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 (file)
--- a/help/help/html/features/clarguments-basic.html
+++ b/help/help/html/features/clarguments-basic.html
@@ -409,7 +409,7 @@
   </p>
 
   <p>
-  <em>Important!</em> If you use <code>--output</code> 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 <code>--headless</code>).  To use Jalview with <code>--output</code> and not assume headless mode, use the <code>--gui</code> or <code>--noheadless</code> argument (the order doesn't matter).
+  <em>Important!</em> If you use <code>--output</code> 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 <code>--headless</code>).  To use Jalview with <code>--output</code> and not assume headless mode, use the <code>--gui</code> argument (the order doesn't matter).
   </p>
 
   <h3><a name="format"></a><code>--format</code></h3>

diff --git a/help/help/html/features/clarguments-reference.html b/help/help/html/features/clarguments-reference.html
index dd0bd52..3532af4 100644 (file)
--- a/help/help/html/features/clarguments-reference.html
+++ b/help/help/html/features/clarguments-reference.html
@@ -65,10 +65,10 @@
     <tr valign="top"><td><code>&#8209;&#8209;help&#8209;all</code></td><td>Help for all arguments</td></tr>
 
     <tr valign="top">
-    <td><code>&#8209;&#8209;headless / &#8209;&#8209;noheadless</code></td>
-    <td>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.
+    <td><code>&#8209;&#8209;headless</code></td>
+    <td>Run Jalview in headless mode.  In headless mode, no GUI interface will be created and Jalview will quit after all arguments have been processed.
     <br/>
-    If you use a command line argument to specify an output file of some kind (<code>--output</code>, <code>--image</code> or <code>--structureimage</code>) then <strong>headless mode will be assumed</strong>.  If you don't want this behaviour use <code>--noheadless</code> or <code>--gui</code>.
+    If you use a command line argument to specify an output file of some kind (<code>--output</code>, <code>--image</code> or <code>--structureimage</code>) then <strong>headless mode will be assumed</strong>.  If you don't want this behaviour use <code>--gui</code>.
     </td>
     </tr>
 

diff --git a/help/help/html/features/clarguments.html b/help/help/html/features/clarguments.html
index b763a81..7c2e9d5 100644 (file)
--- a/help/help/html/features/clarguments.html
+++ b/help/help/html/features/clarguments.html
@@ -163,7 +163,7 @@
   <strong>If you specify an argument for an output file</strong> (one or more of <code>--output</code>, <code>--image</code> or <code>--structureimage</code>) then it will be assumed that you wish to <strong>run in headless mode</strong>.
   </p>
   <p>
-  You can force Jalview to run in graphical mode using the <code>--gui</code> or <code>--noheadless</code> arguments.
+  You can force Jalview to run in graphical mode using the <code>--gui</code> argument.
   </p>
 
   <p>

diff --git a/help/help/icons/jalview_docs_logo.png b/help/help/icons/jalview_docs_logo.png
new file mode 100644 (file)
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 (file)
--- 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 (file)
--- 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 (executable)
--- 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 (executable)
--- 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