[med-svn] r12767 - in trunk/packages/strap-base/trunk/debian: . bin
Christoph Gille
christophgil-guest at alioth.debian.org
Thu Jan 10 21:50:13 UTC 2013
Author: christophgil-guest
Date: 2013-01-10 21:50:13 +0000 (Thu, 10 Jan 2013)
New Revision: 12767
Modified:
trunk/packages/strap-base/trunk/debian/bin/strap_base
trunk/packages/strap-base/trunk/debian/control
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
Log:
Improved man pages
Modified: trunk/packages/strap-base/trunk/debian/bin/strap_base
===================================================================
--- trunk/packages/strap-base/trunk/debian/bin/strap_base 2013-01-10 21:27:18 UTC (rev 12766)
+++ trunk/packages/strap-base/trunk/debian/bin/strap_base 2013-01-10 21:50:13 UTC (rev 12767)
@@ -8,22 +8,19 @@
# Java option max heap size
-xmx=-Xmx200M
+jreArgs=""
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=}":"$CP; fi
+for i in "$@"; do
+ jreArg=${i##JVM_}
+ if [ "$i" != "$jreArg" ]; then
+ jreArgs="$jreArgs $jreArg ";
+ fi
+
+ if [ "$i" != "${i##-cp=}" ]; then CP=${i##-cp=}":"$CP; fi
done
+echo
+set -x
+$JAVA_HOME/bin/java $jreArgs -cp $CP charite.christo.strap.Strap -useDebian -warnInstall=debian -debianStrapBase "$@"
+set +x
-# 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
Modified: trunk/packages/strap-base/trunk/debian/control
===================================================================
--- trunk/packages/strap-base/trunk/debian/control 2013-01-10 21:27:18 UTC (rev 12766)
+++ trunk/packages/strap-base/trunk/debian/control 2013-01-10 21:50:13 UTC (rev 12767)
@@ -15,19 +15,19 @@
Recommends:
Suggests: strap
Enhances:
-Description: Minimal environment for the bioinformatics tool Strap for
- viewing and editing protein sequence alignments and 3D-structure
- 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. Several required packages like Pymol are not installed along
- with strap-base. Users should therefore install the package strap
- which also includes all required bioinformatics tools.
+Description: Essential files for the interactive alignment viewer and
+ editor Strap. Most users should rather install the package strap
+ which in addition installs required debian packages for alignment
+ computation and 3D visualization. A few command line tools can be
+ used for format conversion: strap_to_clustal, strap_to_msf,
+ strap_to_multiple_fasta. The package strap-base may provide
+ interactive alignment visualization and HTML export for other
+ bioinformatics software. The command strap_base with the option
+ -script=file or -script=named_pipe can be used to open a new
+ interactive alignment view. Named pipes are the basis for
+ interprocess communication. The command strap_to_html can be used by
+ other software to produce decorated and annotated alignment outputs
+ suitable for the Web-browser as explained in
+ http://www.bioinformatics.org/strap/alignment-to-html.html.
Modified: trunk/packages/strap-base/trunk/debian/strap_base.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_base.1 2013-01-10 21:27:18 UTC (rev 12766)
+++ trunk/packages/strap-base/trunk/debian/strap_base.1 2013-01-10 21:50:13 UTC (rev 12767)
@@ -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
@@ -12,7 +12,7 @@
.B strap_base [\fIprotein_files\fR] [\fIalignment_files\fR]
-.B strap_base -script=[\fIURL or File\fR]
+.B strap_base -script=[\fIURL or File or named pipe\fR]
.B strap_base -align="PDB:\fIid1\fR PDB:\fIid2\fR UNIPROT:\fIid3\fR PFAM:\fIPF0...\fR ... "
@@ -20,7 +20,6 @@
[\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
@@ -65,7 +64,7 @@
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.
@@ -115,7 +114,7 @@
\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
@@ -130,7 +129,7 @@
-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
@@ -148,13 +147,13 @@
\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
@@ -181,7 +180,7 @@
\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
@@ -213,11 +212,7 @@
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,
@@ -248,8 +243,15 @@
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
@@ -270,18 +272,18 @@
.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
@@ -309,18 +311,8 @@
- 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
Modified: trunk/packages/strap-base/trunk/debian/strap_to_clustal.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_clustal.1 2013-01-10 21:27:18 UTC (rev 12766)
+++ trunk/packages/strap-base/trunk/debian/strap_to_clustal.1 2013-01-10 21:50:13 UTC (rev 12767)
@@ -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_to_clustal 1 "Mai 2012"
.SH NAME
strap_to_clustal \- Reads amino acid sequences and creates a multiple sequence alignment file in clustal format.
@@ -17,7 +17,7 @@
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
+A single alignment file with all sequences is created using clustal format
@@ -54,20 +54,23 @@
r=\fIresidue position range\fR Example: aProtein/10-20
+
\fB-script\fR=\fIscript-line\fR
\fB-script\fR=\fIfile\fR or
+\fB-script\fR=\fInamed_pipe\fR
\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.
+Instead of computing the alignment, the gapped sequences can be directly defined with the script command "aa_sequence".
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.
+See http://www.bioinformatics.org/strap/alignment-to-html.html for details.
-If computations are performed within the script like alignment computations, then consider to use an SQL database for the cache rather than the default
-file based cache. This is described in http://www.bioinformatics.org/strap/cache.html.
+If computations are performed within the script and if more than one Strap instances are running at the same time,
+then the default file based cache is not applicable and the SQL database based cache should be used.
+This is described in http://www.bioinformatics.org/strap/cache.html.
@@ -76,18 +79,18 @@
.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
Modified: trunk/packages/strap-base/trunk/debian/strap_to_fasta.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_fasta.1 2013-01-10 21:27:18 UTC (rev 12766)
+++ trunk/packages/strap-base/trunk/debian/strap_to_fasta.1 2013-01-10 21:50:13 UTC (rev 12767)
@@ -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_to_fasta 1 "Mai 2012"
.SH NAME
strap_to_fasta \- Reads amino acid sequences and creates a fasta formated sequence file for each sequence.
Modified: trunk/packages/strap-base/trunk/debian/strap_to_html.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_html.1 2013-01-10 21:27:18 UTC (rev 12766)
+++ trunk/packages/strap-base/trunk/debian/strap_to_html.1 2013-01-10 21:50:13 UTC (rev 12767)
@@ -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_to_html 1 "Mai 2012"
.SH NAME
strap_to_html \- Reads amino acid sequences and creates an alignment view for web browsers.
@@ -17,7 +17,7 @@
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.
+A html file with the rendered alignment is written. It can be viewed in a web browser.
@@ -54,29 +54,23 @@
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=\fInamed_pipe\fR
\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.
+Instead of computing the alignment, the gapped sequences can be directly defined with the script command "aa_sequence".
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.
+See http://www.bioinformatics.org/strap/alignment-to-html.html for details.
-If computations are performed within the script like alignment computations, then consider to use an SQL database for the cache rather than the default
-file based cache. This is described in http://www.bioinformatics.org/strap/cache.html.
+If computations are performed within the script and if more than one Strap instances are running at the same time,
+then the default file based cache is not applicable and the SQL database based cache should be used.
+This is described in http://www.bioinformatics.org/strap/cache.html.
@@ -93,18 +87,18 @@
.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
Modified: trunk/packages/strap-base/trunk/debian/strap_to_msf.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_msf.1 2013-01-10 21:27:18 UTC (rev 12766)
+++ trunk/packages/strap-base/trunk/debian/strap_to_msf.1 2013-01-10 21:50:13 UTC (rev 12767)
@@ -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_to_msf 1 "Mai 2012"
.SH NAME
strap_to_msf \- Reads amino acid sequences and creates a multiple sequence alignment file in msf format.
@@ -17,7 +17,7 @@
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
+A single alignment file with all sequences is created using msf format
@@ -54,20 +54,23 @@
r=\fIresidue position range\fR Example: aProtein/10-20
+
\fB-script\fR=\fIscript-line\fR
\fB-script\fR=\fIfile\fR or
+\fB-script\fR=\fInamed_pipe\fR
\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.
+Instead of computing the alignment, the gapped sequences can be directly defined with the script command "aa_sequence".
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.
+See http://www.bioinformatics.org/strap/alignment-to-html.html for details.
-If computations are performed within the script like alignment computations, then consider to use an SQL database for the cache rather than the default
-file based cache. This is described in http://www.bioinformatics.org/strap/cache.html.
+If computations are performed within the script and if more than one Strap instances are running at the same time,
+then the default file based cache is not applicable and the SQL database based cache should be used.
+This is described in http://www.bioinformatics.org/strap/cache.html.
@@ -76,18 +79,18 @@
.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
Modified: trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1 2013-01-10 21:27:18 UTC (rev 12766)
+++ trunk/packages/strap-base/trunk/debian/strap_to_multiple_fasta.1 2013-01-10 21:50:13 UTC (rev 12767)
@@ -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_to_multiple_fasta 1 "Mai 2012"
.SH NAME
strap_to_multiple_fasta \- Reads amino acid sequences and creates a multiple fast file.
@@ -17,7 +17,7 @@
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
+A single alignment file with all sequences is created using fasta format
@@ -54,20 +54,23 @@
r=\fIresidue position range\fR Example: aProtein/10-20
+
\fB-script\fR=\fIscript-line\fR
\fB-script\fR=\fIfile\fR or
+\fB-script\fR=\fInamed_pipe\fR
\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.
+Instead of computing the alignment, the gapped sequences can be directly defined with the script command "aa_sequence".
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.
+See http://www.bioinformatics.org/strap/alignment-to-html.html for details.
-If computations are performed within the script like alignment computations, then consider to use an SQL database for the cache rather than the default
-file based cache. This is described in http://www.bioinformatics.org/strap/cache.html.
+If computations are performed within the script and if more than one Strap instances are running at the same time,
+then the default file based cache is not applicable and the SQL database based cache should be used.
+This is described in http://www.bioinformatics.org/strap/cache.html.
@@ -76,18 +79,18 @@
.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
Modified: trunk/packages/strap-base/trunk/debian/strap_to_word.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_to_word.1 2013-01-10 21:27:18 UTC (rev 12766)
+++ trunk/packages/strap-base/trunk/debian/strap_to_word.1 2013-01-10 21:50:13 UTC (rev 12767)
@@ -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_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.
@@ -17,7 +17,7 @@
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.
+A doc-file for word processors (MS-Word, gwrite, OpenOffice) is written.
@@ -54,20 +54,23 @@
r=\fIresidue position range\fR Example: aProtein/10-20
+
\fB-script\fR=\fIscript-line\fR
\fB-script\fR=\fIfile\fR or
+\fB-script\fR=\fInamed_pipe\fR
\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.
+Instead of computing the alignment, the gapped sequences can be directly defined with the script command "aa_sequence".
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.
+See http://www.bioinformatics.org/strap/alignment-to-html.html for details.
-If computations are performed within the script like alignment computations, then consider to use an SQL database for the cache rather than the default
-file based cache. This is described in http://www.bioinformatics.org/strap/cache.html.
+If computations are performed within the script and if more than one Strap instances are running at the same time,
+then the default file based cache is not applicable and the SQL database based cache should be used.
+This is described in http://www.bioinformatics.org/strap/cache.html.
@@ -84,18 +87,18 @@
.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
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