From: James Procter <j.procter@dundee.ac.uk>
Date: Fri, 9 Jun 2023 15:38:21 +0000 (+0100)
Subject: JAL-4041 failing tests to verify we can resolve mixture of 3d-beacons and non-3d... 
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e4c2a9483a41740a85c95ffbf014e23f9afe79f6;p=jalview.git

JAL-4041 failing tests to verify we can resolve mixture of 3d-beacons and non-3d-beacons based sequences in structure chooser
---

diff --git a/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java b/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
index c21add1..39ca0f6 100644
--- a/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
+++ b/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
@@ -60,6 +60,8 @@ public class StructureChooserQuerySourceTest
 
   private Sequence upSeq_fer1_maize;
 
+  private Sequence noUpSeq_fer1_maize;
+
   // same set up as for structurechooser test
 
   @BeforeMethod(alwaysRun = true)
@@ -237,6 +239,9 @@ public class StructureChooserQuerySourceTest
     upSeq_fer1_maize
             .addDBRef(new DBRefEntry("UNIPROT", "0", "P27787", null, true));
     upSeq_fer1_maize.createDatasetSequence();
+    noUpSeq_fer1_maize = new Sequence("O80429_MAIZE","MAATALSMSILRAPPPCFSSPLRLRVAVAKPLAAPMRRQLLRAQATYNVKLITPEGEVELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDVVIETHKEDDLL");
+    noUpSeq_fer1_maize.setDescription("Feredoxin from a Maize");
+    noUpSeq_fer1_maize.createDatasetSequence();
 
   }
 
@@ -247,6 +252,8 @@ public class StructureChooserQuerySourceTest
     upSeq = null;
     upSeq_r1ab = null;
     upSeq_fer1_maize = null;
+    noUpSeq_fer1_maize = null;
+
   }
 
   @SuppressWarnings("deprecation")
@@ -452,13 +459,22 @@ public class StructureChooserQuerySourceTest
             { testUpSeq });
 
   }
+  
+  @Test
+  public void testTdbWithNoUpSeq()
+  {
+    // verify that a 
+    ThreeDBStructureChooserQuerySource tdbquery = new ThreeDBStructureChooserQuerySource();
+
+    Assert.fail("Not yet implemented.");
+  }
 
   @DataProvider(name = "testUpSeqs")
   public Object[][] testUpSeqs() throws Exception
   {
     setUp();
     return new Object[][] { { upSeq }, { upSeq_insulin }, { upSeq_r1ab },
-        { upSeq_fer1_maize } };
+        { upSeq_fer1_maize }, {noUpSeq_fer1_maize }};
   }
 
   @Test(groups = { "Functional" })