From 585dbfeb3c901e3ca234a74c51a01c9e84132ef9 Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Thu, 10 Aug 2023 17:29:17 +0100 Subject: [PATCH] JAL-629 STDOUT documentation. Opt.STDOUT narrower option. Fix for subvals and STDOUT detection. --- help/help/html/features/clarguments-basic.html | 15 +++++++++++++++ help/help/html/features/clarguments-reference.html | 2 ++ src/jalview/bin/argparser/Arg.java | 14 +++++++++----- src/jalview/bin/argparser/BootstrapArgs.java | 16 ++++++++++++---- 4 files changed, 38 insertions(+), 9 deletions(-) diff --git a/help/help/html/features/clarguments-basic.html b/help/help/html/features/clarguments-basic.html index 7a87602..70b42f1 100644 --- a/help/help/html/features/clarguments-basic.html +++ b/help/help/html/features/clarguments-basic.html @@ -393,6 +393,7 @@ phylip (phy),
jalview (jvp, jar). +

For example, to open a FASTA file, append another FASTA file and then save the concatenation as a Stockholm file, do 

@@ -412,6 +413,20 @@
   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).
   

 
+  

+  If you would like to output an alignment file directly to standard output (often referred to as STDOUT), then use the filename - (a single hyphen).  In this case any messages that would normally appear on STDOUT will be diverted to STDERR to avoid invalidating the output file.
+  

+  

+  For example, to open a Stockholm file and pipe it to another command as a Block file, do
+  
+  jalview --open alignment1.stk --output - --format blc | another_command
+  

+  or equivalently
+  
+  jalview alignment1.stk --output=[format=blc]- | another_command
+  

+  

+
   
--format

 
   

diff --git a/help/help/html/features/clarguments-reference.html b/help/help/html/features/clarguments-reference.html
index dd0bd52..48e3a79 100644
--- a/help/help/html/features/clarguments-reference.html
+++ b/help/help/html/features/clarguments-reference.html
@@ -521,6 +521,8 @@
     phylip (phy),
     

     jalview (jvp, jar).
+    

+    To output directly to STDOUT (console output) use the filename - (a single hyphen).  In this case all STDOUT messages will instead go to STDERR.  If no format is supplied then Fasta will be assumed.
     
     format=name
     ✓
diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index 2f25978..0088c60 100644
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -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),
@@ -200,7 +199,7 @@ public enum Arg
                   + "clustal (aln),\n" + "phylip (phy),\n"
                   + "jalview (jvp, jar).",
           Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS, Opt.ALLOWALL,
-          Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.PRIMARY),
+          Opt.REQUIREINPUT, Opt.OUTPUTFILE, Opt.STDOUT, Opt.PRIMARY),
   FORMAT(Type.OUTPUT,
           "Sets the format for the preceding --output file. Valid formats are:\n"
                   + "fasta,\n" + "pfam,\n" + "stockholm,\n" + "pir,\n"
@@ -384,6 +383,11 @@ public enum Arg
      */
     OUTPUTFILE("output file --headless will be assumed unless --gui used"),
     /*
+     * A STDOUT Arg can take an output filename that can be '-' to mean print to STDOUT.
+     */
+    STDOUT("allows the output filename '" + ArgParser.STDOUTFILENAME
+            + "' to mean output to STDOUT"),
+    /*
      * A STORED Arg resets and creates a new set of "opened" linkedIds
      */
     STORED(null),
diff --git a/src/jalview/bin/argparser/BootstrapArgs.java b/src/jalview/bin/argparser/BootstrapArgs.java
index 32eb91a..a989206 100644
--- a/src/jalview/bin/argparser/BootstrapArgs.java
+++ b/src/jalview/bin/argparser/BootstrapArgs.java
@@ -152,11 +152,19 @@ public class BootstrapArgs
           // not a bootstrap arg
 
           // make a check for an output going to stdout
-          if (a != null && a.hasOption(Opt.OUTPUTFILE))
+          if (a != null && a.hasOption(Opt.OUTPUTFILE)
+                  && a.hasOption(Opt.STDOUT))
           {
-            if ((val == null && i + 1 < args.size()
-                    && ArgParser.STDOUTFILENAME.equals(args.get(i + 1)))
-                    || ArgParser.STDOUTFILENAME.equals(val))
+            if (val == null && i + 1 < args.size())
+            {
+              val = args.get(i + 1);
+            }
+            if (val.startsWith("[") && val.indexOf(']') > 0)
+            {
+              val = val.substring(val.indexOf(']') + 1);
+            }
+
+            if (ArgParser.STDOUTFILENAME.equals(val))
             {
               this.outputToStdout = true;
             }
-- 
1.7.10.2