Merge branch 'features/sequenceFeatureRefactor' into develop

[jalview.git] / test / jalview / ext / paradise / TestAnnotate3D.java

diff --git a/test/jalview/ext/paradise/TestAnnotate3D.java b/test/jalview/ext/paradise/TestAnnotate3D.java
index 896b60c..3365c52 100644 (file)
--- a/test/jalview/ext/paradise/TestAnnotate3D.java
+++ b/test/jalview/ext/paradise/TestAnnotate3D.java
@@ -1,13 +1,27 @@
+/*
+ * 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 jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceI;
-import jalview.ext.paradise.Annotate3D;
-import jalview.io.FastaFile;
-import jalview.io.FormatAdapter;
-
 import java.io.BufferedReader;
 import java.io.File;
 import java.io.Reader;
@@ -17,19 +31,24 @@ import org.junit.Assert;
 import org.junit.Test;
 
 import MCview.PDBfile;
-
 import compbio.util.FileUtil;
 
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.io.FastaFile;
+import jalview.io.FormatAdapter;
+
 public class TestAnnotate3D
 {
 
   @Test
   public void test1GIDbyId() throws Exception
   {
-    // use same ID as standard tests given at https://bitbucket.org/fjossinet/pyrna-rest-clients
+    // 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);
+    testRNAMLcontent(ids, null);
   }
 
   @Test
@@ -51,9 +70,13 @@ public class TestAnnotate3D
         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(
@@ -75,7 +98,8 @@ public class TestAnnotate3D
   @Test
   public void testPDBfileVsRNAML() throws Exception
   {
-    PDBfile pdbf = new PDBfile("examples/2GIS.pdb", FormatAdapter.FILE);
+    PDBfile pdbf = new PDBfile(true, false, true, "examples/2GIS.pdb",
+            FormatAdapter.FILE);
     Assert.assertTrue(pdbf.isValid());
     // Comment - should add new FileParse constructor like new FileParse(Reader
     // ..). for direct reading
@@ -100,10 +124,12 @@ public class TestAnnotate3D
         sb.append(line + "\n");
       }
       assertTrue("No data returned by Annotate3D", sb.length() > 0);
-      AlignmentI al = new FormatAdapter().readFile(sb.toString(),
+      final String lines = sb.toString();
+      AlignmentI al = new FormatAdapter().readFile(lines,
               FormatAdapter.PASTE, "RNAML");
-      if (al==null || al.getHeight()==0) {
-        System.out.println(sb.toString());
+      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);
@@ -116,7 +142,8 @@ public class TestAnnotate3D
             String sq_ = new String(sq.getSequence()).toLowerCase();
             for (SequenceI _struseq : pdbf.getSeqsAsArray())
             {
-              if (new String(_struseq.getSequence()).toLowerCase().equals(
+              final String lowerCase = new String(_struseq.getSequence()).toLowerCase();
+              if (lowerCase.equals(
                       sq_))
               {
                 struseq = _struseq;