheses need to be
+quoted. For example \fB'{'\fR \fIprotein1.seq protein2.seq\fR
+\fB'}' '{'\fR \fIprotein3.seq protein4.seq protein5.seq \fR \fB'}'\fR
+would put two proteins into the first and three proteins into the
+second alignment row. If there are more than one sequences in a row,
+only the top most sequence is displayed.
+
+
+.SS Loading of protein entries from remote databases:
+
+The command line options \fB-load="\fR\fI space separated list of
+database entries \fR\fB"\fR loads proteins or alignments given as URL
+or database-colon-id. The option \fB-load="\fR\fI ... \fR\fB"\fR also
+aligns the downloaded proteins.
+
+
+
+.SS File Compression
+
+Supported: .gz, .bz2 and .Z
+
+.SS Parts of proteins
+
+To display only a subset of a protein, a suffix is appended to the
+protein file name.
+Residue subsets are specified by an exclamation mark and a subset
+expression after the protein file. Example:
+"hslv_ecoli.swiss!20-30,50-66". Residue numbering starts with one. To
+refer to pdb-residue numbers use the Rasmol/Jmol syntax \fIPdbResNum\fR:\fIChainLetter\fR. Example: "pdb1ryp.ent!50:A-66:A".
+
+.SH OPTIONS
+
+Program options start with a dash. The values \fBtrue\fR and
+\fBfalse\fR can be abbreviated by \fBt\fR and \fBf\fR. The "=true" or
+"=t" can be ommitted. For example \fB-noSeqres=true\fR can be written
+as \fB-noSeqres=t\fR or \fB-noSeqres\fR. For most settings there is an
+equivalent check-box or choice menu in the graphical user interface.
+
+If the Web-start script http://www.bioinformatics.org/strap/strap.php
+is started, the options are given as web-variable without the leading
+dash. For example for -noSeqres include \fBnoSeqres=t\fR into the
+URL.
+
+\fB-help\fR
+
+Prints this manual
+
+\fB-manual\fR
+
+Generates a comprehensive manual for the web browser.
+
+\fB\-noSeqres\fR
+
+ Skip SEQRES lines of PDB files.
+
+\fB\-noIdentical\fR
+
+Do not load a sequence identical to an already loaded one.
+
+\fB\-dialog\fR=\fIJavaClassNameOfDialog\fR
+
+Opens a certain dialog at start.
+The class name of a dialog is the tab-text can be obtained by opening the help text.
+
+Examples: -dialog=DialogAlign or -dialog=DialogBlast or or -dialog=DialogDotPlot
+
+\fB\-script\fR=\fIURL_or_FilePath_or_ScriptText\fR
+
+Runs a script at start. See http://www.bioinformatics.org/strap/web/strap_script.html.
+Script files in the current directory should be written with a leading
+"./" like "./myScript.txt" since Strap recognizes files by the
+presence of a slash and the absence of white space and colon.
+
+Two or more script files can be given:
+-script5=\fIhttp://...../file\fR -script7=\fIhttp://...../file\fR.
+The optional number suffix defines the order of consecutively executed scripts.
+
+Script commands can be given directly. Assume there are protein files
+in PDB format loaded by Strap. The option
+-script="open_3D viewName, *"
+would display all proteins with 3D-coordinates three-dimensionally
+(See -v3d=). Scripts consisting of more than one line should be
+stored in a file and the file path or URL should be given.
+
+Example:
+
+-script2="open_3D viewName, *" -script3="3D_select $ALL" -script7="3D_ribbons on" -script8="superimpose *"
+
+\fB\-dasRegistry\fR=\fISpace-separated list of URLs of alternative DAS-registries\fR
+
+Only needed for DAS servers that are
+
+\fB\-s3d\fR=\fIJavaClass\fR
+
+Sets the Java class to superimpose proteins.
+
+A short name can be used such as "tm_align" for "Superimpose_TM_align".
+
+Example: -s3d=tm_align or -s3d=ce or -s3d=gangstaplus
+
+\fB\-a3d\fR=\fIJavaClass\fR
+
+Sets the Java class to compute structure based sequence alignments.
+
+Examples: -a3d=tm_align or -a3d=mapsci or -a3d=matt or -a3d=mustang
+
+\fB\-v3d\fR=\fIJavaClass\fR
+
+Sets the Java class to display 3D-structures.
+
+Example: -v3d=jmol or -v3d=pymol or -v3d=astex
+
+\fB\-aligner2\fR=\fIJavaClass\fR
+
+Sets the Java class for aligning two amino acid sequences. Preferably an implementation in Java because native executables take longer to start.
+Default value is PairAlignerNeoBioPROXY.
+
+Example: -aligner2=MultipleAlignerClustalW
+
+
+\fB\-alignerP\fR=\fIJavaClass\fR
+
+Sets the Java class for aligning sequences and structures.
+The default value is clustalW.
+
+Example: -alignerP=t_coffee
+
+
+\fB\-log3d\fR
+
+All 3D-commands which are sent to 3D-protein viewers are printed to stdout.
+
+\fB\-useDebian=false\fR \fB\-useDebian=true\fR
+
+If set to true, use the Debian packages for external programs rather
+than the program versions included in Strap. For example Strap would
+use /usr/bin/pymol instead of downloading and using the Pymol from
+http://www.bioinformatics.org/strap/Binaries/.
+
+\fB\-sysProxies=true\fR or \fB-probeWebProxy=true\fR or \fB-probeWebProxy=false\fR
+
+See section Web proxies.
+
+\fB\-noCache\fR
+
+ Do not use cached results of previous
+computations. This setting can be changed in the graphical user
+interface with a check-box.
+
+This setting influences the result of searches in growing
+databases. For example consider the similarity search method
+Blast. With the cache turned on, Strap would present a previously
+computed Blast result even though new sequences might have been
+published since last run.
+
+\fB\-keepFiles\fR
+
+Do not delete temp-files after the session. This is only important for
+debugging.
+
+\fB\-Xmx500m\fR
+
+This is an option of the java command and not of Strap.
+It sets the heap size to 500 Megabyte.
+
+\fB\-geometry=\fI666x333+11+22\fR
+
+Sets the size and location of the application frame to width 666,
+height 333, horizontal screen position 11 and vertical position 22;
+
+\fB\-laf=\fIlookAndFeel\fR
+
+Examples:
+
+-laf=com.sun.java.swing.plaf.motif.MotifLookAndFeel ( or short -laf=m)
+
+-laf=com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel ( or short -laf=N)
+
+-laf=com.sun.java.swing.plaf.gtk.GTKLookAndFeel ( or short -laf=G)
+
+-laf=javax.swing.plaf.metal.MetalLookAndFeel ( or short -laf=M)
+
+Also non-standard Look-and-Feels can be used. Consider tinylaf which
+can be installed as a Debian package. The following two options would
+apply tinylaf:
+
+ \fB-cp=\fR/usr/share/java/tinylaf.jar
+-laf=de.muntjak.tinylookandfeel.TinyLookAndFeel
+
+See also http://en.wikipedia.org/wiki/Look_and_feel.
+
+\fB\-toFasta\fR \fIProtein or alignment files\fR
+
+Generates a sequence file in Fasta format for each loaded protein.
+
+
+
+.SS Security
+
+\fB\-askUpload\fR[=t/f] The user is asked each time data is uploaded
+to remote servers. The user might not want unpublished sequences to be
+sent to servers.
+
+\fB\-askExec\fR[=t/f] The user is asked when an external program is
+executed. Executing native programs might be regarded as security
+risk. There is a positive and a negative list which can be edited in
+the menu "Security" of the Preferences-menu.
+
+\fB\-allowFileModification\fR According to the default policy, files
+are only modified, created or deleted if they reside in the project
+directory or if the file path contains "StrapAlign". This is to
+prevent files to be lost. With this option file modification control
+is deactivated.
+
+
+.SH ALIGNMENT FILE GENERATION
+
+With the options \fB\-toMultipleFasta\fR or \fB\-toClustal\fR or
+\fB\-toMSF\fR or \fB\-toHTML\fR or \fB\-toWord\fR, Strap can be used as a command line
+tool to generate multiple sequence alignment files. The protein or
+alignment files given in the command line are loaded and the output
+file is generated. Finally the program terminates. Prior file export, the
+proteins may be aligned:
+
+.B STARTS [\fIalignment_files\fR] -script="align *" -toMSF
+
+#define PRG strap_to_html
+#include "EX_PARS.1"
+
+#include "EX_HTML_RS.1"
+
+.SH PROJECT DIRECTORY
+
+The project directory holds information for gaps, 3D-transformations,
+annotations and exported files. Usually, the protein files are also
+located in the project directory. The project directory path must not
+contain white space, such as "My data" or "Eigene Dateien". Therefore
+the project directory can usually not be located in the home directory
+on Windows-XP.
+
+.SH WEB-PROXY
+
+With the option \fB-probeWebProxy=t\fR, strap attempts to access the Web in
+three different ways: (1) Directly, without Web-proxy (2) With the
+settings found in the environment variable http_proxy and (3) using
+the default mechanism of Java to apply the system wide settings. With the
+setting \fB-probeWebProxy=f\fR, however, Strap will directly connect to the
+Internet. with the option \fB-sysProxies=t\fR Strap will use the
+Java-built-in mechanism to find the system wide settings, (which might
+not work properly, depending on the Java system).
+
+.SH ALIGNMENT-FILE-EXPORT
+
+Supported formats are Multiple-Fasta, ClustalW, MSF, HSSP. A
+colorized alignment with highlighted residue selections and secondary
+structure can be exported in HTML and PDF. The colorized HTML output
+can be modified in MS-Word or other text processors. The rendering
+styles of the PDF output can be stored in annotations of residue
+selections.
+
+.SH 3D-VISUALIZATION
+
+The following 3D-protein viewers are tightly linked with the alignment
+view: Pymol, Jmol, OpenAstex. The rendering styles can be stored
+within residue selections. There is a generic Rasmol like scripting
+language which can be applied to all embedded visualization software.
+If the desired effect can not be achieved with this generic commands,
+also specific commands can be associated with residue
+selections.
+
+.SH COPYRIGHT
+
+Christoph Gille \(co 1999-2012
+
+License GPL
+
+.SH "SEE ALSO"
+
+A comprehensive manual is created with the option \fB-manual\fR
+
+.BR jalview (1)
+.BR clustalx (1)
+.BR seaview (1)
+.BR boxshade (1)
+.BR pymol (1)
+.BR openastex (1)
+.BR strap-text-viewer (1)
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