Merge branch 'develop' into feature/JAL-3390hideUnmappedStructure

[jalview.git] / test / jalview / project / Jalview2xmlTests.java

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 5182ad4..eb66416 100644 (file)
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -27,6 +27,21 @@ import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
 
+import java.awt.Color;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.JInternalFrame;
+
+import org.testng.Assert;
+import org.testng.AssertJUnit;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.analysis.scoremodels.SimilarityParams;
 import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
@@ -40,6 +55,7 @@ import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.Mapping;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.Sequence.DBModList;
 import jalview.datamodel.SequenceCollectionI;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
@@ -75,21 +91,6 @@ import jalview.util.matcher.Condition;
 import jalview.viewmodel.AlignmentViewport;
 import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
-import java.awt.Color;
-import java.io.File;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.swing.JInternalFrame;
-
-import org.testng.Assert;
-import org.testng.AssertJUnit;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 @Test(singleThreaded = true)
 public class Jalview2xmlTests extends Jalview2xmlBase
 {
@@ -119,7 +120,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             af.getViewport()
                     .getGlobalColourScheme() instanceof RNAHelicesColour,
             "Couldn't apply RNA helices colourscheme");
-    assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
+    af.saveAlignment(tfile, FileFormat.Jalview);
+    assertTrue(af.isSaveAlignmentSuccessful(),
             "Failed to store as a project.");
     af.closeMenuItem_actionPerformed(true);
     af = null;
@@ -161,7 +163,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
                             .getSchemeName()),
             "Recognise T-Coffee score from string");
 
-    assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
+    af.saveAlignment(tfile, FileFormat.Jalview);
+    assertTrue(af.isSaveAlignmentSuccessful(),
             "Failed to store as a project.");
     af.closeMenuItem_actionPerformed(true);
     af = null;
@@ -207,7 +210,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false);
     sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true);
     af.alignPanel.alignmentChanged();
-    assertTrue(af.saveAlignment(tfile, FileFormat.Jalview),
+    af.saveAlignment(tfile, FileFormat.Jalview);
+    assertTrue(af.isSaveAlignmentSuccessful(),
             "Failed to store as a project.");
     af.closeMenuItem_actionPerformed(true);
     af = null;
@@ -988,7 +992,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     File tfile = File.createTempFile("JalviewTest", ".jvp");
     tfile.deleteOnExit();
     String filePath = tfile.getAbsolutePath();
-    assertTrue(af.saveAlignment(filePath, FileFormat.Jalview),
+    af.saveAlignment(filePath, FileFormat.Jalview);
+    assertTrue(af.isSaveAlignmentSuccessful(),
             "Failed to store as a project.");
 
     /*
@@ -1030,7 +1035,7 @@ 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)
@@ -1237,10 +1242,10 @@ public class Jalview2xmlTests extends Jalview2xmlBase
             DataSourceType.FILE);
     AlignmentViewPanel rap = Desktop.getAlignmentPanels(null)[0];
     SequenceI rpep = rap.getAlignment().getSequenceAt(0);
+    DBModList<DBRefEntry> dbrefs = rpep.getDBRefs();
     assertEquals(rpep.getName(), "P30419");
-    DBRefEntry[] dbrefs = rpep.getDBRefs();
-    assertEquals(dbrefs.length, 3);
-    DBRefEntry dbRef = dbrefs[0];
+    assertEquals(dbrefs.size(), 3);
+    DBRefEntry dbRef = dbrefs.get(0);
     assertFalse(dbRef instanceof GeneLocus);
     assertNull(dbRef.getMap());
     assertEquals(dbRef, dbref1);
@@ -1249,7 +1254,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
      * restored dbrefs with mapping have a different 'map to'
      * sequence but otherwise match the original dbrefs
      */
-    dbRef = dbrefs[1];
+    dbRef = dbrefs.get(1);
     assertFalse(dbRef instanceof GeneLocus);
     assertTrue(dbRef.equalRef(dbref2));
     assertNotNull(dbRef.getMap());
@@ -1261,7 +1266,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     /*
      * GeneLocus map.to is null so can compare Mapping objects
      */
-    dbRef = dbrefs[2];
+    dbRef = dbrefs.get(2);
     assertTrue(dbRef instanceof GeneLocus);
     assertEquals(dbRef, dbref3);
   }