Merge branch 'feature/JAL-629_--output_-_means_output_to_STDOUT' into improvement...

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

diff --git a/src/jalview/bin/argparser/BootstrapArgs.java b/src/jalview/bin/argparser/BootstrapArgs.java
index faa4a43..ec62bcd 100644 (file)
--- 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;
@@ -23,6 +24,12 @@ public class BootstrapArgs
 
   private Set<File> argFiles = new HashSet<>();
 
+  private Set<Opt> argsOptions = new HashSet<>();
+
+  private Set<Type> argsTypes = new HashSet<>();
+
+  private boolean outputToStdout = false;
+
   public static BootstrapArgs getBootstrapArgs(String[] args)
   {
     List<String> argList = new ArrayList<>(Arrays.asList(args));
@@ -48,7 +55,7 @@ public class BootstrapArgs
     {
       if (argFiles.contains(inArgFile))
       {
-        System.err.println(
+        jalview.bin.Console.errPrintln(
                 "Looped argfiles detected: '" + inArgFile.getPath() + "'");
         return;
       }
@@ -104,16 +111,65 @@ public class BootstrapArgs
           }
         }
 
-        if (ArgParser.argMap.containsKey(argName) && val == null)
+        // after all other args, look for Opt.PREFIX args if still not found
+        if (!ArgParser.argMap.containsKey(argName))
         {
-          val = "true";
+          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;
+            }
+          }
         }
 
         Arg a = ArgParser.argMap.get(argName);
 
+        if (a != null)
+        {
+          for (Opt opt : a.getOptions())
+          {
+            if (!argsOptions.contains(opt))
+            {
+              argsOptions.add(opt);
+            }
+          }
+          Type t = a.getType();
+          if (!argsTypes.contains(t))
+          {
+            argsTypes.add(t);
+          }
+        }
+
         if (a == null || !a.hasOption(Opt.BOOTSTRAP))
         {
-          // not a valid bootstrap arg
+          // not a bootstrap arg
+
+          // make a check for an output going to stdout
+          if (a != null && a.hasOption(Opt.OUTPUTFILE)
+                  && a.hasOption(Opt.STDOUT))
+          {
+            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;
+            }
+          }
+
           continue;
         }
 
@@ -149,6 +205,11 @@ public class BootstrapArgs
         }
         else
         {
+          if (val == null)
+          {
+            val = "true";
+          }
+
           add(a, type, val);
         }
       }
@@ -262,7 +323,7 @@ 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;
@@ -274,7 +335,7 @@ public class BootstrapArgs
   {
     if (!bootstrapArgMap.containsKey(a))
       return d;
-    return Boolean.parseBoolean(get(a));
+    return Boolean.parseBoolean(getValue(a));
   }
 
   public boolean getBoolean(Arg a)
@@ -284,8 +345,59 @@ public class BootstrapArgs
       return false;
     }
     if (bootstrapArgMap.containsKey(a))
-      return Boolean.parseBoolean(get(a));
+    {
+      return Boolean.parseBoolean(getValue(a));
+    }
     else
+    {
       return a.getDefaultBoolValue();
+    }
+  }
+
+  public boolean argsHaveOption(Opt opt)
+  {
+    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 has been specified on the command line => headless
+      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;
+  }
+
+  public boolean outputToStdout()
+  {
+    return this.outputToStdout;
   }
 }