X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FStructureChooserTest.java;h=bad536b291e570916bcd51bb8c1ff42e3469a8b2;hb=33ad2b9a53a0e7faec7afddf91de829d98df07bc;hp=1b00c4aff8a513de73739b832aeb6f111b424dda;hpb=8f118c154e74caaef6bec19acd0466904ac424d4;p=jalview.git

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index 1b00c4a..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;
@@ -70,9 +71,36 @@ public class StructureChooserTest
   public void buildQueryTest()
   {
     String query = StructureChooser.buildQuery(seq);
-    System.out.println(">>>>>>>>>> query : " + query);
+    assertEquals("pdb_id:1tim", query);
+    System.out.println("seq >>>> " + seq);
+    seq.getAllPDBEntries().clear();
+    query = StructureChooser.buildQuery(seq);
     assertEquals(
-            "4kqy OR text:1tim OR text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4",
+            "text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4 OR text:4kqy",
+            query);
+    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);
   }
 
@@ -88,6 +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
@@ -103,4 +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));
+  }
 }