JAL-629 Change behaviour of --open GLOB to increment defaultLinkedId to allow --allfr...

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 402024b..f33202d 100644 (file)
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -81,11 +81,11 @@ public class Commands
     headless = h;
     boolean theseArgsWereParsed = false;
 
-    if (argParser != null && argParser.linkedIds() != null)
+    if (argParser != null && argParser.getLinkedIds() != null)
     {
-      for (String id : argParser.linkedIds())
+      for (String id : argParser.getLinkedIds())
       {
-        ArgValuesMap avm = argParser.linkedArgs(id);
+        ArgValuesMap avm = argParser.getLinkedArgs(id);
         theseArgsWereParsed = true;
         if (id == null)
         {
@@ -138,7 +138,7 @@ public class Commands
   protected boolean processLinked(String id)
   {
     boolean theseArgsWereParsed = false;
-    ArgValuesMap avm = argParser.linkedArgs(id);
+    ArgValuesMap avm = argParser.getLinkedArgs(id);
     if (avm == null)
       return true;
 
@@ -571,7 +571,7 @@ public class Commands
 
   protected boolean processImages(String id)
   {
-    ArgValuesMap avm = argParser.linkedArgs(id);
+    ArgValuesMap avm = argParser.getLinkedArgs(id);
     AlignFrame af = afMap.get(id);
 
     if (af == null)

diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index 91cfe4d..6c3e6ae 100644 (file)
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -54,6 +54,12 @@ public enum Arg
              // user.
     ALLOWALL, // This Arg can use the '*' linkedId to apply to all known
               // linkedIds
+    INCREMENTDEFAULTCOUNTER, // If an Arg has this option and the default
+                             // linkedId is used, the defaultLinkedIdCounter is
+                             // incremented *first*.
+    INPUT, // This Arg counts as an input for REQUIREINPUT
+    REQUIREINPUT, // This Arg can only be applied via --allframes if there is an
+                  // input (i.e. --open or --append)
   }
 
   static
@@ -81,9 +87,9 @@ public enum Arg
     SORTBYTREE.setOptions(true, Opt.BOOLEAN);
     USAGESTATS.setOptions(true, Opt.BOOLEAN);
     APPEND.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
-            Opt.ALLOWSUBSTITUTIONS);
-    OPEN.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
-            Opt.ALLOWSUBSTITUTIONS);
+            Opt.ALLOWSUBSTITUTIONS, Opt.INPUT);
+    OPEN.setOptions(Opt.STRING, Opt.LINKED, Opt.INCREMENTDEFAULTCOUNTER,
+            Opt.MULTI, Opt.GLOB, Opt.ALLOWSUBSTITUTIONS, Opt.INPUT);
     PROPS.setOptions(Opt.STRING, Opt.BOOTSTRAP);
     QUESTIONNAIRE.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
     SETPROP.setOptions(Opt.STRING, Opt.MULTI, Opt.BOOTSTRAP);
@@ -93,7 +99,7 @@ public enum Arg
     VSESS.setOptions(Opt.UNARY);
 
     OUTPUT.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS,
-            Opt.ALLOWALL);
+            Opt.ALLOWALL, Opt.REQUIREINPUT);
 
     SSANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
     NOTEMPFAC.setOptions(Opt.UNARY, Opt.LINKED);
@@ -107,7 +113,7 @@ public enum Arg
     STRUCTUREVIEWER.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI);
     WRAP.setOptions(Opt.BOOLEAN, Opt.LINKED);
     IMAGE.setOptions(Opt.STRING, Opt.LINKED, Opt.ALLOWSUBSTITUTIONS,
-            Opt.ALLOWALL);
+            Opt.ALLOWALL, Opt.REQUIREINPUT);
     QUIT.setOptions(Opt.UNARY);
     CLOSE.setOptions(Opt.UNARY, Opt.LINKED, Opt.ALLOWALL);
     DEBUG.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
@@ -123,6 +129,7 @@ public enum Arg
     UNSETARGFILE.setOptions(Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
     WEBSERVICEDISCOVERY.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
     ALLFRAMES.setOptions(Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION);
+
   }
 
   private final String[] argNames;

diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index 19e8bea..415e065 100644 (file)
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -26,7 +26,9 @@ import java.nio.file.Files;
 import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.EnumSet;
+import java.util.Enumeration;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Locale;
@@ -107,12 +109,14 @@ public class ArgParser
 
   protected Map<String, ArgValuesMap> linkedArgs = new HashMap<>();
 
-  protected List<String> linkedOrder = null;
+  protected List<String> linkedOrder = new ArrayList<>();
 
-  protected List<Arg> argList;
+  protected List<Arg> argList = new ArrayList<>();
 
   private static final char ARGFILECOMMENT = '#';
 
+  private int argIndex = 0;
+
   static
   {
     argMap = new HashMap<>();
@@ -193,19 +197,19 @@ public class ArgParser
           boolean allowPrivate)
   {
     this.substitutions = initsubstitutions;
-    int argIndex = 0;
     boolean openEachInitialFilenames = true;
     for (int i = 0; i < args.size(); i++)
     {
       String arg = args.get(i);
 
-      // If the first arguments do not start with "--" or "-" or is "open" and
-      // is a filename that exists it is probably a file/list of files to open
-      // so we fake an Arg.OPEN argument and when adding files only add the
+      // If the first arguments do not start with "--" or "-" or is not "open"
+      // and` is a filename that exists it is probably a file/list of files to
+      // open so we fake an Arg.OPEN argument and when adding files only add the
       // single arg[i] and increment the defaultLinkedIdCounter so that each of
       // these files is opened separately.
       if (openEachInitialFilenames && !arg.startsWith(DOUBLEDASH)
-              && !arg.startsWith("-") && (new File(arg).exists()
+              && !arg.startsWith("-") && !arg.equals("open")
+              && (new File(arg).exists()
                       || HttpUtils.startsWithHttpOrHttps(arg)))
       {
         arg = Arg.OPEN.argString();
@@ -256,7 +260,9 @@ public class ArgParser
         if (a == null)
         {
           // arg not found
-          Console.error("Argument '" + arg + "' not recognised. Ignoring.");
+          Console.error("Argument '" + arg + "' not recognised.  Exiting.");
+          Jalview.exit("Unrecognised command line argument '" + arg + "'",
+                  13);
           continue;
         }
         if (a.hasOption(Opt.PRIVATE) && !allowPrivate)
@@ -367,37 +373,28 @@ public class ArgParser
 
         String autoCounterString = null;
         boolean usingAutoCounterLinkedId = false;
-        String defaultLinkedId = new StringBuilder(DEFAULTLINKEDIDPREFIX)
-                .append(Integer.toString(defaultLinkedIdCounter))
-                .toString();
+        String defaultLinkedId = defaultLinkedId(false);
         boolean usingDefaultLinkedId = false;
         if (a.hasOption(Opt.LINKED))
         {
           if (linkedId == null)
           {
-            if (a == Arg.OPEN)
+            if (a.hasOption(Opt.INCREMENTDEFAULTCOUNTER))
             {
               // use the next default prefixed OPENLINKEDID
-              // NOW using the linkedIdAutoCounter
-              defaultLinkedIdCounter++;
-              linkedId = new StringBuilder(OPENLINKEDIDPREFIX)
-                      .append(Integer.toString(defaultLinkedIdCounter))
-                      .toString();
+              defaultLinkedId = defaultLinkedId(true);
+            }
+            if (allLinkedIds && a.hasOption(Opt.ALLOWALL))
+            {
+              linkedId = MATCHALLLINKEDIDS;
             }
             else
             {
-              if (allLinkedIds && a.hasOption(Opt.ALLOWALL))
-              {
-                linkedId = this.MATCHALLLINKEDIDS;
-              }
-              else
-              {
-                // use default linkedId for linked arguments
-                linkedId = defaultLinkedId;
-                usingDefaultLinkedId = true;
-                Console.debug("Changing linkedId to '" + linkedId
-                        + "' from " + arg);
-              }
+              // use default linkedId for linked arguments
+              linkedId = defaultLinkedId;
+              usingDefaultLinkedId = true;
+              Console.debug("Changing linkedId to '" + linkedId + "' from "
+                      + arg);
             }
           }
           else if (linkedId.contains(LINKEDIDAUTOCOUNTER))
@@ -422,13 +419,13 @@ public class ArgParser
           }
         }
 
-        if (!linkedArgs.containsKey(linkedId))
-          linkedArgs.put(linkedId, new ArgValuesMap());
-
         // do not continue for NOACTION args
         if (a.hasOption(Opt.NOACTION))
           continue;
 
+        if (!linkedArgs.containsKey(linkedId))
+          linkedArgs.put(linkedId, new ArgValuesMap());
+
         ArgValuesMap avm = linkedArgs.get(linkedId);
 
         // not dealing with both NODUPLICATEVALUES and GLOB
@@ -450,7 +447,6 @@ public class ArgParser
           continue;
         }
 
-        boolean argIndexIncremented = false;
         /* TODO
          * Change all avs.addValue() avs.setBoolean avs.setNegated() avs.incrementCount calls to checkfor linkedId == "*"
          * DONE, need to check
@@ -463,11 +459,23 @@ public class ArgParser
           if (a.hasOption(Opt.GLOB) && globVals != null
                   && globVals.size() > 0)
           {
-            for (String v : globVals)
+            Enumeration<String> gve = Collections.enumeration(globVals);
+            while (gve.hasMoreElements())
             {
+              String v = gve.nextElement();
               SubVals vsv = new SubVals(globSubVals, v);
               addValue(linkedId, avs, vsv, v, argIndex++, true);
-              argIndexIncremented = true;
+              // if we're using defaultLinkedId and the arg increments the
+              // counter:
+              if (gve.hasMoreElements() && usingDefaultLinkedId
+                      && a.hasOption(Opt.INCREMENTDEFAULTCOUNTER))
+              {
+                // increment the default linkedId
+                linkedId = defaultLinkedId(true);
+                // get new avm and avs
+                avm = linkedArgs.get(linkedId);
+                avs = avm.getOrCreateArgValues(a);
+              }
             }
           }
           else
@@ -484,28 +492,53 @@ public class ArgParser
         {
           setBoolean(linkedId, avs, true, argIndex);
         }
-        incrementCount(linkedId, avs);
-        if (!argIndexIncremented)
-          argIndex++;
 
-        // store in appropriate place
-        if (a.hasOption(Opt.LINKED))
+        // remove the '*' linkedId that should be empty if it was created
+        if (MATCHALLLINKEDIDS.equals(linkedId)
+                && linkedArgs.containsKey(linkedId))
         {
-          // store the order of linkedIds
-          if (linkedOrder == null)
-            linkedOrder = new ArrayList<>();
-          if (!linkedOrder.contains(linkedId))
-            linkedOrder.add(linkedId);
+          linkedArgs.remove(linkedId);
         }
+      }
+    }
+  }
 
-        // store arg in the list of args used
-        if (argList == null)
-          argList = new ArrayList<>();
-        if (!argList.contains(a))
-          argList.add(a);
+  private void finaliseStoringArgValue(String linkedId, ArgValues avs)
+  {
+    Arg a = avs.arg();
+    incrementCount(linkedId, avs);
+    argIndex++;
+
+    // store in appropriate place
+    if (a.hasOption(Opt.LINKED))
+    {
+      // store the order of linkedIds
+      if (!linkedOrder.contains(linkedId))
+        linkedOrder.add(linkedId);
+    }
+
+    // store arg in the list of args used
+    if (!argList.contains(a))
+      argList.add(a);
+  }
 
+  private String defaultLinkedId(boolean increment)
+  {
+    String defaultLinkedId = new StringBuilder(DEFAULTLINKEDIDPREFIX)
+            .append(Integer.toString(defaultLinkedIdCounter)).toString();
+    if (increment)
+    {
+      while (linkedArgs.containsKey(defaultLinkedId))
+      {
+        defaultLinkedIdCounter++;
+        defaultLinkedId = new StringBuilder(DEFAULTLINKEDIDPREFIX)
+                .append(Integer.toString(defaultLinkedIdCounter))
+                .toString();
       }
     }
+    if (!linkedArgs.containsKey(defaultLinkedId))
+      linkedArgs.put(defaultLinkedId, new ArgValuesMap());
+    return defaultLinkedId;
   }
 
   public String makeSubstitutions(String val, String linkedId)
@@ -618,12 +651,12 @@ public class ArgParser
     return avs == null ? a.getDefaultBoolValue() : avs.getBoolean();
   }
 
-  public List<String> linkedIds()
+  public List<String> getLinkedIds()
   {
     return linkedOrder;
   }
 
-  public ArgValuesMap linkedArgs(String id)
+  public ArgValuesMap getLinkedArgs(String id)
   {
     return linkedArgs.get(id);
   }
@@ -634,16 +667,16 @@ public class ArgParser
     StringBuilder sb = new StringBuilder();
     sb.append("UNLINKED\n");
     sb.append(argValuesMapToString(linkedArgs.get(null)));
-    if (linkedIds() != null)
+    if (getLinkedIds() != null)
     {
       sb.append("LINKED\n");
-      for (String id : linkedIds())
+      for (String id : getLinkedIds())
       {
         // already listed these as UNLINKED args
         if (id == null)
           continue;
 
-        ArgValuesMap avm = linkedArgs(id);
+        ArgValuesMap avm = getLinkedArgs(id);
         sb.append("ID: '").append(id).append("'\n");
         sb.append(argValuesMapToString(avm));
       }
@@ -802,17 +835,23 @@ public class ArgParser
     Arg a = avs.arg();
     if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
     {
-      for (String id : linkedOrder)
+      for (String id : getLinkedIds())
       {
+        if (id == null || MATCHALLLINKEDIDS.equals(id))
+          continue;
         ArgValuesMap avm = linkedArgs.get(id);
-        ArgValues tavs = avm.getArgValues(a);
+        if (a.hasOption(Opt.REQUIREINPUT)
+                && !avm.hasArgWithOption(Opt.INPUT))
+          continue;
+        ArgValues tavs = avm.getOrCreateArgValues(a);
         String val = v;
         if (doSubs)
         {
-          val = makeSubstitutions(v, linkedId);
+          val = makeSubstitutions(v, id);
           sv = new SubVals(sv, val);
         }
         tavs.addValue(sv, val, argIndex);
+        finaliseStoringArgValue(id, tavs);
       }
     }
     else
@@ -824,6 +863,7 @@ public class ArgParser
         sv = new SubVals(sv, val);
       }
       avs.addValue(sv, val, argIndex);
+      finaliseStoringArgValue(linkedId, avs);
     }
   }
 
@@ -833,18 +873,26 @@ public class ArgParser
     Arg a = avs.arg();
     if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
     {
-      for (String id : linkedOrder)
+      for (String id : getLinkedIds())
       {
+        if (id == null || MATCHALLLINKEDIDS.equals(id))
+          continue;
         ArgValuesMap avm = linkedArgs.get(id);
-        ArgValues tavs = avm.getArgValues(a);
-        String val = doSubs ? makeSubstitutions(v, linkedId) : v;
+        // don't set an output if there isn't an input
+        if (a.hasOption(Opt.REQUIREINPUT)
+                && !avm.hasArgWithOption(Opt.INPUT))
+          continue;
+        ArgValues tavs = avm.getOrCreateArgValues(a);
+        String val = doSubs ? makeSubstitutions(v, id) : v;
         tavs.addValue(val, argIndex);
+        finaliseStoringArgValue(id, tavs);
       }
     }
     else
     {
       String val = doSubs ? makeSubstitutions(v, linkedId) : v;
       avs.addValue(val, argIndex);
+      finaliseStoringArgValue(linkedId, avs);
     }
   }
 
@@ -854,16 +902,23 @@ public class ArgParser
     Arg a = avs.arg();
     if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
     {
-      for (String id : linkedOrder)
+      for (String id : getLinkedIds())
       {
+        if (id == null || MATCHALLLINKEDIDS.equals(id))
+          continue;
         ArgValuesMap avm = linkedArgs.get(id);
-        ArgValues tavs = avm.getArgValues(a);
+        if (a.hasOption(Opt.REQUIREINPUT)
+                && !avm.hasArgWithOption(Opt.INPUT))
+          continue;
+        ArgValues tavs = avm.getOrCreateArgValues(a);
         tavs.setBoolean(b, argIndex);
+        finaliseStoringArgValue(id, tavs);
       }
     }
     else
     {
       avs.setBoolean(b, argIndex);
+      finaliseStoringArgValue(linkedId, avs);
     }
   }
 
@@ -872,10 +927,15 @@ public class ArgParser
     Arg a = avs.arg();
     if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
     {
-      for (String id : linkedOrder)
+      for (String id : getLinkedIds())
       {
+        if (id == null || MATCHALLLINKEDIDS.equals(id))
+          continue;
         ArgValuesMap avm = linkedArgs.get(id);
-        ArgValues tavs = avm.getArgValues(a);
+        if (a.hasOption(Opt.REQUIREINPUT)
+                && !avm.hasArgWithOption(Opt.INPUT))
+          continue;
+        ArgValues tavs = avm.getOrCreateArgValues(a);
         tavs.setNegated(b);
       }
     }
@@ -890,10 +950,15 @@ public class ArgParser
     Arg a = avs.arg();
     if (MATCHALLLINKEDIDS.equals(linkedId) && a.hasOption(Opt.ALLOWALL))
     {
-      for (String id : linkedOrder)
+      for (String id : getLinkedIds())
       {
+        if (id == null || MATCHALLLINKEDIDS.equals(id))
+          continue;
         ArgValuesMap avm = linkedArgs.get(id);
-        ArgValues tavs = avm.getArgValues(a);
+        if (a.hasOption(Opt.REQUIREINPUT)
+                && !avm.hasArgWithOption(Opt.INPUT))
+          continue;
+        ArgValues tavs = avm.getOrCreateArgValues(a);
         tavs.incrementCount();
       }
     }

diff --git a/src/jalview/bin/argparser/ArgValuesMap.java b/src/jalview/bin/argparser/ArgValuesMap.java
index 63e5302..cbc6faa 100644 (file)
--- a/src/jalview/bin/argparser/ArgValuesMap.java
+++ b/src/jalview/bin/argparser/ArgValuesMap.java
@@ -226,4 +226,17 @@ public class ArgValuesMap
     return dirname ? FileUtils.getDirname(file)
             : FileUtils.getBasename(file);
   }
+
+  /*
+   * Checks if there is an Arg with Opt
+   */
+  public boolean hasArgWithOption(Opt o)
+  {
+    for (Arg a : getArgKeys())
+    {
+      if (a.hasOption(o))
+        return true;
+    }
+    return false;
+  }
 }

diff --git a/test/jalview/bin/argparser/ArgParserTest.java b/test/jalview/bin/argparser/ArgParserTest.java
index 8d4540a..314b0f0 100644 (file)
--- a/test/jalview/bin/argparser/ArgParserTest.java
+++ b/test/jalview/bin/argparser/ArgParserTest.java
@@ -7,10 +7,12 @@ import java.util.Properties;
 
 import org.testng.Assert;
 import org.testng.annotations.AfterClass;
+import org.testng.annotations.AfterMethod;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
 import jalview.bin.Cache;
+import jalview.gui.Desktop;
 
 @Test(singleThreaded = true)
 public class ArgParserTest
@@ -21,6 +23,13 @@ public class ArgParserTest
     Cache.loadProperties("test/jalview/testProps.jvprops");
   }
 
+  @AfterMethod(alwaysRun = true)
+  public void tearDown()
+  {
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
+  }
+
   @Test(groups = "Functional", dataProvider = "argLines")
   public void parseArgsTest(String commandLineArgs, Arg a, String other)
   {
@@ -35,7 +44,7 @@ public class ArgParserTest
   {
     String[] args = commandLineArgs.split("\\s+");
     ArgParser argparser = new ArgParser(args);
-    ArgValuesMap avm = argparser.linkedArgs(linkedId);
+    ArgValuesMap avm = argparser.getLinkedArgs(linkedId);
     ArgValue av = avm.getArgValue(a);
     SubVals sv = av.getSubVals();
     String testString = null;
@@ -67,7 +76,7 @@ public class ArgParserTest
     // Arg.OPEN, "filename1" },
     String[] args = commandLineArgs.split("\\s+");
     ArgParser argparser = new ArgParser(args);
-    ArgValuesMap avm = argparser.linkedArgs(linkedId);
+    ArgValuesMap avm = argparser.getLinkedArgs(linkedId);
     ArgValue av = avm.getArgValue(a);
     Assert.assertEquals(av.getValue(), filename);
   }
@@ -260,23 +269,63 @@ public class ArgParserTest
         Arg.ARGFILE, "test/jalview/bin/argfiles/testfiles/test1.fa" } };
   }
 
-  @DataProvider(name = "allLinkedIdData")
-  public Object[][] allLinkedIdData()
+  @Test(groups = "Functional", dataProvider = "allLinkedIdsData")
+  public void allLinkedIdsTest(String commandLineArgs, Arg a,
+          String[] values)
+  {
+    String[] args = commandLineArgs.split("\\s+");
+    ArgParser argparser = new ArgParser(args);
+
+    int num = values.length;
+    List<String> linkedIds = argparser.getLinkedIds();
+    Assert.assertEquals(linkedIds.size(), num,
+            "Wrong number of linkedIds: " + linkedIds.toString());
+    for (int i = 0; i < num; i++)
+    {
+      String value = values[i];
+      String linkedId = linkedIds.get(i);
+      ArgValuesMap avm = argparser.getLinkedArgs(linkedId);
+      if (value == null)
+      {
+        Assert.assertTrue(avm.containsArg(a),
+                "Arg value for " + a.argString()
+                        + " not applied correctly to linkedId '" + linkedId
+                        + "'");
+      }
+      else
+      {
+        ArgValues avs = avm.getArgValues(a);
+        ArgValue av = avs.getArgValue();
+        String v = av.getValue();
+        value = new File(value).getAbsolutePath();
+        Assert.assertEquals(v, value, "Arg value for " + a.argString()
+                + " not applied correctly to linkedId '" + linkedId + "'");
+      }
+    }
+
+  }
+
+  @DataProvider(name = "allLinkedIdsData")
+  public Object[][] allLinkedIdsData()
   {
     return new Object[][] {
         //
-        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
+        /*
+        */
+        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --allframes --image={dirname}/{basename}.png --close",
+            Arg.CLOSE, new String[]
+            { null, null,
+                null } },
+        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --allframes --output={dirname}/{basename}.stk --close",
             Arg.OUTPUT, new String[]
-            { "test/jalview/bin/argfiles/testfiles/test1.stk",
-                "test/jalview/bin/argfiles/testfiles/test2.stk",
-                "test/jalview/bin/argfiles/testfiles/test3.stk", } },
-        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
+            { "test/jalview/bin/argparser/testfiles/test1.stk",
+                "test/jalview/bin/argparser/testfiles/test2.stk",
+                "test/jalview/bin/argparser/testfiles/test3.stk", } },
+        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --allframes --image={dirname}/{basename}.png --close",
             Arg.IMAGE, new String[]
-            { "test/jalview/bin/argfiles/testfiles/test1.png",
-                "test/jalview/bin/argfiles/testfiles/test2.png",
-                "test/jalview/bin/argfiles/testfiles/test3.png", } },
-        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
-            Arg.CLOSE, null },
+            { "test/jalview/bin/argparser/testfiles/test1.png",
+                "test/jalview/bin/argparser/testfiles/test2.png",
+                "test/jalview/bin/argparser/testfiles/test3.png", } },
         //
     };
   }