X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2Fseqfetcher%2FDbRefFetcherTest.java;h=d2b5aecdc3b395e4bd485ae09b0dc4612cf291b1;hb=51ff7ec3b6914f3c69b35e91e69d10c88aaf5270;hp=851ab2d0afd497d69dff6a3ebaaa600d4863d464;hpb=8286731258d314669ee6facb627947fe159ac1eb;p=jalview.git

diff --git a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
index 851ab2d..d2b5aec 100644
--- a/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
+++ b/test/jalview/ws/seqfetcher/DbRefFetcherTest.java
@@ -20,12 +20,20 @@
  */
 package jalview.ws.seqfetcher;
 
-import static org.testng.Assert.assertNotEquals;
 import static org.testng.AssertJUnit.assertEquals;
 import static org.testng.AssertJUnit.assertFalse;
 import static org.testng.AssertJUnit.assertNotNull;
 import static org.testng.AssertJUnit.assertTrue;
 
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.junit.Assert;
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
 import jalview.analysis.CrossRef;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
@@ -43,15 +51,6 @@ import jalview.ws.dbsources.EBIAlfaFold;
 import jalview.ws.dbsources.Pdb;
 import jalview.ws.dbsources.Uniprot;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import org.junit.Assert;
-import org.testng.annotations.AfterClass;
-import org.testng.annotations.BeforeClass;
-import org.testng.annotations.Test;
-
 /**
  * @author jimp
  * 
@@ -83,26 +82,28 @@ public class DbRefFetcherTest
   {
   }
 
-  @Test(groups= {"Network"})
+  @Test(groups = { "Network" })
   public void checkUniprotCanonicalFlagSet()
   {
-    // TODO - mock this  - for moment it is a live request.
+    // TODO - mock this - for moment it is a live request.
     SequenceI uniprotSeq = new Sequence("FER1_SPIOL",
             "MAATTTTMMGMATTFVPKPQAPPMMAALPSNTGRSLFGLKTGSRGGRMTMAAYKVTLVTPTGNVEFQCPDDV"
-            + "YILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEE"
-            + "LTA");
+                    + "YILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDVTIETHKEEE"
+                    + "LTA");
     DBRefFetcher dbr = new DBRefFetcher(new SequenceI[] { uniprotSeq });
     dbr.fetchDBRefs(true);
     List<DBRefEntry> primRefs = uniprotSeq.getPrimaryDBRefs();
     assertNotNull(primRefs);
-    assertTrue(primRefs.size()>0);
-    boolean canonicalUp=false;
-    for (DBRefEntry ref:primRefs) {
+    assertTrue(primRefs.size() > 0);
+    boolean canonicalUp = false;
+    for (DBRefEntry ref : primRefs)
+    {
       assertEquals(DBRefSource.UNIPROT, ref.getCanonicalSourceName());
       canonicalUp |= ref.isCanonical();
     }
     assertTrue("No Canonical Uniprot reference detected", canonicalUp);
   }
+
   /**
    * Tests that standard protein database sources include Uniprot (as the first)
    * and also PDB. (Additional sources are dependent on availability of DAS
@@ -161,8 +162,8 @@ public class DbRefFetcherTest
   public void testEmblUniprotProductRecovery() throws Exception
   {
     String retrievalId = "V00488";
-    DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
-            DBRefSource.EMBL).get(0);
+    DbSourceProxy embl = new SequenceFetcher()
+            .getSourceProxy(DBRefSource.EMBL).get(0);
     assertNotNull("Couldn't find the EMBL retrieval client", embl);
     verifyProteinNucleotideXref(retrievalId, embl);
   }
@@ -177,8 +178,8 @@ public class DbRefFetcherTest
   public void testEmblCDSUniprotProductRecovery() throws Exception
   {
     String retrievalId = "AAH29712";
-    DbSourceProxy embl = new SequenceFetcher().getSourceProxy(
-            DBRefSource.EMBLCDS).get(0);
+    DbSourceProxy embl = new SequenceFetcher()
+            .getSourceProxy(DBRefSource.EMBLCDS).get(0);
     assertNotNull("Couldn't find the EMBL retrieval client", embl);
     verifyProteinNucleotideXref(retrievalId, embl);
   }
@@ -198,23 +199,22 @@ public class DbRefFetcherTest
     assertEquals("Didn't retrieve right number of records", 1,
             alsq.getHeight());
     SequenceI seq = alsq.getSequenceAt(0);
-    assertEquals("Wrong sequence name", embl.getDbSource() + "|"
-            + retrievalId, seq.getName());
+    assertEquals("Wrong sequence name",
+            embl.getDbSource() + "|" + retrievalId, seq.getName());
     List<SequenceFeature> sfs = seq.getSequenceFeatures();
     assertFalse("Sequence features missing", sfs.isEmpty());
-    assertTrue(
-            "Feature not CDS",
-            FeatureProperties.isCodingFeature(embl.getDbSource(),
- sfs.get(0).getType()));
+    assertTrue("Feature not CDS", FeatureProperties
+            .isCodingFeature(embl.getDbSource(), sfs.get(0).getType()));
     assertEquals(embl.getDbSource(), sfs.get(0).getFeatureGroup());
     List<DBRefEntry> dr = DBRefUtils.selectRefs(seq.getDBRefs(),
-            new String[] { DBRefSource.UNIPROT });
+            new String[]
+            { DBRefSource.UNIPROT });
     assertNotNull(dr);
     assertEquals("Expected a single Uniprot cross reference", 1, dr.size());
-    assertEquals("Expected cross reference map to be one amino acid", dr.get(0)
-            .getMap().getMappedWidth(), 1);
-    assertEquals("Expected local reference map to be 3 nucleotides", dr.get(0)
-            .getMap().getWidth(), 3);
+    assertEquals("Expected cross reference map to be one amino acid",
+            dr.get(0).getMap().getMappedWidth(), 1);
+    assertEquals("Expected local reference map to be 3 nucleotides",
+            dr.get(0).getMap().getWidth(), 3);
     AlignmentI sprods = new CrossRef(alsq.getSequencesArray(), alsq)
             .findXrefSequences(dr.get(0).getSource(), true);
     assertNotNull(
@@ -223,8 +223,8 @@ public class DbRefFetcherTest
     assertEquals("Didn't xref right number of records", 1,
             sprods.getHeight());
     SequenceI proteinSeq = sprods.getSequenceAt(0);
-    assertEquals(proteinSeq.getSequenceAsString(), dr.get(0).getMap().getTo()
-            .getSequenceAsString());
+    assertEquals(proteinSeq.getSequenceAsString(),
+            dr.get(0).getMap().getTo().getSequenceAsString());
     assertEquals(dr.get(0).getSource() + "|" + dr.get(0).getAccessionId(),
             proteinSeq.getName());
   }
@@ -239,18 +239,21 @@ public class DbRefFetcherTest
   public void testAlphaFoldClien() throws Exception
   {
     DbSourceProxy alphafold = new EBIAlfaFold();
-    AlignmentI resp = alphafold.getSequenceRecords(alphafold.getTestQuery());
+    AlignmentI resp = alphafold
+            .getSequenceRecords(alphafold.getTestQuery());
     assertNotNull(resp);
-    assertEquals("One sequence only",resp.getHeight(), 1);
-    for (AlignmentAnnotation aa:resp.getAlignmentAnnotation()) {
+    assertEquals("One sequence only", resp.getHeight(), 1);
+    for (AlignmentAnnotation aa : resp.getAlignmentAnnotation())
+    {
       if (aa.graph == AlignmentAnnotation.CUSTOMRENDERER)
       {
-        assertTrue("Contact map didn't provide valid contact",resp.getContactListFor(aa, 1).getContactAt(1)!=-1d);
+        assertTrue("Contact map didn't provide valid contact",
+                resp.getContactListFor(aa, 1).getContactAt(1) != -1d);
         // test passes
         return;
       }
     }
-    Assert.fail();
+    Assert.fail("No pAE matrix found for alphafold structure.");
   }
 
 }