JAL-4160 update args used in test suite for new CLI framework

[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 d285b04..0bc41a3 100644 (file)
--- a/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
+++ b/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
@@ -32,7 +32,7 @@ import java.util.Vector;
 
 import org.testng.annotations.BeforeClass;
 
-import MCview.PDBfile;
+import mc_view.PDBfile;
 
 /**
  * This is not a unit test, rather it is a bulk End-to-End scan for sequences
@@ -53,12 +53,17 @@ public class JmolVsJalviewPDBParserEndToEndTest
     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;
     }
 
@@ -72,7 +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)
     {
@@ -81,7 +86,8 @@ public class JmolVsJalviewPDBParserEndToEndTest
       JmolParser jtest = null;
       try
       {
-        mctest = new PDBfile(false, false, false, testFile, DataSourceType.FILE);
+        mctest = new PDBfile(false, false, false, testFile,
+                DataSourceType.FILE);
         jtest = new JmolParser(testFile, DataSourceType.FILE);
       } catch (IOException e)
       {
@@ -113,13 +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)