X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FAnnotatedPDBFileInputTest.java;h=9a07ef789408a18d30b1cd729dde95d6e4601ef2;hb=8b27085fa7fc5f2877e078421284c2636b85b8c6;hp=e8cd3efab4fd03b6391c5ef0ea4fe1cb5dc4c65b;hpb=4a5137b64f7ec23db2a09290bfcd392984a52150;p=jalview.git

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index e8cd3ef..9a07ef7 100644
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -32,6 +32,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
 import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
 
 import java.io.File;
 
@@ -66,7 +67,9 @@ public class AnnotatedPDBFileInputTest
     al = af.getViewport().getAlignment();
     pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
             .get(0).getId();
-    StructureImportSettings.setCurrentDefaultFormat("PDB");
+    StructureImportSettings.setDefaultStructureFileFormat("PDB");
+    // StructureImportSettings
+    // .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
   }
 
   @Test(groups = { "Functional" })
@@ -98,7 +101,11 @@ public class AnnotatedPDBFileInputTest
       {
 
         System.out.println("CalcId: " + aa.getCalcId());
+        if (StructureImportSettings.getDefaultPDBFileParser().equals(
+                StructureParser.JALVIEW_PARSER))
+        {
         assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+        }
       }
     }
   }
@@ -115,9 +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
@@ -125,9 +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
@@ -135,9 +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" })