X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fbin%2FCommandsTest2.java;h=a31b77dd9d2ffb8c97407a0b6e9ae7498053a5ab;hb=1d1edb58c9ee8baec12686a512eb18d97b9bdba1;hp=34b802e9198242e634f3358b59c548420418b100;hpb=89d2d876e6f62e428c11eb0facf618ea4c57aa8d;p=jalview.git

diff --git a/test/jalview/bin/CommandsTest2.java b/test/jalview/bin/CommandsTest2.java
index 34b802e..a31b77d 100644
--- a/test/jalview/bin/CommandsTest2.java
+++ b/test/jalview/bin/CommandsTest2.java
@@ -57,14 +57,24 @@ public class CommandsTest2
 
   @Test(
     groups =
-    { "Functional" },
-    dataProvider = "structureOpeningArgsParams")
+    { "Functional", "testTask1" },
+    dataProvider = "structureOpeningArgsParams",
+    singleThreaded = true)
   public void structureOpeningArgsTest(String cmdLine, int seqNum,
           int annNum, int viewerNum)
   {
     String[] args = cmdLine.split("\\s+");
 
     Jalview.main(args);
+    try
+    {
+      // sleep for slow build server to open annotations and viewer windows
+      Thread.sleep(seqNum * 50 + annNum * 50 + viewerNum * 500);
+    } catch (InterruptedException e)
+    {
+      e.printStackTrace();
+    }
+
     AlignFrame[] afs = Desktop.getAlignFrames();
     Assert.assertNotNull(afs);
     Assert.assertTrue(afs.length > 0);
@@ -88,6 +98,7 @@ public class CommandsTest2
 
     AlignmentAnnotation[] aas = al.getAlignmentAnnotation();
     int visibleAnn = 0;
+    int dcount = 0;
     for (AlignmentAnnotation aa : aas)
     {
       if (aa.visible)
@@ -99,23 +110,12 @@ public class CommandsTest2
 
     if (viewerNum > -1)
     {
-      try
-      {
-        // sleep for slow build server to open viewer window
-        Thread.sleep(2000);
-      } catch (InterruptedException e)
-      {
-        e.printStackTrace();
-      }
       List<StructureViewerBase> openViewers = Desktop.instance
               .getStructureViewers(ap, null);
       Assert.assertNotNull(openViewers);
       int count = 0;
-      int dcount = 0;
       for (StructureViewerBase svb : openViewers)
       {
-        System.err.println("##### DIAGNOSIS: annotation " + dcount
-                + " is called '" + svb.getName() + "'");
         if (svb.isVisible())
           count++;
       }
@@ -131,55 +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 },
+        /*
+         */
         //
     };
   }