Merge branch 'feature/JAL-1713_overviewInProject' into bug/JAL-3785autoOverviewTitle

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

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 42d68a9..783dd1c 100644 (file)
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -23,11 +23,13 @@ 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;
 
 import java.awt.Color;
+import java.awt.Rectangle;
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
@@ -48,6 +50,7 @@ import jalview.api.AlignViewportI;
 import jalview.api.AlignmentViewPanel;
 import jalview.api.FeatureColourI;
 import jalview.api.ViewStyleI;
+import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
@@ -69,8 +72,10 @@ import jalview.gui.AlignViewport;
 import jalview.gui.AlignmentPanel;
 import jalview.gui.Desktop;
 import jalview.gui.JvOptionPane;
+import jalview.gui.OverviewPanel;
 import jalview.gui.PCAPanel;
 import jalview.gui.PopupMenu;
+import jalview.gui.Preferences;
 import jalview.gui.SliderPanel;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
@@ -160,8 +165,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertNotNull(
             ColourSchemeProperty.getColourScheme(viewport,
                     viewport.getAlignment(),
-                    viewport.getGlobalColourScheme()
-                            .getSchemeName()),
+                    viewport.getGlobalColourScheme().getSchemeName()),
             "Recognise T-Coffee score from string");
 
     af.saveAlignment(tfile, FileFormat.Jalview);
@@ -450,9 +454,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Assert.assertEquals(Desktop.getAlignFrames().length,
             Desktop.getAlignmentPanels(
                     af.getViewport().getSequenceSetId()).length);
-    Assert.assertEquals(
-            Desktop.getAlignmentPanels(
-                    af.getViewport().getSequenceSetId()).length,
+    Assert.assertEquals(Desktop
+            .getAlignmentPanels(af.getViewport().getSequenceSetId()).length,
             oldviews);
   }
 
@@ -1207,7 +1210,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData,
             DataSourceType.PASTE);
     assertNotNull(af, "Didn't read in the example file correctly.");
-  
+
     AlignmentViewPanel ap = Desktop.getAlignmentPanels(null)[0];
     SequenceI pep = ap.getAlignment().getSequenceAt(0);
     SequenceI cds = ap.getAlignment().getSequenceAt(1);
@@ -1239,7 +1242,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       Assert.fail("Didn't save the state", e);
     }
     Desktop.instance.closeAll_actionPerformed(null);
-  
+
     new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
             DataSourceType.FILE);
     AlignmentViewPanel rap = Desktop.getAlignmentPanels(null)[0];
@@ -1272,4 +1275,117 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertTrue(dbRef instanceof GeneLocus);
     assertEquals(dbRef, dbref3);
   }
+
+  /**
+   * test store and recovery of Overview windows
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" }, enabled = true)
+  public void testStoreAndRecoverOverview() throws Exception
+  {
+    Desktop.instance.closeAll_actionPerformed(null);
+
+    Cache.setProperty("SHOW_OVERVIEW", "false");
+    Cache.setProperty(Preferences.USE_LEGACY_GAP, "false");
+    Cache.setColourProperty(Preferences.GAP_COLOUR, Color.green);
+    Cache.setColourProperty(Preferences.HIDDEN_COLOUR, Color.yellow);
+    Cache.setProperty(Preferences.SHOW_OV_HIDDEN_AT_START, "true");
+
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+
+    /*
+     * open and resize / reposition overview 
+     */
+    af.overviewMenuItem_actionPerformed(null);
+    OverviewPanel ov1 = af.alignPanel.getOverviewPanel();
+    assertNotNull(ov1);
+    ov1.setFrameBounds(20, 30, 200, 400);
+    assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa");
+    assertTrue(ov1.isShowHiddenRegions());
+
+    /*
+     * open a New View and its Overview and reposition it
+     */
+    af.newView_actionPerformed(null);
+    af.overviewMenuItem_actionPerformed(null);
+    OverviewPanel ov2 = af.alignPanel.getOverviewPanel();
+    assertNotNull(ov2);
+    assertNotSame(ov1, ov2);
+    ov2.setFrameBounds(25, 35, 205, 405);
+    assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original");
+    assertEquals(ov2.getTitle(), "Overview examples/uniref50.fa View 1");
+
+    File tfile = File.createTempFile("testStoreAndRecoverOverview", ".jvp");
+    new Jalview2XML(false).saveState(tfile);
+    Desktop.instance.closeAll_actionPerformed(null);
+
+    /*
+     * change preferences (should _not_ affect reloaded Overviews)
+     */
+    Cache.setProperty("SHOW_OVERVIEW", "true");
+    Cache.setProperty(Preferences.USE_LEGACY_GAP, "true");
+    Cache.setColourProperty(Preferences.GAP_COLOUR, Color.blue);
+    Cache.setColourProperty(Preferences.HIDDEN_COLOUR, Color.orange);
+    Cache.setProperty(Preferences.SHOW_OV_HIDDEN_AT_START, "false");
+
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            DataSourceType.FILE);
+
+    /*
+     * workaround: explicitly select View 1 (not in focus after restore)
+     */
+    af.tabSelectionChanged(1);
+
+    /*
+     * verify restored overview for View 1
+     */
+    ov2 = af.alignPanel.getOverviewPanel();
+    assertEquals(ov2.getCanvas().getGapColour(), Color.green);
+    // 'non-legacy' colouring uses white for non-gapped residues
+    assertEquals(ov2.getCanvas().getResidueColour(), Color.white);
+    assertEquals(ov2.getCanvas().getHiddenColour(), Color.yellow);
+    assertEquals(ov2.getTitle(), "Overview examples/uniref50.fa View 1");
+    assertEquals(ov2.getFrameBounds(), new Rectangle(25, 35, 205, 405));
+    assertTrue(ov2.isShowHiddenRegions());
+
+    /*
+     * verify restored overview for Original view
+     */
+    af.tabSelectionChanged(0);
+    ov1 = af.alignPanel.getOverviewPanel();
+    assertEquals(ov1.getCanvas().getGapColour(), Color.green);
+    // 'non-legacy' colouring uses white for non-gapped residues
+    assertEquals(ov1.getCanvas().getResidueColour(), Color.white);
+    assertEquals(ov1.getCanvas().getHiddenColour(), Color.yellow);
+    assertEquals(ov1.getTitle(), "Overview examples/uniref50.fa Original");
+    assertEquals(ov1.getFrameBounds(), new Rectangle(20, 30, 200, 400));
+    assertTrue(ov1.isShowHiddenRegions());
+  }
+
+  /**
+   * Test that a view with no Overview is restored with no Overview, even if
+   * 'Open Overview' is selected in Preferences
+   * 
+   * @throws Exception
+   */
+  @Test(groups = { "Functional" }, enabled = true)
+  public void testStoreAndRecoverNoOverview() throws Exception
+  {
+    Cache.setProperty("SHOW_OVERVIEW", "false");
+    Desktop.instance.closeAll_actionPerformed(null);
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            ">seq1\nMATRSQFLVNF\n", DataSourceType.PASTE);
+
+    File tfile = File.createTempFile("testStoreAndRecoverOverview", ".jvp");
+    new Jalview2XML(false).saveState(tfile);
+    Desktop.instance.closeAll_actionPerformed(null);
+
+    Cache.setProperty("SHOW_OVERVIEW", "true");
+    af = new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(),
+            DataSourceType.FILE);
+
+    assertNull(af.alignPanel.getOverviewPanel());
+  }
 }