From: Ben Soares Date: Thu, 17 Aug 2023 11:43:26 +0000 (+0100) Subject: JAL-3830 JAL-4160 Remove --noheadless as --gui does this. Simplifies wrapper scripts X-Git-Tag: Release_2_11_3_0~8^2~30^2~2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3778008766299b5db71d77e8530a9c0fe9b6916d;hp=e63e442ec4eea069cb7caa4ebe0c7e6f04855c74;p=jalview.git JAL-3830 JAL-4160 Remove --noheadless as --gui does this. Simplifies wrapper scripts --- diff --git a/help/help/html/features/clarguments-basic.html b/help/help/html/features/clarguments-basic.html index 7a87602..e2f984f 100644 --- a/help/help/html/features/clarguments-basic.html +++ b/help/help/html/features/clarguments-basic.html @@ -409,7 +409,7 @@

- 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 or --noheadless 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).

--format

diff --git a/help/help/html/features/clarguments-reference.html b/help/help/html/features/clarguments-reference.html index dd0bd52..3532af4 100644 --- a/help/help/html/features/clarguments-reference.html +++ b/help/help/html/features/clarguments-reference.html @@ -65,10 +65,10 @@ ‑‑help‑allHelp for all arguments - ‑‑headless / ‑‑noheadless - Run Jalview in headless (/ or not in headless) mode. In headless mode, no GUI interface will be created and Jalview will quit after all arguments have been processed. + ‑‑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 --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. diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html index b763a81..7c2e9d5 100644 --- a/help/help/html/features/clarguments.html +++ b/help/help/html/features/clarguments.html @@ -163,7 +163,7 @@ 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 or --noheadless arguments. + You can force Jalview to run in graphical mode using the --gui argument.

diff --git a/help/help/icons/jalview_docs_logo.png b/help/help/icons/jalview_docs_logo.png new file mode 100644 index 0000000..21f5386 Binary files /dev/null and b/help/help/icons/jalview_docs_logo.png differ diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java index 2f25978..ec915f5 100644 --- a/src/jalview/bin/argparser/Arg.java +++ b/src/jalview/bin/argparser/Arg.java @@ -29,8 +29,8 @@ public enum Arg Opt.UNARY, Opt.BOOTSTRAP), HEADLESS(Type.CONFIG, "Run Jalview in headless mode. No GUI interface will be created and Jalview will quit after all arguments have been processed. " - + "Headless mode is assumed if an output file is to be generated, this can be overridden with --noheadless or --gui.", - Opt.BOOLEAN, Opt.BOOTSTRAP), + + "Headless mode is assumed if an output file is to be generated, this can be overridden with --gui.", + Opt.UNARY, Opt.BOOTSTRAP), GUI(Type.CONFIG, "Do not run Jalview in headless mode. This overrides the assumption of headless mode when an output file is to be generated.", Opt.UNARY, Opt.BOOTSTRAP), @@ -93,11 +93,10 @@ public enum Arg + "turn-propensity,\n" + "buried-index,\n" + "nucleotide,\n" + "nucleotide-ambiguity,\n" + "purine-pyrimidine,\n" + "rna-helices,\n" - + "t-coffee-scores,\n" + "sequence-id.\n" - +"\n" + + "t-coffee-scores,\n" + "sequence-id.\n" + "\n" + "Names of user defined colourschemes will also work,\n" - +"and jalview colourscheme specifications like\n" - +"--colour=\"D,E=red; K,R,H=0022FF; C,c=yellow\"", + + "and jalview colourscheme specifications like\n" + + "--colour=\"D,E=red; K,R,H=0022FF; C,c=yellow\"", Opt.STRING, Opt.LINKED, Opt.ALLOWALL), FEATURES(Type.OPENING, "Add a feature file or URL to the open alignment.", Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.ALLOWSUBSTITUTIONS), diff --git a/src/jalview/bin/argparser/BootstrapArgs.java b/src/jalview/bin/argparser/BootstrapArgs.java index 4b7b180..f51e4c5 100644 --- a/src/jalview/bin/argparser/BootstrapArgs.java +++ b/src/jalview/bin/argparser/BootstrapArgs.java @@ -362,7 +362,7 @@ public class BootstrapArgs } else if (this.contains(Arg.HEADLESS)) { - // --headless, --noheadless specified => use value + // --headless has been specified on the command line => headless isHeadless = this.getBoolean(Arg.HEADLESS); } else if (this.argsHaveOption(Opt.OUTPUTFILE)) diff --git a/utils/conda/jalview.sh b/utils/conda/jalview.sh index c9ec026..995195f 100755 --- a/utils/conda/jalview.sh +++ b/utils/conda/jalview.sh @@ -66,21 +66,19 @@ HEADLESS=0 GUI=0 HELP=0 DEBUG=0 -for ARG in "${@}"; do +for RAWARG in "${@}"; do + ARG="${RAWARG%%=*}" case "${ARG}" in - "--headless") + --headless|--output|--image|--structureimage) HEADLESS=1 ;; - "--help") + --help|--help-*|--version) HELP=1 ;; - --help-*) - HELP=1 - ;; - "--gui") + --gui) GUI=1 ;; - "--debug") + --debug) DEBUG=1 ;; esac @@ -174,7 +172,7 @@ fi JVMARGS=( "${JVMARGS[@]}" "-DCONSOLEWIDTH=${COLUMNS}" ) if [ "${DEBUG}" = 1 ]; then - echo Shell running: "${JAVA}" "${JVMARGS[@]}" -jar \""${JARPATH}"\" jalview.bin.Launcher "${ARGS[@]}" + echo Shell running: "${JAVA}" "${JVMARGS[@]}" -jar \""${JARPATH}"\" "${ARGS[@]}" fi -"${JAVA}" "${JVMARGS[@]}" -jar "${JARPATH}" jalview.bin.Launcher "${ARGS[@]}" +"${JAVA}" "${JVMARGS[@]}" -jar "${JARPATH}" "${ARGS[@]}" diff --git a/utils/getdown/bin/jalview.sh b/utils/getdown/bin/jalview.sh index 371bfcd..9281be2 100755 --- a/utils/getdown/bin/jalview.sh +++ b/utils/getdown/bin/jalview.sh @@ -41,21 +41,19 @@ HEADLESS=0 GUI=0 HELP=0 DEBUG=0 -for ARG in "${@}"; do +for RAWARG in "${@}"; do + ARG="${RAWARG%%=*}" case "${ARG}" in - "--headless") + --headless|--output|--image|--structureimage) HEADLESS=1 ;; - "--help") + --help|--help-*|--version) HELP=1 ;; - --help-*) - HELP=1 - ;; - "--gui") + --gui) GUI=1 ;; - "--debug") + --debug) DEBUG=1 ;; esac