From 17aaf80d4e11248d8cb947b310303a898426092e Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Tue, 9 May 2023 10:27:02 +0100 Subject: [PATCH] JAL-629 more docs --- .../help/html/features/clarguments-ng-summary.html | 315 ++++++++++++++++++++ help/help/html/features/clarguments-ng.html | 29 +- 2 files changed, 332 insertions(+), 12 deletions(-) create mode 100644 help/help/html/features/clarguments-ng-summary.html diff --git a/help/help/html/features/clarguments-ng-summary.html b/help/help/html/features/clarguments-ng-summary.html new file mode 100644 index 0000000..a85dc24 --- /dev/null +++ b/help/help/html/features/clarguments-ng-summary.html @@ -0,0 +1,315 @@ + + +Summary of Command Line Arguments (version 2.11.3.0 onwards) + + +

Summary of Command Line Arguments (version 2.11.3.0 onwards)

+ +

+ See Jalview Command Line Arguments (next generation) + for more explanation about using Jalview's command line arguments. +

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
argumentactionsubval modifiers (optional)linked (optional)
--open filename/URL ... + Opens one or more alignment files in new alignment windows. + Examples. + + + colour=colourscheme, + title=title, + features=featurefile, + annotations=annotationfile, + tree=treefile, + showannotations, + ssannotations, + sortbytree, + wrap + + ✓
--append filename/URL ...Appends one or more alignment files to an open alignment window (or opens a new alignment if none already open). + + colour=colourscheme, + title=title, + features=featurefile, + annotations=annotationfile, + tree=treefile, + showannotations, + ssannotations, + sortbytree, + wrap + . + Examples. + ✓
--title "title"Specifies the title for the open alignment window.✓
--colour colourschemeApplies the given colour scheme to the open alignment window. Valid values are: + clustal, + blosum62, + pc-identity, + zappo, + taylor, + gecos-flower, + gecos-blossom, + gecos-sunset, + gecos-ocean, + hydrophobic, + helix-propensity, + strand-propensity, + turn-propensity, + buried-index, + nucleotide, + nucleotide-ambiguity, + purine-pyrimidine, + rna-helices, + t-coffee-scores, + sequence-id. + Examples. + ✓
--features filename/URLAdd a feature file to the open alignment.✓
--tree filename/URLAdd a tree file to the open alignment.✓
--sortbytree / --nosortbytreeEnforces sorting (or not sorting) the alignment in the order of an attached phylogenetic tree.✓
--annotations filename/URLAdd an annotations file to the open alignment.✓
--showannotations / --noshowannotationsEnforces showing (or not showing) alignment annotations.✓
--structure filename/URLLoad a structure file attached to a sequence in the open alignment. + + seqid=sequenceid or sequence index, + paefile=paefilename, + tempfac=temperature factor type, + ssannotations, + notempfac, + structureviewer=structure viewer + ✓
--paematrix filenameAdd a PAE file to the preceding --structure✓
--tempfac temperature factor typeSet the type of temperature factor. Possible values are + default, + plddt + ✓
--structureviewer structure viewerSet the structure viewer to use to open the 3d structure file specified in previous --structure. Possible values are: +
+ none, +
+ jmol, +
+ chimera - requires installation, might need configuring in Preferences, +
+ chimerax - requires installation, might need configuring in Preferences, +
+ pymol - requires installation, might need configuring in Preferences + 		✓
--notempfacDo not show the temperature factor annotation for the preceding --structure✓
--groovy filenameProcess a groovy script in the file for the open alignment.✓
--image new filenameOutput an image of the open alignment window. Format is specified by the subval modifier, a following --type argument or guessed from the file extension. Valid formats/extensions are: + svg, + png, + eps, + html, + biojs + + type=image format, + textrenderer=text format + ✓
--type image formatSet the image format for the preceding --image. Valid values are: + svg, + png, + eps, + html, + biojs + ✓
--textrenderer text formatSets whether text in a vector image format (SVG, HTML, EPS) should be rendered as text or vector line-art. Possible values are: + text, + lineart + ✓
--output outputfilenameExport the open alignment. Format is specified by the subval modifier, a following --format argument or guessed from the file extension. Valid formats/extensions are: +
+ Fasta (fa, fasta), +
+ + 		✓
-- ✓
-- ✓
-- ✓
diff --git a/help/help/html/features/clarguments-ng.html b/help/help/html/features/clarguments-ng.html index 4a173d2..5f2ef5a 100644 --- a/help/help/html/features/clarguments-ng.html +++ b/help/help/html/features/clarguments-ng.html @@ -25,6 +25,11 @@

Jalview Command Line Arguments (version 2.11.3.0 and later)

+ For a summary of Jalview command line arguments see Summary + of Command Line Arguments. +

+ +

From version 2.11.3.0 Jalview processes a new set of command line arguments which allow more powerful and flexible combinations of arguments, though can also be used for very simple use cases too. @@ -73,7 +78,7 @@ in typical use cases you may still want to think of it as doing so.
For more advanced use please see - Advanced Command Line Arguments. +

@@ -82,7 +87,7 @@

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

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

   jalview filename1 filename2 ...
@@ -104,10 +109,10 @@ after the initial filenames.)

-
--open
+
--open

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

@@ -130,14 +135,14 @@

-
--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 frame 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
 
@@ -146,13 +151,13 @@
   

 
   

-  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 frames 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 frames, use --new to move on to a new alignment frame:
+  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
   

@@ -232,7 +237,7 @@
   
--annotations

 
   

-  You can specify whether the currently opened alignment frame should show alignment annotations (e.g. Conservation, Quality, Consensus...) or not with either --annotations or --noannotations.  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 --annotations or --noannotations.  If you don't specify then your saved preference will be used.
   
   jalview --open examples/uniref50.fa --noannotations
   

@@ -241,7 +246,7 @@
   
--title

 
   

-  If you would like to give the alignment frame 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"
   

@@ -250,7 +255,7 @@
   
--structure

 
   

-  You can add a 3D structure file to a sequence in the current alignment frame 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
   

-- 
1.7.10.2