From: Ben Soares <b.soares@dundee.ac.uk>
Date: Thu, 4 May 2023 15:49:00 +0000 (+0100)
Subject: JAL-629 More NG arguments: --features, --annotations, --sortbytree, --tree, --groovy... 
X-Git-Tag: Release_2_11_3_0~14^2~69
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=adff51745d97ff4fd30a188a68efa29cc83202e3;p=jalview.git

JAL-629 More NG arguments: --features, --annotations, --sortbytree, --tree, --groovy.  More consistent arg naming and processing of test output.  Actual java process tests for ng commandline.  Store BootstrapArgs in ArgParser.
---

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 79b6ab6..7e33b17 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -42,6 +42,7 @@ import jalview.io.FileFormats;
 import jalview.io.FileLoader;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
 import jalview.structure.StructureImportSettings.TFType;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.HttpUtils;
@@ -92,6 +93,7 @@ public class Commands
         ArgValuesMap avm = argParser.getLinkedArgs(id);
         theseArgsWereParsed = true;
         theseArgsWereParsed &= processLinked(id);
+        processGroovyScript(id);
         boolean processLinkedOkay = theseArgsWereParsed;
         theseArgsWereParsed &= processImages(id);
         if (processLinkedOkay)
@@ -110,7 +112,7 @@ public class Commands
       }
 
     }
-    if (argParser.getBool(Arg.QUIT))
+    if (argParser.getBoolean(Arg.QUIT))
     {
       Jalview.getInstance().quit();
       return true;
@@ -219,21 +221,11 @@ public class Commands
         if (af == null || "true".equals(av.getSubVal("new"))
                 || a == Arg.OPEN || format == FileFormat.Jalview)
         {
-          /*
-           * this approach isn't working yet // get default annotations before opening
-           * AlignFrame if (m.get(Arg.SSANNOTATIONS) != null) {
-           * Console.debug("##### SSANNOTATIONS=" + m.get(Arg.SSANNOTATIONS).getBoolean());
-           * } if (m.get(Arg.NOTEMPFAC) != null) { Console.debug( "##### NOTEMPFAC=" +
-           * m.get(Arg.NOTEMPFAC).getBoolean()); } boolean showSecondaryStructure =
-           * (m.get(Arg.SSANNOTATIONS) != null) ? m.get(Arg.SSANNOTATIONS).getBoolean() :
-           * false; boolean showTemperatureFactor = (m.get(Arg.NOTEMPFAC) != null) ?
-           * !m.get(Arg.NOTEMPFAC).getBoolean() : false; Console.debug("##### tempfac=" +
-           * showTemperatureFactor + ", showSS=" + showSecondaryStructure);
-           * StructureSelectionManager ssm = StructureSelectionManager
-           * .getStructureSelectionManager(Desktop.instance); if (ssm != null) {
-           * ssm.setAddTempFacAnnot(showTemperatureFactor);
-           * ssm.setProcessSecondaryStructure(showSecondaryStructure); }
-           */
+          if (a == Arg.OPEN)
+          {
+            Jalview.testoutput(argParser, Arg.OPEN, "examples/uniref50.fa",
+                    openFile);
+          }
 
           Console.debug(
                   "Opening '" + openFile + "' in new alignment frame");
@@ -241,45 +233,91 @@ public class Commands
 
           af = fileLoader.LoadFileWaitTillLoaded(openFile, protocol,
                   format);
-          boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm,
-                  Arg.ANNOTATIONS, av.getSubVals(), null,
-                  "SHOW_ANNOTATIONS", true);
-          af.setAnnotationsVisibility(showAnnotations, false, true);
 
           // wrap alignment?
           boolean wrap = ArgParser.getFromSubValArgOrPref(avm, Arg.WRAP, sv,
                   null, "WRAP_ALIGNMENT", false);
           af.getCurrentView().setWrapAlignment(wrap);
 
-          // colour aligment?
+          // colour alignment?
           String colour = ArgParser.getFromSubValArgOrPref(avm, av,
                   Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
-
           if ("" != colour)
           {
             af.changeColour_actionPerformed(colour);
+            Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
           }
 
-          // change alignment frame title
+          // Change alignment frame title
           String title = ArgParser.getFromSubValArgOrPref(avm, av,
                   Arg.TITLE, sv, null, null, null);
           if (title != null)
+          {
             af.setTitle(title);
+            Jalview.testoutput(argParser, Arg.TITLE, "test title", title);
+          }
+
+          // Add features
+          String featuresfile = ArgParser.getValueFromSubValOrArg(avm, av,
+                  Arg.FEATURES, sv);
+          if (featuresfile != null)
+          {
+            af.parseFeaturesFile(featuresfile,
+                    AppletFormatAdapter.checkProtocol(featuresfile));
+            Jalview.testoutput(argParser, Arg.FEATURES,
+                    "examples/testdata/plantfdx.features", featuresfile);
+          }
 
-          // show secondary structure annotations?
+          // Add annotations from file
+          String annotationsfile = ArgParser.getValueFromSubValOrArg(avm,
+                  av, Arg.ANNOTATIONS, sv);
+          if (annotationsfile != null)
+          {
+            af.loadJalviewDataFile(annotationsfile, null, null, null);
+            Jalview.testoutput(argParser, Arg.ANNOTATIONS,
+                    "examples/testdata/plantfdx.annotations",
+                    annotationsfile);
+          }
+
+          // Set or clear the sortbytree flag
+          boolean sortbytree = ArgParser.getBoolFromSubValOrArg(avm,
+                  Arg.SORTBYTREE, sv);
+          if (sortbytree)
+          {
+            af.getViewport().setSortByTree(true);
+            Jalview.testoutput(argParser, Arg.SORTBYTREE);
+          }
+
+          // Load tree from file
+          String treefile = ArgParser.getValueFromSubValOrArg(avm, av,
+                  Arg.TREE, sv);
+          if (treefile != null)
+          {
+            try
+            {
+              NewickFile nf = new NewickFile(treefile,
+                      AppletFormatAdapter.checkProtocol(treefile));
+              af.getViewport().setCurrentTree(
+                      af.showNewickTree(nf, treefile).getTree());
+              Jalview.testoutput(argParser, Arg.TREE,
+                      "examples/testdata/uniref50_test_tree", treefile);
+            } catch (IOException e)
+            {
+              Console.warn("Couldn't add tree " + treefile, e);
+            }
+          }
+
+          // Show secondary structure annotations?
           boolean showSSAnnotations = ArgParser.getFromSubValArgOrPref(avm,
                   Arg.SSANNOTATIONS, av.getSubVals(), null,
                   "STRUCT_FROM_PDB", true);
-          if (avm.getBoolean(Arg.SSANNOTATIONS))
-          {
-            af.setAnnotationsVisibility(showSSAnnotations, true, false);
-            /*
-            AlignmentUtils.showOrHideSequenceAnnotations(
-                    af.getCurrentView().getAlignment(),
-                    Collections.singleton("Secondary Structure"), null,
-                    false, false);
-             */
-          }
+          af.setAnnotationsVisibility(showSSAnnotations, true, false);
+
+          // Show sequence annotations?
+          boolean showAnnotations = ArgParser.getFromSubValArgOrPref(avm,
+                  Arg.SHOWANNOTATIONS, av.getSubVals(), null,
+                  "SHOW_ANNOTATIONS", true);
+          af.setAnnotationsVisibility(showAnnotations, false, true);
 
           // show temperature factor annotations?
           if (avm.getBoolean(Arg.NOTEMPFAC))
@@ -521,8 +559,8 @@ public class Commands
           }
 
           String sViewer = ArgParser.getFromSubValArgOrPref(avm,
-                  Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals,
-                  "viewer", null, "jmol");
+                  Arg.STRUCTUREVIEWER, Position.AFTER, av, subVals, null,
+                  null, "jmol");
           ViewerType viewerType = null;
           if (!"none".equals(sViewer))
           {
@@ -569,6 +607,30 @@ public class Commands
     return theseArgsWereParsed;
   }
 
+  protected void processGroovyScript(String id)
+  {
+    ArgValuesMap avm = argParser.getLinkedArgs(id);
+    AlignFrame af = afMap.get(id);
+
+    if (af == null)
+    {
+      Console.warn("Did not have an alignment window for id=" + id);
+      return;
+    }
+
+    if (avm.containsArg(Arg.GROOVY))
+    {
+      String groovyscript = avm.getValue(Arg.GROOVY);
+      if (groovyscript != null)
+      {
+        // Execute the groovy script after we've done all the rendering stuff
+        // and before any images or figures are generated.
+        Console.info("Executing script " + groovyscript);
+        Jalview.getInstance().executeGroovyScript(groovyscript, af);
+      }
+    }
+  }
+
   protected boolean processImages(String id)
   {
     ArgValuesMap avm = argParser.getLinkedArgs(id);
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 4c204fa..895268d 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -67,6 +67,7 @@ import com.threerings.getdown.util.LaunchUtil;
 import groovy.lang.Binding;
 import groovy.util.GroovyScriptEngine;
 import jalview.bin.argparser.Arg;
+import jalview.bin.argparser.Arg.Opt;
 import jalview.bin.argparser.ArgParser;
 import jalview.bin.argparser.BootstrapArgs;
 import jalview.ext.so.SequenceOntology;
@@ -436,6 +437,8 @@ public class Jalview
     {
       System.out.println(
               "CMD [-props " + usrPropsFile + "] executed successfully!");
+      testoutput(bootstrapArgs, Arg.PROPS,
+              "test/jalview/bin/testProps.jvprops", usrPropsFile);
     }
 
     // new ArgParser
@@ -445,12 +448,14 @@ public class Jalview
     {
       argparser = ArgParser.parseArgFiles(
               bootstrapArgs.getList(Arg.ARGFILE),
-              bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS));
+              bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
+              bootstrapArgs);
     }
     else
     {
       argparser = new ArgParser(args,
-              bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS));
+              bootstrapArgs.getBoolean(Arg.INITSUBSTITUTIONS),
+              bootstrapArgs);
     }
 
     if (!Platform.isJS())
@@ -489,7 +494,9 @@ public class Jalview
       // allow https handshakes to download intermediate certs if necessary
       System.setProperty("com.sun.security.enableAIAcaIssuers", "true");
 
-      final String jabawsUrl = aparser.getValue("jabaws");
+      String jabawsUrl = bootstrapArgs.get(Arg.JABAWS);
+      if (jabawsUrl == null)
+        jabawsUrl = aparser.getValue("jabaws");
       if (jabawsUrl != null)
       {
         try
@@ -497,6 +504,8 @@ public class Jalview
           Jws2Discoverer.getDiscoverer().setPreferredUrl(jabawsUrl);
           System.out.println(
                   "CMD [-jabaws " + jabawsUrl + "] executed successfully!");
+          testoutput(bootstrapArgs, Arg.JABAWS,
+                  "http://www.compbio.dundee.ac.uk/jabaws", jabawsUrl);
         } catch (MalformedURLException e)
         {
           System.err.println(
@@ -639,25 +648,37 @@ public class Jalview
           }
         }
 
-        boolean doWebServiceDiscovery = !aparser
-                .contains("nowebservicediscovery");
-        if (bootstrapArgs.contains(Arg.WEBSERVICEDISCOVERY))
-          doWebServiceDiscovery = bootstrapArgs
-                  .getBoolean(Arg.WEBSERVICEDISCOVERY);
-        if (doWebServiceDiscovery)
+        boolean webservicediscovery = bootstrapArgs
+                .getBoolean(Arg.WEBSERVICEDISCOVERY);
+        if (aparser.contains("nowebservicediscovery"))
+          webservicediscovery = false;
+        if (webservicediscovery)
         {
           desktop.startServiceDiscovery();
         }
-        if (!aparser.contains("nousagestats"))
+        else
+        {
+          testoutput(argparser, Arg.WEBSERVICEDISCOVERY);
+        }
+
+        boolean usagestats = bootstrapArgs.getBoolean(Arg.USAGESTATS);
+        if (aparser.contains("nousagestats"))
+          usagestats = false;
+        if (usagestats)
         {
           startUsageStats(desktop);
+          testoutput(argparser, Arg.USAGESTATS);
         }
         else
         {
-          System.err.println("CMD [-nousagestats] executed successfully!");
+          System.out.println("CMD [-nousagestats] executed successfully!");
+          testoutput(argparser, Arg.USAGESTATS);
         }
 
-        if (!aparser.contains("noquestionnaire"))
+        boolean questionnaire = bootstrapArgs.getBoolean(Arg.QUESTIONNAIRE);
+        if (aparser.contains("noquestionnaire"))
+          questionnaire = false;
+        if (questionnaire)
         {
           String url = aparser.getValue("questionnaire");
           if (url != null)
@@ -687,8 +708,9 @@ public class Jalview
         }
         else
         {
-          System.err
+          System.out
                   .println("CMD [-noquestionnaire] executed successfully!");
+          testoutput(argparser, Arg.QUESTIONNAIRE);
         }
 
         if ((!aparser.contains("nonews")
@@ -1492,7 +1514,7 @@ public class Jalview
    *          the Jalview Desktop object passed in to the groovy binding as the
    *          'Jalview' object.
    */
-  private void executeGroovyScript(String groovyscript, AlignFrame af)
+  protected void executeGroovyScript(String groovyscript, AlignFrame af)
   {
     /**
      * for scripts contained in files
@@ -1653,4 +1675,111 @@ public class Jalview
     if (exitcode > -1)
       System.exit(exitcode);
   }
+
+  /*
+   * testoutput for string values
+   */
+  protected static void testoutput(ArgParser ap, Arg a, String s1,
+          String s2)
+  {
+    BootstrapArgs bsa = ap.getBootstrapArgs();
+    if (!bsa.getBoolean(Arg.TESTOUTPUT))
+      return;
+    if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
+    {
+      Console.debug("testoutput with unmatching values '" + s1 + "' and '"
+              + s2 + "' for arg " + a.argString());
+      return;
+    }
+    boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
+            : ap.isSet(a);
+    if (!isset)
+    {
+      Console.warn("Arg '" + a.getName() + "' not set at all");
+      return;
+    }
+    testoutput(true, a, s1, s2);
+  }
+
+  protected static void testoutput(BootstrapArgs bsa, Arg a, String s1,
+          String s2)
+  {
+    if (!bsa.getBoolean(Arg.TESTOUTPUT))
+      return;
+    if (!((s1 == null && s2 == null) || (s1 != null && s1.equals(s2))))
+    {
+      Console.debug("testoutput with unmatching values '" + s1 + "' and '"
+              + s2 + "' for arg " + a.argString());
+      return;
+    }
+    if (!a.hasOption(Opt.BOOTSTRAP))
+    {
+      Console.error("Non-bootstrap Arg '" + a.getName()
+              + "' given to testoutput(BootstrapArgs bsa, Arg a, String s1, String s2) with only BootstrapArgs");
+    }
+    if (!bsa.contains(a))
+    {
+      Console.warn("Arg '" + a.getName() + "' not set at all");
+      return;
+    }
+    testoutput(true, a, s1, s2);
+  }
+
+  private static void testoutput(boolean yes, Arg a, String s1, String s2)
+  {
+    if (yes && ((s1 == null && s2 == null)
+            || (s1 != null && s1.equals(s2))))
+    {
+      System.out.println("[TESTOUTPUT] arg " + a.argString() + "='" + s1
+              + "' was set");
+    }
+  }
+
+  /*
+   * testoutput for boolean values
+   */
+  protected static void testoutput(ArgParser ap, Arg a)
+  {
+    if (ap == null)
+      return;
+    BootstrapArgs bsa = ap.getBootstrapArgs();
+    if (bsa == null)
+      return;
+    if (!bsa.getBoolean(Arg.TESTOUTPUT))
+      return;
+    boolean val = a.hasOption(Opt.BOOTSTRAP) ? bsa.getBoolean(a)
+            : ap.getBoolean(a);
+    boolean isset = a.hasOption(Opt.BOOTSTRAP) ? bsa.contains(a)
+            : ap.isSet(a);
+    if (!isset)
+    {
+      Console.warn("Arg '" + a.getName() + "' not set at all");
+      return;
+    }
+    testoutput(val, a);
+  }
+
+  protected static void testoutput(BootstrapArgs bsa, Arg a)
+  {
+    if (!bsa.getBoolean(Arg.TESTOUTPUT))
+      return;
+    if (!a.hasOption(Opt.BOOTSTRAP))
+    {
+      Console.warn("Non-bootstrap Arg '" + a.getName()
+              + "' given to testoutput(BootstrapArgs bsa, Arg a) with only BootstrapArgs");
+
+    }
+    if (!bsa.contains(a))
+    {
+      Console.warn("Arg '" + a.getName() + "' not set at all");
+      return;
+    }
+    testoutput(bsa.getBoolean(a), a);
+  }
+
+  private static void testoutput(boolean yes, Arg a)
+  {
+    System.out.println("[TESTOUTPUT] arg "
+            + (yes ? a.argString() : a.negateArgString()) + " was set");
+  }
 }
diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index f8454df..f83f267 100644
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -9,16 +9,17 @@ import java.util.stream.Collectors;
 
 public enum Arg
 {
-  HELP("h"), CALCULATION, MENUBAR, STATUS, SHOWOVERVIEW, ANNOTATIONS,
-  COLOUR, FEATURES, GROOVY, GROUPS, HEADLESS, JABAWS, DISPLAY, GUI, NEWS,
-  SORTBYTREE, USAGESTATS, APPEND, OPEN, PROPS, QUESTIONNAIRE, SETPROP, TREE,
-  VDOC, VSESS, OUTPUT, SSANNOTATIONS, NOTEMPFAC, TEMPFAC, TITLE, PAEMATRIX,
-  WRAP, NOSTRUCTURE, STRUCTURE, STRUCTUREVIEWER, IMAGE, TYPE, FORMAT,
-  OVERWRITE, RENDERER, QUIT, CLOSE, DEBUG("d"), TRACE, QUIET("q"), ARGFILE,
-  NEW, NPP("n++"), SUBSTITUTIONS, INITSUBSTITUTIONS, NIL, SPLASH,
-  SETARGFILE, UNSETARGFILE, WEBSERVICEDISCOVERY, ALL, BACKUPS;
-
-  protected static enum Opt
+  HELP("h"), CALCULATION, MENUBAR, STATUS, SHOWOVERVIEW, SHOWANNOTATIONS,
+  COLOUR("color"), FEATURES, ANNOTATIONS, GROOVY, GROUPS, HEADLESS, JABAWS,
+  DISPLAY, NEWS, SORTBYTREE, USAGESTATS, APPEND, OPEN, PROPS, QUESTIONNAIRE,
+  SETPROP, TREE, VDOC, VSESS, OUTPUT, SSANNOTATIONS, NOTEMPFAC, TEMPFAC,
+  TITLE, PAEMATRIX, WRAP, NOSTRUCTURE, STRUCTURE, STRUCTUREVIEWER, IMAGE,
+  TYPE, FORMAT, OVERWRITE, RENDERER, QUIT, CLOSE, DEBUG("d"), TRACE,
+  QUIET("q"), ARGFILE, NEW, NPP("n++"), SUBSTITUTIONS, INITSUBSTITUTIONS,
+  NIL, SPLASH, SETARGFILE, UNSETARGFILE, WEBSERVICEDISCOVERY, ALL, BACKUPS,
+  TESTOUTPUT;
+
+  public static enum Opt
   {
     BOOLEAN, // This Arg can be specified as --arg or --noarg to give true or
              // false. A default can be given with setOptions(bool, Opt....).
@@ -70,30 +71,33 @@ public enum Arg
     MENUBAR.setOptions(true, Opt.BOOLEAN);
     STATUS.setOptions(true, Opt.BOOLEAN);
     SHOWOVERVIEW.setOptions(Opt.UNARY, Opt.LINKED);
-    ANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
+    SHOWANNOTATIONS.setOptions(Opt.BOOLEAN, Opt.LINKED);
     COLOUR.setOptions(Opt.STRING, Opt.LINKED);
     FEATURES.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
             Opt.ALLOWSUBSTITUTIONS);
+    ANNOTATIONS.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
+            Opt.ALLOWSUBSTITUTIONS);
+    TREE.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
+            Opt.ALLOWSUBSTITUTIONS);
     GROOVY.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI,
             Opt.ALLOWSUBSTITUTIONS);
     GROUPS.setOptions(Opt.STRING, Opt.LINKED);
     HEADLESS.setOptions(Opt.UNARY, Opt.BOOTSTRAP);
-    JABAWS.setOptions(Opt.STRING);
+    TESTOUTPUT.setOptions(Opt.UNARY, Opt.BOOTSTRAP);
+    JABAWS.setOptions(Opt.STRING, Opt.BOOTSTRAP);
     DISPLAY.setOptions(true, Opt.BOOLEAN);
-    GUI.setOptions(true, Opt.BOOLEAN);
     NEWS.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
     SPLASH.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
-    // expects a string value
-    SORTBYTREE.setOptions(true, Opt.BOOLEAN);
-    USAGESTATS.setOptions(true, Opt.BOOLEAN);
+    SORTBYTREE.setOptions(true, Opt.LINKED, Opt.BOOLEAN);
+    QUESTIONNAIRE.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
+    USAGESTATS.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
+    WEBSERVICEDISCOVERY.setOptions(true, Opt.BOOLEAN, Opt.BOOTSTRAP);
     APPEND.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
             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);
-    TREE.setOptions(Opt.STRING);
 
     VDOC.setOptions(Opt.UNARY);
     VSESS.setOptions(Opt.UNARY);
@@ -135,7 +139,6 @@ public enum Arg
     NIL.setOptions(Opt.UNARY, Opt.LINKED, Opt.MULTI, Opt.NOACTION);
     SETARGFILE.setOptions(Opt.STRING, Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
     UNSETARGFILE.setOptions(Opt.MULTI, Opt.PRIVATE, Opt.NOACTION);
-    WEBSERVICEDISCOVERY.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
     ALL.setOptions(Opt.BOOLEAN, Opt.MULTI, Opt.NOACTION);
 
   }
diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index 42868ae..dd863d1 100644
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -118,6 +118,8 @@ public class ArgParser
 
   private int argIndex = 0;
 
+  private BootstrapArgs bootstrapArgs = null;
+
   static
   {
     argMap = new HashMap<>();
@@ -147,10 +149,11 @@ public class ArgParser
 
   public ArgParser(String[] args)
   {
-    this(args, false);
+    this(args, false, null);
   }
 
-  public ArgParser(String[] args, boolean initsubstitutions)
+  public ArgParser(String[] args, boolean initsubstitutions,
+          BootstrapArgs bsa)
   {
     // Make a mutable new ArrayList so that shell globbing parser works.
     // (When shell file globbing is used, there are a sequence of non-Arg
@@ -158,16 +161,17 @@ public class ArgParser
     // consumed by the --append/--argfile/etc Arg which is most easily done by
     // removing these filenames from the list one at a time. This can't be done
     // with an ArrayList made with only Arrays.asList(String[] args). )
-    this(new ArrayList<>(Arrays.asList(args)), initsubstitutions);
+    this(new ArrayList<>(Arrays.asList(args)), initsubstitutions, false,
+            bsa);
   }
 
   public ArgParser(List<String> args, boolean initsubstitutions)
   {
-    this(args, initsubstitutions, false);
+    this(args, initsubstitutions, false, null);
   }
 
   public ArgParser(List<String> args, boolean initsubstitutions,
-          boolean allowPrivate)
+          boolean allowPrivate, BootstrapArgs bsa)
   {
     // do nothing if there are no "--" args and (some "-" args || >0 arg is
     // "open")
@@ -191,6 +195,10 @@ public class ArgParser
       parse(new ArrayList<String>(), false, false);
       return;
     }
+    if (bsa != null)
+      this.bootstrapArgs = bsa;
+    else
+      this.bootstrapArgs = BootstrapArgs.getBootstrapArgs(args);
     parse(args, initsubstitutions, allowPrivate);
   }
 
@@ -620,9 +628,24 @@ public class ArgParser
     return vals;
   }
 
+  public BootstrapArgs getBootstrapArgs()
+  {
+    return bootstrapArgs;
+  }
+
   public boolean isSet(Arg a)
   {
-    return a.hasOption(Opt.LINKED) ? isSet("", a) : isSet(null, a);
+    return a.hasOption(Opt.LINKED) ? isSetAtAll(a) : isSet(null, a);
+  }
+
+  public boolean isSetAtAll(Arg a)
+  {
+    for (String linkedId : linkedOrder)
+    {
+      if (isSet(linkedId, a))
+        return true;
+    }
+    return false;
   }
 
   public boolean isSet(String linkedId, Arg a)
@@ -631,7 +654,7 @@ public class ArgParser
     return avm == null ? false : avm.containsArg(a);
   }
 
-  public boolean getBool(Arg a)
+  public boolean getBoolean(Arg a)
   {
     if (!a.hasOption(Opt.BOOLEAN) && !a.hasOption(Opt.UNARY))
     {
@@ -698,7 +721,7 @@ public class ArgParser
   }
 
   public static ArgParser parseArgFiles(List<String> argFilenameGlobs,
-          boolean initsubstitutions)
+          boolean initsubstitutions, BootstrapArgs bsa)
   {
     List<File> argFiles = new ArrayList<>();
 
@@ -708,11 +731,11 @@ public class ArgParser
       argFiles.addAll(FileUtils.getFilesFromGlob(pattern));
     }
 
-    return parseArgFileList(argFiles, initsubstitutions);
+    return parseArgFileList(argFiles, initsubstitutions, bsa);
   }
 
   public static ArgParser parseArgFileList(List<File> argFiles,
-          boolean initsubstitutions)
+          boolean initsubstitutions, BootstrapArgs bsa)
   {
     List<String> argsList = new ArrayList<>();
     for (File argFile : argFiles)
@@ -740,7 +763,7 @@ public class ArgParser
     }
     // Third param "true" uses Opt.PRIVATE args --setargile=argfile and
     // --unsetargfile
-    return new ArgParser(argsList, initsubstitutions, true);
+    return new ArgParser(argsList, initsubstitutions, true, bsa);
   }
 
   protected static List<String> readArgFile(File argFile)
diff --git a/src/jalview/bin/argparser/BootstrapArgs.java b/src/jalview/bin/argparser/BootstrapArgs.java
index 4829ef8..14b7fe6 100644
--- a/src/jalview/bin/argparser/BootstrapArgs.java
+++ b/src/jalview/bin/argparser/BootstrapArgs.java
@@ -25,6 +25,11 @@ public class BootstrapArgs
     return new BootstrapArgs(argList);
   }
 
+  public static BootstrapArgs getBootstrapArgs(List<String> args)
+  {
+    return new BootstrapArgs(args);
+  }
+
   private BootstrapArgs(List<String> args)
   {
     parse(args, null);
diff --git a/src/jalview/io/FileFormat.java b/src/jalview/io/FileFormat.java
index b701963..43c6dcf 100644
--- a/src/jalview/io/FileFormat.java
+++ b/src/jalview/io/FileFormat.java
@@ -30,7 +30,7 @@ import jalview.structure.StructureImportSettings;
 
 public enum FileFormat implements FileFormatI
 {
-  Fasta("Fasta", "fa, fasta, mfa, fastq", true, true)
+  Fasta("Fasta", "fa,fasta,mfa,fastq", true, true)
   {
     @Override
     public AlignmentFileReaderI getReader(FileParse source)
@@ -92,7 +92,7 @@ public enum FileFormat implements FileFormatI
       return new PIRFile();
     }
   },
-  BLC("BLC", "BLC", true, true)
+  BLC("BLC", "blc", true, true)
   {
     @Override
     public AlignmentFileReaderI getReader(FileParse source)
@@ -244,7 +244,7 @@ public enum FileFormat implements FileFormatI
       return new PhylipFile();
     }
   },
-  GenBank("GenBank Flatfile", "gb, gbk", true, false)
+  GenBank("GenBank Flatfile", "gb,gbk", true, false)
   {
     @Override
     public AlignmentFileReaderI getReader(FileParse source)
@@ -379,7 +379,7 @@ public enum FileFormat implements FileFormatI
       return true;
     }
   },
-  Jalview("Jalview", "jvp, jar", true, true)
+  Jalview("Jalview", "jvp,jar", true, true)
   {
     @Override
     public AlignmentFileReaderI getReader(FileParse source)
diff --git a/test/jalview/bin/CommandLineOperations.java b/test/jalview/bin/CommandLineOperations.java
index 9b9adf8..0ab18d9 100644
--- a/test/jalview/bin/CommandLineOperations.java
+++ b/test/jalview/bin/CommandLineOperations.java
@@ -34,7 +34,6 @@ import java.util.ArrayList;
 import org.testng.Assert;
 import org.testng.FileAssert;
 import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeTest;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
@@ -213,13 +212,13 @@ public class CommandLineOperations
     }
   }
 
-  @BeforeTest(alwaysRun = true)
+  @BeforeClass(alwaysRun = true)
   public void initialize()
   {
     new CommandLineOperations();
   }
 
-  @BeforeTest(alwaysRun = true)
+  @BeforeClass(alwaysRun = true)
   public void setUpForHeadlessCommandLineInputOperations()
           throws IOException
   {
@@ -239,7 +238,7 @@ public class CommandLineOperations
     }
   }
 
-  @BeforeTest(alwaysRun = true)
+  @BeforeClass(alwaysRun = true)
   public void setUpForCommandLineInputOperations() throws IOException
   {
     String cmds = "-open examples/uniref50.fa -noquestionnaire -nousagestats";
@@ -261,7 +260,7 @@ public class CommandLineOperations
         int count = 0;
         try
         {
-          while ((ln = worker.getErrorReader().readLine()) != null)
+          while ((ln = worker.getOutputReader().readLine()) != null)
           {
             System.out.println(ln);
             successfulCMDs.add(ln);
diff --git a/test/jalview/bin/CommandLineOperationsNG.java b/test/jalview/bin/CommandLineOperationsNG.java
new file mode 100644
index 0000000..4d05c4e
--- /dev/null
+++ b/test/jalview/bin/CommandLineOperationsNG.java
@@ -0,0 +1,455 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.bin;
+
+import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertTrue;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.testng.Assert;
+import org.testng.FileAssert;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.DataProvider;
+import org.testng.annotations.Test;
+
+import io.github.classgraph.ClassGraph;
+import jalview.gui.JvOptionPane;
+
+public class CommandLineOperationsNG
+{
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  // Note longer timeout needed on full test run than on individual tests
+  private static final int TEST_TIMEOUT = 13000;
+
+  private static final int SETUP_TIMEOUT = 9500;
+
+  private static final int MINFILESIZE_SMALL = 2096;
+
+  private static final int MINFILESIZE_BIG = 4096;
+
+  private List<String> successfulCMDs = new ArrayList<>();
+
+  /***
+   * from
+   * http://stackoverflow.com/questions/808276/how-to-add-a-timeout-value-when
+   * -using-javas-runtime-exec
+   * 
+   * @author jimp
+   * 
+   */
+  private static class Worker extends Thread
+  {
+    private final Process process;
+
+    private BufferedReader outputReader;
+
+    private BufferedReader errorReader;
+
+    private Integer exit;
+
+    private Worker(Process process)
+    {
+      this.process = process;
+    }
+
+    @Override
+    public void run()
+    {
+      try
+      {
+        exit = process.waitFor();
+      } catch (InterruptedException ignore)
+      {
+        return;
+      }
+    }
+
+    public BufferedReader getOutputReader()
+    {
+      return outputReader;
+    }
+
+    public void setOutputReader(BufferedReader outputReader)
+    {
+      this.outputReader = outputReader;
+    }
+
+    public BufferedReader getErrorReader()
+    {
+      return errorReader;
+    }
+
+    public void setErrorReader(BufferedReader errorReader)
+    {
+      this.errorReader = errorReader;
+    }
+  }
+
+  private static ClassGraph scanner = null;
+
+  private static String classpath = null;
+
+  private static String modules = null;
+
+  private static String java_exe = null;
+
+  public synchronized static String getClassPath()
+  {
+    // if (scanner == null)
+    // {
+    // scanner = new ClassGraph();
+    // ScanResult scan = scanner.scan();
+    // classpath = scan.getClasspath();
+    modules = "";
+    // for (ModuleRef mr : scan.getModules())
+    // {
+    // modules.concat(mr.getName());
+    // }
+    java_exe = System.getProperty("java.home") + File.separator + "bin"
+            + File.separator + "java";
+
+    // }
+
+    // while (classpath == null)
+    // {
+    // try
+    // {
+    // Thread.sleep(10);
+    // } catch (InterruptedException x)
+    // {
+    //
+    // }
+    // }
+    return classpath;
+  }
+
+  private Worker getJalviewDesktopRunner(boolean withAwt, String cmd,
+          int timeout)
+  {
+    // Note: JAL-3065 - don't include quotes for lib/* because the arguments are
+    // not expanded by the shell
+    // String classpath = getClassPath();
+    getClassPath();
+    boolean win = System.getProperty("os.name").indexOf("Win") >= 0;
+    String pwd = "";
+    try
+    {
+      Path currentRelativePath = Paths.get("");
+      pwd = currentRelativePath.toAbsolutePath().toString();
+    } catch (Exception q)
+    {
+      q.printStackTrace();
+    }
+    if (pwd == null || pwd.length() == 0)
+      pwd = ".";
+    String[] classpaths = new String[] { pwd + "/bin/main",
+        pwd + "/j11lib/*", pwd + "/resources", pwd + "/help" };
+    String classpath = String.join(win ? ";" : ":", classpaths);
+    String _cmd = java_exe + " "
+            + (withAwt ? "-Djava.awt.headless=true" : "") + " -classpath "
+            + classpath
+            + ((modules != null && modules.length() > 2)
+                    ? "--add-modules=\"" + modules + "\""
+                    : "")
+            + " jalview.bin.Jalview ";
+    Process ls2_proc = null;
+    Worker worker = null;
+    try
+    {
+      cmd = " --testoutput " + cmd;
+      System.out.println("Running '" + _cmd + cmd + "'");
+      ls2_proc = Runtime.getRuntime().exec(_cmd + cmd);
+    } catch (Throwable e1)
+    {
+      e1.printStackTrace();
+    }
+    if (ls2_proc != null)
+    {
+      BufferedReader outputReader = new BufferedReader(
+              new InputStreamReader(ls2_proc.getInputStream()));
+      BufferedReader errorReader = new BufferedReader(
+              new InputStreamReader(ls2_proc.getErrorStream()));
+      worker = new Worker(ls2_proc);
+      worker.start();
+      try
+      {
+        worker.join(timeout);
+      } catch (InterruptedException e)
+      {
+        System.err.println("Thread interrupted");
+      }
+      worker.setOutputReader(outputReader);
+      worker.setErrorReader(errorReader);
+    }
+    return worker;
+  }
+
+  @Test(groups = { "Functional" })
+  public void reportCurrentWorkingDirectory()
+  {
+    try
+    {
+      Path currentRelativePath = Paths.get("");
+      String s = currentRelativePath.toAbsolutePath().toString();
+      System.out.println("Test CWD is " + s);
+    } catch (Exception q)
+    {
+      q.printStackTrace();
+    }
+  }
+
+  @BeforeClass(alwaysRun = true)
+  public void initialize()
+  {
+    new CommandLineOperationsNG();
+  }
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpForHeadlessCommandLineInputOperations()
+          throws IOException
+  {
+    String cmds = "--headless " + "--open examples/uniref50.fa "
+            + "--sortbytree "
+            + "--props test/jalview/bin/testProps.jvprops "
+            + "--colour zappo "
+            + "--jabaws http://www.compbio.dundee.ac.uk/jabaws "
+            + "--features examples/testdata/plantfdx.features "
+            + "--annotations examples/testdata/plantfdx.annotations "
+            + "--tree examples/testdata/uniref50_test_tree "
+            + "--nousagestats ";
+    Worker worker = getJalviewDesktopRunner(true, cmds, SETUP_TIMEOUT);
+    String ln = null;
+    while ((ln = worker.getOutputReader().readLine()) != null)
+    {
+      System.out.println(ln);
+      successfulCMDs.add(ln);
+    }
+    while ((ln = worker.getErrorReader().readLine()) != null)
+    {
+      System.err.println(ln);
+    }
+  }
+
+  @BeforeClass(alwaysRun = true)
+  public void setUpForCommandLineInputOperations() throws IOException
+  {
+    String cmds = "--open examples/uniref50.fa --noquestionnaire --nousagestats";
+    final Worker worker = getJalviewDesktopRunner(false, cmds,
+            SETUP_TIMEOUT);
+
+    // number of lines expected on STDERR when Jalview starts up normally
+    // may need to adjust this if Jalview is excessively noisy ?
+    final int STDERR_SETUPLINES = 50;
+
+    // thread monitors stderr - bails after SETUP_TIMEOUT or when
+    // STDERR_SETUPLINES have been read
+    Thread runner = new Thread(new Runnable()
+    {
+      @Override
+      public void run()
+      {
+        String ln = null;
+        int count = 0;
+        try
+        {
+          while ((ln = worker.getOutputReader().readLine()) != null)
+          {
+            System.out.println(ln);
+            successfulCMDs.add(ln);
+            if (++count > STDERR_SETUPLINES)
+            {
+              break;
+            }
+          }
+        } catch (Exception e)
+        {
+          System.err.println(
+                  "Unexpected Exception reading stderr from the Jalview process");
+          e.printStackTrace();
+        }
+      }
+    });
+    long t = System.currentTimeMillis() + SETUP_TIMEOUT;
+    runner.start();
+    while (!runner.isInterrupted() && System.currentTimeMillis() < t)
+    {
+      try
+      {
+        Thread.sleep(500);
+      } catch (InterruptedException e)
+      {
+      }
+    }
+    runner.interrupt();
+    if (worker != null && worker.exit == null)
+    {
+      worker.interrupt();
+      Thread.currentThread().interrupt();
+      worker.process.destroy();
+    }
+  }
+
+  @Test(groups = { "Functional" }, dataProvider = "allInputOperationsData")
+  public void testAllInputOperations(String expectedString,
+          String failureMsg)
+  {
+    if ("[TESTOUTPUT] arg --nousagestats was set".equals(expectedString))
+      Assert.assertTrue(successfulCMDs.contains(expectedString),
+              failureMsg);
+  }
+
+  @Test(
+    groups =
+    { "Functional" },
+    dataProvider = "headlessModeOutputOperationsData")
+  public void testHeadlessModeOutputOperations(String harg, String type,
+          String fileName, boolean withAWT, int expectedMinFileSize,
+          int timeout)
+  {
+    String cmd = harg + type + " " + fileName;
+    // System.out.println(">>>>>>>>>>>>>>>> Command : " + cmd);
+    File file = new File(fileName);
+    file.deleteOnExit();
+    Worker worker = getJalviewDesktopRunner(withAWT, cmd, timeout);
+    assertNotNull(worker, "worker is null");
+    String msg = "Didn't create an output" + type + " file.[" + cmd + "]";
+    assertTrue(file.exists(), msg);
+    FileAssert.assertFile(file, msg);
+    FileAssert.assertMinLength(file, expectedMinFileSize);
+    if (worker != null && worker.exit == null)
+    {
+      worker.interrupt();
+      Thread.currentThread().interrupt();
+      worker.process.destroy();
+      Assert.fail("Jalview did not exit after " + type
+              + " generation (try running test again to verify - timeout at "
+              + timeout + "ms). [" + harg + "]");
+    }
+    file.delete();
+  }
+
+  @DataProvider(name = "allInputOperationsData")
+  public Object[][] getHeadlessModeInputParams()
+  {
+    return new Object[][] {
+        // headless mode input operations
+        { "[TESTOUTPUT] arg --colour='zappo' was set",
+            "Failed setting arg --colour" },
+        { "[TESTOUTPUT] arg --props='test/jalview/bin/testProps.jvprops' was set",
+            "Failed setting arg --props" },
+        { "[TESTOUTPUT] arg --sortbytree was set",
+            "Failed setting arg --sortbytree" },
+        { "[TESTOUTPUT] arg --jabaws='http://www.compbio.dundee.ac.uk/jabaws' was set",
+            "Failed setting arg --jabaws" },
+        { "[TESTOUTPUT] arg --open='examples/uniref50.fa' was set",
+            "Failed setting arg --open" },
+        { "[TESTOUTPUT] arg --features='examples/testdata/plantfdx.features' was set",
+            "Failed setting arg --features" },
+        { "[TESTOUTPUT] arg --annotations='examples/testdata/plantfdx.annotations' was set",
+            "Failed setting arg --annotations" },
+        { "[TESTOUTPUT] arg --tree='examples/testdata/uniref50_test_tree' was set",
+            "Failed setting arg --tree" },
+        // non headless mode input operations
+        { "[TESTOUTPUT] arg --nousagestats was set",
+            "Failed setting arg --nousagestats" },
+        { "[TESTOUTPUT] arg --noquestionnaire was set",
+            "Failed setting arg --noquestionnaire" }
+        //
+    };
+  }
+
+  @DataProvider(name = "headlessModeOutputOperationsData")
+  public static Object[][] getHeadlessModeOutputParams()
+  {
+    // JBPNote: I'm not clear why need to specify full path for output file
+    // when running tests on build server, but we will keep this patch for now
+    // since it works.
+    // https://issues.jalview.org/browse/JAL-1889?focusedCommentId=21609&page=com.atlassian.jira.plugin.system.issuetabpanels:comment-tabpanel#comment-21609
+    String workingDir = "test/jalview/bin/";
+    return new Object[][] {
+        //
+        { "--headless --open examples/uniref50.fa", " --image",
+            workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
+        { "--headless --open examples/uniref50.fa", " --image",
+            workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
+        { "--headless --open examples/uniref50.fa", " --image",
+            workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
+        { "--headless --open examples/uniref50.fa", " --image",
+            workingDir + "test_uniref50_out.eps", false, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
+        { "--headless --open examples/uniref50.fa", " --image",
+            workingDir + "test_uniref50_out.eps", true, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
+        { "--headless --open examples/uniref50.fa", " --image",
+            workingDir + "test_uniref50_out.svg", false, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
+        { "--headless --open examples/uniref50.fa", " --image",
+            workingDir + "test_uniref50_out.png", true, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
+        { "--headless --open examples/uniref50.fa", " --image",
+            workingDir + "test_uniref50_out.html", true, MINFILESIZE_BIG,
+            TEST_TIMEOUT },
+        { "--headless --open examples/uniref50.fa", " --output",
+            workingDir + "test_uniref50_out.mfa", true, MINFILESIZE_SMALL,
+            TEST_TIMEOUT },
+        { "--headless --open examples/uniref50.fa", " --output",
+            workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
+            TEST_TIMEOUT },
+        { "--headless --open examples/uniref50.fa", " --output",
+            workingDir + "test_uniref50_out.msf", true, MINFILESIZE_SMALL,
+            TEST_TIMEOUT },
+        { "--headless --open examples/uniref50.fa", " --output",
+            workingDir + "test_uniref50_out.aln", true, MINFILESIZE_SMALL,
+            TEST_TIMEOUT },
+        { "--headless --open examples/uniref50.fa", " --output",
+            workingDir + "test_uniref50_out.pir", true, MINFILESIZE_SMALL,
+            TEST_TIMEOUT },
+        { "--headless --open examples/uniref50.fa", " --output",
+            workingDir + "test_uniref50_out.pfam", true, MINFILESIZE_SMALL,
+            TEST_TIMEOUT },
+        { "--headless --open examples/uniref50.fa", " --output",
+            workingDir + "test_uniref50_out.blc", true, MINFILESIZE_SMALL,
+            TEST_TIMEOUT },
+        { "--headless --open examples/uniref50.fa", " --output",
+            workingDir + "test_uniref50_out.jvp", true, MINFILESIZE_SMALL,
+            TEST_TIMEOUT },
+        //
+    };
+  }
+}
diff --git a/test/jalview/bin/CommandsTest2.java b/test/jalview/bin/CommandsTest2.java
index dc7d061..40faccc 100644
--- a/test/jalview/bin/CommandsTest2.java
+++ b/test/jalview/bin/CommandsTest2.java
@@ -161,21 +161,21 @@ public class CommandsTest2
                 + "--colour=gecos-flower "
                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
-                + "--noannotations "
+                + "--noshowannotations "
                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
             15, 3, 1 },
         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
                 + "--colour=gecos-flower "
                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
-                + "--noannotations " + "--nossannotations "
+                + "--noshowannotations " + "--nossannotations "
                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
             15, 0, 1 },
         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
                 + "--colour=gecos-flower "
                 + "--structure=[seqid=FER1_SPIOL]examples/AlphaFold/AF-P00221-F1-model_v4.cif "
                 + "--paematrix=examples/AlphaFold/AF-P00221-F1-predicted_aligned_error_v4.json "
-                + "--noannotations " + "--nossannotations "
+                + "--noshowannotations " + "--nossannotations "
                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
             15, 0, 1 },
         { "--nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ",
diff --git a/test/jalview/bin/commandsTest2.argfile1 b/test/jalview/bin/commandsTest2.argfile1
index bb1a250..8a19038 100644
--- a/test/jalview/bin/commandsTest2.argfile1
+++ b/test/jalview/bin/commandsTest2.argfile1
@@ -1,6 +1,6 @@
 --substitutions
 --append=examples/test_fab41.result/sample.a2m
---annotations
+--showannotations
 --ssannotations
 --colour=gecos-flower
 --structure=[viewer=jmol,tempfac=plddt,paematrix={dirname}/test_fab41_unrelaxed_rank_1_model_3_scores.json]{dirname}/test_fab41_unrelaxed_rank_1_model_3.pdb
diff --git a/test/jalview/bin/commandsTest2.argfile2 b/test/jalview/bin/commandsTest2.argfile2
index 30cecf7..ea7f0bc 100644
--- a/test/jalview/bin/commandsTest2.argfile2
+++ b/test/jalview/bin/commandsTest2.argfile2
@@ -3,7 +3,7 @@
 --nosplash
 --substitutions
 --append=examples/test_fab41.result/sample.a2m
---noannotations
+--noshowannotations
 --nossannotations
 --colour=gecos-flower
 --structure=[tempfac=plddt,paematrix={dirname}/test_fab41_unrelaxed_rank_1_model_3_scores.json]{dirname}/test_fab41_unrelaxed_rank_1_model_3.pdb
@@ -16,7 +16,7 @@
 --structureviewer=jmol
 --paematrix={dirname}/test_fab41_unrelaxed_rank_3_model_2_scores.json
 --tempfac=plddt
---structure=[viewer=none]{dirname}/test_fab41_unrelaxed_rank_4_model_5.pdb
+--structure=[structureviewer=none]{dirname}/test_fab41_unrelaxed_rank_4_model_5.pdb
 --paematrix={dirname}/test_fab41_unrelaxed_rank_4_model_5_scores.json
 --tempfac=plddt
 --structure={dirname}/test_fab41_unrelaxed_rank_5_model_1.pdb