Merge branch 'develop' into trialMerge

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

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index f3504e9..d8ae999 100644 (file)
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -31,7 +31,9 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.gui.JvOptionPane;
 import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
 
 import java.io.File;
 
@@ -43,6 +45,13 @@ import org.testng.annotations.Test;
 public class AnnotatedPDBFileInputTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   AlignmentI al;
 
   String pdbId;
@@ -62,7 +71,7 @@ public class AnnotatedPDBFileInputTest
             Boolean.TRUE.toString());
     FileLoader loader = new FileLoader(false);
     AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
-            FormatAdapter.FILE);
+            DataSourceType.FILE);
     al = af.getViewport().getAlignment();
     pdbId = al.getSequenceAt(0).getDatasetSequence().getAllPDBEntries()
             .get(0).getId();
@@ -84,8 +93,8 @@ 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]);
       }
     }
   }
@@ -100,11 +109,11 @@ public class AnnotatedPDBFileInputTest
       {
 
         System.out.println("CalcId: " + aa.getCalcId());
-        // if (StructureImportSettings.getDefaultPDBFileParser().equals(
-        // StructureParser.JALVIEW_PARSER))
-        // {
-        // assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
-        // }
+        if (StructureImportSettings.getDefaultPDBFileParser().equals(
+                StructureParser.JALVIEW_PARSER))
+        {
+          assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+        }
       }
     }
   }
@@ -203,14 +212,14 @@ public class AnnotatedPDBFileInputTest
     String tfile = File.createTempFile("JalviewTest", ".jvp")
             .getAbsolutePath();
     AlignFrame af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(
-            inFile, FormatAdapter.FILE);
+            inFile, DataSourceType.FILE);
     assertTrue("Didn't read input file " + inFile, af != null);
     assertTrue("Failed to store as a project.",
-            af.saveAlignment(tfile, "Jalview"));
+            af.saveAlignment(tfile, FileFormat.Jalview));
     af.closeMenuItem_actionPerformed(true);
     af = null;
     af = new jalview.io.FileLoader().LoadFileWaitTillLoaded(tfile,
-            FormatAdapter.FILE);
+            DataSourceType.FILE);
     assertTrue("Failed to import new project", af != null);
     for (SequenceI asq : af.getViewport().getAlignment().getSequences())
     {