JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / test / jalview / io / AnnotatedPDBFileInputTest.java

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index d3d9ff8..b8c12c6 100644 (file)
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -85,8 +85,8 @@ public class AnnotatedPDBFileInputTest
     {
       for (int q = p + 1; q < avec.length; q++)
       {
-        assertTrue("Found a duplicate annotation row "
-                + avec[p].label, avec[p] != avec[q]);
+        assertTrue("Found a duplicate annotation row " + avec[p].label,
+                avec[p] != avec[q]);
       }
     }
   }
@@ -104,7 +104,7 @@ public class AnnotatedPDBFileInputTest
         if (StructureImportSettings.getDefaultPDBFileParser().equals(
                 StructureParser.JALVIEW_PARSER))
         {
-        assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+          assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
         }
       }
     }
@@ -122,9 +122,9 @@ public class AnnotatedPDBFileInputTest
     SequenceFeature[] sf = al.getSequenceAt(0).getSequenceFeatures();
     assertEquals(296, sf.length);
     assertEquals("RESNUM", sf[0].getType());
-    assertEquals("GLU:19 1gaqA", sf[0].getDescription());
+    assertEquals("GLU:  19  1gaqA", sf[0].getDescription());
     assertEquals("RESNUM", sf[295].getType());
-    assertEquals("TYR:314 1gaqA", sf[295].getDescription());
+    assertEquals("TYR: 314  1gaqA", sf[295].getDescription());
 
     /*
      * 1GAQ/B
@@ -132,9 +132,9 @@ public class AnnotatedPDBFileInputTest
     sf = al.getSequenceAt(1).getSequenceFeatures();
     assertEquals(98, sf.length);
     assertEquals("RESNUM", sf[0].getType());
-    assertEquals("ALA:1 1gaqB", sf[0].getDescription());
+    assertEquals("ALA:   1  1gaqB", sf[0].getDescription());
     assertEquals("RESNUM", sf[97].getType());
-    assertEquals("ALA:98 1gaqB", sf[97].getDescription());
+    assertEquals("ALA:  98  1gaqB", sf[97].getDescription());
 
     /*
      * 1GAQ/C
@@ -142,9 +142,9 @@ public class AnnotatedPDBFileInputTest
     sf = al.getSequenceAt(2).getSequenceFeatures();
     assertEquals(296, sf.length);
     assertEquals("RESNUM", sf[0].getType());
-    assertEquals("GLU:19 1gaqC", sf[0].getDescription());
+    assertEquals("GLU:  19  1gaqC", sf[0].getDescription());
     assertEquals("RESNUM", sf[295].getType());
-    assertEquals("TYR:314 1gaqC", sf[295].getDescription());
+    assertEquals("TYR: 314  1gaqC", sf[295].getDescription());
   }
 
   @Test(groups = { "Functional" })
@@ -221,8 +221,8 @@ public class AnnotatedPDBFileInputTest
         sq = sq.getDatasetSequence();
       }
       assertNotNull(sq.getAllPDBEntries());
-      assertEquals("Expected only one PDB ID",
-              sq.getAllPDBEntries().size(), 1);
+      assertEquals("Expected only one PDB ID", 1, sq.getAllPDBEntries()
+              .size());
       for (PDBEntry pdbentry : sq.getAllPDBEntries())
       {
         System.err.println("PDB Entry " + pdbentry.getId() + " "