X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=79d622c6e068065de8cbf53c2c65a71b0bdadf9e;hb=3352c2b216fc2c4051410efe7a564b790c79ebd9;hp=80ed4c1e993451834244c29f6bd9ea5560499841;hpb=4fa02869e039bb879849419737510b4b29ea5a4c;p=jalview.git

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 80ed4c1..79d622c 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -33,6 +33,7 @@ import java.io.IOException;
 import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
+import java.util.Locale;
 import java.util.Map;
 
 import javax.swing.JInternalFrame;
@@ -159,8 +160,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertNotNull(
             ColourSchemeProperty.getColourScheme(viewport,
                     viewport.getAlignment(),
-                    viewport.getGlobalColourScheme()
-                            .getSchemeName()),
+                    viewport.getGlobalColourScheme().getSchemeName()),
             "Recognise T-Coffee score from string");
 
     af.saveAlignment(tfile, FileFormat.Jalview);
@@ -449,9 +449,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Assert.assertEquals(Desktop.getAlignFrames().length,
             Desktop.getAlignmentPanels(
                     af.getViewport().getSequenceSetId()).length);
-    Assert.assertEquals(
-            Desktop.getAlignmentPanels(
-                    af.getViewport().getSequenceSetId()).length,
+    Assert.assertEquals(Desktop
+            .getAlignmentPanels(af.getViewport().getSequenceSetId()).length,
             oldviews);
   }
 
@@ -804,6 +803,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase
               "Mismatch PDBEntry 'Type'");
       Assert.assertNotNull(recov.getFile(),
               "Recovered PDBEntry should have a non-null file entry");
+      Assert.assertEquals(
+              recov.getFile().toLowerCase(Locale.ENGLISH)
+                      .lastIndexOf("pdb"),
+              recov.getFile().length() - 3,
+              "Recovered PDBEntry file should have PDB suffix");
     }
   }
 
@@ -1035,7 +1039,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertEquals(fr.getFeatureFilter("type2").toStableString(),
             "(Score LE 2.4) AND (Score GT 1.1)");
     assertEquals(fr.getFeatureFilter("type3").toStableString(),
-            "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)");
+            "(AF Contains X) OR (CSQ:PolyPhen NE 0)");
   }
 
   private void addFeature(SequenceI seq, String featureType, int score)
@@ -1205,7 +1209,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
             DataSourceType.PASTE);
     assertNotNull(af, "Didn't read in the example file correctly.");
-  
+
     AlignmentViewPanel ap = Desktop.getAlignmentPanels(null)[0];
     SequenceI pep = ap.getAlignment().getSequenceAt(0);
     SequenceI cds = ap.getAlignment().getSequenceAt(1);
@@ -1237,7 +1241,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       Assert.fail("Didn't save the state", e);
     }
     Desktop.instance.closeAll_actionPerformed(null);
-  
+
     new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
             DataSourceType.FILE);
     AlignmentViewPanel rap = Desktop.getAlignmentPanels(null)[0];