X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=06df70ab6c7aa972572f6b1f214d1e24e69bd478;hb=14985603cea28569e295ddabb219da8034f1c7b2;hp=3a60a72677fb7f44c677e3ff5fefb1c9d9fd0134;hpb=3ab582bfeeab1563bedf60e97994e63e672d2e31;p=jalview.git

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 3a60a72..06df70a 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -35,10 +35,13 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SearchResultsI;
 import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.io.DataSourceType;
 import jalview.io.FileLoader;
-import jalview.io.FormatAdapter;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.PIDColourScheme;
 import jalview.structure.StructureSelectionManager;
@@ -54,6 +57,13 @@ import org.testng.annotations.Test;
 public class AlignViewportTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   AlignmentI al;
 
   AlignViewport testee;
@@ -61,7 +71,8 @@ public class AlignViewportTest
   @BeforeClass(alwaysRun = true)
   public static void setUpBeforeClass() throws Exception
   {
-    Jalview.main(new String[] { "-props", "test/jalview/testProps.jvprops" });
+    Jalview.main(new String[] { "-nonews", "-props",
+        "test/jalview/testProps.jvprops" });
   }
 
   @BeforeMethod(alwaysRun = true)
@@ -138,7 +149,7 @@ public class AlignViewportTest
      * alignment with reference to mappings
      */
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
-            ">Seq1\nCAGT\n", FormatAdapter.PASTE);
+            ">Seq1\nCAGT\n", DataSourceType.PASTE);
 
     SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
     AlignedCodonFrame acf1 = new AlignedCodonFrame();
@@ -187,9 +198,9 @@ public class AlignViewportTest
     ssm.resetAll();
 
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
-            ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
+            ">Seq1\nRSVQ\n", DataSourceType.PASTE);
     AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
-            ">Seq2\nDGEL\n", FormatAdapter.PASTE);
+            ">Seq2\nDGEL\n", DataSourceType.PASTE);
     SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
     SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
     SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
@@ -250,9 +261,9 @@ public class AlignViewportTest
     ssm.resetAll();
 
     AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
-            ">Seq1\nRSVQ\n", FormatAdapter.PASTE);
+            ">Seq1\nRSVQ\n", DataSourceType.PASTE);
     AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
-            ">Seq2\nDGEL\n", FormatAdapter.PASTE);
+            ">Seq2\nDGEL\n", DataSourceType.PASTE);
     SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
     SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
     SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
@@ -319,7 +330,7 @@ public class AlignViewportTest
     Cache.applicationProperties.setProperty("SHOW_IDENTITY",
             Boolean.FALSE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/uniref50.fa", FormatAdapter.FILE);
+            "examples/uniref50.fa", DataSourceType.FILE);
     AlignmentAnnotation[] anns = af.viewport.getAlignment()
             .getAlignmentAnnotation();
     assertNotNull("No annotations found", anns);
@@ -336,15 +347,61 @@ public class AlignViewportTest
   public void testSetGlobalColourScheme()
   {
     /*
-     * test for JAL-2283 don't inadvertently turn on colour by conservation
+     * test for JAL-2283: don't inadvertently turn on colour by conservation
      */
-    Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "NONE");
+    Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "None");
     Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
             Boolean.TRUE.toString());
     AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
-            "examples/uniref50.fa", FormatAdapter.FILE);
+            "examples/uniref50.fa", DataSourceType.FILE);
     ColourSchemeI cs = new PIDColourScheme();
     af.getViewport().setGlobalColourScheme(cs);
-    assertFalse(cs.conservationApplied());
+    assertFalse(af.getViewport().getResidueShading()
+            .conservationApplied());
+  }
+
+  @Test(groups = { "Functional" })
+  public void testSetGetHasSearchResults()
+  {
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+    SearchResultsI sr = new SearchResults();
+    SequenceI s1 = af.getViewport().getAlignment().getSequenceAt(0);
+
+    // create arbitrary range on first sequence
+    sr.addResult(s1, s1.getStart() + 10, s1.getStart() + 15);
+
+    // test set
+    af.getViewport().setSearchResults(sr);
+    // has -> true
+    assertTrue(af.getViewport().hasSearchResults());
+    // get == original
+    assertEquals(sr, af.getViewport().getSearchResults());
+
+    // set(null) results in has -> false
+
+    af.getViewport().setSearchResults(null);
+    assertFalse(af.getViewport().hasSearchResults());
+  }
+
+  /**
+   * Verify that setting the selection group has the side-effect of setting the
+   * context on the group, unless it already has one
+   */
+  @Test(groups = { "Functional" })
+  public void testSetSelectionGroup()
+  {
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+    AlignViewport av = af.getViewport();
+    SequenceGroup sg1 = new SequenceGroup();
+    SequenceGroup sg2 = new SequenceGroup();
+
+    av.setSelectionGroup(sg1);
+    assertSame(sg1.getContext(), av.getAlignment()); // context set
+
+    sg2.setContext(sg1);
+    av.setSelectionGroup(sg2);
+    assertSame(sg2.getContext(), sg1); // unchanged
   }
 }