[med-svn] r12768 - in trunk/packages/strap/trunk/debian: . bin
Christoph Gille
christophgil-guest at alioth.debian.org
Thu Jan 10 21:50:32 UTC 2013
Author: christophgil-guest
Date: 2013-01-10 21:50:31 +0000 (Thu, 10 Jan 2013)
New Revision: 12768
Modified:
trunk/packages/strap/trunk/debian/bin/strap_protein_alignment
trunk/packages/strap/trunk/debian/control
trunk/packages/strap/trunk/debian/copyright
trunk/packages/strap/trunk/debian/strap_protein_alignment.1
Log:
Improved man pages
Modified: trunk/packages/strap/trunk/debian/bin/strap_protein_alignment
===================================================================
--- trunk/packages/strap/trunk/debian/bin/strap_protein_alignment 2013-01-10 21:50:13 UTC (rev 12767)
+++ trunk/packages/strap/trunk/debian/bin/strap_protein_alignment 2013-01-10 21:50:31 UTC (rev 12768)
@@ -5,6 +5,6 @@
-/bin/sh /usr/bin/strap_base -probeWebProxy -stdout $*
+/bin/sh /usr/bin/strap_base -probeWebProxy -stdout "$@"
\ No newline at end of file
Modified: trunk/packages/strap/trunk/debian/control
===================================================================
--- trunk/packages/strap/trunk/debian/control 2013-01-10 21:50:13 UTC (rev 12767)
+++ trunk/packages/strap/trunk/debian/control 2013-01-10 21:50:31 UTC (rev 12768)
@@ -15,7 +15,7 @@
Recommends: muscle, mafft, t-coffee, probcons, dialign, dialign-t, amap-align, chemical-mime-data
Suggests:
Enhances: clustalw, tm-align, pymol, mustang, muscle, mafft, t-coffee, probcons, dialign, dialign-t, amap-align
-Description: Aligning proteins by sequence and structure.
+Description: Interactive alignment editor - aligning proteins by sequence and structure.
Strap can be used to display, edit and compute multiple sequence
alignments, structure alignments and 3D-structure superpositions. It
aids structure / function prediction and database searching. Modern
@@ -26,11 +26,9 @@
Information can be attached to residue selections such as free text
notes, cross-references as well as 3D and 1D display style commands.
The alignment can be exported in several formats: Multiple-Fasta,
- ClustalW, MSF, HSSP, Jalview. The alignment together with residue
+ ClustalW, MSF, HSSP, Jalview. Decorated alignments with residue
annotations can be exported to PDF and HTML and can be edited with
MS-Word or gwrite to create figures in publication quality - see
http://3d-alignment.eu/ for details. Strap is scriptable and can be
- used by programs and web-services to display sequence alignments and
- 3D-superpositions. The current alignment including all residue
- underlinings can be displayed in Web pages either as HTML or as an
- interactive Java based alignment view.
\ No newline at end of file
+ used by other programs to display sequence alignments and
+ 3D-superpositions.
\ No newline at end of file
Modified: trunk/packages/strap/trunk/debian/copyright
===================================================================
--- trunk/packages/strap/trunk/debian/copyright 2013-01-10 21:50:13 UTC (rev 12767)
+++ trunk/packages/strap/trunk/debian/copyright 2013-01-10 21:50:31 UTC (rev 12768)
@@ -22,3 +22,432 @@
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’
+
+File: texhade.sty
+Copyright 1999-2009 Eric Beitz
+License: GPL Version 2
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Modified: trunk/packages/strap/trunk/debian/strap_protein_alignment.1
===================================================================
--- trunk/packages/strap/trunk/debian/strap_protein_alignment.1 2013-01-10 21:50:13 UTC (rev 12767)
+++ trunk/packages/strap/trunk/debian/strap_protein_alignment.1 2013-01-10 21:50:31 UTC (rev 12768)
@@ -1,4 +1,4 @@
-.\"" Do not edit this file. It is generated by a script. Contact Christoph Gille for changes.
+.\"" Do not edit this file. It is generated from a template file. Contact Christoph Gille for changes.
.TH Strap 1 "October 2011"
.SH NAME
@@ -9,7 +9,7 @@
.B strap_protein_alignment [\fIprotein_files\fR] [\fIalignment_files\fR]
-.B strap_protein_alignment -script=[\fIURL or File\fR]
+.B strap_protein_alignment -script=[\fIURL or File or named pipe\fR]
.B strap_protein_alignment -align="PDB:\fIid1\fR PDB:\fIid2\fR UNIPROT:\fIid3\fR PFAM:\fIPF0...\fR ... "
@@ -17,7 +17,6 @@
[\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
@@ -62,7 +61,7 @@
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
+or database-colon-id. The option \fB-align="\fR\fI ... \fR\fB"\fR also
aligns the downloaded proteins.
@@ -112,7 +111,7 @@
\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.
+The Java class name of a dialog is shown in the tool tip of the help button when the shift key is pressed.
Examples: -dialog=DialogAlign or -dialog=DialogBlast or or -dialog=DialogDotPlot
@@ -127,7 +126,7 @@
-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
+Script commands can be given directly. Consider a few protein files
in PDB format loaded by Strap. The option
-script="open_3D viewName, *"
would display all proteins with 3D-coordinates three-dimensionally
@@ -145,13 +144,13 @@
\fB\-dasRegistry\fR=\fISpace-separated list of URLs of alternative DAS-registries\fR
-Only needed for DAS servers that are
+Only needed to access unregistered DAS servers.
\fB\-s3d\fR=\fIJavaClass\fR
-Sets the Java class to superimpose proteins.
+Sets the Java class for superimposing proteins.
-A short name can be used such as "tm_align" for "Superimpose_TM_align".
+The short name or the full Java class name can be used such as "tm_align" for "Superimpose_TM_align".
Example: -s3d=tm_align or -s3d=ce or -s3d=gangstaplus
@@ -178,7 +177,7 @@
\fB\-alignerP\fR=\fIJavaClass\fR
Sets the Java class for aligning sequences and structures.
-The default value is clustalW.
+The default is clustalW.
Example: -alignerP=t_coffee
@@ -210,11 +209,7 @@
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,
@@ -245,8 +240,15 @@
Generates a sequence file in Fasta format for each loaded protein.
+.SS Interprocess communication
+Strap can be controled from another application using named pipes.
+The -script option does not only take files and URLS but also named
+pipes. Other applications can write script commands to the pipe which
+are then executed by Strap.
+
+
.SS Security
\fB\-askUpload\fR[=t/f] The user is asked each time data is uploaded
@@ -267,18 +269,18 @@
.SH Parameters for the Java virtual machine
-Even if Strap is started indirectly with a UNIX script file,
-parameters can still be passed directly to the Java command.
+If the java process is started from a script file,
+parameters can be passed directly to the Java command.
Those parameters need to be prefixed with "JVM_".
This does not (yet) work for MS-Windows.
Examples:
-\fB JVM_-Xmx200M\fR
-\fB JVM_-Dapple.laf.useScreenMenuBar=true\fR
-\fB JVM_-DproxyHost=realproxy.charite.de JVM_-DproxyPort=888 \fR
-\fB JVM_-ea\fR
+\fB JVM_-Xmx200M\fR Setting the heap size to 200 Megabyte.
+\fB JVM_-Dapple.laf.useScreenMenuBar=true\fR Screen menu bar for MacOS
+\fB JVM_-DproxyHost=realproxy.charite.de JVM_-DproxyPort=888 \fR Setting the web proxy
+\fB JVM_-ea\fR Enable assertions
@@ -306,18 +308,8 @@
- 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
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