JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/test/jalview/ext/jmol/PDBFileWithJmolTest.java b/test/jalview/ext/jmol/PDBFileWithJmolTest.java
index 39b679a..fa3922b 100644 (file)
--- a/test/jalview/ext/jmol/PDBFileWithJmolTest.java
+++ b/test/jalview/ext/jmol/PDBFileWithJmolTest.java
@@ -1,40 +1,136 @@
-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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 static org.junit.Assert.*;
-
-import java.util.Vector;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.io.AppletFormatAdapter;
+import jalview.io.FileLoader;
+
+import java.util.Vector;
 
-import org.junit.Test;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import MCview.PDBfile;
 
 /**
  * @author jimp
- *
+ * 
  */
 public class PDBFileWithJmolTest
 {
+  String[] testFile = new String[] { "./examples/1GAQ.txt",
+      "./test/jalview/ext/jmol/1QCF.pdb" }; // ,
+
+  // "./examples/DNMT1_MOUSE.pdb"
+  // };
+
+  @BeforeMethod(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+            Boolean.TRUE.toString());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testAlignmentLoader() throws Exception
+  {
+    for (String f : testFile)
+    {
+      FileLoader fl = new jalview.io.FileLoader(false);
+      AlignFrame af = fl
+              .LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
+      validateSecStrRows(af.getViewport().getAlignment());
+    }
+  }
+
+  @Test(groups = { "Functional" })
+  public void testFileParser() throws Exception
+  {
+    for (String pdbStr : testFile)
+    {
+      PDBfile mctest = new PDBfile(false, false, false, pdbStr,
+              AppletFormatAdapter.FILE);
+      PDBFileWithJmol jtest = new PDBFileWithJmol(pdbStr,
+              jalview.io.AppletFormatAdapter.FILE);
+      Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
 
-  @Test
-  public void test() throws Exception
+      assertTrue(
+              "No sequences extracted from testfile\n"
+                      + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
+                              : "(No warnings raised)"), seqs != null
+                      && seqs.size() > 0);
+      for (SequenceI sq : seqs)
+      {
+        assertEquals("JMol didn't process " + pdbStr
+                + " to the same sequence as MCView",
+                sq.getSequenceAsString(), mcseqs.remove(0)
+                        .getSequenceAsString());
+        AlignmentI al = new Alignment(new SequenceI[] { sq });
+        validateSecStrRows(al);
+      }
+    }
+  }
+
+  private void validateSecStrRows(AlignmentI al)
   {
-    PDBFileWithJmol jtest=new PDBFileWithJmol("./examples/1GAQ.txt", jalview.io.AppletFormatAdapter.FILE);
-    Vector<SequenceI> seqs=jtest.getSeqs();
-    
-    assertTrue("No sequences extracted from testfile\n"+(jtest.hasWarningMessage() ? jtest.getWarningMessage(): "(No warnings raised)"), seqs!=null && seqs.size()>0);
-    for (SequenceI sq:seqs)
+    if (!al.isNucleotide())
     {
-      AlignmentI al = new Alignment(new SequenceI[] { sq});
-      if (!al.isNucleotide())
+      for (SequenceI asq : al.getSequences())
       {
-        assertTrue("No secondary structure assigned for protein sequence.",sq.getAnnotation()!=null && sq.getAnnotation().length>=1 && sq.getAnnotation()[0].hasIcons);
+        SequenceI sq = asq;
+        boolean hasDs = false;
+        while (sq.getDatasetSequence() != null
+                && sq.getAnnotation() == null)
+        {
+          sq = sq.getDatasetSequence();
+          hasDs = true;
+        }
+        checkFirstAAIsAssoc(sq);
+        if (hasDs)
+        {
+          // also verify if alignment sequence has annotation on it
+          // that is correctly mapped
+          checkFirstAAIsAssoc(asq);
+        }
       }
     }
   }
 
+  private void checkFirstAAIsAssoc(SequenceI sq)
+  {
+    assertTrue("No secondary structure assigned for protein sequence.",
+            sq.getAnnotation() != null && sq.getAnnotation().length >= 1
+                    && sq.getAnnotation()[0].hasIcons);
+    assertTrue(
+            "Secondary structure not associated for sequence "
+                    + sq.getName(), sq.getAnnotation()[0].sequenceRef == sq);
+  }
 }