X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=test%2Fjalview%2Fgui%2FStructureChooserTest.java;h=bad536b291e570916bcd51bb8c1ff42e3469a8b2;hb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;hp=28b9b83b434956f922b396c79b6e0abcf972542c;hpb=639715a37f34db96f6149ef25efd395398ecfbeb;p=jalview.git

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index 28b9b83..bad536b 100644
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -24,6 +24,7 @@ import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
@@ -60,7 +61,7 @@ public class StructureChooserTest
     seq.setPDBId(pdbIds);
   }
 
-  @AfterMethod
+  @AfterMethod(alwaysRun = true)
   public void tearDown() throws Exception
   {
     seq = null;
@@ -80,6 +81,27 @@ public class StructureChooserTest
     seq.setDBRefs(null);
     query = StructureChooser.buildQuery(seq);
     assertEquals("text:4kqy", query);
+
+    DBRefEntry uniprotDBRef = new DBRefEntry();
+    uniprotDBRef.setAccessionId("P12345");
+    uniprotDBRef.setSource(DBRefSource.UNIPROT);
+    seq.addDBRef(uniprotDBRef);
+
+    DBRefEntry pdbDBRef = new DBRefEntry();
+    pdbDBRef.setAccessionId("1XYZ");
+    pdbDBRef.setSource(DBRefSource.PDB);
+    seq.addDBRef(pdbDBRef);
+
+    for (int x = 1; x < 5; x++)
+    {
+      DBRefEntry dbRef = new DBRefEntry();
+      dbRef.setAccessionId("XYZ_" + x);
+      seq.addDBRef(dbRef);
+    }
+    query = StructureChooser.buildQuery(seq);
+    assertEquals(
+            "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
+            query);
   }
 
   @Test(groups = { "Functional" })
@@ -94,6 +116,13 @@ public class StructureChooserTest
 
     sc.setStructuresDiscovered(true);
     sc.populateFilterComboBox();
+    try
+    {
+      Thread.sleep(2000);
+    } catch (InterruptedException e)
+    {
+      e.printStackTrace();
+    }
     optionsSize = sc.getCmbFilterOption().getItemCount();
     assertTrue(optionsSize > 3); // if structures are found, filter options
                                  // should be populated
@@ -109,4 +138,22 @@ public class StructureChooserTest
     assertTrue(sc.getDiscoveredStructuresSet().size() > 0);
 
   }
+
+  @Test(groups = { "Functional" })
+  public void sanitizeSeqNameTest()
+  {
+    String name = "ab_cdEF|fwxyz012349";
+    assertEquals(name, StructureChooser.sanitizeSeqName(name));
+
+    // remove a [nn] substring
+    name = "abcde12[345]fg";
+    assertEquals("abcde12fg", StructureChooser.sanitizeSeqName(name));
+
+    // remove characters other than a-zA-Z0-9 | or _
+    name = "ab[cd],.\t£$*!- \\\"@:e";
+    assertEquals("abcde", StructureChooser.sanitizeSeqName(name));
+
+    name = "abcde12[345a]fg";
+    assertEquals("abcde12345afg", StructureChooser.sanitizeSeqName(name));
+  }
 }