X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandsTest2.java;h=a31b77dd9d2ffb8c97407a0b6e9ae7498053a5ab;hb=e67a74ee1dac618d941fce0fc5ef4561f76380b1;hp=34966ae7f3cc9c4ac10b4a3202758eaabf8629fc;hpb=bf95499e2c08367f60183e13cde467408fdba591;p=jalview.git

diff --git a/test/jalview/bin/CommandsTest2.java b/test/jalview/bin/CommandsTest2.java
index 34966ae..a31b77d 100644
--- a/test/jalview/bin/CommandsTest2.java
+++ b/test/jalview/bin/CommandsTest2.java
@@ -57,7 +57,7 @@ public class CommandsTest2
 
   @Test(
     groups =
-    { "Functional" },
+    { "Functional", "testTask1" },
     dataProvider = "structureOpeningArgsParams",
     singleThreaded = true)
   public void structureOpeningArgsTest(String cmdLine, int seqNum,
@@ -69,7 +69,7 @@ public class CommandsTest2
     try
     {
       // sleep for slow build server to open annotations and viewer windows
-      Thread.sleep(seqNum * 100 + annNum * 200 + viewerNum * 1500);
+      Thread.sleep(seqNum * 50 + annNum * 50 + viewerNum * 500);
     } catch (InterruptedException e)
     {
       e.printStackTrace();
@@ -101,8 +101,6 @@ public class CommandsTest2
     int dcount = 0;
     for (AlignmentAnnotation aa : aas)
     {
-      System.err.println("##### DIAGNOSIS: annotation " + ++dcount
-              + " is labelled '" + aa.label + "'");
       if (aa.visible)
         visibleAnn++;
     }
@@ -133,55 +131,72 @@ public class CommandsTest2
       String cmdLine,
       int seqNum,
       int annNum,
-      int viewerNum,
-      String propsFile
+      int structureViewerNum,
      */
     return new Object[][] {
         //
         /*
          */
         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
-                + "--colour=gecos:flower "
+                + "--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 "
+                + "--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 " + "--append=examples/uniref50.fa "
-                + "--colour=gecos:flower "
+                + "--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 "
+                + "--noshowssannotations "
                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
             15, 4, 1 },
         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
-                + "--colour=gecos:flower "
+                + "--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 "
+                + "--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 " + "--noshowssannotations "
                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
             15, 0, 1 },
         { "--nonews --nosplash --debug " + "--append=examples/uniref50.fa "
-                + "--colour=gecos:flower "
+                + "--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 " + "--noshowssannotations "
                 + "--props=test/jalview/bin/commandsTest2.jvprops1 ",
             15, 0, 1 },
-        { "--argfile=test/jalview/bin/commandsTest2.argfile1 ", 16, 19, 3 },
-        { "--argfile=test/jalview/bin/commandsTest2.argfile2 ", 16, 0, 2 },
+        { "--nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile1 ",
+            16, 19, 3 },
+        { "--nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --argfile=test/jalview/bin/commandsTest2.argfile2 ",
+            16, 0, 2 },
+        { "--nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
+                + "--allstructures "
+                + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+                + "--structureviewer=none "
+                + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb "
+                + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb",
+            16, 10, 0 },
+        { "--nonews --nosplash --debug --nowebservicediscovery --props=test/jalview/bin/commandsTest.jvprops --open=./examples/test_fab41.result/sample.a2m "
+                + "--allstructures "
+                + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
+                + "--noallstructures " + "--structureviewer=none "
+                + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_2_model_4.pdb "
+                + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_3_model_2.pdb",
+            16, 10, 2 },
+        /*
+         */
         //
     };
   }