X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fsifts%2FSiftsClientTest.java;h=45c5412545aa45a47f6478ff37c4ac0fa8da59a8;hb=483e7163b1fb8d4bcb9393014816c944befce328;hp=9141bad941942d524b2c452d91e166eda6e68025;hpb=63117948459c9ee4748cb1ebbcea963bdf26796c;p=jalview.git

diff --git a/test/jalview/ws/sifts/SiftsClientTest.java b/test/jalview/ws/sifts/SiftsClientTest.java
index 9141bad..45c5412 100644
--- a/test/jalview/ws/sifts/SiftsClientTest.java
+++ b/test/jalview/ws/sifts/SiftsClientTest.java
@@ -21,11 +21,13 @@
 package jalview.ws.sifts;
 
 import jalview.api.DBRefEntryI;
+import jalview.bin.Cache;
 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;
 
@@ -37,6 +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;
 
@@ -46,6 +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
@@ -67,7 +77,7 @@ public class SiftsClientTest
 
   @BeforeTest(alwaysRun = true)
   public void populateExpectedMapping() throws SiftsException
-   {
+  {
     expectedMapping.put(51, new int[] { 1, 2 });
     expectedMapping.put(52, new int[] { 2, 7 });
     expectedMapping.put(53, new int[] { 3, 12 });
@@ -165,11 +175,13 @@ public class SiftsClientTest
     expectedMapping.put(145, new int[] { 95, 714 });
     expectedMapping.put(146, new int[] { 96, 722 });
     expectedMapping.put(147, new int[] { 97, 729 });
-   }
-   
+  }
+
   @BeforeTest(alwaysRun = true)
   public void setUpSiftsClient() throws SiftsException
   {
+    // read test props before manipulating config
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
     // SIFTs entries are updated weekly - so use saved SIFTs file to enforce
     // test reproducibility
     new SiftsSettings();
@@ -182,7 +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)
     {
@@ -233,7 +245,6 @@ public class SiftsClientTest
     }
   }
 
-
   @Test(groups = { "Functional" })
   public void getAllMappingAccessionTest()
   {
@@ -251,16 +262,13 @@ public class SiftsClientTest
 
     // TODO delete when auto-fetching of DBRefEntry is implemented
     DBRefEntry dbRef = new DBRefEntry("uniprot", "", "P00221");
-    dbRef.setStartRes(1);
-    dbRef.setEndRes(147);
     testSeq.addDBRef(dbRef);
     // testSeq.setSourceDBRef(dbRef);
 
     try
     {
       HashMap<Integer, int[]> actualMapping = siftsClient.getGreedyMapping(
-              "A", testSeq,
-              null);
+              "A", testSeq, null);
       Assert.assertEquals(testSeq.getStart(), 1);
       Assert.assertEquals(testSeq.getEnd(), 147);
       Assert.assertEquals(actualMapping, expectedMapping);
@@ -305,7 +313,7 @@ public class SiftsClientTest
   private void populateAtomPositionsNullTest1()
           throws IllegalArgumentException, SiftsException
   {
-      siftsClient.populateAtomPositions(null, null);
+    siftsClient.populateAtomPositions(null, null);
   }
 
   @Test(
@@ -327,8 +335,6 @@ public class SiftsClientTest
       DBRefEntryI expectedDBRef = new DBRefEntry();
       expectedDBRef.setSource(DBRefSource.UNIPROT);
       expectedDBRef.setAccessionId("P00221");
-      expectedDBRef.setStartRes(1);
-      expectedDBRef.setEndRes(147);
       expectedDBRef.setVersion("");
       Assert.assertEquals(actualValidSrcDBRef, expectedDBRef);
     } catch (Exception e)
@@ -341,7 +347,7 @@ public class SiftsClientTest
     expectedExceptions = SiftsException.class)
   public void getValidSourceDBRefExceptionTest() throws SiftsException
   {
-      SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
+    SequenceI invalidTestSeq = new Sequence("testSeq", "ABCDEFGH");
     try
     {
       siftsClient.getValidSourceDBRef(invalidTestSeq);
@@ -376,8 +382,6 @@ public class SiftsClientTest
     DBRefEntryI validDBRef = new DBRefEntry();
     validDBRef.setSource(DBRefSource.UNIPROT);
     validDBRef.setAccessionId("P00221");
-    validDBRef.setStartRes(1);
-    validDBRef.setEndRes(147);
     validDBRef.setVersion("");
     Assert.assertTrue(siftsClient.isValidDBRefEntry(validDBRef));
   }
@@ -392,8 +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"
@@ -454,14 +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)
     {
@@ -477,4 +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);
+
+  }
 }