JAL-3829 3d-beacons structure chooser logic (not yet finished)

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

diff --git a/test/jalview/gui/StructureChooserTest.java b/test/jalview/gui/StructureChooserTest.java
index f69e6b5..31f5f8b 100644 (file)
--- a/test/jalview/gui/StructureChooserTest.java
+++ b/test/jalview/gui/StructureChooserTest.java
@@ -30,7 +30,10 @@ import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 import jalview.fts.api.FTSData;
+import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
+import jalview.gui.structurechooser.StructureChooserQuerySource;
 import jalview.jbgui.GStructureChooser.FilterOption;
+import jalview.ws.params.InvalidArgumentException;
 
 import java.util.Collection;
 import java.util.Vector;
@@ -82,19 +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();
@@ -113,7 +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);
@@ -158,17 +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));
   }
 }