Merge branch 'develop' into spike/JAL-4047/JAL-4048_columns_in_sequenceID

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

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index c0038a1..1b62ce3 100644 (file)
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -24,6 +24,15 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.io.File;
+import java.util.List;
+
+import org.junit.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -32,19 +41,11 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.features.SequenceFeatures;
 import jalview.gui.AlignFrame;
+import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
 import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureImportSettings.StructureParser;
 
-import java.io.File;
-import java.util.List;
-
-import org.junit.Assert;
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
 public class AnnotatedPDBFileInputTest
 {
 
@@ -116,7 +117,7 @@ public class AnnotatedPDBFileInputTest
         if (StructureImportSettings.getDefaultPDBFileParser()
                 .equals(StructureParser.JALVIEW_PARSER))
         {
-          assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+          assertTrue(mc_view.PDBfile.isCalcIdForFile(aa, pdbId));
         }
       }
     }
@@ -182,10 +183,9 @@ public class AnnotatedPDBFileInputTest
             break;
           }
         }
-        assertTrue(
-                "Couldn't find sequence associated annotation "
-                        + aa.label
-                        + " on the sequence it is associated with.\nSequence associated editing will fail.",
+        assertTrue("Couldn't find sequence associated annotation "
+                + aa.label
+                + " on the sequence it is associated with.\nSequence associated editing will fail.",
                 found);
       }
     }
@@ -197,8 +197,9 @@ public class AnnotatedPDBFileInputTest
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    jalview.bin.Jalview.main(new String[] { "-props",
-        "test/jalview/io/testProps.jvprops" });
+    jalview.bin.Jalview
+            .main(new String[]
+            { "-props", "test/jalview/io/testProps.jvprops" });
   }
 
   /**
@@ -207,8 +208,8 @@ public class AnnotatedPDBFileInputTest
   @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
-    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
-
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
   }
 
   @Test(groups = { "Functional" })
@@ -218,11 +219,12 @@ public class AnnotatedPDBFileInputTest
     String inFile = "examples/1gaq.txt";
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
-    AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
-            inFile, DataSourceType.FILE);
+    AlignFrame af = new jalview.io.FileLoader()
+            .LoadFileWaitTillLoaded(inFile, DataSourceType.FILE);
     assertTrue("Didn't read input file " + inFile, af != null);
+    af.saveAlignment(tfile, FileFormat.Jalview);
     assertTrue("Failed to store as a project.",
-            af.saveAlignment(tfile, FileFormat.Jalview));
+            af.isSaveAlignmentSuccessful());
     af.closeMenuItem_actionPerformed(true);
     af = null;
     af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
@@ -236,21 +238,21 @@ public class AnnotatedPDBFileInputTest
         sq = sq.getDatasetSequence();
       }
       assertNotNull(sq.getAllPDBEntries());
-      assertEquals("Expected only one PDB ID", 1, sq.getAllPDBEntries()
-              .size());
+      assertEquals("Expected only one PDB ID", 1,
+              sq.getAllPDBEntries().size());
       for (PDBEntry pdbentry : sq.getAllPDBEntries())
       {
-        System.err.println("PDB Entry " + pdbentry.getId() + " "
-                + pdbentry.getFile());
+        System.err.println(
+                "PDB Entry " + pdbentry.getId() + " " + pdbentry.getFile());
         boolean exists = false, found = false;
         for (AlignmentAnnotation ana : sq.getAnnotation())
         {
           System.err.println("CalcId " + ana.getCalcId());
           if (ana.getCalcId() != null
-                  && MCview.PDBfile.isCalcIdHandled(ana.getCalcId()))
+                  && mc_view.PDBfile.isCalcIdHandled(ana.getCalcId()))
           {
             exists = true;
-            if (MCview.PDBfile.isCalcIdForFile(ana, pdbentry.getId()))
+            if (mc_view.PDBfile.isCalcIdForFile(ana, pdbentry.getId()))
             {
               found = true;
             }
@@ -258,8 +260,10 @@ public class AnnotatedPDBFileInputTest
         }
         if (exists)
         {
-          assertTrue("Couldn't find any annotation for " + pdbentry.getId()
-                  + " (file handle " + pdbentry.getFile() + ")", found);
+          assertTrue(
+                  "Couldn't find any annotation for " + pdbentry.getId()
+                          + " (file handle " + pdbentry.getFile() + ")",
+                  found);
         }
       }
     }