Merge branch 'Jalview-JS/jim/JAL-3253-JAL-3418' into Jalview-JS/JAL-3253-applet

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

diff --git a/test/jalview/io/AnnotatedPDBFileInputTest.java b/test/jalview/io/AnnotatedPDBFileInputTest.java
index e14a478..beeb52f 100644 (file)
--- a/test/jalview/io/AnnotatedPDBFileInputTest.java
+++ b/test/jalview/io/AnnotatedPDBFileInputTest.java
@@ -39,6 +39,7 @@ 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;
@@ -67,9 +68,9 @@ public class AnnotatedPDBFileInputTest
   @BeforeMethod(alwaysRun = true)
   public void setup() throws Exception
   {
-    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+    Cache.setPropertyNoSave("STRUCT_FROM_PDB",
             Boolean.TRUE.toString());
-    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+    Cache.setPropertyNoSave("ADD_SS_ANN",
             Boolean.TRUE.toString());
     FileLoader loader = new FileLoader(false);
     AlignFrame af = loader.LoadFileWaitTillLoaded("examples/1gaq.txt",
@@ -101,20 +102,21 @@ public class AnnotatedPDBFileInputTest
     }
   }
 
-  @Test(groups = { "Functional" })
+  @Test(groups = { "Functional" }, enabled = false)
   public void checkPDBannotationSource()
   {
-
+    Assert.fail(
+            "This test is incorrect - does not verify that JmolParser's annotation rows can be recognised as generated by the Jmol parser.");
     for (SequenceI asq : al.getSequences())
     {
       for (AlignmentAnnotation aa : asq.getAnnotation())
       {
 
         System.out.println("CalcId: " + aa.getCalcId());
-        if (StructureImportSettings.getDefaultPDBFileParser().equals(
-                StructureParser.JALVIEW_PARSER))
+        if (StructureImportSettings.getDefaultPDBFileParser()
+                .equals(StructureParser.JALVIEW_PARSER))
         {
-          assertTrue(MCview.PDBfile.isCalcIdForFile(aa, pdbId));
+          assertTrue(mc_view.PDBfile.isCalcIdForFile(aa, pdbId));
         }
       }
     }
@@ -205,7 +207,7 @@ public class AnnotatedPDBFileInputTest
   @AfterClass(alwaysRun = true)
   public static void tearDownAfterClass() throws Exception
   {
-    jalview.gui.Desktop.instance.closeAll_actionPerformed(null);
+    jalview.gui.Desktop.getInstance().closeAll_actionPerformed(null);
 
   }
 
@@ -219,8 +221,9 @@ public class AnnotatedPDBFileInputTest
     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,
@@ -245,10 +248,10 @@ public class AnnotatedPDBFileInputTest
         {
           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;
             }