Merge branch 'releases/Release_2_11_3_Branch'

[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 8a89830..0bc41a3 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
@@ -23,12 +46,24 @@ 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)
     {
-      System.err
-              .println("You must provide a PDB directory in the launch argument");
+      System.err.println(
+              "You must provide a PDB directory in the launch argument");
       return;
     }
 
@@ -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)
     {
@@ -52,9 +87,8 @@ public class JmolVsJalviewPDBParserEndToEndTest
       try
       {
         mctest = new PDBfile(false, false, false, testFile,
-                AppletFormatAdapter.FILE);
-        jtest = new JmolParser(false, false, false, testFile,
-                jalview.io.AppletFormatAdapter.FILE);
+                DataSourceType.FILE);
+        jtest = new JmolParser(testFile, DataSourceType.FILE);
       } catch (IOException e)
       {
         System.err.println("Exception thrown while parsing : " + pdbStr);
@@ -66,15 +100,15 @@ public class JmolVsJalviewPDBParserEndToEndTest
       {
         try
         {
-        String testSeq = mcseqs.remove(0).getSequenceAsString();
+          String testSeq = mcseqs.remove(0).getSequenceAsString();
           if (!sq.getSequenceAsString().equals(testSeq))
-        {
-          ++totalFail;
+          {
+            ++totalFail;
             System.err.println("Test Failed for " + pdbStr + ". Diff:");
-          System.err.println(sq.getSequenceAsString());
-          System.err.println(testSeq);
-          failedFiles.add(pdbStr);
-        }
+            System.err.println(sq.getSequenceAsString());
+            System.err.println(testSeq);
+            failedFiles.add(pdbStr);
+          }
           ++totalSeqScanned;
         } catch (Exception e)
         {
@@ -85,13 +119,12 @@ public class JmolVsJalviewPDBParserEndToEndTest
     int count = 0;
 
     System.out.println("\n\nTotal sequence Scanned : " + totalSeqScanned);
-    System.out.println("Total sequence passed : "
-            + (totalSeqScanned - totalFail));
+    System.out.println(
+            "Total sequence passed : " + (totalSeqScanned - totalFail));
     System.out.println("Total sequence failed : " + totalFail);
-    System.out
-            .println("Success rate: "
-                    + ((totalSeqScanned - totalFail) * 100)
-                    / totalSeqScanned + "%");
+    System.out.println("Success rate: "
+            + ((totalSeqScanned - totalFail) * 100) / totalSeqScanned
+            + "%");
     System.out.println("\nList of " + failedFiles.size()
             + " file(s) with sequence diffs:");
     for (String problemFile : failedFiles)