JAL-629 Help and code with threads

[jalview.git] / src / jalview / bin / argparser / Arg.java

diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index 46de01b..384e843 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -179,7 +179,7 @@ public enum Arg
   OPENED("Apply the following output arguments to all of the last --open'ed set of linked arguments.",
           Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION),
   QUIT("After all files have been opened, appended and output, quit Jalview. In ‑‑headless mode this already happens.",
-          Opt.UNARY),
+          Opt.UNARY, Opt.BOOTSTRAP),
 
   // secret options
   TESTOUTPUT(
@@ -198,18 +198,18 @@ public enum Arg
   UNSETARGFILE(
           "Unsets the current value of the argfilename.  Inserted after argfile contents.",
           Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.PRIVATE, Opt.NOACTION),
+  THREADS("When opening multiple alignment windows, set a limit to alignments being processed at one time.  The default is 3.",
+          Opt.BOOTSTRAP, Opt.STRING, Opt.NODUPLICATEVALUES, Opt.NOACTION),
 
   // these last two have no purpose in the normal Jalview application but are
   // used by jalview.bin.Launcher to set memory settings. They are not used by
   // argparser but are here for Usage statement reasons.
   JVMMEMPC(
-          "Only available with standalone executable jar or jalview.bin.Launcher.\n"
-                  + "Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected.\n"
+          "Limit maximum heap size (memory) to PERCENT% of total physical memory detected. This defaults to 90 if total physical memory can be detected.\n"
                   + "The equals sign (\"=\") separator must be used with no spaces.",
           Opt.NOACTION, Opt.BOOTSTRAP, Opt.STRING),
   JVMMEMMAX(
-          "Only available with standalone executable jar or jalview.bin.Launcher.\n"
-                  + "Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.\n"
+          "Limit maximum heap size (memory) to MAXMEMORY. MAXMEMORY can be specified in bytes, kilobytes(k), megabytes(m), gigabytes(g) or if you're lucky enough, terabytes(t). This defaults to 32g if total physical memory can be detected, or to 8g if total physical memory cannot be detected.\n"
                   + "The equals sign (\"=\") separator must be used with no spaces.",
           Opt.NOACTION, Opt.BOOTSTRAP, Opt.STRING),