JAL-3210 Barebones gradle/buildship/eclipse. See README

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

diff --git a/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java b/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
deleted file mode 100644 (file)
index 382e208..0000000
--- a/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
+++ /dev/null
@@ -1,135 +0,0 @@
-/*
- * 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.gui.JvOptionPane;
-import jalview.io.DataSourceType;
-
-import java.io.File;
-import java.io.IOException;
-import java.util.HashSet;
-import java.util.Set;
-import java.util.Vector;
-
-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
- * 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
-{
-
-  @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");
-      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<>();
-    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, DataSourceType.FILE);
-        jtest = new JmolParser(testFile, DataSourceType.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);
-    }
-  }
-}