[med-svn] r11032 - in trunk/packages/strap/trunk/debian: . bin

[Christoph Gille]

Author: christophgil-guest
Date: 2012-05-28 14:41:13 +0000 (Mon, 28 May 2012)
New Revision: 11032

Modified:
   trunk/packages/strap/trunk/debian/bin/strap
   trunk/packages/strap/trunk/debian/strap.1
   trunk/packages/strap/trunk/debian/strap.manpages
Log:


Modified: trunk/packages/strap/trunk/debian/bin/strap
===================================================================
--- trunk/packages/strap/trunk/debian/bin/strap	2012-05-28 02:07:14 UTC (rev 11031)
+++ trunk/packages/strap/trunk/debian/bin/strap	2012-05-28 14:41:13 UTC (rev 11032)
@@ -19,15 +19,16 @@
 
 
 
-echo The maximum heap size option is $xmx. To change,
-echo add a program line option like -Xmx500M which means a heap size of 500 Megabytes.
+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 -probeWebProxy -stdout -askUpload  $*"
-
+EXEC="$JAVA_HOME/bin/java $xmx -cp $CP charite.christo.strap.Strap -useDebian -warnInstall=debian $S3D -a3d=mustang -aligner2=clustalw -probeWebProxy -stdout -askUpload  $*"
+ 
 echo
 echo $EXEC
 echo
-exec $EXEC
+$EXEC 
 
 

Modified: trunk/packages/strap/trunk/debian/strap.1
===================================================================
--- trunk/packages/strap/trunk/debian/strap.1	2012-05-28 02:07:14 UTC (rev 11031)
+++ trunk/packages/strap/trunk/debian/strap.1	2012-05-28 14:41:13 UTC (rev 11032)
@@ -128,10 +128,6 @@
 
 -script2="open_3D viewName, *" -script3="3D_select $ALL" -script7="3D_ribbons on" -script8="superimpose *"
 
-\fB\-showScriptText\fR
-
- Displays the script defined with the -script option.
-
 \fB\-dasRegistry\fR=\fISpace-separated list of URLs of alternative DAS-registries\fR
 
 Only needed for DAS servers that are  
@@ -156,6 +152,14 @@
 
 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.
@@ -231,6 +235,17 @@
 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 The user might not want unpublished sequences to be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,

Modified: trunk/packages/strap/trunk/debian/strap.manpages
===================================================================
--- trunk/packages/strap/trunk/debian/strap.manpages	2012-05-28 02:07:14 UTC (rev 11031)
+++ trunk/packages/strap/trunk/debian/strap.manpages	2012-05-28 14:41:13 UTC (rev 11032)
@@ -1 +1 @@
-debian/*1
+debian/strap.1