From: Ben Soares <b.soares@dundee.ac.uk>
Date: Sun, 23 Apr 2023 11:35:42 +0000 (+0100)
Subject: JAL-629 Change --open to --append and --opennew to --open. Make --open(new) part... 
X-Git-Tag: Release_2_11_4_0~388
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=2bb9cad4fa36d64cebbe09bc63732e8dbb4dcb32;p=jalview.git

JAL-629 Change --open to --append and --opennew to --open. Make --open(new) part of the same default linkedId scheme.  Add and adjust tests.
---

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index fc2ee1a..dafc342 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -2,16 +2,15 @@ package jalview.bin;
 
 import java.io.File;
 import java.io.IOException;
-import java.util.AbstractMap;
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Collections;
 import java.util.EnumSet;
 import java.util.HashMap;
 import java.util.Iterator;
 import java.util.List;
 import java.util.Locale;
 import java.util.Map;
-import java.util.Map.Entry;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.bin.argparser.Arg;
@@ -150,7 +149,7 @@ public class Commands
      * m.get(Arg.OPEN).getValue(); String data = null; FileFormatI format = null;
      * DataSourceType protocol = null;
      */
-    if (avm.containsArg(Arg.OPEN) || avm.containsArg(Arg.OPENNEW))
+    if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
     {
       commandArgsProvided = true;
       long progress = -1;
@@ -158,21 +157,16 @@ public class Commands
       boolean first = true;
       boolean progressBarSet = false;
       AlignFrame af;
-      // Combine the OPEN and OPENNEW files into one list, along with whether it
-      // was OPEN or OPENNEW
-      List<Entry<Arg, ArgValue>> openAvList = new ArrayList<>();
-      avm.getArgValueList(Arg.OPEN).stream()
-              .forEachOrdered(av -> openAvList.add(
-                      new AbstractMap.SimpleEntry<Arg, ArgValue>(Arg.OPEN,
-                              av)));
-      avm.getArgValueList(Arg.OPENNEW).stream()
-              .forEachOrdered(av -> openAvList
-                      .add(new AbstractMap.SimpleEntry<Arg, ArgValue>(
-                              Arg.OPENNEW, av)));
-      for (Entry<Arg, ArgValue> aav : openAvList)
+      // Combine the APPEND and OPEN files into one list, along with whether it
+      // was APPEND or OPEN
+      List<ArgValue> openAvList = new ArrayList<>();
+      openAvList.addAll(avm.getArgValueList(Arg.OPEN));
+      openAvList.addAll(avm.getArgValueList(Arg.APPEND));
+      // sort avlist based on av.getArgIndex()
+      Collections.sort(openAvList);
+      for (ArgValue av : openAvList)
       {
-        Arg a = aav.getKey();
-        ArgValue av = aav.getValue();
+        Arg a = av.getArg();
         String openFile = av.getValue();
         if (openFile == null)
           continue;
@@ -221,7 +215,7 @@ public class Commands
 
         af = afMap.get(id);
         if (af == null || "true".equals(av.getSubVal("new"))
-                || a == Arg.OPENNEW || format == FileFormat.Jalview)
+                || a == Arg.OPEN || format == FileFormat.Jalview)
         {
           /*
            * this approach isn't working yet // get default annotations before opening
@@ -340,7 +334,7 @@ public class Commands
           af.getCurrentView().addFile(new File(openFile), format, false);
         }
 
-        Console.debug("Command " + Arg.OPEN + " executed successfully!");
+        Console.debug("Command " + Arg.APPEND + " executed successfully!");
 
       }
       if (first) // first=true means nothing opened
diff --git a/src/jalview/bin/argparser/Arg.java b/src/jalview/bin/argparser/Arg.java
index f712010..07d8c28 100644
--- a/src/jalview/bin/argparser/Arg.java
+++ b/src/jalview/bin/argparser/Arg.java
@@ -11,7 +11,7 @@ public enum Arg
 {
   HELP("h"), CALCULATION, MENUBAR, STATUS, SHOWOVERVIEW, ANNOTATIONS,
   COLOUR, FEATURES, GROOVY, GROUPS, HEADLESS, JABAWS, DISPLAY, GUI, NEWS,
-  SORTBYTREE, USAGESTATS, OPEN, OPENNEW, PROPS, QUESTIONNAIRE, SETPROP,
+  SORTBYTREE, USAGESTATS, APPEND, OPEN, PROPS, QUESTIONNAIRE, SETPROP,
   TREE, VDOC, VSESS, OUTPUT, OUTPUTTYPE, SSANNOTATIONS, NOTEMPFAC, TEMPFAC,
   TITLE, PAEMATRIX, WRAP, NOSTRUCTURE, STRUCTURE, STRUCTUREVIEWER, IMAGE,
   QUIT, CLOSE, DEBUG("d"), QUIET("q"), ARGFILE, INCREMENT, NPP("n++"),
@@ -47,9 +47,9 @@ public enum Arg
     // expects a string value
     SORTBYTREE.setOptions(true, Opt.BOOLEAN);
     USAGESTATS.setOptions(true, Opt.BOOLEAN);
-    OPEN.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
+    APPEND.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
             Opt.ALLOWSUBSTITUTIONS);
-    OPENNEW.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
+    OPEN.setOptions(Opt.STRING, Opt.LINKED, Opt.MULTI, Opt.GLOB,
             Opt.ALLOWSUBSTITUTIONS);
     PROPS.setOptions(Opt.STRING, Opt.BOOTSTRAP);
     QUESTIONNAIRE.setOptions(Opt.BOOLEAN, Opt.BOOTSTRAP);
diff --git a/src/jalview/bin/argparser/ArgParser.java b/src/jalview/bin/argparser/ArgParser.java
index 70ed5d1..b31beab 100644
--- a/src/jalview/bin/argparser/ArgParser.java
+++ b/src/jalview/bin/argparser/ArgParser.java
@@ -55,11 +55,12 @@ public class ArgParser
   // the substitution string used to use the defaultLinkedIdCounter
   private static final String DEFAULTLINKEDIDCOUNTER = "{}";
 
-  // the counter added to the default linked id prefix
-  private int opennewLinkedIdCounter = 0;
+  // the counter added to the default linked id prefix. NOW using
+  // linkedIdAutoCounter
+  // private int openLinkedIdCounter = 0;
 
-  // the linked id prefix used for --opennew files
-  protected static final String OPENNEWLINKEDIDPREFIX = "OPENNEW:";
+  // the linked id prefix used for --open files. NOW the same as DEFAULT
+  protected static final String OPENLINKEDIDPREFIX = DEFAULTLINKEDIDPREFIX;
 
   // the counter used for {n} substitutions
   private int linkedIdAutoCounter = 0;
@@ -71,12 +72,12 @@ public class ArgParser
   // the linked id substitution string used to use the idCounter
   private static final String LINKEDIDAUTOCOUNTER = "{n}";
 
-  // the linked id substitution string used to use the base filename of --open
-  // or --opennew
+  // the linked id substitution string used to use the base filename of --append
+  // or --open
   private static final String LINKEDIDBASENAME = "{basename}";
 
-  // the linked id substitution string used to use the dir path of --open
-  // or --opennew
+  // the linked id substitution string used to use the dir path of --append
+  // or --open
   private static final String LINKEDIDDIRNAME = "{dirname}";
 
   // the current argfile
@@ -141,7 +142,7 @@ public class ArgParser
     // Make a mutable new ArrayList so that shell globbing parser works.
     // (When shell file globbing is used, there are a sequence of non-Arg
     // arguments (which are the expanded globbed filenames) that need to be
-    // consumed by the --open/--argfile/etc Arg which is most easily done by
+    // 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);
@@ -197,7 +198,7 @@ public class ArgParser
       if (openEachInitialFilenames && !arg.startsWith(DOUBLEDASH)
               && !arg.startsWith("-") && new File(arg).exists())
       {
-        arg = Arg.OPENNEW.argString();
+        arg = Arg.OPEN.argString();
       }
       else
       {
@@ -360,13 +361,14 @@ public class ArgParser
         {
           if (linkedId == null)
           {
-            if (a == Arg.OPENNEW)
+            if (a == Arg.OPEN)
             {
-              // use the next default prefixed OPENNEWLINKEDID
-              linkedId = new StringBuilder(OPENNEWLINKEDIDPREFIX)
-                      .append(Integer.toString(opennewLinkedIdCounter))
+              // use the next default prefixed OPENLINKEDID
+              // NOW using the linkedIdAutoCounter
+              defaultLinkedIdCounter++;
+              linkedId = new StringBuilder(OPENLINKEDIDPREFIX)
+                      .append(Integer.toString(defaultLinkedIdCounter))
                       .toString();
-              opennewLinkedIdCounter++;
             }
             else
             {
diff --git a/src/jalview/bin/argparser/ArgValue.java b/src/jalview/bin/argparser/ArgValue.java
index c9e86b8..36901df 100644
--- a/src/jalview/bin/argparser/ArgValue.java
+++ b/src/jalview/bin/argparser/ArgValue.java
@@ -3,8 +3,10 @@ package jalview.bin.argparser;
 /**
  * A helper class to keep an index of argument position with argument values
  */
-public class ArgValue
+public class ArgValue implements Comparable<ArgValue>
 {
+  private Arg arg;
+
   private int argIndex;
 
   private String value;
@@ -13,20 +15,27 @@ public class ArgValue
 
   private SubVals subVals;
 
-  protected ArgValue(SubVals sv, String content, int argIndex)
+  protected ArgValue(Arg a, SubVals sv, String content, int argIndex)
   {
+    this.arg = a;
     this.value = content;
     this.argIndex = argIndex;
     this.subVals = sv == null ? new SubVals("") : sv;
   }
 
-  protected ArgValue(String value, int argIndex)
+  protected ArgValue(Arg a, String value, int argIndex)
   {
+    this.arg = a;
     this.argIndex = argIndex;
     this.subVals = new SubVals(value);
     this.value = getSubVals().getContent();
   }
 
+  public Arg getArg()
+  {
+    return arg;
+  }
+
   public String getValue()
   {
     return value;
@@ -63,4 +72,10 @@ public class ArgValue
   {
     this.subVals.put(key, val);
   }
+
+  @Override
+  public int compareTo(ArgValue o)
+  {
+    return this.getArgIndex() - o.getArgIndex();
+  }
 }
\ No newline at end of file
diff --git a/src/jalview/bin/argparser/ArgValues.java b/src/jalview/bin/argparser/ArgValues.java
index c166da0..4a60efd 100644
--- a/src/jalview/bin/argparser/ArgValues.java
+++ b/src/jalview/bin/argparser/ArgValues.java
@@ -105,12 +105,12 @@ public class ArgValues
 
   protected void addValue(String val, int argIndex)
   {
-    addArgValue(new ArgValue(val, argIndex));
+    addArgValue(new ArgValue(arg(), val, argIndex));
   }
 
   protected void addValue(SubVals sv, String content, int argIndex)
   {
-    addArgValue(new ArgValue(sv, content, argIndex));
+    addArgValue(new ArgValue(arg(), sv, content, argIndex));
   }
 
   protected void addArgValue(ArgValue av)
diff --git a/src/jalview/bin/argparser/ArgValuesMap.java b/src/jalview/bin/argparser/ArgValuesMap.java
index 176dc7c..63e5302 100644
--- a/src/jalview/bin/argparser/ArgValuesMap.java
+++ b/src/jalview/bin/argparser/ArgValuesMap.java
@@ -193,7 +193,7 @@ public class ArgValuesMap
   }
 
   /*
-   * This method returns the basename of the first --open or --opennew value. 
+   * This method returns the basename of the first --append or --open value. 
    * Used primarily for substitutions in output filenames.
    */
   public String getBasename()
@@ -202,7 +202,7 @@ public class ArgValuesMap
   }
 
   /*
-   * This method returns the dirname of the first --open or --opennew value. 
+   * This method returns the dirname of the first --append or --open value. 
    * Used primarily for substitutions in output filenames.
    */
   public String getDirname()
@@ -213,12 +213,12 @@ public class ArgValuesMap
   public String getDirOrBasename(boolean dirname)
   {
     String filename = null;
+    String appendVal = getValue(Arg.APPEND);
     String openVal = getValue(Arg.OPEN);
-    String opennewVal = getValue(Arg.OPENNEW);
-    if (openVal != null)
+    if (appendVal != null)
+      filename = appendVal;
+    if (filename == null && openVal != null)
       filename = openVal;
-    if (filename == null && opennewVal != null)
-      filename = opennewVal;
     if (filename == null)
       return null;
 
diff --git a/src/jalview/util/FileUtils.java b/src/jalview/util/FileUtils.java
index 9b56c64..4d35cd2 100644
--- a/src/jalview/util/FileUtils.java
+++ b/src/jalview/util/FileUtils.java
@@ -130,7 +130,7 @@ public class FileUtils
   }
 
   /*
-   * This method returns the basename of the first --open or --opennew value. 
+   * This method returns the basename of the first --append or --open value. 
    * Used primarily for substitutions in output filenames.
    */
   public static String getBasename(File file)
@@ -153,7 +153,7 @@ public class FileUtils
   }
 
   /*
-   * This method returns the dirname of the first --open or --opennew value. 
+   * This method returns the dirname of the first --append or --open value. 
    * Used primarily for substitutions in output filenames.
    */
   public static String getDirname(File file)
diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index fda047c..2d3724b 100644
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.java
@@ -83,7 +83,8 @@ public class CommandsTest
     Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
             "Overall command parse and operation is false");
 
-    Assert.assertEquals(Desktop.getAlignFrames().length, numFrames);
+    Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
+            "Wrong number of AlignFrames");
 
     if (sequences != null)
     {
@@ -147,11 +148,11 @@ public class CommandsTest
         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
         { "--argfile=" + testfiles + "/dir*/argfile.txt", new String[]
         { testfiles + "/dir1/test1.png", testfiles + "/dir2/test1.png" } },
-        { "--initsubstitutions --open examples/uniref50.fa --image "
+        { "--initsubstitutions --append examples/uniref50.fa --image "
                 + testfiles + "/{basename}.png",
             new String[]
             { testfiles + "/uniref50.png" } },
-        { "--open examples/uniref50.fa --image " + testfiles
+        { "--append examples/uniref50.fa --image " + testfiles
                 + "/{basename}.png",
             new String[]
             { testfiles + "/{basename}.png" } } };
@@ -166,24 +167,28 @@ public class CommandsTest
     String[] t2 = new String[] { "TEST2" };
     String[] t3 = new String[] { "TEST3" };
     return new Object[][] {
-        { "--open=examples/uniref50.fa", true, 1, someUniref50Seqs },
-        { "--open examples/uniref50.fa", true, 1, someUniref50Seqs },
-        { "--open=examples/uniref50*.fa", true, 1, someUniref50Seqs },
+        /*
+        */
+        { "--append=examples/uniref50.fa", true, 1, someUniref50Seqs },
+        { "--append examples/uniref50.fa", true, 1, someUniref50Seqs },
+        { "--append=examples/uniref50*.fa", true, 1, someUniref50Seqs },
         // NOTE we cannot use shell expansion in tests, so list all files!
-        { "--open examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
+        { "--append examples/uniref50.fa examples/uniref50_mz.fa", true, 1,
             someUniref50Seqs },
-        { "--open=[new]examples/uniref50*.fa", true, 2, someUniref50Seqs },
-        { "--opennew=examples/uniref50*.fa", true, 2, someUniref50Seqs },
+        { "--append=[new]examples/uniref50*.fa", true, 2,
+            someUniref50Seqs },
+        { "--open=examples/uniref50*.fa", true, 2, someUniref50Seqs },
         { "examples/uniref50.fa", true, 1, someUniref50Seqs },
         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2,
             ArrayUtils.concatArrays(someUniref50Seqs, t1) },
         { "examples/uniref50.fa " + testfiles + "/test1.fa", true, 2, t1 },
         { "--argfile=" + testfiles + "/argfile0.txt", true, 1,
             ArrayUtils.concatArrays(t1, t3) },
-        { "--argfile=" + testfiles + "/argfile*.txt", true, 4,
+        { "--argfile=" + testfiles + "/argfile*.txt", true, 5,
             ArrayUtils.concatArrays(t1, t2, t3) },
         { "--argfile=" + testfiles + "/argfile.autocounter", true, 3,
             ArrayUtils.concatArrays(t1, t2) } };
+
   }
 
   public static boolean lookForSequenceName(String sequenceName)
diff --git a/test/jalview/bin/CommandsTest2.java b/test/jalview/bin/CommandsTest2.java
index 71452e2..ca0d3e4 100644
--- a/test/jalview/bin/CommandsTest2.java
+++ b/test/jalview/bin/CommandsTest2.java
@@ -125,40 +125,44 @@ public class CommandsTest2
       int viewerNum,
       String propsFile
      */
-    return new Object[][] { { "--nonews --nosplash --debug "
-            + "--open=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 "
-            + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
-        15, 7, 1 },
-        { "--nonews --nosplash --debug " + "--open=examples/uniref50.fa "
+    return new Object[][] {
+        //
+        /*
+         */
+        { "--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 "
+                + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
+            15, 7, 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 "
                 + "--props=test/jalview/bin/commandsTest2.jvprops2 ",
             15, 4, 1 },
-        { "--nonews --nosplash --debug " + "--open=examples/uniref50.fa "
+        { "--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 "
                 + "--nossannotations "
                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
             15, 4, 1 },
-        { "--nonews --nosplash --debug " + "--open=examples/uniref50.fa "
+        { "--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 "
                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
             15, 3, 1 },
-        { "--nonews --nosplash --debug " + "--open=examples/uniref50.fa "
+        { "--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 "
                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
             15, 0, 1 },
-        { "--nonews --nosplash --debug " + "--open=examples/uniref50.fa "
+        { "--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 "
diff --git a/test/jalview/bin/argparser/ArgParserTest.java b/test/jalview/bin/argparser/ArgParserTest.java
index 6d7f88f..efd6cb8 100644
--- a/test/jalview/bin/argparser/ArgParserTest.java
+++ b/test/jalview/bin/argparser/ArgParserTest.java
@@ -63,8 +63,8 @@ public class ArgParserTest
   public void parseAutoIndexAndSubstitutionsTest(String commandLineArgs,
           String linkedId, Arg a, String filename)
   {
-    // { "--open=filename0 --increment --open=filename1", "JALVIEW:1", Arg.OPEN,
-    // "filename1" },
+    // { "--append=filename0 --increment --append=filename1", "JALVIEW:1",
+    // Arg.OPEN, "filename1" },
     String[] args = commandLineArgs.split("\\s+");
     ArgParser argparser = new ArgParser(args);
     ArgValuesMap avm = argparser.linkedArgs(linkedId);
@@ -118,7 +118,7 @@ public class ArgParserTest
     BootstrapArgs b = BootstrapArgs.getBootstrapArgs(args);
 
     Assert.assertTrue(b.contains(a));
-    Assert.assertFalse(b.contains(Arg.OPEN));
+    Assert.assertFalse(b.contains(Arg.APPEND));
     if (a == Arg.PROPS)
     {
       Properties bP = Cache.bootstrapProperties(b.get(Arg.PROPS));
@@ -141,11 +141,11 @@ public class ArgParserTest
   public Object[][] argLines()
   {
     return new Object[][] { {
-        "--open=test/jalview/bin/argparser/testfiles/test1.fa --props=test/jalview/bin/argparser/testfiles/testProps.jvprops",
+        "--append=test/jalview/bin/argparser/testfiles/test1.fa --props=test/jalview/bin/argparser/testfiles/testProps.jvprops",
         Arg.PROPS, "true" },
-        { "--debug --open=test/jalview/bin/argparser/testfiles/test1.fa",
+        { "--debug --append=test/jalview/bin/argparser/testfiles/test1.fa",
             Arg.DEBUG, null },
-        { "--open=test/jalview/bin/argparser/testfiles/test1.fa --headless",
+        { "--append=test/jalview/bin/argparser/testfiles/test1.fa --headless",
             Arg.HEADLESS, null },
 
         { "--argfile test/jalview/bin/argparser/testfiles/argfile0.txt",
@@ -176,37 +176,65 @@ public class ArgParserTest
   public Object[][] argSubValsAndLinkedIds()
   {
     return new Object[][] { {
-        "--debug --open=[hi]test/jalview/bin/argparser/testfiles/test1.fa",
-        "JALVIEW:0", Arg.OPEN, "hi", "true", true },
-        { "--open[linkedId1]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
-            "linkedId1", Arg.OPEN, "new", "true", true },
-        { "--open[linkedId2]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
-            "linkedId2", Arg.OPEN, "hello", "world", true },
-        { "--open[linkedId3]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
-            "linkedId3", Arg.OPEN, "GETINDEX", "1", true },
-        { "--open[linkedId4]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --open[linkedId5]=[notnew;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
-            "linkedId5", Arg.OPEN, "new", "true", false },
-        { "--open[linkedId5]=[new;hello=worlddomination;1]test/jalview/bin/argparser/testfiles/test1.fa --open[linkedId2]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
-            "linkedId5", Arg.OPEN, "hello", "world", false },
-        { "--open[linkedId6]=[new;hello=world;0]test/jalview/bin/argparser/testfiles/test1.fa --open[linkedId7]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
-            "linkedId7", Arg.OPEN, "GETINDEX", "0", false }, };
+        "--debug --append=[hi]test/jalview/bin/argparser/testfiles/test1.fa",
+        "JALVIEW:0", Arg.APPEND, "hi", "true", true },
+        { "--append[linkedId1]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+            "linkedId1", Arg.APPEND, "new", "true", true },
+        { "--append[linkedId2]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+            "linkedId2", Arg.APPEND, "hello", "world", true },
+        { "--append[linkedId3]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+            "linkedId3", Arg.APPEND, "GETINDEX", "1", true },
+        { "--append[linkedId4]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --append[linkedId5]=[notnew;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+            "linkedId5", Arg.APPEND, "new", "true", false },
+        { "--append[linkedId5]=[new;hello=worlddomination;1]test/jalview/bin/argparser/testfiles/test1.fa --append[linkedId2]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+            "linkedId5", Arg.APPEND, "hello", "world", false },
+        { "--append[linkedId6]=[new;hello=world;0]test/jalview/bin/argparser/testfiles/test1.fa --append[linkedId7]=[new;hello=world;1]test/jalview/bin/argparser/testfiles/test1.fa --headless",
+            "linkedId7", Arg.APPEND, "GETINDEX", "0", false }, };
   }
 
   @DataProvider(name = "argAutoIndexAndSubstitutions")
   public Object[][] argAutoIndexAndSubstitutions()
   {
-    return new Object[][] { { "--open=filename0 --open=filename1",
-        "JALVIEW:0", Arg.OPEN, "filename0" },
-        { "--open=filename0 --increment --open=filename1", "JALVIEW:1",
-            Arg.OPEN, "filename1" },
-        { "--open=filename0 --increment --increment --open=filename2",
-            "JALVIEW:0", Arg.OPEN, "filename0" },
-        { "--open=filename0 --increment --increment --open=filename2",
-            "JALVIEW:2", Arg.OPEN, "filename2" },
-        { "--open[linkA-{n}]=filenameA0 --open[linkA-{++n}]=filenameA1",
+    return new Object[][] {
+        //
+        /*
+         */
+        { "--append=filename0 --append=filename1", "JALVIEW:0", Arg.APPEND,
+            "filename0" },
+        { "--append=filename0 --increment --append=filename1", "JALVIEW:1",
+            Arg.APPEND, "filename1" },
+        { "--append=filename0 --increment --increment --append=filename2",
+            "JALVIEW:0", Arg.APPEND, "filename0" },
+        { "--append=filename0 --increment --increment --append=filename2",
+            "JALVIEW:2", Arg.APPEND, "filename2" },
+        { "--append[linkA-{n}]=filenameA0 --append[linkA-{++n}]=filenameA1",
+            "linkA-0", Arg.APPEND, "filenameA0" },
+        { "--append[linkB-{n}]=filenameB0 --append[linkB-{++n}]=filenameB1",
+            "linkB-1", Arg.APPEND, "filenameB1" },
+        { "--append[linkC-{n}]=filenameC0 --image[linkC-{n}]=outputC{n}.txt",
+            "linkC-0", Arg.IMAGE, "outputC{n}.txt" },
+        { "--append[linkD-{n}]=filenameD0 --substitutions --image[linkD-{n}]=outputD{n}.txt",
+            "linkD-0", Arg.IMAGE, "outputD0.txt" },
+        { "--append[linkE-{n}]=filenameE0 --substitutions --image[linkE-{n}]=output-E{n}.txt --nil[{++n}] --image[linkE-{n}]=outputE{n}.txt",
+            "linkE-0", Arg.IMAGE, "output-E0.txt" },
+        { "--append[linkF-{n}]=filenameF0 --substitutions --image[linkF-{n}]=output-F{n}.txt --nil[{++n}] --image[linkF-{n}]=outputF{n}.txt",
+            "linkF-1", Arg.IMAGE, "outputF1.txt" },
+        { "--append[linkG-{n}]=filenameG0 --substitutions --image[linkG-{n}]=output-G{n}.txt --nil[{++n}] --nosubstitutions --image[linkG-{n}]=outputG{n}.txt",
+            "linkG-1", Arg.IMAGE, "outputG{n}.txt" },
+        { "--append[linkH-{n}]=filenameH0 --substitutions --image[linkH-{n}]=output-H{n}.txt --nil[{++n}] --nosubstitutions --image[linkH-{n}]=outputH{n}.txt",
+            "linkH-0", Arg.IMAGE, "output-H0.txt" },
+        { "--open=filename0 --append=filename1", "JALVIEW:1", Arg.OPEN,
+            "filename0" },
+        { "--open=filename0 --increment --append=filename1", "JALVIEW:2",
+            Arg.APPEND, "filename1" },
+        { "--open=filename0 --increment --increment --append=filename2",
+            "JALVIEW:1", Arg.OPEN, "filename0" },
+        { "--open=filename0 --increment --increment --append=filename2",
+            "JALVIEW:3", Arg.APPEND, "filename2" },
+        { "--open[linkA-{n}]=filenameA0 --append[linkA-{++n}]=filenameA1",
             "linkA-0", Arg.OPEN, "filenameA0" },
-        { "--open[linkB-{n}]=filenameB0 --open[linkB-{++n}]=filenameB1",
-            "linkB-1", Arg.OPEN, "filenameB1" },
+        { "--open[linkB-{n}]=filenameB0 --append[linkB-{++n}]=filenameB1",
+            "linkB-1", Arg.APPEND, "filenameB1" },
         { "--open[linkC-{n}]=filenameC0 --image[linkC-{n}]=outputC{n}.txt",
             "linkC-0", Arg.IMAGE, "outputC{n}.txt" },
         { "--open[linkD-{n}]=filenameD0 --substitutions --image[linkD-{n}]=outputD{n}.txt",
@@ -218,7 +246,10 @@ public class ArgParserTest
         { "--open[linkG-{n}]=filenameG0 --substitutions --image[linkG-{n}]=output-G{n}.txt --nil[{++n}] --nosubstitutions --image[linkG-{n}]=outputG{n}.txt",
             "linkG-1", Arg.IMAGE, "outputG{n}.txt" },
         { "--open[linkH-{n}]=filenameH0 --substitutions --image[linkH-{n}]=output-H{n}.txt --nil[{++n}] --nosubstitutions --image[linkH-{n}]=outputH{n}.txt",
-            "linkH-0", Arg.IMAGE, "output-H0.txt" }, };
+            "linkH-0", Arg.IMAGE, "output-H0.txt" },
+
+        //
+    };
   }
 
   @DataProvider(name = "argFiles")
diff --git a/test/jalview/bin/argparser/testfiles/argfile.autocounter b/test/jalview/bin/argparser/testfiles/argfile.autocounter
index 7eaf95e..e35a99e 100644
--- a/test/jalview/bin/argparser/testfiles/argfile.autocounter
+++ b/test/jalview/bin/argparser/testfiles/argfile.autocounter
@@ -3,5 +3,5 @@
 --open[{++n}]=test/jalview/bin/argparser/testfiles/test2.fa
 --colour[{n}]=zappo
 --open[{++n}]=test/jalview/bin/argparser/testfiles/test1.fa
---open[{n}]=test/jalview/bin/argparser/testfiles/test2.fa
+--append[{n}]=test/jalview/bin/argparser/testfiles/test2.fa
 --colour[{n}]=taylor
diff --git a/test/jalview/bin/argparser/testfiles/argfile0.txt b/test/jalview/bin/argparser/testfiles/argfile0.txt
index 6e5185e..e8a8cdc 100644
--- a/test/jalview/bin/argparser/testfiles/argfile0.txt
+++ b/test/jalview/bin/argparser/testfiles/argfile0.txt
@@ -1,2 +1,2 @@
 --open=test/jalview/bin/argparser/testfiles/test1.fa
---open=test/jalview/bin/argparser/testfiles/test3.fa
+--append=test/jalview/bin/argparser/testfiles/test3.fa
diff --git a/test/jalview/bin/argparser/testfiles/argfile1.txt b/test/jalview/bin/argparser/testfiles/argfile1.txt
index bb33f21..e2d0fa4 100644
--- a/test/jalview/bin/argparser/testfiles/argfile1.txt
+++ b/test/jalview/bin/argparser/testfiles/argfile1.txt
@@ -1,4 +1,4 @@
 --open[all]=test/jalview/bin/argparser/testfiles/test1.fa
---open[all]=test/jalview/bin/argparser/testfiles/test2.fa
+--append[all]=test/jalview/bin/argparser/testfiles/test2.fa
 --open[1]=test/jalview/bin/argparser/testfiles/test1.fa
 --open[2]=test/jalview/bin/argparser/testfiles/test2.fa
diff --git a/test/jalview/bin/argparser/testfiles/dir1/argfile.txt b/test/jalview/bin/argparser/testfiles/dir1/argfile.txt
index cd6b31b..ee9580d 100644
--- a/test/jalview/bin/argparser/testfiles/dir1/argfile.txt
+++ b/test/jalview/bin/argparser/testfiles/dir1/argfile.txt
@@ -1,6 +1,6 @@
 --substitutions
 --increment
---open={argfiledirname}/*.fa
+--append={argfiledirname}/*.fa
 --colour=gecos:flower
 --image={argfiledirname}/{basename}.png
 --close
diff --git a/test/jalview/bin/argparser/testfiles/dir2/argfile.txt b/test/jalview/bin/argparser/testfiles/dir2/argfile.txt
index cd6b31b..ee9580d 100644
--- a/test/jalview/bin/argparser/testfiles/dir2/argfile.txt
+++ b/test/jalview/bin/argparser/testfiles/dir2/argfile.txt
@@ -1,6 +1,6 @@
 --substitutions
 --increment
---open={argfiledirname}/*.fa
+--append={argfiledirname}/*.fa
 --colour=gecos:flower
 --image={argfiledirname}/{basename}.png
 --close
diff --git a/test/jalview/bin/argparser/testfiles/dir3/subdir/subdirfile.txt b/test/jalview/bin/argparser/testfiles/dir3/subdir/subdirfile.txt
index cd6b31b..ee9580d 100644
--- a/test/jalview/bin/argparser/testfiles/dir3/subdir/subdirfile.txt
+++ b/test/jalview/bin/argparser/testfiles/dir3/subdir/subdirfile.txt
@@ -1,6 +1,6 @@
 --substitutions
 --increment
---open={argfiledirname}/*.fa
+--append={argfiledirname}/*.fa
 --colour=gecos:flower
 --image={argfiledirname}/{basename}.png
 --close
diff --git a/test/jalview/bin/commandsTest2.argfile1 b/test/jalview/bin/commandsTest2.argfile1
index a9c602d..e46b746 100644
--- a/test/jalview/bin/commandsTest2.argfile1
+++ b/test/jalview/bin/commandsTest2.argfile1
@@ -2,7 +2,7 @@
 --nonews
 --nosplash
 --substitutions
---open=examples/test_fab41.result/sample.a2m
+--append=examples/test_fab41.result/sample.a2m
 --annotations
 --ssannotations
 --colour=gecos:flower
diff --git a/test/jalview/bin/commandsTest2.argfile2 b/test/jalview/bin/commandsTest2.argfile2
index d057858..f8f1c65 100644
--- a/test/jalview/bin/commandsTest2.argfile2
+++ b/test/jalview/bin/commandsTest2.argfile2
@@ -2,7 +2,7 @@
 --nonews
 --nosplash
 --substitutions
---open=examples/test_fab41.result/sample.a2m
+--append=examples/test_fab41.result/sample.a2m
 --noannotations
 --nossannotations
 --colour=gecos:flower