Merge branch 'improvement/JAL-4409_implement_extra_schemes_in_getdown' into develop

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

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index 12e1b1d..e7cca35 100644 (file)
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -33,11 +33,13 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
 
+import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.bin.Jalview;
 import jalview.bin.Jalview.ExitCode;
 import jalview.bin.argparser.Arg.Opt;
 import jalview.bin.argparser.Arg.Type;
+import jalview.util.ArgParserUtils;
 import jalview.util.FileUtils;
 import jalview.util.HttpUtils;
 
@@ -317,6 +319,14 @@ public class ArgParser
       return;
     }
 
+    // preprocess for associated files only if no actual --args supplied
+    Console.debug("Supplied args are " + args);
+    if (!dd && !Cache.getDefault("NOARGPREPROCESSING", false))
+    {
+      ArgParserUtils.preProcessArgs(args);
+      Console.debug("Preprocessed args are " + args);
+    }
+
     if (bsa != null)
     {
       this.bootstrapArgs = bsa;