X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fjmol%2FPDBFileWithJmolTest.java;h=fa3922b3c78c7d7be3bddc37a3a9dabd0d95e90b;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=900e47cf2e4bc66fa224061f1a3d64c76c910593;hpb=7ab5d6b0ba5fec1ea4a4239e79c476d841622485;p=jalview.git

diff --git a/test/jalview/ext/jmol/PDBFileWithJmolTest.java b/test/jalview/ext/jmol/PDBFileWithJmolTest.java
index 900e47c..fa3922b 100644
--- a/test/jalview/ext/jmol/PDBFileWithJmolTest.java
+++ b/test/jalview/ext/jmol/PDBFileWithJmolTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,15 +20,23 @@
  */
 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
@@ -36,32 +44,93 @@ import org.junit.Test;
  */
 public class PDBFileWithJmolTest
 {
+  String[] testFile = new String[] { "./examples/1GAQ.txt",
+      "./test/jalview/ext/jmol/1QCF.pdb" }; // ,
+
+  // "./examples/DNMT1_MOUSE.pdb"
+  // };
 
-  @Test
-  public void test() throws Exception
+  @BeforeMethod(alwaysRun = true)
+  public void setUp()
   {
-    PDBFileWithJmol jtest = new PDBFileWithJmol("./examples/1GAQ.txt",
-            jalview.io.AppletFormatAdapter.FILE);
-    Vector<SequenceI> seqs = jtest.getSeqs();
+    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+            Boolean.TRUE.toString());
+  }
 
-    assertTrue(
-            "No sequences extracted from testfile\n"
-                    + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
-                            : "(No warnings raised)"),
-            seqs != null && seqs.size() > 0);
-    for (SequenceI sq : seqs)
+  @Test(groups = { "Functional" })
+  public void testAlignmentLoader() throws Exception
+  {
+    for (String f : testFile)
     {
-      AlignmentI al = new Alignment(new SequenceI[]
-      { sq });
-      if (!al.isNucleotide())
+      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();
+
+      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)
+  {
+    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);
+  }
 }