Merge branch 'bug/JAL-4277_dirname_substitution_always_absolute' into improvement...

[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 3862375..b300c67 100644 (file)
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -37,6 +37,7 @@ 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.FileUtils;
@@ -150,12 +151,6 @@ public class ArgParser
   private boolean allLinkedIds = false;
 
   /**
-   * flag to say whether the default linkedId is the current default linked id
-   * or OPENED linkedIds
-   */
-  private boolean openedLinkedIds = false;
-
-  /**
    * flag to say whether the structure arguments should be applied to all
    * structures with this linked id
    */
@@ -177,6 +172,15 @@ public class ArgParser
 
   private BootstrapArgs bootstrapArgs = null;
 
+  private boolean oldArguments = false;
+
+  private boolean mixedArguments = false;
+
+  /**
+   * saved examples of mixed arguments
+   */
+  private String[] mixedExamples = new String[] { null, null };
+
   static
   {
     argMap = new HashMap<>();
@@ -241,19 +245,39 @@ public class ArgParser
       if (arg.startsWith(DOUBLEDASH))
       {
         dd = true;
-        break;
+        if (mixedExamples[1] == null)
+        {
+          mixedExamples[1] = arg;
+        }
       }
       else if (arg.startsWith("-") || arg.equals("open"))
       {
         d = true;
+        if (mixedExamples[0] == null)
+        {
+          mixedExamples[0] = arg;
+        }
+      }
+    }
+    if (d)
+    {
+      if (dd)
+      {
+        mixedArguments = true;
+      }
+      else
+      {
+        oldArguments = true;
       }
     }
-    if (d && !dd)
+
+    if (oldArguments || mixedArguments)
     {
       // leave it to the old style -- parse an empty list
       parse(new ArrayList<String>(), false, false);
       return;
     }
+
     if (bsa != null)
       this.bootstrapArgs = bsa;
     else
@@ -379,10 +403,12 @@ public class ArgParser
         {
           // arg not found
           Console.error("Argument '" + arg + "' not recognised.  Exiting.");
-          Jalview.exit("Invalid argument used." + System.lineSeparator()
-                  + "Use" + System.lineSeparator() + "jalview "
-                  + Arg.HELP.argString() + System.lineSeparator()
-                  + "for a usage statement.", 13);
+          Jalview.exit(
+                  "Invalid argument used." + System.lineSeparator() + "Use"
+                          + System.lineSeparator() + "jalview "
+                          + Arg.HELP.argString() + System.lineSeparator()
+                          + "for a usage statement.",
+                  ExitCode.INVALID_ARGUMENT);
           continue;
         }
         if (a.hasOption(Opt.PRIVATE) && !allowPrivate)
@@ -484,12 +510,6 @@ public class ArgParser
         else if (a == Arg.ALL)
         {
           allLinkedIds = !negated;
-          openedLinkedIds = false;
-        }
-        else if (a == Arg.OPENED)
-        {
-          openedLinkedIds = !negated;
-          allLinkedIds = false;
         }
         else if (a == Arg.ALLSTRUCTURES)
         {
@@ -516,35 +536,25 @@ public class ArgParser
         {
           if (linkedId == null)
           {
-            if (a.hasOption(Opt.OUTPUTFILE) && a.hasOption(Opt.ALLOWALL)
-                    && val.startsWith(MATCHALLLINKEDIDS))
+            if (a.hasOption(Opt.OUTPUTFILE) && a.hasOption(Opt.ALLOWMULTIID)
+                    && val.contains(MATCHALLLINKEDIDS))
             {
-              // --output=*.ext is shorthand for --all --output {basename}.ext
+              // --output=*.ext is shorthand for --output {basename}.ext
+              // --output=*/*.ext is shorthand for
+              // --output {dirname}/{basename}.ext
               // (or --image=*.ext)
-              allLinkedIds = true;
-              openedLinkedIds = false;
-              linkedId = MATCHALLLINKEDIDS;
-              val = LINKEDIDDIRNAME + File.separator + LINKEDIDBASENAME
-                      + val.substring(MATCHALLLINKEDIDS.length());
+              linkedId = allLinkedIds ? MATCHALLLINKEDIDS
+                      : MATCHOPENEDLINKEDIDS;
+              val = FileUtils.convertWildcardsToPath(val, MATCHALLLINKEDIDS,
+                      LINKEDIDDIRNAME, LINKEDIDBASENAME);
             }
-            else if (a.hasOption(Opt.OUTPUTFILE)
-                    && a.hasOption(Opt.ALLOWALL)
-                    && val.startsWith(MATCHOPENEDLINKEDIDS))
-            {
-              // --output=open*.ext is shorthand for --opened --output
-              // {basename}.ext
-              // (or --image=open*.ext)
-              openedLinkedIds = true;
-              allLinkedIds = false;
-              linkedId = MATCHOPENEDLINKEDIDS;
-              val = LINKEDIDDIRNAME + File.separator + LINKEDIDBASENAME
-                      + val.substring(MATCHOPENEDLINKEDIDS.length());
-            }
-            else if (allLinkedIds && a.hasOption(Opt.ALLOWALL))
+            else if (allLinkedIds && a.hasOption(Opt.ALLOWMULTIID))
             {
               linkedId = MATCHALLLINKEDIDS;
             }
-            else if (openedLinkedIds && a.hasOption(Opt.ALLOWALL))
+            else if (a.hasOption(Opt.ALLOWMULTIID)
+                    && this.storedLinkedIds != null
+                    && this.storedLinkedIds.size() > 0)
             {
               linkedId = MATCHOPENEDLINKEDIDS;
             }
@@ -668,9 +678,8 @@ public class ArgParser
         // remove the '*' or 'open*' linkedId that should be empty if it was
         // created
         if ((MATCHALLLINKEDIDS.equals(linkedId)
+                || MATCHOPENEDLINKEDIDS.equals(linkedId))
                 && linkedArgs.containsKey(linkedId))
-                || (MATCHOPENEDLINKEDIDS.equals(linkedId)
-                        && linkedArgs.containsKey(linkedId)))
         {
           linkedArgs.remove(linkedId);
         }
@@ -915,7 +924,7 @@ public class ArgParser
       {
         String message = Arg.ARGFILE.argString() + EQUALS + "\""
                 + argFile.getPath() + "\": File does not exist.";
-        Jalview.exit(message, 2);
+        Jalview.exit(message, ExitCode.FILE_NOT_FOUND);
       }
       try
       {
@@ -929,7 +938,7 @@ public class ArgParser
       {
         String message = Arg.ARGFILE.argString() + "=\"" + argFile.getPath()
                 + "\": File could not be read.";
-        Jalview.exit(message, 3);
+        Jalview.exit(message, ExitCode.FILE_NOT_READABLE);
       }
     }
     // Third param "true" uses Opt.PRIVATE args --setargile=argfile and
@@ -955,7 +964,7 @@ public class ArgParser
         String message = Arg.ARGFILE.argString() + "=\"" + argFile.getPath()
                 + "\": File could not be read.";
         Console.debug(message, e);
-        Jalview.exit(message, 3);
+        Jalview.exit(message, ExitCode.FILE_NOT_READABLE);
       }
     }
     return args;
@@ -1202,7 +1211,7 @@ public class ArgParser
     Arg a = avs.arg();
 
     List<String> wildcardLinkedIds = null;
-    if (a.hasOption(Opt.ALLOWALL))
+    if (a.hasOption(Opt.ALLOWMULTIID))
     {
       switch (linkedId)
       {
@@ -1233,7 +1242,9 @@ public class ArgParser
         // skip incorrectly stored wildcard ids!
         if (id == null || MATCHALLLINKEDIDS.equals(id)
                 || MATCHOPENEDLINKEDIDS.equals(id))
+        {
           continue;
+        }
         ArgValuesMap avm = linkedArgs.get(id);
         // don't set an output if there isn't an input
         if (a.hasOption(Opt.REQUIREINPUT)
@@ -1341,4 +1352,18 @@ public class ArgParser
     return linkedArgs.get(linkedId);
   }
 
+  public boolean isOldStyle()
+  {
+    return oldArguments;
+  }
+
+  public boolean isMixedStyle()
+  {
+    return mixedArguments;
+  }
+
+  public String[] getMixedExamples()
+  {
+    return mixedExamples;
+  }
 }
\ No newline at end of file