JAL-2189 format tests

[jalview.git] / test / jalview / datamodel / SequenceTest.java

diff --git a/test/jalview/datamodel/SequenceTest.java b/test/jalview/datamodel/SequenceTest.java
index 25804bc..065bed7 100644 (file)
--- a/test/jalview/datamodel/SequenceTest.java
+++ b/test/jalview/datamodel/SequenceTest.java
@@ -70,11 +70,11 @@ public class SequenceTest
   public void testIsProtein()
   {
     // test Protein
-    assertTrue(new Sequence("prot","ASDFASDFASDF").isProtein());
+    assertTrue(new Sequence("prot", "ASDFASDFASDF").isProtein());
     // test DNA
-    assertFalse(new Sequence("prot","ACGTACGTACGT").isProtein());
+    assertFalse(new Sequence("prot", "ACGTACGTACGT").isProtein());
     // test RNA
-    SequenceI sq = new Sequence("prot","ACGUACGUACGU");
+    SequenceI sq = new Sequence("prot", "ACGUACGUACGU");
     assertFalse(sq.isProtein());
     // change sequence, should trigger an update of cached result
     sq.setSequence("ASDFASDFADSF");
@@ -336,7 +336,6 @@ public class SequenceTest
     assertEquals(1, sfs.length);
     assertSame(sf, sfs[0]);
 
-
     /*
      * SequenceFeature on sequence and dataset sequence; returns that on
      * sequence
@@ -425,7 +424,7 @@ public class SequenceTest
   @Test(groups = { "Functional" })
   public void testCreateDatasetSequence()
   {
-    SequenceI sq = new Sequence("my","ASDASD");
+    SequenceI sq = new Sequence("my", "ASDASD");
     assertNull(sq.getDatasetSequence());
     SequenceI rds = sq.createDatasetSequence();
     assertNotNull(rds);
@@ -459,12 +458,11 @@ public class SequenceTest
     sq.addPDBId(new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1"));
     sq.addPDBId(new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2"));
     sq.addPDBId(new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2"));
-    
+
     // these are the same as ones already added
     DBRefEntry pdb1pdb = new DBRefEntry("PDB", "version1", "1PDB");
     DBRefEntry pdb2pdb = new DBRefEntry("PDB", "version2", "2PDB");
 
-    
     List<DBRefEntry> primRefs = Arrays.asList(new DBRefEntry[] { pdb1pdb,
         pdb2pdb });
 
@@ -474,15 +472,15 @@ public class SequenceTest
             new DBRefEntry("PDB", "version3", "3PDB")); // should do nothing
     sq.getDatasetSequence().addDBRef(
             new DBRefEntry("PDB", "version4", "4PDB")); // should do nothing
-    
-    PDBEntry pdbe1a=new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1");
+
+    PDBEntry pdbe1a = new PDBEntry("1PDB", "A", Type.PDB, "filePath/test1");
     PDBEntry pdbe1b = new PDBEntry("1PDB", "B", Type.PDB, "filePath/test1");
-    PDBEntry pdbe2a=new PDBEntry("2PDB", "A", Type.MMCIF, "filePath/test2");
-    PDBEntry pdbe2b = new PDBEntry("2PDB", "B", Type.MMCIF, "filePath/test2");
-    sq.getDatasetSequence().addPDBId(
-            pdbe1a);
-    sq.getDatasetSequence().addPDBId(
-            pdbe1b);
+    PDBEntry pdbe2a = new PDBEntry("2PDB", "A", Type.MMCIF,
+            "filePath/test2");
+    PDBEntry pdbe2b = new PDBEntry("2PDB", "B", Type.MMCIF,
+            "filePath/test2");
+    sq.getDatasetSequence().addPDBId(pdbe1a);
+    sq.getDatasetSequence().addPDBId(pdbe1b);
     sq.getDatasetSequence().addPDBId(pdbe2a);
     sq.getDatasetSequence().addPDBId(pdbe2b);
 
@@ -544,7 +542,7 @@ public class SequenceTest
     assertNotNull(sq.getSequenceFeatures());
     assertArrayEquals(sq.getSequenceFeatures(),
             derived.getSequenceFeatures());
-    
+
     /*
      *  verify we have primary db refs *just* for PDB IDs with associated
      *  PDBEntry objects
@@ -599,7 +597,7 @@ public class SequenceTest
             12.4f, "group"));
     seq1.addPDBId(new PDBEntry("1A70", "B", Type.PDB, "File"));
     seq1.addDBRef(new DBRefEntry("EMBL", "1.2", "AZ12345"));
-    
+
     SequenceI copy = new Sequence(seq1);
 
     assertNull(copy.getDatasetSequence());
@@ -675,9 +673,13 @@ public class SequenceTest
     // copy has a copy of the sequence feature:
     SequenceFeature[] sfs = copy.getSequenceFeatures();
     assertEquals(1, sfs.length);
-    if (seq1.getDatasetSequence()!=null && copy.getDatasetSequence()==seq1.getDatasetSequence()) {
+    if (seq1.getDatasetSequence() != null
+            && copy.getDatasetSequence() == seq1.getDatasetSequence())
+    {
       assertTrue(sfs[0] == seq1.getSequenceFeatures()[0]);
-    } else {
+    }
+    else
+    {
       assertFalse(sfs[0] == seq1.getSequenceFeatures()[0]);
     }
     assertTrue(sfs[0].equals(seq1.getSequenceFeatures()[0]));
@@ -867,11 +869,11 @@ public class SequenceTest
   public void testGetPrimaryDBRefs_nucleotide()
   {
     SequenceI sq = new Sequence("aseq", "TGATCACTCGACTAGCATCAGCATA", 10, 34);
-  
+
     // primary - Ensembl
     DBRefEntry dbr1 = new DBRefEntry("ENSEMBL", "0", "ENSG1234");
     sq.addDBRef(dbr1);
-  
+
     // not primary - Ensembl 'transcript' mapping of sub-sequence
     DBRefEntry dbr2 = new DBRefEntry("ENSEMBL", "0", "ENST1234");
     dbr2.setMap(new Mapping(null, new MapList(new int[] { 15, 25 },
@@ -891,7 +893,7 @@ public class SequenceTest
     // not primary - to protein
     DBRefEntry dbr5 = new DBRefEntry("UNIPROT", "0", "Q87654");
     sq.addDBRef(dbr5);
-  
+
     List<DBRefEntry> primaryDBRefs = sq.getPrimaryDBRefs();
     assertEquals(2, primaryDBRefs.size());
     assertTrue(primaryDBRefs.contains(dbr1));
@@ -913,7 +915,7 @@ public class SequenceTest
     seq.addDBRef(new DBRefEntry("PDB", "0", "3a6sB"));
     // 7 is not a valid chain code:
     seq.addDBRef(new DBRefEntry("PDB", "0", "2GIS7"));
-    
+
     seq.updatePDBIds();
     List<PDBEntry> pdbIds = seq.getAllPDBEntries();
     assertEquals(4, pdbIds.size());