X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fparadise%2FTestAnnotate3D.java;h=6d54f156b1116182de18036e227ef0c26369e3a2;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=d358c44bbbcd51f52374f8ce155b663cd63966ea;hpb=4675e195cd7ebca7bf5e1198595eb0e8cff5c7c7;p=jalview.git

diff --git a/test/jalview/ext/paradise/TestAnnotate3D.java b/test/jalview/ext/paradise/TestAnnotate3D.java
index d358c44..6d54f15 100644
--- a/test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/test/jalview/ext/paradise/TestAnnotate3D.java
@@ -1,42 +1,181 @@
+/*
+ * 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.paradise;
 
-import static org.junit.Assert.assertTrue;
+import java.util.Locale;
 
-import jalview.ext.paradise.Annotate3D;
+import static org.testng.AssertJUnit.assertTrue;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
+import jalview.io.FastaFile;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
 
 import java.io.BufferedReader;
 import java.io.File;
+import java.io.Reader;
+import java.util.Iterator;
 
-import org.junit.Test;
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
 
 import compbio.util.FileUtil;
+import mc_view.PDBfile;
 
 public class TestAnnotate3D
 {
 
-  @Test
-  public void testIdVsContent() throws Exception
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @Test(groups = { "Network" }, enabled = true)
+  public void test1GIDbyId() throws Exception
+  {
+    // use same ID as standard tests given at
+    // https://bitbucket.org/fjossinet/pyrna-rest-clients
+    Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("1GID");
+    assertTrue("Didn't retrieve 1GID by id.", ids != null);
+    testRNAMLcontent(ids, null);
+  }
+
+  @Test(groups = { "Network" }, enabled = true)
+  public void testIdVsContent2GIS() throws Exception
   {
-    BufferedReader id = (BufferedReader) Annotate3D.getRNAMLForPDBId("2GIS");
-    assertTrue("Didn't retrieve 2GIS by id.", id != null);
-    BufferedReader file = (BufferedReader) Annotate3D.getRNAMLForPDBFileAsString(FileUtil
-            .readFileToString(new File("examples/2GIS.pdb")));
-    assertTrue("Didn't retrieve using examples/2GIS.pdb.", file != null);
-    String iline, fline;
-    do
+    Iterator<Reader> ids = Annotate3D.getRNAMLForPDBId("2GIS");
+    assertTrue("Didn't retrieve 2GIS by id.", ids != null);
+    Iterator<Reader> files = Annotate3D.getRNAMLForPDBFileAsString(
+            FileUtil.readFileToString(new File("examples/2GIS.pdb")));
+    assertTrue("Didn't retrieve using examples/2GIS.pdb.", files != null);
+    int i = 0;
+    while (ids.hasNext() && files.hasNext())
     {
-      iline = id.readLine();
-      fline = file.readLine();
-      if (iline != null)
-        System.out.println(iline);
-      if (fline != null)
-        System.out.println(fline);
-
-      assertTrue("Results differ for ID and file upload based retrieval",
-              ((iline == fline && iline == null) || (iline != null
-                      && fline != null && iline.equals(fline))));
-
-    } while (iline != null);
+      BufferedReader file = new BufferedReader(files.next()),
+              id = new BufferedReader(ids.next());
+      String iline, fline;
+      do
+      {
+        iline = id.readLine();
+        fline = file.readLine();
+        if (iline != null)
+        {
+          System.out.println(iline);
+        }
+        if (fline != null)
+        {
+          System.out.println(fline);
+        }
+        // next assert fails for latest RNAview - because the XMLID entries
+        // change between file and ID based RNAML generation.
+        assertTrue(
+                "Results differ for ID and file upload based retrieval (chain entry "
+                        + (++i) + ")",
+                ((iline == fline && iline == null) || (iline != null
+                        && fline != null && iline.equals(fline))));
+
+      } while (iline != null);
+    }
+  }
+
+  /**
+   * test to demonstrate JAL-1142 - compare sequences in RNAML returned from
+   * Annotate3d vs those extracted by Jalview from the originl PDB file
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Network" }, enabled = true)
+  public void testPDBfileVsRNAML() throws Exception
+  {
+    PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
+            DataSourceType.FILE);
+    Assert.assertTrue(pdbf.isValid());
+    // Comment - should add new FileParse constructor like new FileParse(Reader
+    // ..). for direct reading
+    Iterator<Reader> readers = Annotate3D.getRNAMLForPDBFileAsString(
+            FileUtil.readFileToString(new File("examples/2GIS.pdb")));
+    testRNAMLcontent(readers, pdbf);
   }
 
+  private void testRNAMLcontent(Iterator<Reader> readers, PDBfile pdbf)
+          throws Exception
+  {
+    StringBuffer sb = new StringBuffer();
+    int r = 0;
+    while (readers.hasNext())
+    {
+      System.out.println("Testing RNAML input number " + (++r));
+      BufferedReader br = new BufferedReader(readers.next());
+      String line;
+      while ((line = br.readLine()) != null)
+      {
+        sb.append(line + "\n");
+      }
+      assertTrue("No data returned by Annotate3D", sb.length() > 0);
+      final String lines = sb.toString();
+      AlignmentI al = new FormatAdapter().readFile(lines,
+              DataSourceType.PASTE, FileFormat.Rnaml);
+      if (al == null || al.getHeight() == 0)
+      {
+        System.out.println(lines);
+      }
+      assertTrue("No alignment returned.", al != null);
+      assertTrue("No sequences in returned alignment.", al.getHeight() > 0);
+      if (pdbf != null)
+      {
+        for (SequenceI sq : al.getSequences())
+        {
+          {
+            SequenceI struseq = null;
+            String sq_ = sq.getSequenceAsString().toLowerCase(Locale.ROOT);
+            for (SequenceI _struseq : pdbf.getSeqsAsArray())
+            {
+              final String lowerCase = _struseq.getSequenceAsString()
+                      .toLowerCase(Locale.ROOT);
+              if (lowerCase.equals(sq_))
+              {
+                struseq = _struseq;
+                break;
+              }
+            }
+            if (struseq == null)
+            {
+              AssertJUnit.fail(
+                      "Couldn't find this sequence in original input:\n"
+                              + new FastaFile().print(new SequenceI[]
+                              { sq }, true) + "\n\nOriginal input:\n"
+                              + new FastaFile().print(pdbf.getSeqsAsArray(),
+                                      true)
+                              + "\n");
+            }
+          }
+        }
+      }
+    }
+  }
 }