X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FStructureChooserTest.java;h=c187c60ef1600b3078ead0b886efe18407bc887f;hb=bf5bc203579d7a291844f3b34d5e8431984ee8e2;hp=4535c93c1b3121e0820e0794d288606bab388e2f;hpb=4dc268e8e7f986a2fd34df2019996e4494ceb74c;p=jalview.git

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index 4535c93..c187c60 100644
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -21,6 +21,7 @@
 package jalview.gui;
 
 import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.datamodel.DBRefEntry;
@@ -28,8 +29,13 @@ import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
-import jalview.jbgui.GStructureChooser.FilterOption;
+import jalview.fts.api.FTSData;
+import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
+import jalview.gui.structurechooser.StructureChooserQuerySource;
+import jalview.jbgui.FilterOption;
+import jalview.ws.params.InvalidArgumentException;
 
+import java.util.Collection;
 import java.util.Vector;
 
 import org.testng.annotations.AfterMethod;
@@ -37,6 +43,8 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import junit.extensions.PA;
+
 public class StructureChooserTest
 {
 
@@ -65,7 +73,7 @@ public class StructureChooserTest
     PDBEntry dbRef = new PDBEntry();
     dbRef.setId("1tim");
 
-    Vector<PDBEntry> pdbIds = new Vector<PDBEntry>();
+    Vector<PDBEntry> pdbIds = new Vector<>();
     pdbIds.add(dbRef);
 
     seq.setPDBId(pdbIds);
@@ -77,19 +85,22 @@ public class StructureChooserTest
     seq = null;
   }
 
+  @SuppressWarnings("deprecation")
   @Test(groups = { "Functional" })
   public void buildQueryTest()
   {
-    String query = StructureChooser.buildQuery(seq);
-    assertEquals("pdb_id:1tim", query);
     System.out.println("seq >>>> " + seq);
+    StructureChooserQuerySource scquery = StructureChooserQuerySource.getPDBfts();
+    String query = scquery.buildQuery(seq);
+    assertEquals("pdb_id:1tim", query);
     seq.getAllPDBEntries().clear();
-    query = StructureChooser.buildQuery(seq);
+    query = scquery.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);
+    query = scquery.buildQuery(seq);
+    System.out.println(query);
     assertEquals("text:4kqy", query);
 
     DBRefEntry uniprotDBRef = new DBRefEntry();
@@ -108,7 +119,10 @@ public class StructureChooserTest
       dbRef.setAccessionId("XYZ_" + x);
       seq.addDBRef(dbRef);
     }
-    query = StructureChooser.buildQuery(seq);
+    System.out.println("");
+    System.out.println(seq.getDBRefs());
+    System.out.println(query);
+    query = scquery.buildQuery(seq);
     assertEquals(
             "uniprot_accession:P12345 OR uniprot_id:P12345 OR pdb_id:1xyz",
             query);
@@ -133,7 +147,7 @@ public class StructureChooserTest
     assertTrue(sc.getCmbFilterOption().getSelectedItem() != null);
     FilterOption filterOpt = (FilterOption) sc.getCmbFilterOption()
             .getSelectedItem();
-    assertEquals("Cached PDB Entries", filterOpt.getName());
+    assertEquals("Cached Structures", filterOpt.getName());
   }
 
   @Test(groups = { "Network" })
@@ -142,8 +156,10 @@ public class StructureChooserTest
     SequenceI[] selectedSeqs = new SequenceI[] { seq };
     StructureChooser sc = new StructureChooser(selectedSeqs, seq, null);
     sc.fetchStructuresMetaData();
-    assertTrue(sc.getDiscoveredStructuresSet() != null);
-    assertTrue(sc.getDiscoveredStructuresSet().size() > 0);
+    Collection<FTSData> ss = (Collection<FTSData>) PA.getValue(sc,
+            "discoveredStructuresSet");
+    assertNotNull(ss);
+    assertTrue(ss.size() > 0);
 
   }
 
@@ -151,17 +167,17 @@ public class StructureChooserTest
   public void sanitizeSeqNameTest()
   {
     String name = "ab_cdEF|fwxyz012349";
-    assertEquals(name, StructureChooser.sanitizeSeqName(name));
+    assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
 
     // remove a [nn] substring
     name = "abcde12[345]fg";
-    assertEquals("abcde12fg", StructureChooser.sanitizeSeqName(name));
+    assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 
     // remove characters other than a-zA-Z0-9 | or _
     name = "ab[cd],.\t£$*!- \\\"@:e";
-    assertEquals("abcde", StructureChooser.sanitizeSeqName(name));
+    assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
 
     name = "abcde12[345a]fg";
-    assertEquals("abcde12345afg", StructureChooser.sanitizeSeqName(name));
+    assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
   }
 }