X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2Fargparser%2FBootstrapArgs.java;h=4b7b180a799d8f83ff90fdd53a7f152b01e45459;hb=65ed1da9a1710a9ce132c7edfce54955dc1ddf99;hp=a6bad2449158549f4a5a9288100aaed77a433b5d;hpb=4fd4608b88401dbb1a86a29f8d607c7481145e27;p=jalview.git

diff --git a/src/jalview/bin/argparser/BootstrapArgs.java b/src/jalview/bin/argparser/BootstrapArgs.java
index a6bad24..4b7b180 100644
--- a/src/jalview/bin/argparser/BootstrapArgs.java
+++ b/src/jalview/bin/argparser/BootstrapArgs.java
@@ -4,6 +4,7 @@ import java.io.File;
 import java.util.AbstractMap;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.EnumSet;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
@@ -25,6 +26,8 @@ public class BootstrapArgs
 
   private Set<Opt> argsOptions = new HashSet<>();
 
+  private Set<Type> argsTypes = new HashSet<>();
+
   public static BootstrapArgs getBootstrapArgs(String[] args)
   {
     List<String> argList = new ArrayList<>(Arrays.asList(args));
@@ -106,6 +109,24 @@ public class BootstrapArgs
           }
         }
 
+        // after all other args, look for Opt.PREFIX args if still not found
+        if (!ArgParser.argMap.containsKey(argName))
+        {
+          for (Arg potentialArg : EnumSet.allOf(Arg.class))
+          {
+            if (potentialArg.hasOption(Opt.PREFIXKEV) && argName != null
+                    && argName.startsWith(potentialArg.getName())
+                    && val != null)
+            {
+              val = argName.substring(potentialArg.getName().length())
+                      + ArgParser.EQUALS + val;
+              argName = argName.substring(0,
+                      potentialArg.getName().length());
+              break;
+            }
+          }
+        }
+
         if (ArgParser.argMap.containsKey(argName) && val == null)
         {
           val = "true";
@@ -122,6 +143,11 @@ public class BootstrapArgs
               argsOptions.add(opt);
             }
           }
+          Type t = a.getType();
+          if (!argsTypes.contains(t))
+          {
+            argsTypes.add(t);
+          }
         }
 
         if (a == null || !a.hasOption(Opt.BOOTSTRAP))
@@ -275,7 +301,7 @@ public class BootstrapArgs
    * Retrieves the first value even if MULTI.
    * A convenience for non-MULTI args.
    */
-  public String get(Arg a)
+  public String getValue(Arg a)
   {
     if (!bootstrapArgMap.containsKey(a))
       return null;
@@ -287,7 +313,7 @@ public class BootstrapArgs
   {
     if (!bootstrapArgMap.containsKey(a))
       return d;
-    return Boolean.parseBoolean(get(a));
+    return Boolean.parseBoolean(getValue(a));
   }
 
   public boolean getBoolean(Arg a)
@@ -298,7 +324,7 @@ public class BootstrapArgs
     }
     if (bootstrapArgMap.containsKey(a))
     {
-      return Boolean.parseBoolean(get(a));
+      return Boolean.parseBoolean(getValue(a));
     }
     else
     {
@@ -310,4 +336,41 @@ public class BootstrapArgs
   {
     return argsOptions.contains(opt);
   }
+
+  public boolean argsHaveType(Type type)
+  {
+    return argsTypes.contains(type);
+  }
+
+  public boolean isHeadless()
+  {
+    boolean isHeadless = false;
+    if (this.argsHaveType(Type.HELP))
+    {
+      // --help, --help-all, ... specified => headless
+      isHeadless = true;
+    }
+    else if (this.contains(Arg.VERSION))
+    {
+      // --version specified => headless
+      isHeadless = true;
+    }
+    else if (this.contains(Arg.GUI))
+    {
+      // --gui specified => forced NOT headless
+      isHeadless = !this.getBoolean(Arg.GUI);
+    }
+    else if (this.contains(Arg.HEADLESS))
+    {
+      // --headless, --noheadless specified => use value
+      isHeadless = this.getBoolean(Arg.HEADLESS);
+    }
+    else if (this.argsHaveOption(Opt.OUTPUTFILE))
+    {
+      // --output file.fa, --image pic.png, --structureimage struct.png =>
+      // assume headless unless above has been already specified
+      isHeadless = true;
+    }
+    return isHeadless;
+  }
 }