From 190af5d9e60121fdfba0dee0bcfb1c2fa037d72d Mon Sep 17 00:00:00 2001
From: tcofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Wed, 27 Jul 2016 13:02:07 +0100
Subject: [PATCH] JAL-1919 added codes for End-2-End scan for sequence
 consistency for PDB files parse with JmolParser vs.
 Jalview's PDBfile parser

---
 .../jmol/JmolVsJalviewPDBParserEndToEndTest.java   |  102 ++++++++++++++++++++
 1 file changed, 102 insertions(+)
 create mode 100644 test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java

diff --git a/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java b/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
new file mode 100644
index 0000000..8a89830
--- /dev/null
+++ b/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
@@ -0,0 +1,102 @@
+package jalview.ext.jmol;
+
+import jalview.datamodel.SequenceI;
+import jalview.io.AppletFormatAdapter;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.HashSet;
+import java.util.Set;
+import java.util.Vector;
+
+import MCview.PDBfile;
+
+/**
+ * This is not a unit test, rather it is a bulk End-to-End scan for sequences
+ * consistency for PDB files parsed with JmolParser vs. Jalview's PDBfile
+ * parser. The directory of PDB files to test must be provided in the launch
+ * args.
+ * 
+ * @author tcnofoegbu
+ *
+ */
+public class JmolVsJalviewPDBParserEndToEndTest
+{
+
+  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");
+      return;
+    }
+
+    // args[0] must provide the directory of PDB files to run the test with
+    String testDir = args[0];
+    System.out.println("PDB directory : " + testDir);
+    File pdbDir = new File(testDir);
+    String testFiles[] = pdbDir.list();
+    testFileParser(testDir, testFiles);
+  }
+
+  public static void testFileParser(String testDir, String[] testFiles)
+  {
+    Set<String> failedFiles = new HashSet<String>();
+    int totalSeqScanned = 0, totalFail = 0;
+    for (String pdbStr : testFiles)
+    {
+      String testFile = testDir + "/" + pdbStr;
+      PDBfile mctest = null;
+      JmolParser jtest = null;
+      try
+      {
+        mctest = new PDBfile(false, false, false, testFile,
+                AppletFormatAdapter.FILE);
+        jtest = new JmolParser(false, false, false, testFile,
+                jalview.io.AppletFormatAdapter.FILE);
+      } catch (IOException e)
+      {
+        System.err.println("Exception thrown while parsing : " + pdbStr);
+      }
+      Vector<SequenceI> seqs = jtest.getSeqs();
+      Vector<SequenceI> mcseqs = mctest.getSeqs();
+
+      for (SequenceI sq : seqs)
+      {
+        try
+        {
+        String testSeq = mcseqs.remove(0).getSequenceAsString();
+          if (!sq.getSequenceAsString().equals(testSeq))
+        {
+          ++totalFail;
+            System.err.println("Test Failed for " + pdbStr + ". Diff:");
+          System.err.println(sq.getSequenceAsString());
+          System.err.println(testSeq);
+          failedFiles.add(pdbStr);
+        }
+          ++totalSeqScanned;
+        } catch (Exception e)
+        {
+          e.printStackTrace();
+        }
+      }
+    }
+    int count = 0;
+
+    System.out.println("\n\nTotal sequence Scanned : " + totalSeqScanned);
+    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("\nList of " + failedFiles.size()
+            + " file(s) with sequence diffs:");
+    for (String problemFile : failedFiles)
+    {
+      System.out.println(++count + ". " + problemFile);
+    }
+  }
+}
-- 
1.7.10.2