JAL-2319 corrected reporting of SIFTS mapping

[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 9141bad..3f67c4c 100644 (file)
--- a/test/jalview/ws/sifts/SiftsClientTest.java
+++ b/test/jalview/ws/sifts/SiftsClientTest.java
@@ -21,6 +21,7 @@
 package jalview.ws.sifts;
 
 import jalview.api.DBRefEntryI;
+import jalview.bin.Cache;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.Sequence;
@@ -67,7 +68,7 @@ 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 +166,13 @@ 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();
@@ -233,7 +236,6 @@ public class SiftsClientTest
     }
   }
 
-
   @Test(groups = { "Functional" })
   public void getAllMappingAccessionTest()
   {
@@ -251,16 +253,13 @@ 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 +304,7 @@ public class SiftsClientTest
   private void populateAtomPositionsNullTest1()
           throws IllegalArgumentException, SiftsException
   {
-      siftsClient.populateAtomPositions(null, null);
+    siftsClient.populateAtomPositions(null, null);
   }
 
   @Test(
@@ -327,8 +326,6 @@ 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 +338,7 @@ 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 +373,6 @@ 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 +387,8 @@ 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"
@@ -454,7 +449,7 @@ public class SiftsClientTest
   }
 
   @Test(groups = { "Functional" })
-  public void getEntityByMostOptimalMatchedIdTest()
+  public void getEntityByMostOptimalMatchedIdTest1()
   {
     SiftsClient siftsClientX = null;
     PDBfile pdbFile;
@@ -477,4 +472,34 @@ 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", AppletFormatAdapter.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);
+
+  }
 }