JAL-4134 properly resolve positions in associated aligned sequence for matrix group...

[jalview.git] / test / jalview / bin / argparser / ArgParserTest.java

diff --git a/test/jalview/bin/argparser/ArgParserTest.java b/test/jalview/bin/argparser/ArgParserTest.java
index 314b0f0..ca63e44 100644 (file)
--- a/test/jalview/bin/argparser/ArgParserTest.java
+++ b/test/jalview/bin/argparser/ArgParserTest.java
@@ -72,7 +72,7 @@ public class ArgParserTest
   public void parseAutoIndexAndSubstitutionsTest(String commandLineArgs,
           String linkedId, Arg a, String filename)
   {
-    // { "--append=filename0 --newframe --append=filename1", "JALVIEW:1",
+    // { "--append=filename0 --new --append=filename1", "JALVIEW:1",
     // Arg.OPEN, "filename1" },
     String[] args = commandLineArgs.split("\\s+");
     ArgParser argparser = new ArgParser(args);
@@ -97,7 +97,7 @@ public class ArgParserTest
     }
     else if (a == Arg.ARGFILE)
     {
-      List<String> filenames = b.getList(a);
+      List<String> filenames = b.getValueList(a);
       boolean found = false;
       for (String s : filenames)
       {
@@ -184,9 +184,12 @@ public class ArgParserTest
   @DataProvider(name = "argSubValsAndLinkedIds")
   public Object[][] argSubValsAndLinkedIds()
   {
-    return new Object[][] { {
-        "--debug --append=[hi]test/jalview/bin/argparser/testfiles/test1.fa",
-        "JALVIEW:0", Arg.APPEND, "hi", "true", true },
+    return new Object[][] {
+        //
+        /*
+         */
+        { "--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",
@@ -198,7 +201,11 @@ public class ArgParserTest
         { "--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 }, };
+            "linkedId7", Arg.APPEND, "GETINDEX", "0", false },
+        /*
+         */
+        //
+    };
   }
 
   @DataProvider(name = "argAutoIndexAndSubstitutions")
@@ -210,12 +217,12 @@ public class ArgParserTest
          */
         { "--append=filename0 --append=filename1", "JALVIEW:0", Arg.APPEND,
             "filename0" },
-        { "--append=filename0 --newframe --append=filename1", "JALVIEW:1",
+        { "--append=filename0 --new --append=filename1", "JALVIEW:1",
             Arg.APPEND, "filename1" },
-        { "--append=filename0 --newframe --newframe --append=filename2",
-            "JALVIEW:0", Arg.APPEND, "filename0" },
-        { "--append=filename0 --newframe --newframe --append=filename2",
-            "JALVIEW:2", Arg.APPEND, "filename2" },
+        { "--append=filename0 --new --new --append=filename2", "JALVIEW:0",
+            Arg.APPEND, "filename0" },
+        { "--append=filename0 --new --new --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",
@@ -232,14 +239,14 @@ public class ArgParserTest
             "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,
+        { "--open=filename0 --append=filename1", "JALVIEW:0", Arg.OPEN,
             "filename0" },
-        { "--open=filename0 --newframe --append=filename1", "JALVIEW:2",
+        { "--open=filename0 --new --append=filename1", "JALVIEW:1",
             Arg.APPEND, "filename1" },
-        { "--open=filename0 --newframe --newframe --append=filename2",
-            "JALVIEW:1", Arg.OPEN, "filename0" },
-        { "--open=filename0 --newframe --newframe --append=filename2",
-            "JALVIEW:3", Arg.APPEND, "filename2" },
+        { "--open=filename0 --new --new --append=filename2", "JALVIEW:0",
+            Arg.OPEN, "filename0" },
+        { "--open=filename0 --new --new --append=filename2", "JALVIEW:2",
+            Arg.APPEND, "filename2" },
         { "--open[linkA-{n}]=filenameA0 --append[linkA-{++n}]=filenameA1",
             "linkA-0", Arg.OPEN, "filenameA0" },
         { "--open[linkB-{n}]=filenameB0 --append[linkB-{++n}]=filenameB1",
@@ -256,6 +263,8 @@ public class ArgParserTest
             "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" },
+        /*
+         */
 
         //
     };
@@ -271,7 +280,7 @@ public class ArgParserTest
 
   @Test(groups = "Functional", dataProvider = "allLinkedIdsData")
   public void allLinkedIdsTest(String commandLineArgs, Arg a,
-          String[] values)
+          String[] values, String[] nonvalues)
   {
     String[] args = commandLineArgs.split("\\s+");
     ArgParser argparser = new ArgParser(args);
@@ -312,20 +321,22 @@ public class ArgParserTest
         //
         /*
         */
-        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --allframes --image={dirname}/{basename}.png --close",
+        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --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",
+            { null, null, null },
+            null },
+        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --output={dirname}/{basename}.stk --close",
             Arg.OUTPUT, new String[]
             { "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",
+                "test/jalview/bin/argparser/testfiles/test3.stk", },
+            null },
+        { "--open=test/jalview/bin/argparser/testfiles/*.fa --substitutions --all --image={dirname}/{basename}.png --close",
             Arg.IMAGE, new String[]
             { "test/jalview/bin/argparser/testfiles/test1.png",
                 "test/jalview/bin/argparser/testfiles/test2.png",
-                "test/jalview/bin/argparser/testfiles/test3.png", } },
+                "test/jalview/bin/argparser/testfiles/test3.png", },
+            null },
         //
     };
   }