X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments-old.html;fp=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments-old.html;h=c0f4c42d428855c0276075006c08561ef50dfe20;hb=5eca2a7ffd0c6b38898655d8b1c95310535cdfc8;hp=0000000000000000000000000000000000000000;hpb=ec24991b1786e17158a43f713c8ae9c4f8647393;p=jalview.git diff --git a/help/help/html/features/clarguments-old.html b/help/help/html/features/clarguments-old.html new file mode 100644 index 0000000..c0f4c42 --- /dev/null +++ b/help/help/html/features/clarguments-old.html @@ -0,0 +1,276 @@ + + +Jalview Command Line Arguments + +

+ The Jalview Executable's Command Line Arguments +

+ See + running Jalview from the command line + for more information. +
+
Jalview processes arguments on the command line sequentially. If + you would like to pass a 'JVL' file containing + memory settings or any other launch + parameters, then include it at the beginning of the command line to + ensure they are processed before any remaining arguments. +
+ Typical command line execution follows the following pattern: + 
+  jalview -open <Alignment File/URL> [additional import arguments] [export arguments]
+
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
-nodisplay
Run Jalview without + User Interface. (automatically disables questionnaire, version + and usage stats checks)
-nowebservicediscovery
Do not query configured servers to + discover web services (Since 2.11.2.0)
-open FILE/URL
Specify the alignment file to + open or process by providing additional arguments.
-props FILE/URL
Use the given Jalview properties + file instead of users default.
-setprop PROPERTY=value
(JalviewJS ONLY) sets the given + property to the given value
-features FILE/URL
+

+ Use the given file to add sequence features to an alignment. + See Features + File (Known as Groups file prior to 2.08) description. +

+ +
+
-colour COLOURSCHEME
+ 		Set the colourscheme for the alignment. This can be any + of the built-in colourschemes, a name of a predefined + colourscheme (defined in the Jalview properties file), or an + 'inline' colourscheme (see the applet's colour parameter for + more information).
+
-annotations FILE/URL
+ 		Add precalculated annotations to the alignment. See Annotation + File description. +
+
-no-annotation
+ 		Do not display annotation below the alignment. +
+
-tree FILE/URL
+ 		+
Load the given newick format tree file + onto the alignment
+
+
-questionnaire URL
+ 		+
Queries the given URL for information + about any Jalview user questionnaires
+
+
-noquestionnaire
+ 		+
Turn off questionnaire check
+
+
-nonews
+ 		+
+ Disable check for Jalview + news on startup (not recommended other than for classroom / + demo usage) +
+
+
-nousagestats
+ 		+
Turn off google analytics usage tracking
+
+
-[no]sortbytree
+ 		+
Enable or disable automatic sorting of + associated view when a new tree is displayed
+
+
-groovy FILE/URL
+ 		+
Execute groovy script in FILE (where + FILE may be 'STDIN' to read from the standard input) after all + other arguments have been processed
+
+
-jabaws URL
+ 		+
Specify the URL of the preferred JABAWS + server
+
+
-fasta FILE
+ 		+
Create alignment file FILE in Fasta + format.
+
-clustal FILE
Create alignment file FILE in + Clustal format.
-msf FILE
Create alignment file FILE in MSF + format.
-pileup FILE
Create alignment file FILE in + Pileup format.
-pir FILE
Create alignment file FILE in PIR + format.
-pfam FILE
Create alignment file FILE in + PFAM format.
-blc FILE
Create alignment file FILE in BLC + format.
-json FILE
Create alignment file FILE in + JSON format.
-jalview FILE
Create alignment file FILE in + Jalview format.
-png FILE
Create PNG image FILE from + alignment.
-imgMap FILE
Create HTML file FILE with image + map of PNG image.
-eps FILE
Create EPS file FILE from + alignment.
-svg FILE
Create Scalable Vector Graphics + file FILE from alignment.
-biojsMSA FILE
Write an HTML page to display + the alignment with the + BioJS MSAviewer MSA +
+
-jvmmempc=PERCENT
Only available with standalone executable jar or jalview.bin.Launcher. + Limit maximum heap size (memory) to PERCENT% of total physical memory detected. + This defaults to 90 if total physical memory can be detected. + See Memory usage settings for Jalview for more details. +
+
-jvmmemmax=MAXMEMORY
Only available with standalone executable jar or jalview.bin.Launcher. + Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), + gigabytes(g) or if you're lucky enough, terabytes(t). + This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected. + See Memory usage settings for Jalview for more details. +
+
+ +