From 9c970ce520ca5480fcd289c8ef32ed78284cde29 Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Wed, 20 Sep 2023 11:19:59 +0100 Subject: [PATCH] JAL-629 Make arguments appear correctly using all non-breaking hyphens --- help/help/html/features/clarguments-advanced.html | 16 +- help/help/html/features/clarguments-argfiles.html | 4 +- help/help/html/features/clarguments-basic.html | 212 ++++++++++---------- help/help/html/features/clarguments-reference.html | 18 +- help/help/html/features/clarguments.html | 36 ++-- 5 files changed, 143 insertions(+), 143 deletions(-) diff --git a/help/help/html/features/clarguments-advanced.html b/help/help/html/features/clarguments-advanced.html index a235727..eea97fb 100644 --- a/help/help/html/features/clarguments-advanced.html +++ b/help/help/html/features/clarguments-advanced.html @@ -49,11 +49,11 @@

Alignment linked IDs

- Jalview's alignment related arguments are linked together using a linked ID. In all of the basic usage examples this linked ID is assigned using a default formula of JALVIEW:n where n starts at 0 and increments every time there is an --opened file (or a first use of --append) or the --new argument is used. + Jalview's alignment related arguments are linked together using a linked ID. In all of the basic usage examples this linked ID is assigned using a default formula of JALVIEW:n where n starts at 0 and increments every time there is an ‑‑opened file (or a first use of ‑‑append) or the ‑‑new argument is used.

- When another alignment related argument is used (without a specified linked ID), it is assigned this default linked ID. When the --all argument is used, following alignment related arguments are applied to all of the linked IDs (made so far). + When another alignment related argument is used (without a specified linked ID), it is assigned this default linked ID. When the ‑‑all argument is used, following alignment related arguments are applied to all of the linked IDs (made so far).

@@ -67,7 +67,7 @@

- A specified linked ID will also take precedence over a wildcard or --all set linked ID. e.g. + A specified linked ID will also take precedence over a wildcard or ‑‑all set linked ID. e.g. 

   jalview --open[myID] examples/uniref50.fa --all --colour taylor --colour[myID] gecos-blossom
@@ -82,11 +82,11 @@

- There is also an incrementor integer value {n} that can be put into both linked IDs and filenames and works across different linked IDs. Whenever you use {n} in a linked ID or filename value it is replaced with the current value of n. The initial value is 0, and it can be incremented by using the argument --npp or --n++, or using a another special substitution {++n} in either a linked ID or filename value which increments the value and is replaced with the new incremented value of n. + There is also an incrementor integer value {n} that can be put into both linked IDs and filenames and works across different linked IDs. Whenever you use {n} in a linked ID or filename value it is replaced with the current value of n. The initial value is 0, and it can be incremented by using the argument ‑‑npp or ‑‑n++, or using a another special substitution {++n} in either a linked ID or filename value which increments the value and is replaced with the new incremented value of n.

- In the same way that the --all argument enables (some) following arguments to apply to all opened alignments so far, the special linked ID * will also apply an individual argument to all opened linked IDs (in fact when you use the --all argument it simply changes the default linked ID to *). + In the same way that the ‑‑all argument enables (some) following arguments to apply to all opened alignments so far, the special linked ID * will also apply an individual argument to all opened linked IDs (in fact when you use the ‑‑all argument it simply changes the default linked ID to *). 

   jalview --open[myId1] fileA.fa --open[myId2] fileB.fa --open[myId3] fileC.fa --colour[*] taylor --all --image tmp/image-{++n}.png --headless
@@ -118,7 +118,7 @@

- One benefit of this is seen above in the --image argument, the special "alloutput" wildcard filename *.png will not be expanded by the shell, so does not need to be escaped or surrounded with quotation marks. + One benefit of this is seen above in the ‑‑image argument, the special "alloutput" wildcard filename *.png will not be expanded by the shell, so does not need to be escaped or surrounded with quotation marks.

@@ -150,7 +150,7 @@

- Some arguments (such as --scale=n) are used to modify the behaviour of other "primary" arguments (such as --image=filename). These arguments can alternatively be specifed as sub-value modifiers of the values given to the primary argument. If specified as a sub-value modifier, this modifier takes precedence over any following linked argument if given. e.g + Some arguments (such as ‑‑scale=n) are used to modify the behaviour of other "primary" arguments (such as ‑‑image=filename). These arguments can alternatively be specifed as sub-value modifiers of the values given to the primary argument. If specified as a sub-value modifier, this modifier takes precedence over any following linked argument if given. e.g 

   jalview --open=[colour=zappo]examples/*.fa
@@ -166,7 +166,7 @@

- You can specify multiple sub-value modifiers separating them with a comma (','). If you wish to specify a "boolean" argument, such as --wrap or --nowrap then simply use the argument name without a value, like this: + You can specify multiple sub-value modifiers separating them with a comma (','). If you wish to specify a "boolean" argument, such as ‑‑wrap or ‑‑nowrap then simply use the argument name without a value, like this: 

   jalview --open=[colour=gecos-flower,wrap,noannotations,features=examples/plantfdx.features]examples/plantfdx.fa
diff --git a/help/help/html/features/clarguments-argfiles.html b/help/help/html/features/clarguments-argfiles.html index 5c71d16..ad27751 100644 --- a/help/help/html/features/clarguments-argfiles.html +++ b/help/help/html/features/clarguments-argfiles.html @@ -86,7 +86,7 @@

- Because --argfiles takes a filename argument, and multiple --argfiles can be read on the command line, you can also use file globs to specify multiple --argfile values. If you produce an argument file for each set of alignment files that you wish to associate then you can act on all of them with, e.g. + Because ‑‑argfiles takes a filename argument, and multiple ‑‑argfiles can be read on the command line, you can also use file globs to specify multiple ‑‑argfile values. If you produce an argument file for each set of alignment files that you wish to associate then you can act on all of them with, e.g. 

   jalview --argfile=*/argfile.txt --headless
@@ -124,7 +124,7 @@

Only argument files

- When you use an --argfile argument, all other non-initialising arguments on the command line will be ignored. Only the initialising arguments and any and all --argfiles arguments on the command line will be used. You can also set initialising arguments in argument files. + When you use an ‑‑argfile argument, all other non-initialising arguments on the command line will be ignored. Only the initialising arguments and any and all ‑‑argfiles arguments on the command line will be used. You can also set initialising arguments in argument files.

diff --git a/help/help/html/features/clarguments-basic.html b/help/help/html/features/clarguments-basic.html index 9de0e08..44c3459 100644 --- a/help/help/html/features/clarguments-basic.html +++ b/help/help/html/features/clarguments-basic.html @@ -47,7 +47,7 @@
  • The all output wildcard
    • -

    Opening alignments (--open, --append, --new)

    +

    Opening alignments (‑‑open, ‑‑append, ‑‑new)

    To simply open one or more alignment files in different alignment windows just put the filenames as the first arguments: @@ -68,14 +68,14 @@

    - (Using initial filenames is the same as using the --open argument, and further arguments can be used + (Using initial filenames is the same as using the ‑‑open argument, and further arguments can be used after the initial filenames.)

    -

    --open

    +

    ‑‑open

    - Use the --open argument to open alignment files each in their own window. + Use the ‑‑open argument to open alignment files each in their own window.

    @@ -98,14 +98,14 @@

    -

    --append

    +

    ‑‑append

    To append several alignment files together use: 

       jalview --open filename1.fa --append filename2.fa filename3.fa
    - or, if you haven't previously used --open then you can use --append to open one new window and keep appending each set of alignments: + or, if you haven't previously used ‑‑open then you can use --append to open one new window and keep appending each set of alignments: 
       jalview --append these/filename*.fa --append more/filename*.fa
 
@@ -114,34 +114,34 @@
   
    
 
   
    
-  Note that whilst you can include a Jalview Project File (.jvp) as an --append value, the items in the file will always open in their original windows and not append to another.
+  Note that whilst you can include a Jalview Project File (.jvp) as an ‑‑append value, the items in the file will always open in their original windows and not append to another.
   
    
 
-  
    --new
    
+  
    ‑‑new
    
 
   
    
-  To append different sets of alignment files in different windows, use --new to move on to a new alignment window:
+  To append different sets of alignment files in different windows, use ‑‑new to move on to a new alignment window:
   
       jalview --append these/filename*.fa --new --append other/filename*.fa
   
    
   
    
 
   
    
-  --open is like using --new --append applied to every filename/URL given to --open
+  ‑‑open is like using ‑‑new --append applied to every filename/URL given to ‑‑open
   
    
 
 
-  
    Alignment options (--colour, --wrap, --showannotations, --title)
    
+  
    Alignment options (‑‑colour, ‑‑wrap, ‑‑showannotations, ‑‑title)
    
 
   
    
-  An opened alignment window (or set of opened alignment windows) can be modified in its appearance using the following arguments before the next --open argument.  These modifying arguments apply to the one or more files that were opened with the preceding --open argument.  E.g. --open file.fa --colour gecos-flower will colour the one alignment window with file.fa.  However, --open *.fa --colour gecos-flower will colour every alignment window matching file*.fa, and  --open file1.fa file2.fa --colour gecos-flower
+  An opened alignment window (or set of opened alignment windows) can be modified in its appearance using the following arguments before the next ‑‑open argument.  These modifying arguments apply to the one or more files that were opened with the preceding ‑‑open argument.  E.g. ‑‑open file.fa --colour gecos-flower will colour the one alignment window with file.fa.  However, ‑‑open *.fa --colour gecos-flower will colour every alignment window matching file*.fa, and  --open file1.fa file2.fa --colour gecos-flower
   will colour both opened alignment windows.
   
    
 
-  
    --colour
    
+  
    ‑‑colour
    
 
   
    
-  You can specify a residue/base colouring for the alignment using the --colour option (note spelling -- Jalview is made in Scotland!):
+  You can specify a residue/base colouring for the alignment using the ‑‑colour option (note spelling -- Jalview is made in Scotland!):
   
       jalview --open examples/uniref50.fa --colour gecos-flower
   
    
@@ -190,31 +190,31 @@
   sequence-id
   
    
 
-  
    --wrap
    
+  
    ‑‑wrap
    
   
    
-  An alignment should open with your usual preferences stored in the .jalview_properties file.  To open an alignment with the sequences (definitely) wrapped, following your --open (or first --append) argument use the argument --wrap:
+  An alignment should open with your usual preferences stored in the .jalview_properties file.  To open an alignment with the sequences (definitely) wrapped, following your ‑‑open (or first ‑‑append) argument use the argument ‑‑wrap:
   
       jalview --open examples/uniref50.fa --wrap
   
    
-  To ensure an alignment is not wrapped use --nowrap:
+  To ensure an alignment is not wrapped use ‑‑nowrap:
   
       jalview --open examples/uniref50.fa --nowrap
   
    
   
    
 
-  
    --showannotations / --noshowannotations
    
+  
    ‑‑showannotations / ‑‑noshowannotations
    
 
   
    
-  You can specify whether the currently opened alignment window should show alignment annotations (e.g. Conservation, Quality, Consensus...) or not with either --showannotations or --noshowannotations.  If you don't specify then your saved preference will be used.
+  You can specify whether the currently opened alignment window should show alignment annotations (e.g. Conservation, Quality, Consensus...) or not with either ‑‑showannotations or ‑‑noshowannotations.  If you don't specify then your saved preference will be used.
   
       jalview --open examples/uniref50.fa --noshowannotations
   
    
   
    
 
-  
    --title
    
+  
    ‑‑title
    
 
   
    
-  If you would like to give the alignment window a specific title you can do so with the --title option:
+  If you would like to give the alignment window a specific title you can do so with the ‑‑title option:
   
       jalview --open examples/uniref50.fa --title "My example alignment"
   
    
@@ -223,28 +223,28 @@
 
 
 
-  
    Adding 3D structures (--structure, --seqid, --structureviewer, --paematrix, --tempfac, --showssannotations)
    
+  
    Adding 3D structures (‑‑structure, ‑‑seqid, ‑‑structureviewer, ‑‑paematrix, ‑‑tempfac, ‑‑showssannotations)
    
 
   
    
   
    
 
-  
    --structure
    
+  
    ‑‑structure
    
 
   
    
-  You can add a 3D structure file to a sequence in the current alignment window with the --structure option:
+  You can add a 3D structure file to a sequence in the current alignment window with the ‑‑structure option:
   
       jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb
   
    
   By default this attaches to the first sequence in the alignment but most likely you will want to attach it to a specific sequence.
   
    
 
-  
    --seqid
    
+  
    ‑‑seqid
    
 
   
    
-  The easiest way to specify a sequence ID for your structure is to follow the --structure argument with a --seqid argument with a value of a sequence ID in the alignment.  This does of course require some knowledge of the sequences in the alignment files
+  The easiest way to specify a sequence ID for your structure is to follow the ‑‑structure argument with a ‑‑seqid argument with a value of a sequence ID in the alignment.  This does of course require some knowledge of the sequences in the alignment files
   that have been opened.
   
    
-  Alternatively you can specify a sub-value with the --structure argument value.  You do this by preceding the value with square brackets and seqid=SequenceId,
+  Alternatively you can specify a sub-value with the ‑‑structure argument value.  You do this by preceding the value with square brackets and seqid=SequenceId,
   like this:
   
       jalview --open examples/uniref50.fa --structure [seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.pdb
@@ -256,7 +256,7 @@
   
    
 
   
    
-  The sub-value seqid=FER1_SPIOL takes precedence over the following argument --seqid FER1_SPIOL if you accidentally specify both (in which case the argument will probably be completely unused).
+  The sub-value seqid=FER1_SPIOL takes precedence over the following argument ‑‑seqid FER1_SPIOL if you accidentally specify both (in which case the argument will probably be completely unused).
   
    
 
   
    
@@ -270,10 +270,10 @@
   Remember that you might need to escape any spaces in the sequence ID or enclose the ID in quotation marks.
   
    
 
-  
    --structureviewer
    
+  
    ‑‑structureviewer
    
 
   
    
-  You can specify which structure viewer (or none) to use to open the structure using either the --structureviewer argument or the structureviewer sub-value.  Multiple sub-values can be specified together, separated by a comma ','.  Possible values for the structureviewer are:
+  You can specify which structure viewer (or none) to use to open the structure using either the ‑‑structureviewer argument or the structureviewer sub-value.  Multiple sub-values can be specified together, separated by a comma ','.  Possible values for the structureviewer are:
   
    
   none,
   
    
@@ -296,19 +296,19 @@
   
    
   
    
 
-  
    --paematrix
    
+  
    ‑‑paematrix
    
 
   
    
-  If you are opening a structure file that has a PAE matrix (provided as a JSON file), such as from an AlphaFold model or an nf-core pipeline, you can add the PAE matrix as an annotation by following the --structure argument with a --paematrix argument with the filename.  You can also specify a paematrix=filename sub-value.
+  If you are opening a structure file that has a PAE matrix (provided as a JSON file), such as from an AlphaFold model or an nf-core pipeline, you can add the PAE matrix as an annotation by following the ‑‑structure argument with a ‑‑paematrix argument with the filename.  You can also specify a paematrix=filename sub-value.
   
       jalview --open examples/uniref50.fa --structure [seqid=FER1+SPIOL,structureviewer=pymol]examples/AlphaFold/AF-P00221-F1-model_v4.pdb --paematrix examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json
   
    
   
    
 
-  
    --tempfac
    
+  
    ‑‑tempfac
    
 
   
    
-  Structure files may have a temperature factor associated with the structure component positions.  If the temperature factor is a pLDDT confidence score, such as with an AlphaFold model, you can specify this by using a following argument of --tempfac with a value of plddt.  This will enable standard pLDDT colouring of the temperature factor annotation.  Valid values are:
+  Structure files may have a temperature factor associated with the structure component positions.  If the temperature factor is a pLDDT confidence score, such as with an AlphaFold model, you can specify this by using a following argument of ‑‑tempfac with a value of plddt.  This will enable standard pLDDT colouring of the temperature factor annotation.  Valid values are:
   default,
   plddt.
   More types of temperature factor may be added in future releases of Jalview.
@@ -327,10 +327,10 @@
 
   
 
-  
    --showssannotations / --noshowssannotations
    
+  
    ‑‑showssannotations / ‑‑noshowssannotations
    
 
   
    
-  You can specify whether the currently opened alignment window should show secondary structure annotations or not with either --showssannotations or --noshowssannotations.  If you don't specify then your saved preference will be used.
+  You can specify whether the currently opened alignment window should show secondary structure annotations or not with either ‑‑showssannotations or ‑‑noshowssannotations.  If you don't specify then your saved preference will be used.
   
       jalview --open examples/uniref50.fa --structure examples/AlphaFold/AF-P00221-F1-model_v4.pdb --noshowssannotations
   
    
@@ -340,7 +340,7 @@

    -

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

    +

    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: @@ -367,10 +367,10 @@ In bitmap formats (currently only PNG, but what else would you want?!) you can specify a scaling factor to improve the resolution of the output image.

    -

    --output

    +

    ‑‑output

    - To save the open alignment in a new alignment file use --output filename. The format for the file can be found from the extension of filename, or if you are using a non-standard extension you can use a following --format argument, or specify it as a sub-value modifier. + To save the open alignment in a new alignment file use ‑‑output filename. The format for the file can be found from the extension of filename, or if you are using a non-standard extension you can use a following ‑‑format argument, or specify it as a sub-value modifier.

    Recognised formats and their recognised extensions are: @@ -415,7 +415,7 @@

    - Important! If you use --output or any other argument that outputs a file, then it will be assumed you want to run Jalview in headless mode (as if you had specified --headless). To use Jalview with --output and not assume headless mode, use the --gui argument (the order doesn't matter). + Important! If you use ‑‑output or any other argument that outputs a file, then it will be assumed you want to run Jalview in headless mode (as if you had specified ‑‑headless). To use Jalview with ‑‑output and not assume headless mode, use the ‑‑gui argument (the order doesn't matter).

    @@ -432,15 +432,15 @@

    -

    --format

    +

    ‑‑format

    - To specify the format of the output file (if using an unrecognised file extension) use the --format argument to specify a value (see above). A sub-value modifier on the --output value can also be used. + To specify the format of the output file (if using an unrecognised file extension) use the ‑‑format argument to specify a value (see above). A sub-value modifier on the ‑‑output value can also be used.

    -

    --image

    +

    ‑‑image

    - To export the open alignment window as an image, use the --image argument, which will give an image of the alignment and annotations as it appears (or would appear if not in --headless mode) in the alignment window if it was large enough for the whole alignment, including colour scheme and features. + To export the open alignment window as an image, use the ‑‑image argument, which will give an image of the alignment and annotations as it appears (or would appear if not in ‑‑headless mode) in the alignment window if it was large enough for the whole alignment, including colour scheme and features. 

    @@ -448,9 +448,9 @@

    -

    --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). + 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). 

    @@ -462,10 +462,10 @@
   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
    
+  
    ‑‑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:
+  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),
   
    
@@ -490,57 +490,57 @@
   Let's increase the resolution of the PNG image:
   
    
 
-  
    --scale
    
+  
    ‑‑scale
    
 
   
    
-  We can increase the size of the PNG image by a factor of S by following the --image or --structureimage argument with a --scale S argument and value.  The value doesn't have to be an integer and should be given as an integer or floating point formatted number, e.g.
+  We can increase the size of the PNG image by a factor of S by following the ‑‑image or ‑‑structureimage argument with a ‑‑scale S argument and value.  The value doesn't have to be an integer and should be given as an integer or floating point formatted number, e.g.
   
       jalview --open examples/uniref50.fa --colour gecos-ocean --image mypic.png --scale 5.5 --headless
   
    
-  which will produce a PNG image 5.5 times larger (and more detailed) than without the --scale argument.
+  which will produce a PNG image 5.5 times larger (and more detailed) than without the ‑‑scale argument.
   
    
   
    
   However, since you won't necessarily already know the size of an alignment's exported image you can specify either an exact width or height (in pixels) with either one of the
-  --width and --height arguments:
+  ‑‑width and ‑‑height arguments:
 
-  
    --width
    
+  
    ‑‑width
    
 
   
    
-  Specify an exact width of an exported PNG image with --width:
+  Specify an exact width of an exported PNG image with ‑‑width:
   
       jalview --headless --open https://www.ebi.ac.uk/interpro/api/entry/pfam/PF03760/?annotation=alignment%3Aseed --noshowannotations --colour gecos-sunset --image wallpaper.png --width 3840
   
    
   
    
 
-  
    --height
    
+  
    ‑‑height
    
 
   
    
-  Alternatively specify an exact height with the --height argument:
+  Alternatively specify an exact height with the ‑‑height argument:
   
       jalview --headless --open https://www.ebi.ac.uk/interpro/api/entry/pfam/PF03760/?annotation=alignment%3Aseed --noshowannotations --colour gecos-ocean --image wallpaper.png --height 2160
   
    
   
    
 
   
    
-  You can specify two or all of --scale, --width and --height as limits to the size of the image (think of one or two bounding boxes) and the one which produces the smallest scale of image is used.  You can also specify each of these as sub-value modifiers to the --image or --structureimage value:
+  You can specify two or all of ‑‑scale, ‑‑width and ‑‑height as limits to the size of the image (think of one or two bounding boxes) and the one which produces the smallest scale of image is used.  You can also specify each of these as sub-value modifiers to the ‑‑image or ‑‑structureimage value:
   
       jalview --headless --open https://www.ebi.ac.uk/interpro/api/entry/pfam/PF03760/?annotation=alignment%3Aseed --noshowannotations --colour gecos-flower --image [scale=0.25,width=320,height=240]thumbnail.png
   
    
   
    
 
-  
    --imagecolour
    
+  
    ‑‑imagecolour
    
 
   
    
-  Specify a colour scheme to use just for this image using the --imagecolour argument:
+  Specify a colour scheme to use just for this image using the ‑‑imagecolour argument:
   
       jalview --open examples/uniref50.fa --colour gecos-flower --image uniref50-residues.png --height 2160 --image uniref50-helix.png --imagecolour helix-propensity --width 800 --image uniref50-turn.png --imagecolour turn-propensity --width 800
   
    
   
    
 
-  
    --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.
+  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.
   
    
   
    
   E.g.
@@ -560,7 +560,7 @@
   
       jalview --open examples/uniref50.fa --colour gecos-flower --image printable.eps
   
    
-  The image format can be specified with the --type argument or as a sub-value modifier on the --image value.  If neither is used the type will be guessed from the image file extension.  The following three examples should produce the same contents:
+  The image format can be specified with the ‑‑type argument or as a sub-value modifier on the ‑‑image value.  If neither is used the type will be guessed from the image file extension.  The following three examples should produce the same contents:
   
       jalview --open examples/uniref50.fa --colour gecos-flower --image printable.eps
   jalview --open examples/uniref50.fa --colour gecos-flower --image printable.postscript --type eps
@@ -568,10 +568,10 @@
   
    
   
    
 
-  
    --textrenderer
    
+  
    ‑‑textrenderer
    
 
   
    
-  In a vector format any text that appears on the page (including residue/base labels) can be saved in the image file either as text or as lineart using the --textrenderer argument.  This is only available for eps, svg and html formats.
+  In a vector format any text that appears on the page (including residue/base labels) can be saved in the image file either as text or as lineart using the ‑‑textrenderer argument.  This is only available for eps, svg and html formats.
   
    
 
   
    
@@ -582,7 +582,7 @@
   
    
 
   
    
-  The type of --textrenderer can be specified with an argument following --image or as a sub-value modifier:
+  The type of ‑‑textrenderer can be specified with an argument following ‑‑image or as a sub-value modifier:
   
       jalview --open examples/uniref50.fa --colour gecos-flower --image printable.html --type biojs
   jalview --open examples/uniref50.fa --colour gecos-flower --image [type=eps,textrenderer=lineart]printable.ps
@@ -591,25 +591,25 @@
 
   
    Output behaviour
    
 
-  
    --overwrite
    
+  
    ‑‑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.
+  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
    
+  
    ‑‑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.
+  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
    
+  
    ‑‑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.
+  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)
    
+  
    Filename substitutions and batch processing (‑‑substitutions, ‑‑close, ‑‑all)
    
 
   
    
   One of the more powerful aspects of Jalview's command line operations is that stores all of the different opened alignment arguments (before opening them) and can apply some arguments to all of the alignments as they are opened.  This includes display and output arguments.
@@ -630,7 +630,7 @@
   
    
 
   
    
-  Specifically for --structureimage output, you can also use substitutions using parts of the structure filename:
+  Specifically for ‑‑structureimage output, you can also use substitutions using parts of the structure filename:
   
      
   
    • {structuredirname} -- is replaced by the directory path to the opened structure file.
      • 
   
    • {structurebasename} -- is replaced by the base of the filename of the opened structure file. This is without the path or file extension (if there is one).
      • 
@@ -642,7 +642,7 @@
   These filename substitutions are on by default, but if for whatever reason you wish to disable the substitutions, they can be turned off (or back on again) through the list of arguments with:
   
      
 
-  
      --substitutions / --nosubstitutions
      
+  
      ‑‑substitutions / --nosubstitutions
      
 
   
      
   Enable (or disable) filename substitutions in the following argument values and sub-value modifier values.
@@ -652,54 +652,54 @@
   
      
 
   
      
-  For opening single files this is less useful, since you could obviously just type the output filename, but for multiple opened alignments you can also use these substituted values and they will be replaced by the relevant part of the filename given for each opened alignment window.  Normally an --output or --image argument will only be applied to the latest opened alignment window, but you can tell Jalview to apply some arguments to all alignments that have been opened (so far) by using the --all argument.
+  For opening single files this is less useful, since you could obviously just type the output filename, but for multiple opened alignments you can also use these substituted values and they will be replaced by the relevant part of the filename given for each opened alignment window.  Normally an ‑‑output or ‑‑image argument will only be applied to the latest opened alignment window, but you can tell Jalview to apply some arguments to all alignments that have been opened (so far) by using the ‑‑all argument.
   
      
 
-  
      --all / -noall
      
+  
      ‑‑all / -noall
      
 
   
      
-  When using the --all argument, following arguments will apply to all of the previously opened alignment windows.  You can turn this behaviour off again for following arguments using the --noall argument.  The arguments that can apply to all previously opened alignments are:
+  When using the ‑‑all argument, following arguments will apply to all of the previously opened alignment windows.  You can turn this behaviour off again for following arguments using the ‑‑noall argument.  The arguments that can apply to all previously opened alignments are:
   
      
-  --colour
+  ‑‑colour
   
      
-  --sortbytree
+  ‑‑sortbytree
   
      
-  --showannotations
+  ‑‑showannotations
   
      
-  --wrap
+  ‑‑wrap
   
      
-  --nostructure
+  ‑‑nostructure
   
      
-  --notempfac
+  ‑‑notempfac
   
      
-  --showssannotations
+  ‑‑showssannotations
   
      
-  --image
+  ‑‑image
   
      
-  --type
+  ‑‑type
   
      
-  --textrenderer
+  ‑‑textrenderer
   
      
-  --scale
+  ‑‑scale
   
      
-  --width
+  ‑‑width
   
      
-  --height
+  ‑‑height
   
      
-  --output
+  ‑‑output
   
      
-  --format
+  ‑‑format
   
      
-  --groovy
+  ‑‑groovy
   
      
-  --backups
+  ‑‑backups
   
      
-  --overwrite
+  ‑‑overwrite
   
      
-  --close
+  ‑‑close
   
      
   
      
-  In particular, for our example above, we can use -all and --output like this (--close will be explained in a moment):
+  In particular, for our example above, we can use -all and ‑‑output like this (‑‑close will be explained in a moment):
   
         jalview --open all_my_fasta_files/*.fa --all --output all_my_converted_stockholm_files/{basename}.stk --close --headless
   
      
@@ -716,31 +716,31 @@
   
    
   
    
 
-  
    --close
    
+  
    ‑‑close
    
 
   
    
-  The --close tag is used to close an alignment window after all output files or image exports are performed.  This reduces memory use, especially if an --open value is set to open many files.  These will be opened, formatted and output sequentially so since they are closed before the next one is opened memory use will not build up over a large number of alignments.
+  The ‑‑close tag is used to close an alignment window after all output files or image exports are performed.  This reduces memory use, especially if an ‑‑open value is set to open many files.  These will be opened, formatted and output sequentially so since they are closed before the next one is opened memory use will not build up over a large number of alignments.
   
       
    
   
    
 
 
-  
    The all output wildcard: --output "*/*.ext",  --image "*/*.ext"
    
+  
    The all output wildcard: ‑‑output "*/*.ext",  ‑‑image "*/*.ext"
    
 
   
    
-  Purely as an intuitive syntactic sweetener, you can use the --output wildcard * in two places as part of an output path and filename.
+  Purely as an intuitive syntactic sweetener, you can use the ‑‑output wildcard * in two places as part of an output path and filename.
   
    
 
   
    
-  Using an asterisk (*) as a filename before an extension, e.g. --image "tmp/*.png" will result in that asterisk being treated as a {basename} substitution.
+  Using an asterisk (*) as a filename before an extension, e.g. ‑‑image "tmp/*.png" will result in that asterisk being treated as a {basename} substitution.
   
    
 
   
    
-  Using an asterisk (*) before a file separator (usually /), e.g. --image "tmp/*/file1.png" will result in that asterisk being treated as a {dirname} substitution.
+  Using an asterisk (*) before a file separator (usually /), e.g. ‑‑image "tmp/*/file1.png" will result in that asterisk being treated as a {dirname} substitution.
   
    
 
   
    
-  You can combine these, using an asterisk (*) before and after the last file separator, e.g. --image "tmp/*/*.png" will result in being substituted like tmp/{dirname}/{basename}.png.
+  You can combine these, using an asterisk (*) before and after the last file separator, e.g. ‑‑image "tmp/*/*.png" will result in being substituted like tmp/{dirname}/{basename}.png.
   
    
 
   
    
@@ -748,7 +748,7 @@
   
       jalview --open */*.fa --image "*/*.png" --colour gecos-flower --width 256 --height 256 --close --headless
   
    
-  Here we move the --colour argument after the --output argument (it will still be applied before the image export or file output) so that it is included after the implied --all argument.  The thumbnails will be placed in the same directory as the alignment file with the same filename except for a different extension of .png.
+  Here we move the ‑‑colour argument after the ‑‑output argument (it will still be applied before the image export or file output) so that it is included after the implied ‑‑all argument.  The thumbnails will be placed in the same directory as the alignment file with the same filename except for a different extension of .png.
   
    
 
   
    
@@ -763,7 +763,7 @@
   
    
 
   
    
-  An alternative is to use an equals sign ('=') with no spaces between the argument and the value, --output=*.ext, which Jalview will interpret the same, but the shell will not automatically expand before it is sent to Jalview, e.g.
+  An alternative is to use an equals sign ('=') with no spaces between the argument and the value, ‑‑output=*.ext, which Jalview will interpret the same, but the shell will not automatically expand before it is sent to Jalview, e.g.
   
       jalview --open all_my_fasta_files/*.fa --output=*.stk --close --headless
   
    
diff --git a/help/help/html/features/clarguments-reference.html b/help/help/html/features/clarguments-reference.html
index 484d62a..62ef374 100644
--- a/help/help/html/features/clarguments-reference.html
+++ b/help/help/html/features/clarguments-reference.html
@@ -67,13 +67,13 @@
     ‑‑headless
     Run Jalview in headless mode.  In headless mode, no GUI interface will be created and Jalview will quit after all arguments have been processed.
     
    
-    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.
+    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
-    Force Jalview to run in graphical mode.  This can be used to counter the assumption of headless mode when an argument that creates an output file is used.  --gui takes precedence over --headless.
+    Force Jalview to run in graphical mode.  This can be used to counter the assumption of headless mode when an argument that creates an output file is used.  ‑‑gui takes precedence over ‑‑headless.
     
 
     
@@ -575,7 +575,7 @@
 
     
     ‑‑mkdirs
-    Enable automatic creation of new directories and parent directories for filenames given, or created through substitutions, in --output, --image or --structureimage arguments.
+    Enable automatic creation of new directories and parent directories for filenames given, or created through substitutions, in ‑‑output, ‑‑image or ‑‑structureimage arguments.
     
     ✓
     
@@ -690,7 +690,7 @@ Automatically create directories when outputting a file to a new directory
 
     
     ‑‑scale number
-    Sets a scaling for bitmap image format (PNG).  Should be given as a floating point number.  Applies to the preceding ‑‑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).
+    Sets a scaling for bitmap image format (PNG).  Should be given as a floating point number.  Applies to the preceding ‑‑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).
     
     
     ✓
@@ -698,7 +698,7 @@ Automatically create directories when outputting a file to a new directory
 
     
     ‑‑width number
-    Sets a width for bitmap image format (PNG) with the height 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 --height then the smallest size 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.  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 ‑‑height then the smallest size will be used (scale, width and height provide bounds for the image).
     
     
     ✓
@@ -706,14 +706,14 @@ Automatically create directories when outputting a file to a new directory
 
     
     ‑‑height number
-    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).
+    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).
     
     ✓
     
 
     
     ‑‑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 preceded by a hash (#) character (e.g. #ffffff, 00ffff).  Note that you made need to quote a hashed RGB hex string.  This can also be set as a sub-value modifier to the --structureimage value.
+    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 preceded by a hash (#) character (e.g. #ffffff, 00ffff).  Note that you made need to quote a hashed RGB hex string.  This can also be set as a sub-value modifier to the ‑‑structureimage value.
     
     ✓
     
@@ -741,7 +741,7 @@ Automatically create directories when outputting a file to a new directory
     
     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.
     
     
 
@@ -800,7 +800,7 @@ Automatically create directories when outputting a file to a new directory
     
     ‑‑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.
     
     
 
diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html
index 7c2e9d5..6df40b5 100644
--- a/help/help/html/features/clarguments.html
+++ b/help/help/html/features/clarguments.html
@@ -44,7 +44,7 @@
   
    
 
   
    
-  These new arguments are all accessed with a --doubledash form of
+  These new arguments are all accessed with a ‑‑doubledash form of
   command line argument (with the one exception where simply opening one or more
   files can be performed without any arguments other than the filenames).
   
    
@@ -60,7 +60,7 @@
   
    
   However, you cannot mix old and new style arguments, so if you use any
   -singledash arguments (with the exception of -help or -h), they will all be interpreted as
-  old style arguments with the new --doubledash
+  old style arguments with the new ‑‑doubledash
   arguments being ignored.  If you have a script
   that uses the old arguments without any dashes, and uses the bare-word
   open then these will also be interpreted as old style arguments.
@@ -97,52 +97,52 @@
     
  • 
         For arguments that require a value, the value can be given after an equals-sign ('=') or a space (' ').
         
    
-        --arg value
+        ‑‑arg value
         
    
-        --arg=value
+        ‑‑arg=value
     
    • 
     
  • 
         For arguments that can take multiple values (these will be filenames), the multiple filenames should appear after a space. If you use a filename wildcard you can put this after a space (which will be expanded by the shell unto multiple filenames before they reach Jalview), or you can put it after an equals-sign, which will be used by Jalview to find a list of files.  You cannot use an equals-sign and value followed by further values.
         
    
-        --arg file1.fa otherfile.stk
+        ‑‑arg file1.fa otherfile.stk
         
    
-        --arg filename*.fa (filenames expanded by shell)
+        ‑‑arg filename*.fa (filenames expanded by shell)
         
    
-        --arg=filename*.fa (filenames expanded by Jalview)
+        ‑‑arg=filename*.fa (filenames expanded by Jalview)
     
    • 
     
  • 
         For arguments that act as a switch, most can be negated by preceding the argument name with no.
         
    
-        --switch
+        ‑‑switch
         
    
-        --noswitch
+        ‑‑noswitch
     
    • 
     
  • 
-        Some values can be modified, or may need additional information (for instance an --image output can be modified with a --scale=number factor, or a --structure can refer to a sequence with a --seqid=ID).  This additional information can be added in a number of different ways.
+        Some values can be modified, or may need additional information (for instance an ‑‑image output can be modified with a ‑‑scale=number factor, or a ‑‑structure can refer to a sequence with a ‑‑seqid=ID).  This additional information can be added in a number of different ways.
         
      
           
    • 
               An argument immediately following the main argument.
               
      
-              --image output.png --scale 2.5
+              ‑‑image output.png --scale 2.5
           
      • 
           
    • 
               A sub-value modifier, which is where one or more (comma-separated) values are added to the start of the main value, placed in square brackets.
               
      
-              --open=[nowrap,colour=gecos-blossom]uniref50.fa
+              ‑‑open=[nowrap,colour=gecos-blossom]uniref50.fa
               
      
               Sub-value modifiers with a value must use an equals-sign separator, and those that act as a switch can simply be included without an equals-sign or value, and can be preceded with no to negate the value, as with the argument name.
           
      • 
           
    • 
               Another argument with the same linked ID.  A linked ID is an optional identifier for a particular open alignment, placed in square brackets immediately following the argument name (before the equals-sign or space).  If linked IDs are specified they do not need to be near to each other.
               
      
-              --image[MYID]=output.png --other --args --scale[MYID]=2.5
+              ‑‑image[MYID]=output.png --other --args --scale[MYID]=2.5
           
      • 
           
    • 
               An argument that is designated as applying to all linked IDs
               
      
-              --image=output.png --other --args --all --scale=2.5
+              ‑‑image=output.png --other --args --all --scale=2.5
               
      
-              --image=output.png --other --args --scale[*]=2.5
+              ‑‑image=output.png --other --args --scale[*]=2.5
           
      • 
         
    
     
    • 
@@ -157,13 +157,13 @@
   
    Headless mode
    
 
   
    
-  Jalview can be run in headless mode, i.e. without the usual graphical user interface (GUI), by specifying the --headless argument.  With command line arguments you can specify operations for Jalview to perform on one or more files and then stop running.  Most likely you will want to output another file, either an alignment for image file.
+  Jalview can be run in headless mode, i.e. without the usual graphical user interface (GUI), by specifying the ‑‑headless argument.  With command line arguments you can specify operations for Jalview to perform on one or more files and then stop running.  Most likely you will want to output another file, either an alignment for image file.
   
    
   
    
-  If you specify an argument for an output file (one or more of --output, --image or --structureimage) then it will be assumed that you wish to run in headless mode.
+  If you specify an argument for an output file (one or more of ‑‑output, ‑‑image or ‑‑structureimage) then it will be assumed that you wish to run in headless mode.
   
    
   
    
-  You can force Jalview to run in graphical mode using the --gui argument.
+  You can force Jalview to run in graphical mode using the ‑‑gui argument.
   
    
 
   
    
-- 
1.7.10.2