‑‑help‑all‑‑headless / ‑‑noheadless‑‑headless--output, --image or --structureimage) then headless mode will be assumed. If you don't want this behaviour use --noheadless or --gui.
+ If you use a command line argument to specify an output file of some kind (‑‑output, ‑‑image or ‑‑structureimage) then headless mode will be assumed. If you don't want this behaviour use ‑‑gui.
‑‑gui--gui takes precedence over --headless.‑‑gui takes precedence over ‑‑headless.phylip (phy),
jalview (jvp, jar).
+ - (a single hyphen). In this case all STDOUT messages will instead go to STDERR. If no format is supplied then Fasta will be assumed.
format=name‑‑mkdirs‑‑output, ‑‑image or ‑‑structureimage arguments.
+ biojs.
type=name,
- textrenderer=name,
- scale=number,
- width=number,
- height=number
+
+ type=name,
+
+ textrenderer=name,
+
+ scale=number,
+
+ width=number,
+
+ height=number,
+
+ imagecolour=name
+
+ ‑‑structureimage filename‑‑structureimage filename will output a file for each ‑‑structureimage that has been applied to the open alignment window. In this situation, to avoid overwriting the same file with each structure, additional substitutions {structuredirname}, {structurebasename} and {structureextname} are available being substituted with the directory path, file basename and file extension of each structure file. Image formats can be:
+ svg,
+ png,
+ eps.
+
+ type=name,
+
+ textrenderer=name,
+
+ scale=number,
+
+ width=number,
+
+ height=number,
+
+ imagecolour=name
+
+ bgcolour=name
+
‑‑type name‑‑image to name. Valid values for name are:
+ ‑‑image or ‑‑structureimage to name. Valid values for name are:
svg,
‑‑textrenderer name‑‑image or ‑‑structureimage. Valid values for name are:
text,
‑‑scale number--image value. If used in conjunction with --width and --height then the smallest scaling will be used (scale, width and height provide bounds for the image).
+ ‑‑image or ‑‑structureimage. This can also be set as a sub-value modifier to the ‑‑image or ‑‑structureimage value. If used in conjunction with ‑‑width and ‑‑height then the smallest size will be used (scale, width and height provide bounds for the image).
‑‑width number--image value. If used in conjunction with --scale and --height then the smallest scaling will be used (scale, width and height provide bounds for the image).
+ ‑‑image or ‑‑structureimage. Should be given as a positive integer. This can also be set as a sub-value modifier to the ‑‑image or ‑‑structureimage value. If used in conjunction with ‑‑scale and ‑‑height then the smallest size will be used (scale, width and height provide bounds for the image).
‑‑height number--image value. If used in conjunction with --scale and --width then the smallest scaling will be used (scale, width and height provide bounds for the image).‑‑groovy filenamejmol only)| argument | -action | -sub-value modifiers (optional) | -linked (optional) | -||
‑‑structureimage filename |
- Export an image of a 3D structure opened in JMOL. Image formats can be:
- - svg,
- - png,
- - eps.
- |
-
- structureimagetype=name,
- |
- ✓ | -||
‑‑structureimagetype name |
- Set the structure image format for the preceding --structureimage. Valid values are:
- - svg,
- - png,
- - eps.
- |
- - | ✓ | -||
‑‑structureimagetextrenderer name |
- Sets whether text in a vector structure image format (SVG, EPS) should be rendered as text or vector line-art. Possible values are:
- - text,
- - lineart.
- |
+ Sets a height for bitmap image format (PNG) with the width maintaining the aspect ratio. Applies to the preceding ‑‑image or ‑‑structureimage. Should be given as a positive integer. This can also be set as a sub-value modifier to the ‑‑image or ‑‑structureimage value. If used in conjunction with ‑‑scale and ‑‑width then the smallest size will be used (scale, width and height provide bounds for the image). |
✓ | ||
‑‑structureimagescale number |
- Sets a scaling for bitmap structure image format (PNG). Should be given as a floating point number. If used in conjunction with --structureimagewidth and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image). - | +‑‑bgcolour name |
+ Only applies to structure images (opened with jmol structure viewer). Sets the background colour of the preceding ‑‑structureimage. name should be either a named colour (e.g. white, cyan) known to Jmol, or can be given as a six digit RGB hex string (e.g. ffffff, 00ffff). This can also be set as a sub-value modifier to the ‑‑structureimage value. |
✓ | |
‑‑structureimagewidth number |
- Sets a width for bitmap structure image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimageheight then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image). - | -- | ✓ | -||
‑‑structureimageheight number |
- Sets a height for bitmap structure image format (PNG) with the width maintaining the aspect ratio. Should be given as a positive integer. If used in conjunction with --structureimagescale and --structureimagewidth then the smallest scaling will be used (structureimagescale, structureimagewidth and structureimageheight provide bounds for the structure image). - | +‑‑groovy filename |
+ Process a groovy script in the file for the open alignment. | ✓ |
Move on to a new alignment window. This will ensure ‑‑append will start a new alignment window and other linked arguments will apply to the new alignment window.
- Note that --open already starts a new alignment window for each file it opens.
+ Note that ‑‑open already starts a new alignment window for each file it opens.
|
‑‑substitutions / ‑‑nosubstitutions |
The following argument values allow (or don't allow) subsituting filename parts. This is initially true. Valid substitutions are
+ {basename} - the filename-without-extension of the currently ‑‑opened file (or first ‑‑appended file),
{dirname}, - the directory (folder) name of the currently ‑‑opened file (or first ‑‑appended file),
+ {extension}, - the extension of the filename of the currently ‑‑opened file (or first ‑‑appended file),
{argfilebasename} - the filename-without-extension of the current ‑‑argfile,
{argfiledirname} - the directory (folder) name of the current ‑‑argfile,
+ {structurebasename} - the filename-without-extension of the ‑‑structure file. Only available to ‑‑structureimage .
+ + {structuredirname}, - the directory (folder) name of the ‑‑structure file. Only available to ‑‑structureimage .
+ + {structureextension}, - the extension of the filename of the ‑‑structure file. Only available to ‑‑structureimage .
+ {n} - the value of the index counter (starting at 0).
- {++n} - increase and substitute the value of the index counter,
+ {++n} - increase and substitute the value of the index counter.
+ + {m} - the value of the on-the-fly counter (starting at 0). Only available to ‑‑structureimage .
+ + {++m} - increase and substitute the (incremented) value of the on-the-fly counter. Only available to ‑‑structureimage .
{} - the value of the current alignment window default index.
|
@@ -815,7 +800,7 @@
||||
‑‑allstructures / ‑‑noallstructures |
- Apply (or stop applying) the following 3D structure formatting arguments to all structures within the current open alignment. Whilst --allstructures will continue to operate for a --new alignment, the structure formatting arguments must be set again for each new alignment.
+ Apply (or stop applying) the following 3D structure formatting arguments to all structures within the current open alignment. Whilst ‑‑allstructures will continue to operate for a ‑‑new alignment, the structure formatting arguments must be set again for each new alignment.
|