From: Ben Soares Date: Wed, 20 Sep 2023 10:15:57 +0000 (+0100) Subject: JAL-629 Added/corrected/tidied documentation X-Git-Tag: Release_2_11_4_0~174^2~11 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=33a18c18d0ec58e651de30890437cdf4e6eb542d;p=jalview.git JAL-629 Added/corrected/tidied documentation --- diff --git a/help/help/html/features/clarguments-basic.html b/help/help/html/features/clarguments-basic.html index f3c053d..9de0e08 100644 --- a/help/help/html/features/clarguments-basic.html +++ b/help/help/html/features/clarguments-basic.html @@ -340,7 +340,7 @@

-

Outputting/converting alignment files and images (--output, --format, --image, --type, --textrenderer, --scale, --backups, --overwrite)

+

Outputting/converting alignment files and images (--output, --format, --image, --structureimage, --type, --scale, --width, --height, --imagecolour, --bgcolour, --textrenderer, --overwrite, --backups, --mkdirs)

You can save an alignment as an alignment file, or exported as an image, in different formats. Jalview's alignment output formats are: @@ -448,7 +448,7 @@

-

--structureimage

+

--structureimage

To export an open structure as an image, use the --structureimage argument, which will give an image of the structure as it appears (or would appear if not in --headless mode) in a Jmol window including colour scheme. --structureimage can currently only be used with structures opened with the jmol structureviewer (the default viewer).

@@ -462,6 +462,22 @@ These by default produce a PNG image of screen or webpage resolution, which you will probably want to improve upon. There are two ways of doing this with Jalview: increasing the scale of the PNG image, or using a vector based image format (EPS, SVG, HTML).

+

--type

+ +

+ To specify the type of image file to write (if using an unrecognised file extension) use the --type argument to specify a value (see above). A sub-value modifier on the --image and --structureimage value can also be used. Valid values are: +
+ png - A Portable Network Graphics image (bitmap, default), +
+ svg - A Scalable Vector Graphics image (vector), +
+ eps - An Encapsulated PostScript file (vector), +
+ html - An HTML rendition of the alignment with embedded source data (vector/web browser), +
+ biojs - An HTML rendition of the alignment with interactive MSA viewer BioJS-MSA (vector). +

+

Bitmap image types (png)

@@ -512,7 +528,7 @@

-

--imagecolour

+

--imagecolour

Specify a colour scheme to use just for this image using the --imagecolour argument: @@ -521,7 +537,7 @@

-

--bgcolour

+

--bgcolour

Only applies to --structureimage. Specify a background colour for a structure image. The colour can be specified as a named colour recognised by Java (e.g. "white", "cyan") or as a #RRGGBB hash-6-digit-hex-string as used in web pages (e.g. "#ffffff", "#00ffff"). Note that if you're using a hash in a bash-like shell then you should quote the string to avoid problems with it being interpreted as a comment character. @@ -537,7 +553,7 @@ Next we look at vector image formats, which maintain detail at all resolutions.

-

Vector image export

+

Vector image export (svg, eps, html, biojs)

Jalview can export an alignment in Encapsulated PostScript (eps), Scalable Vector Graphics (svg), HTML (html) or BioJSON -- another HTML format (biojs), by using, e.g. @@ -573,6 +589,25 @@

+

Output behaviour

+ +

--overwrite

+ +

+ By default, Jalview will refuse to overwrite an output file (alignment or image) unless backups are in operation (alignment files only). To force overwriting files, use the --overwrite argument. +

+ +

--backups / --nobackups

+ +

+ Jalview should honour your preferences for backup files of output alignment files. Using --backups or --nobackups forces the behaviour. With no backups set, you will need to use --overwrite to overwrite an existing file. Note that Jalview does not make backup files of exported images. +

+ +

--mkdirs

+ +

+ If you want to output a file into a folder that doesn't yet exist (this might happen particularly when using {dirname} substitutions -- see below), then Jalview will fail to write the file since the parent directory doesn't exist. You can use --mkdirs to tell Jalview to make the new directory (or directories, it will create several nested directories if necessary) before writing the file. --mkdirs is cautious and will generally refuse to make a new directory using a relative path with .. in. +

Filename substitutions and batch processing (--substitutions, --close, --all)