Merge branch 'develop' into bug/JAL-2210_ensembl_uniprot_primaryrefs_alternate

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

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index 44b51f2..1e41a16 100644 (file)
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -1,9 +1,30 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.gui;
 
 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;
@@ -18,12 +39,12 @@ public class StructureChooserTest
 {
   Sequence seq;
 
-  @BeforeMethod
+  @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
   {
     seq = new Sequence("PDB|4kqy|4KQY|A", "ABCDEFGHIJKLMNOPQRSTUVWXYZ", 1,
             26);
-    seq.setDatasetSequence(seq);
+    seq.createDatasetSequence();
     for (int x = 1; x < 5; x++)
     {
       DBRefEntry dbRef = new DBRefEntry();
@@ -40,52 +61,91 @@ public class StructureChooserTest
     seq.setPDBId(pdbIds);
   }
 
-  @AfterMethod
+  @AfterMethod(alwaysRun = true)
   public void tearDown() throws Exception
   {
     seq = null;
   }
 
-
-
-  @Test
+  @Test(groups = { "Functional" })
   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(
+            "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(
-            "4kqy OR text:1tim OR text:XYZ_1 OR text:XYZ_2 OR text:XYZ_3 OR text:XYZ_4",
+            "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
             query);
   }
 
-  @Test
-  public void populateFilterComboBoxTest()
+  @Test(groups = { "Functional" })
+  public void populateFilterComboBoxTest() throws InterruptedException
   {
-    SequenceI[] selectedSeqs = new SequenceI[]
-    { seq };
-    StructureChooser sc = new StructureChooser(selectedSeqs, seq,
-            null);
-    sc.populateFilterComboBox();
+    SequenceI[] selectedSeqs = new SequenceI[] { seq };
+    StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
+    sc.populateFilterComboBox(false);
     int optionsSize = sc.getCmbFilterOption().getItemCount();
     assertEquals(3, optionsSize); // if structures are not discovered then don't
                                   // populate filter options
 
-    sc.setStructuresDiscovered(true);
-    sc.populateFilterComboBox();
+    sc.populateFilterComboBox(true);
     optionsSize = sc.getCmbFilterOption().getItemCount();
     assertTrue(optionsSize > 3); // if structures are found, filter options
                                  // should be populated
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void fetchStructuresInfoTest()
   {
-    SequenceI[] selectedSeqs = new SequenceI[]
-    { seq };
+    SequenceI[] selectedSeqs = new SequenceI[] { seq };
     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
     sc.fetchStructuresMetaData();
     assertTrue(sc.getDiscoveredStructuresSet() != null);
     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));
+  }
 }