JAL-4090 JAL-1551 source license

[jalview.git] / test / jalview / bin / CommandsTest.java

diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index 66250d8..42b93a9 100644 (file)
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.java
@@ -1,12 +1,35 @@
+/*
+ * 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 java.io.File;
 import java.io.IOException;
+import java.lang.reflect.InvocationTargetException;
 import java.nio.file.Files;
 import java.util.Date;
 import java.util.HashSet;
 import java.util.Set;
 
+import javax.swing.SwingUtilities;
+
 import org.testng.Assert;
 import org.testng.annotations.AfterClass;
 import org.testng.annotations.AfterMethod;
@@ -48,7 +71,24 @@ public class CommandsTest
   @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
-    Desktop.closeDesktop();
+    try
+    {
+      // occasionally we are blocked by Jmol redraws
+      SwingUtilities.invokeAndWait(new Runnable()
+      {
+
+        @Override
+        public void run()
+        {
+          Desktop.closeDesktop();
+        }
+      });
+    } catch (Exception foo)
+    {
+      System.err.println("Failed during teardown with exception");
+      foo.printStackTrace();
+    }
+
   }
 
   public static void callJalviewMain(String[] args)
@@ -76,7 +116,7 @@ public class CommandsTest
   }
   */
 
-  @Test(groups = "Functional", dataProvider = "cmdLines")
+  @Test(groups = { "Functional", "testTask3" }, dataProvider = "cmdLines")
   public void commandsOpenTest(String cmdLine, boolean cmdArgs,
           int numFrames, String[] sequences)
   {
@@ -91,13 +131,13 @@ public class CommandsTest
       Assert.assertEquals(cmds.argsWereParsed(), cmdArgs,
               "Overall command parse and operation is false");
 
-      Assert.assertEquals(Desktop.getAlignFrames().length, numFrames,
+      Assert.assertEquals(Desktop.getDesktopAlignFrames().length, numFrames,
               "Wrong number of AlignFrames");
 
       if (sequences != null)
       {
         Set<String> openedSequenceNames = new HashSet<>();
-        AlignFrame[] afs = Desktop.getAlignFrames();
+        AlignFrame[] afs = Desktop.getDesktopAlignFrames();
         for (AlignFrame af : afs)
         {
           openedSequenceNames.addAll(
@@ -127,7 +167,7 @@ public class CommandsTest
 
   @Test(
     groups =
-    { "Functional", "testTask1" },
+    { "Functional", "testTask3" },
     dataProvider = "structureImageOutputFiles")
   public void structureImageOutputTest(String cmdLine, String[] filenames)
           throws IOException
@@ -214,11 +254,11 @@ public class CommandsTest
                 + "--open=./examples/test_fab41.result/sample.a2m "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
                 + "--structureimage=" + testfiles
-                + "/structureimage2.png --structureimagescale=1.5"
+                + "/structureimage2.png --scale=1.5 "
                 + "--open=./examples/test_fab41.result/sample.a2m "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
                 + "--structureimage=" + testfiles
-                + "/structureimage3.png --structureimagescale=2.0",
+                + "/structureimage3.png --scale=2.0 ",
             new String[]
             { testfiles + "/structureimage1.png",
                 testfiles + "/structureimage2.png",
@@ -229,11 +269,11 @@ public class CommandsTest
                 + "--open=./examples/test_fab41.result/sample.a2m "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
                 + "--structureimage=" + testfiles
-                + "/structureimage2.png --structureimagescale=1.5"
+                + "/structureimage2.png --scale=1.5 "
                 + "--open=./examples/test_fab41.result/sample.a2m "
                 + "--structure=./examples/test_fab41.result/test_fab41_unrelaxed_rank_1_model_3.pdb "
                 + "--structureimage=" + testfiles
-                + "/structureimage3.png --structureimagescale=2.0",
+                + "/structureimage3.png --scale=2.0 ",
             new String[]
             { testfiles + "/structureimage1.png",
                 testfiles + "/structureimage2.png",
@@ -305,7 +345,7 @@ public class CommandsTest
 
   public static boolean lookForSequenceName(String sequenceName)
   {
-    AlignFrame[] afs = Desktop.getAlignFrames();
+    AlignFrame[] afs = Desktop.getDesktopAlignFrames();
     for (AlignFrame af : afs)
     {
       for (String name : af.getViewport().getAlignment().getSequenceNames())