Merge branch 'develop' into trialMerge

[jalview.git] / test / jalview / gui / AlignViewportTest.java

diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 341a814..d6b2454 100644 (file)
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -35,10 +35,14 @@ 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.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;
 import jalview.util.MapList;
 
@@ -136,7 +140,7 @@ 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();
@@ -185,9 +189,9 @@ 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);
@@ -248,9 +252,9 @@ 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);
@@ -317,7 +321,7 @@ 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);
@@ -329,4 +333,44 @@ public class AlignViewportTest
     assertNotNull("Quality in column 1 is null", annotations[0]);
     assertTrue("No quality value in column 1", annotations[0].value > 10f);
   }
+
+  @Test(groups = { "Functional" })
+  public void testSetGlobalColourScheme()
+  {
+    /*
+     * test for JAL-2283 don't inadvertently turn on colour by conservation
+     */
+    Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "NONE");
+    Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+            Boolean.TRUE.toString());
+    AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+            "examples/uniref50.fa", DataSourceType.FILE);
+    ColourSchemeI cs = new PIDColourScheme();
+    af.getViewport().setGlobalColourScheme(cs);
+    assertFalse(cs.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());
+  }
 }