From 51909770452369f94b4a0070482ab0acdd96fada Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Sat, 20 May 2023 11:45:36 +0100
Subject: [PATCH] JAL-4187 JAL-629 JAL-3830 adjustments to Cygwin and WSL
 parts of bash launcher script and usage statement after
 testing

---
 src/jalview/bin/argparser/Arg.java |   17 +++++++----------
 utils/getdown/bin/jalview.sh       |    4 +---
 2 files changed, 8 insertions(+), 13 deletions(-)

diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index 958569e..2a080fc 100644
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -198,7 +198,7 @@ public enum Arg
           Opt.UNARY, Opt.MULTI, Opt.NOACTION, Opt.INCREMENTDEFAULTCOUNTER),
   SUBSTITUTIONS(Type.FLOW,
           "The following argument values allow (or don't allow) subsituting filename parts. This is initially true. Valid substitutions are {basename} - the filename-without-extension of the currently --opened file (or first --appended file),\n"
-                  + "{dirname}, - the directory (folder) name of the currently --opened file (or first --appended file),\n"
+                  + "{dirname} - the directory (folder) name of the currently --opened file (or first --appended file),\n"
                   + "{argfilebasename} - the filename-without-extension of the current --argfile,\n"
                   + "{argfiledirname} - the directory (folder) name of the current --argfile,\n"
                   + "{n} - the value of the index counter (starting at 0).\n"
@@ -703,15 +703,8 @@ public enum Arg
       while (line.length() > descLength)
       {
         int splitIndex = line.lastIndexOf(" ", descLength);
-        if (splitIndex > descLength)
-        {
-          break;
-        }
-        else
-        {
-          splitDescLinesList.add(line.substring(0, splitIndex));
-          line = line.substring(splitIndex + 1);
-        }
+        splitDescLinesList.add(line.substring(0, splitIndex));
+        line = line.substring(splitIndex + 1);
       }
       splitDescLinesList.add(line);
     }
@@ -723,11 +716,15 @@ public enum Arg
       while (splitDescLines.hasNext())
       {
         if (first)
+        {
           sb.append(ARGDESCRIPTIONSEPARATOR);
+        }
         else
+        {
           sb.append(String.format("%-"
                   + (maxArgLength + ARGDESCRIPTIONSEPARATOR.length()) + "s",
                   ""));
+        }
         sb.append(splitDescLines.next());
         sb.append(System.lineSeparator());
         first = false;
diff --git a/utils/getdown/bin/jalview.sh b/utils/getdown/bin/jalview.sh
index 912f1ad..62da28c 100755
--- a/utils/getdown/bin/jalview.sh
+++ b/utils/getdown/bin/jalview.sh
@@ -80,7 +80,6 @@ fi
 if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoid
   if [ "$(uname -o)" = "Cygwin" ]; then
   # CYGWIN
-    echo "When using relative paths in args within Cygwin, please start with './' or '../'" >&2
     CLASSPATH=$(cygpath -pw "${CLASSPATH}")
     # now for some arg paths fun. only translating paths starting with './', '../', '/' or '~'
     ARGS=()
@@ -91,9 +90,8 @@ if [ "${ISMACOS}" != 1 ]; then # older macos doesn't like uname -o, best to avoi
         ARGS=( "${ARGS[@]}" "${ARG}" )
       fi
     done
-  elif uname -r | grep Microsoft >/dev/null; then
+  elif uname -r | grep -i microsoft | grep -i wsl >/dev/null; then
   # WSL
-    echo "When using relative paths in args within WSL, please start with './' or '../'" >&2
     CLASSPATH=""
     for JARPATH in "${JARPATHS[@]}"; do
       [ -n "${CLASSPATH}" ] && CLASSPATH="${CLASSPATH};"
-- 
1.7.10.2