JAL-3210 task jalviewjsIDE_checkJ2sPlugin compares installed net.sf.j2s.core with...

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

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 5f1256c..0609ee5 100644 (file)
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -51,7 +51,6 @@ import jalview.gui.AlignFrame;
 import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
-import jalview.gui.FeatureRenderer;
 import jalview.gui.JvOptionPane;
 import jalview.gui.PCAPanel;
 import jalview.gui.PopupMenu;
@@ -74,6 +73,7 @@ import jalview.structure.StructureImportSettings;
 import jalview.util.MapList;
 import jalview.util.matcher.Condition;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
 
 import java.awt.Color;
 import java.io.File;
@@ -119,7 +119,8 @@ 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 +162,8 @@ 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 +209,8 @@ 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;
@@ -842,13 +845,16 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     /*
      * create a group with Strand colouring, 30% Conservation
      * and 40% PID threshold
+     * (notice menu action applies to selection group even if mouse click
+     * is at a sequence not in the group)
      */
     SequenceGroup sg = new SequenceGroup();
     sg.addSequence(al.getSequenceAt(0), false);
     sg.setStartRes(15);
     sg.setEndRes(25);
     av.setSelectionGroup(sg);
-    PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null);
+    PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(2),
+            null);
     popupMenu.changeColour_actionPerformed(
             JalviewColourScheme.Strand.toString());
     assertTrue(sg.getColourScheme() instanceof StrandColourScheme);
@@ -924,7 +930,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     /*
      * set colour schemes for features
      */
-    FeatureRenderer fr = af.getFeatureRenderer();
+    FeatureRendererModel fr = af.getFeatureRenderer();
     fr.findAllFeatures(true);
 
     // type1: red
@@ -985,7 +991,8 @@ 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.");
 
     /*
@@ -1235,7 +1242,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     AlignmentViewPanel rap = Desktop.getAlignmentPanels(null)[0];
     SequenceI rpep = rap.getAlignment().getSequenceAt(0);
     assertEquals(rpep.getName(), "P30419");
-    DBRefEntry[] dbrefs = rpep.getDBRefs();
+    DBRefEntry[] dbrefs = (DBRefEntry[]) rpep.getDBRefs().toArray();
     assertEquals(dbrefs.length, 3);
     DBRefEntry dbRef = dbrefs[0];
     assertFalse(dbRef instanceof GeneLocus);