From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Thu, 21 Nov 2019 16:37:49 +0000 (+0000)
Subject: JAL-3484 unit test for restoring two views' annotation ordering
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=9e66ffdd391a2467fd6821abf9f8f0ca66e5a18d;p=jalview.git

JAL-3484 unit test for restoring two views' annotation ordering
---

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 3e7279c..d08ae7d 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -23,6 +23,7 @@ package jalview.project;
 import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertFalse;
 import static org.testng.Assert.assertNotNull;
+import static org.testng.Assert.assertNotSame;
 import static org.testng.Assert.assertNull;
 import static org.testng.Assert.assertSame;
 import static org.testng.Assert.assertTrue;
@@ -72,6 +73,7 @@ import jalview.schemes.TCoffeeColourScheme;
 import jalview.structure.StructureImportSettings;
 import jalview.util.matcher.Condition;
 import jalview.viewmodel.AlignmentViewport;
+import jalview.viewmodel.AlignmentViewport.AutoAnnotation;
 
 import java.awt.Color;
 import java.io.File;
@@ -1183,7 +1185,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   }
 
   /**
-   * Test that annotation ordering is faithfully restored
+   * Tests that annotation ordering is faithfully restored, on project reload or
+   * New View, even if preference settings have changed
    * 
    * @throws Exception
    */
@@ -1289,34 +1292,106 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     newPanel.closePanel();
 
     /*
-     * reload the project with Preferences set to not create Occupancy;
-     * this should still appear, as it is in the saved project
+     * reload the project with Preferences set to not create Occupancy, but to
+     * create Quality; annotations should still appear as saved in the project;
+     * preferences should be left unchanged (after temporary override)
      */
     Desktop.instance.closeAll_actionPerformed(null);
     Cache.setProperty("SHOW_OCCUPANCY", "false");
+    Cache.removeProperty("SHOW_QUALITY"); // will default to true
+    Map<String, String> originalPreferences = Cache.getProperties(
+            AutoAnnotation.OCCUPANCY.preferenceKey,
+            AutoAnnotation.CONSERVATION.preferenceKey,
+            AutoAnnotation.QUALITY.preferenceKey,
+            AutoAnnotation.CONSENSUS.preferenceKey);
     af = new FileLoader().LoadFileWaitTillLoaded(
             projectFile.getAbsolutePath(), DataSourceType.FILE);
-    anns = af.getViewport().getAlignment().getAlignmentAnnotation();
+    alignment = af.getViewport().getAlignment();
+    anns = alignment.getAlignmentAnnotation();
     assertEquals(anns.length, 4);
     assertEquals(anns[0].label, "Occupancy");
     assertEquals(anns[1].label, "hello");
     assertEquals(anns[2].label, "Conservation");
     assertEquals(anns[3].label, "world");
+    Map<String, String> newPreferences = Cache.getProperties(
+            AutoAnnotation.OCCUPANCY.preferenceKey,
+            AutoAnnotation.CONSERVATION.preferenceKey,
+            AutoAnnotation.QUALITY.preferenceKey,
+            AutoAnnotation.CONSENSUS.preferenceKey);
+    assertEquals(originalPreferences, newPreferences);
+    assertNull(Cache.getProperty(AutoAnnotation.QUALITY.preferenceKey));
+
+    /*
+     * make a new view, reorder its annotations, and delete and hide 
+     * a different annotation in each of the two views
+     */
+    newPanel = af.newView("new", true);
+    af.getViewport().setViewName("Original");
+    
+    /*
+     * just for interest - new view has the same manual annotation objects,
+     * but new auto-calculated annotations
+     */
+    AlignmentI newAlignment = newPanel.getAlignment();
+    newAnns = newAlignment.getAlignmentAnnotation();
+    assertNotSame(anns[0], newAnns[0]);
+    assertSame(anns[1], newAnns[1]);
+    assertNotSame(anns[2], newAnns[2]);
+    assertSame(anns[3], newAnns[3]);
+
+    alignment.deleteAnnotation(anns[2]); // delete Conservation view 1
+    anns[1].visible = false; // hide 'hello' view 1
+
+    tmp = newAnns[0];
+    newAnns[0] = newAnns[3]; // 'world' moved to top of new view
+    newAnns[3] = tmp; // then hello, Conservation, Occupancy
+    newAnns[0].visible = false; // hide 'world' in new view
+    newAnns[3].graphHeight = 99; // set height of Occupancy
+    newAlignment.deleteAnnotation(newAnns[1]); // delete 'hello' in new view
 
     /*
-     * reload the project with Preferences set to create Quality annotation;
-     * this should not appear, as it is not in the saved project
+     * save, reload and verify annotations in both views
      */
+    ((AlignViewport) newPanel.getAlignViewport()).setViewName("New View");
+    projectFile = File.createTempFile("jvTest", ".jvp");
+    new Jalview2XML(false).saveState(projectFile);
     Desktop.instance.closeAll_actionPerformed(null);
-    Cache.setProperty("SHOW_OCCUPANCY", "false");
-    Cache.setProperty("SHOW_QUALITY", "true");
     af = new FileLoader().LoadFileWaitTillLoaded(
             projectFile.getAbsolutePath(), DataSourceType.FILE);
-    anns = af.getViewport().getAlignment().getAlignmentAnnotation();
-    assertEquals(anns.length, 4);
+    assertEquals(af.getAlignPanels().size(), 2);
+
+    /*
+     * check first view
+     */
+    AlignViewportI firstViewport = af.getAlignPanels().get(0)
+            .getAlignViewport();
+    assertEquals(((AlignViewport) firstViewport).getViewName(), "Original");
+    alignment = firstViewport.getAlignment();
+    anns = alignment.getAlignmentAnnotation();
+    assertEquals(anns.length, 3);
     assertEquals(anns[0].label, "Occupancy");
     assertEquals(anns[1].label, "hello");
-    assertEquals(anns[2].label, "Conservation");
-    assertEquals(anns[3].label, "world");
+    assertEquals(anns[2].label, "world");
+    assertFalse(anns[0].visible);
+    assertFalse(anns[1].visible);
+    assertFalse(anns[2].visible);
+
+    /*
+     * check second view
+     */
+    AlignViewportI secondViewport = af.getAlignPanels().get(1)
+            .getAlignViewport();
+    assertEquals(((AlignViewport) secondViewport).getViewName(),
+            "New View");
+    alignment = secondViewport.getAlignment();
+    anns = alignment.getAlignmentAnnotation();
+    assertEquals(anns.length, 3);
+    assertEquals(anns[0].label, "world");
+    assertEquals(anns[1].label, "Conservation");
+    assertEquals(anns[2].label, "Occupancy");
+    assertFalse(anns[0].visible);
+    assertTrue(anns[1].visible);
+    assertFalse(anns[2].visible);
+    assertEquals(anns[2].graphHeight, 99);
   }
 }