Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

[jalview.git] / test / jalview / ext / jmol / JmolVsJalviewPDBParserEndToEndTest.java

diff --git a/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java b/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
index b6aa375..382e208 100644 (file)
--- a/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
+++ b/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
@@ -1,7 +1,28 @@
+/*
+ * 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.ext.jmol;
 
 import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
 
 import java.io.File;
 import java.io.IOException;
@@ -9,7 +30,9 @@ import java.util.HashSet;
 import java.util.Set;
 import java.util.Vector;
 
-import MCview.PDBfile;
+import org.testng.annotations.BeforeClass;
+
+import mc_view.PDBfile;
 
 /**
  * This is not a unit test, rather it is a bulk End-to-End scan for sequences
@@ -23,6 +46,18 @@ import MCview.PDBfile;
 public class JmolVsJalviewPDBParserEndToEndTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  /**
+   * 
+   * @param args
+   * @j2sIgnore
+   */
   public static void main(String[] args)
   {
     if (args == null || args[0] == null)
@@ -42,7 +77,7 @@ public class JmolVsJalviewPDBParserEndToEndTest
 
   public static void testFileParser(String testDir, String[] testFiles)
   {
-    Set<String> failedFiles = new HashSet<String>();
+    Set<String> failedFiles = new HashSet<>();
     int totalSeqScanned = 0, totalFail = 0;
     for (String pdbStr : testFiles)
     {
@@ -51,9 +86,8 @@ public class JmolVsJalviewPDBParserEndToEndTest
       JmolParser jtest = null;
       try
       {
-        mctest = new PDBfile(false, false, false, testFile,
-                AppletFormatAdapter.FILE);
-        jtest = new JmolParser(testFile, AppletFormatAdapter.FILE);
+        mctest = new PDBfile(false, false, false, testFile, DataSourceType.FILE);
+        jtest = new JmolParser(testFile, DataSourceType.FILE);
       } catch (IOException e)
       {
         System.err.println("Exception thrown while parsing : " + pdbStr);