X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments.html;fp=help%2Fhelp%2Fhtml%2Ffeatures%2Fclarguments.html;h=d1ee915e95dde87301a88e40d32bb2d055fc0d44;hb=1d1edb58c9ee8baec12686a512eb18d97b9bdba1;hp=437392f2f6402b845c29fcdf4bc8338c534d0be3;hpb=173c541c3bdef7cee4f72a76cc8e23e8902a8614;p=jalview.git diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html index 437392f..d1ee915 100644 --- a/help/help/html/features/clarguments.html +++ b/help/help/html/features/clarguments.html @@ -406,10 +406,36 @@ ✓ + + ‑‑close + Close the open alignment window. This occurs after other output, processing and image export arguments. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all. + + ✓ + + + + + +

Processing alignments

+ + + + + + + + + + + + + + +
argumentactionsub-value modifiers (optional)linked (optional)
‑‑groovy filenameProcess a groovy script in the file for the open alignment.✓
-

Outputting files

+

Outputting alignment files

@@ -484,6 +510,33 @@ + + + + + + + + + + + + + +
‑‑backups / ‑‑nobackupsEnable (or disable) writing backup files when saving an ‑‑output file. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all.✓
‑‑overwrite / ‑‑nooverwriteEnable (or disable) overwriting of output files without backups enabled. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all.✓
+ + +

Exporting image files

+ + + + + + + + + + - + - + @@ -565,23 +620,85 @@ +
argumentactionsub-value modifiers (optional)linked (optional)
‑‑image filename Output an image of the open alignment window. Format is specified by the sub-value modifier, a following ‑‑type argument or guessed from the file extension. Valid formats/extensions are:
@@ -539,14 +592,16 @@
‑‑scale numberSets a scaling for bitmap image format (PNG). Should be given as a floating point number. This can also be set as a sub-value modifier to the --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).Sets a scaling for bitmap image format (PNG). Should be given as a floating point number. This can also be set as a sub-value modifier to the --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). + ✓
‑‑width numberSets a width for bitmap image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. This can also be set as a sub-value modifier to the --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).Sets a width for bitmap image format (PNG) with the height maintaining the aspect ratio. Should be given as a positive integer. This can also be set as a sub-value modifier to the --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). + ✓
✓
+ + +

Exporting 3D structure image files (jmol only)

+ + + + + + + + + + + + + + + + + + + + + + + - - + + - - + + - - + + + + + + + + + @@ -647,6 +764,13 @@ + + + + +
argumentactionsub-value modifiers (optional)linked (optional)
‑‑structureimage filenameExport an image of a 3D structure opened in JMOL. Image formats can be: +
+ svg, +
+ png, +
+ eps. + 		+ structureimagetype=name, + structureimagetextrenderer=name, + structureimagescale=number, + structureimagewidth=number, + structureimageheight=number + ✓
‑‑structureimagetype nameSet the structure image format for the preceding --structureimage. Valid values are: +
+ svg, +
+ png, +
+ eps. + 		✓
‑‑backups / ‑‑nobackupsEnable (or disable) writing backup files when saving an ‑‑output file. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all.‑‑structureimagetextrenderer nameSets whether text in a vector structure image format (SVG, EPS) should be rendered as text or vector line-art. Possible values are: +
+ text, +
+ lineart. + 		✓
‑‑overwrite / ‑‑nooverwriteEnable (or disable) overwriting of output files without backups enabled. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all.‑‑structureimagescale numberSets 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). + ✓
‑‑closeClose the current open alignment window. This occurs after other output arguments. This applies to the current open alignment -- to apply to all ‑‑output and ‑‑image files, use after ‑‑all.‑‑structureimagewidth numberSets 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 numberSets 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). + ✓
‑‑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. +
‑‑quit After all files have been opened, appended and output, quit Jalview. In ‑‑headless mode this already happens.