Merge branch 'develop' into trialMerge

[jalview.git] / test / jalview / ws / sifts / SiftsClientTest.java

diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java
index 8d26c45..45c5412 100644 (file)
--- a/test/jalview/ws/sifts/SiftsClientTest.java
+++ b/test/jalview/ws/sifts/SiftsClientTest.java
@@ -26,7 +26,8 @@ import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.gui.JvOptionPane;
+import jalview.io.DataSourceType;
 import jalview.structure.StructureMapping;
 import jalview.xml.binding.sifts.Entry.Entity;
 
@@ -38,6 +39,7 @@ import java.util.HashMap;
 import org.testng.Assert;
 import org.testng.FileAssert;
 import org.testng.annotations.AfterTest;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeTest;
 import org.testng.annotations.Test;
 
@@ -47,6 +49,13 @@ import MCview.PDBfile;
 public class SiftsClientTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
           .getProperty("user.home")
           + File.separatorChar
@@ -185,7 +194,7 @@ public class SiftsClientTest
     try
     {
       pdbFile = new PDBfile(false, false, false, "test/jalview/io/"
-              + testPDBId + ".pdb", AppletFormatAdapter.FILE);
+              + testPDBId + ".pdb", DataSourceType.FILE);
       siftsClient = new SiftsClient(pdbFile);
     } catch (Exception e)
     {
@@ -387,8 +396,8 @@ public class SiftsClientTest
               testSeq, testPDBId, "A");
       String expectedMappingOutput = "\nSequence ⟷ Structure mapping details\n"
               + "Method: SIFTS\n\n"
-              + "P00221 :  1 - 97 Maps to \n"
-              + "1A70|A :  51 - 147\n\n"
+              + "P00221 :  51 - 147 Maps to \n"
+              + "1A70|A :  1 - 97\n\n"
               + "P00221 AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n"
               + "       |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||\n"
               + "1A70|A AAYKVTLVTPTGNVEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLD\n\n"
@@ -449,14 +458,14 @@ public class SiftsClientTest
   }
 
   @Test(groups = { "Functional" })
-  public void getEntityByMostOptimalMatchedIdTest()
+  public void getEntityByMostOptimalMatchedIdTest1()
   {
     SiftsClient siftsClientX = null;
     PDBfile pdbFile;
     try
     {
       pdbFile = new PDBfile(false, false, false, "test/jalview/io/2nq2"
-              + ".pdb", AppletFormatAdapter.FILE);
+              + ".pdb", DataSourceType.FILE);
       siftsClientX = new SiftsClient(pdbFile);
     } catch (Exception e)
     {
@@ -472,4 +481,34 @@ public class SiftsClientTest
     Assert.assertEquals(entityD.getEntityId(), "D");
 
   }
+
+  @Test(groups = { "Functional" })
+  public void getEntityByMostOptimalMatchedIdTest2()
+  {
+    // This test is for a SIFTS file in which entity A should map to chain P for
+    // the given PDB Id. All the other chains shouldn't be mapped as there are
+    // no SIFTS entity records for them.
+    SiftsClient siftsClientX = null;
+    PDBfile pdbFile;
+    try
+    {
+      pdbFile = new PDBfile(false, false, false,
+              "test/jalview/io/3ucu.cif", DataSourceType.FILE);
+      siftsClientX = new SiftsClient(pdbFile);
+    } catch (Exception e)
+    {
+      e.printStackTrace();
+    }
+    Entity entityA = siftsClientX.getEntityByMostOptimalMatchedId("P");
+    Entity entityP = siftsClientX.getEntityByMostOptimalMatchedId("A");
+    Entity entityR = siftsClientX.getEntityByMostOptimalMatchedId("R");
+    Assert.assertEquals(entityA.getEntityId(), "A");
+    Assert.assertNotEquals(entityR, "A");
+    Assert.assertNotEquals(entityP, "A");
+    Assert.assertNotEquals(entityR, "R");
+    Assert.assertNotEquals(entityP, "P");
+    Assert.assertNull(entityR);
+    Assert.assertNull(entityP);
+
+  }
 }