[med-svn] r12770 - in trunk/packages/strap-base/trunk/debian: . bin etc etc/bash_completion.d
Christoph Gille
christophgil-guest at alioth.debian.org
Sun Jan 13 11:28:26 UTC 2013
Author: christophgil-guest
Date: 2013-01-13 11:28:26 +0000 (Sun, 13 Jan 2013)
New Revision: 12770
Added:
trunk/packages/strap-base/trunk/debian/etc/
trunk/packages/strap-base/trunk/debian/etc/bash_completion.d/
trunk/packages/strap-base/trunk/debian/etc/bash_completion.d/strap_to_fasta
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.install
trunk/packages/strap-base/trunk/debian/strap_base.1
Log:
Added support for bash tabulator completion. Improved description.
Modified: trunk/packages/strap-base/trunk/debian/bin/strap_base
===================================================================
--- trunk/packages/strap-base/trunk/debian/bin/strap_base 2013-01-13 11:28:16 UTC (rev 12769)
+++ trunk/packages/strap-base/trunk/debian/bin/strap_base 2013-01-13 11:28:26 UTC (rev 12770)
@@ -2,12 +2,21 @@
# See http://3d-alignment.eu/
+COMPL=/etc/bash_completion.d/strap_to_fasta
+if [ "$_strap_base_defined" = "" ] && [ -f $COMPL ]; then
+ echo
+ echo "Howto enable tabulator word completion for Strap's command line options? Run:"
+ echo " . /etc/bash_completion"
+ echo
+fi
. /usr/lib/java-wrappers/java-wrappers.sh
find_java_runtime java6
# Java option max heap size
+
+
jreArgs=""
CP=/usr/lib/strap-base/strap-protein-alignment-1.jar:
for i in "$@"; do
Modified: trunk/packages/strap-base/trunk/debian/control
===================================================================
--- trunk/packages/strap-base/trunk/debian/control 2013-01-13 11:28:16 UTC (rev 12769)
+++ trunk/packages/strap-base/trunk/debian/control 2013-01-13 11:28:26 UTC (rev 12770)
@@ -15,19 +15,19 @@
Recommends:
Suggests: strap
Enhances:
-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
+Description: Essential files for the interactive alignment viewer and editor Strap.
+ Most users should install the package strap which in addition
+ installs required debian packages for alignment computation and 3D
+ visualization. Strap-base provides utilities for protein and
+ alignment file format conversion: strap_to_clustal, strap_to_msf,
+ strap_to_fasta, strap_to_multiple_fasta. It also provides
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
+ -script=file or -script=named_pipe opens a new interactive alignment
+ view. Named pipes are the basis for interprocess communication. The
+ command strap_to_html is a command line tool to produce
+ decorated and annotated alignments suitable for web-browsers with
+ script commands as explained in
http://www.bioinformatics.org/strap/alignment-to-html.html.
Added: trunk/packages/strap-base/trunk/debian/etc/bash_completion.d/strap_to_fasta
===================================================================
--- trunk/packages/strap-base/trunk/debian/etc/bash_completion.d/strap_to_fasta (rev 0)
+++ trunk/packages/strap-base/trunk/debian/etc/bash_completion.d/strap_to_fasta 2013-01-13 11:28:26 UTC (rev 12770)
@@ -0,0 +1,110 @@
+export _strap_base_defined="x"
+_strap_base() {
+ local cur prev opts
+ COMPREPLY=()
+ _get_comp_words_by_ref -n = cur
+ #cur="${COMP_WORDS[COMP_CWORD]}"
+ prev="${COMP_WORDS[COMP_CWORD-1]}"
+ opts="-align= -load= -pdb= \
+ -allowFileModification=true \
+ -warnInstall -askExec=true -askUpload=true -noCache=true -noSound=true \
+ -cp= \
+ -dialog=
+ -edtftp=true \
+ -laf= \
+ -log3d=true \
+ -manual \
+ -noIdentical=true -noSeqres=true \
+ -probeWebProxy=true -stdout=true -stdout=false \
+ -script= -geometry=
+"
+ case $cur in
+ JVM_*)
+
+ COMPREPLY=( $(compgen -W "JVM_-Xmx300M JVM_-ea JVM_-DproxyHost=proxy JVM_-DproxyPort=888 " -- ${cur}) )
+ return 0
+ ;;
+ -geometry=*)
+cur=${cur#*=}
+COMPREPLY=( $(compgen -W "1400x900+100+10 1000x500+10+20" -- ${cur}) )
+return 0
+;;
+-cp=*)
+cur=${cur#*=}
+cp=$(ls --color=never /usr/share/java/*laf.jar)
+COMPREPLY=( $(compgen -W "${cp}" -- ${cur}) )
+return 0
+;;
+-laf=*)
+cur=${cur#*=}
+lafs="de.muntjak.tinylookandfeel.TinyLookAndFeel com.sun.java.swing.plaf.gtk.GTKLookAndFeel com.sun.java.swing.plaf.motif.MotifLookAndFeel com.sun.java.swing.plaf.nimbus.NimbusLookAndFeel"
+COMPREPLY=( $(compgen -W "${lafs}" -- ${cur}) )
+return 0
+;;
+
+-dialog=*)
+cur=${cur#*=}
+COMPREPLY=( $(compgen -W "DialogAlign DialogAlignOneToAll DialogBarChart DialogBlast DialogCompareProteins DialogDifferentResidues DialogDotPlot DialogExportAlignment DialogExportWord DialogFetchPdb DialogFetchSRS DialogGenbank DialogHighlightPattern DialogImportMFA DialogInferCDS DialogNeighbors DialogNewProtein DialogPhylogeneticTree DialogPlot DialogPredictCoiledCoil DialogPredictSecondaryStructures DialogPredictTexshade DialogPredictTmHelices2 DialogPublishAlignment DialogRenameProteins DialogResidueAnnotationChanges DialogResidueAnnotationList DialogSelectionOfResiduesMain DialogSuperimpose3 DialogExportProteins Dialog_bl2seq" -- ${cur}) )
+return 0
+;;
+
+-*)
+COMPREPLY=( $(compgen -W "${opts}" -- ${cur}) )
+if [[ $COMPREPLY == *= ]]; then compopt -o nospace; fi
+
+return 0
+;;
+esac
+
+COMPREPLY=( $(compgen -f -- ${cur}) )
+
+}
+
+
+
+
+_strap_export() {
+ local cur prev opts
+ COMPREPLY=()
+ _get_comp_words_by_ref -n = cur
+ #cur="${COMP_WORDS[COMP_CWORD]}"
+ prev="${COMP_WORDS[COMP_CWORD-1]}"
+ opts=" -o \
+ -script= \
+ -allowFileModification=true \
+ -warnInstall -askExec=true -askUpload=true -noCache=true \
+ -noIdentical=true -noSeqres=true \
+ -stdout=true -stdout=false \
+"
+
+ case $cur in
+ -*)
+ COMPREPLY=( $(compgen -W "${opts}" -- ${cur}) )
+ if [[ $COMPREPLY == *= ]]; then compopt -o nospace; fi
+ return 0
+ ;;
+ esac
+ COMPREPLY=( $(compgen -f -- ${cur}) )
+
+}
+
+
+complete -F _strap_base strap_protein_alignment
+complete -F _strap_base strap_base
+
+complete -F _strap_export strap_to_fasta
+complete -F _strap_export strap_to_multiple_fasta
+complete -F _strap_export strap_to_word
+complete -F _strap_export strap_to_msf
+complete -F _strap_export strap_to_clustal
+
+
+
+
+# Local variables:
+# mode: shell-script
+# sh-basic-offset: 4
+# sh-indent-comment: t
+# indent-tabs-mode: nil
+# End:
+# ex: ts=4 sw=4 et filetype=sh
Modified: trunk/packages/strap-base/trunk/debian/strap-base.install
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap-base.install 2013-01-13 11:28:16 UTC (rev 12769)
+++ trunk/packages/strap-base/trunk/debian/strap-base.install 2013-01-13 11:28:26 UTC (rev 12770)
@@ -8,4 +8,4 @@
debian/bin/strap_to_html usr/bin
debian/bin/strap_to_word usr/bin
debian/bin/strap_base usr/bin
-
+debian/etc/bash_completion.d/strap_to_fasta etc/bash_completion.d
Modified: trunk/packages/strap-base/trunk/debian/strap_base.1
===================================================================
--- trunk/packages/strap-base/trunk/debian/strap_base.1 2013-01-13 11:28:16 UTC (rev 12769)
+++ trunk/packages/strap-base/trunk/debian/strap_base.1 2013-01-13 11:28:26 UTC (rev 12770)
@@ -377,5 +377,4 @@
.BR seaview (1)
.BR boxshade (1)
.BR pymol (1)
-.BR openastex (1)
-.BR strap-text-viewer (1)
+
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