X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2FPDBSequenceFetcherTest.java;h=fda01983927f8db5b407ee161a07a03382fcb250;hb=0f40a8334651302a74a223ecd3e583451302bb42;hp=adf53f53ac2a13da00ab3531b8110622f372b1aa;hpb=02059a2675d81af6de5f8d54a7a1e4db94351365;p=jalview.git

diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index adf53f5..fda0198 100644
--- a/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -25,6 +25,8 @@ import static org.testng.AssertJUnit.assertTrue;
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
+import jalview.structure.StructureImportSettings;
+import jalview.structure.StructureImportSettings.StructureParser;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
 import java.util.List;
@@ -37,7 +39,7 @@ public class PDBSequenceFetcherTest
 
   SequenceFetcher sf;
 
- @BeforeMethod(alwaysRun = true)
+  @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
   {
     // ensure 'add annotation from structure' is selected
@@ -57,10 +59,13 @@ public class PDBSequenceFetcherTest
    * 
    * @throws Exception
    */
-  @Test(groups =
-  { "Network" }, enabled = true)
+  @Test(groups = { "Network" }, enabled = true)
   public void testRnaSeqRetrieve() throws Exception
   {
+    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("DEFAULT_STRUCTURE_FORMAT",
+            "PDB");
     List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
     AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
     assertTrue(response != null);
@@ -69,11 +74,52 @@ public class PDBSequenceFetcherTest
     {
       assertTrue("No annotation transfered to sequence.",
               sq.getAnnotation().length > 0);
-      assertTrue("No PDBEntry on sequence.", sq.getAllPDBEntries().size() > 0);
+      assertTrue("No PDBEntry on sequence.",
+              sq.getAllPDBEntries().size() > 0);
       assertTrue(
               "No RNA annotation on sequence, possibly http://arn-ibmc.in2p3.fr/api/compute/2d not available?",
               sq.getRNA() != null);
     }
   }
 
+  @Test(groups = { "Network" }, enabled = true)
+  public void testPdbSeqRetrieve() throws Exception
+  {
+    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+            Boolean.TRUE.toString());
+    StructureImportSettings.setDefaultStructureFileFormat("PDB");
+    StructureImportSettings
+            .setDefaultPDBFileParser(StructureParser.JALVIEW_PARSER);
+
+    testRetrieveProteinSeqFromPDB();
+  }
+
+  @Test(groups = { "Network" }, enabled = true)
+  public void testmmCifSeqRetrieve() throws Exception
+  {
+    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+            Boolean.TRUE.toString());
+    StructureImportSettings.setDefaultStructureFileFormat("mmCIF");
+    testRetrieveProteinSeqFromPDB();
+  }
+
+  private void testRetrieveProteinSeqFromPDB() throws Exception
+  {
+    List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
+    AlignmentI response = sps.get(0).getSequenceRecords("1QIP");
+    assertTrue(response != null);
+    assertTrue(response.getHeight() == 4);
+    for (SequenceI sq : response.getSequences())
+    {
+      assertTrue("No annotation transfered to sequence.",
+              sq.getAnnotation().length > 0);
+      assertTrue("No PDBEntry on sequence.",
+              sq.getAllPDBEntries().size() > 0);
+      org.testng.Assert
+              .assertEquals(sq.getEnd() - sq.getStart() + 1,
+                      sq.getLength(),
+                      "Sequence start/end doesn't match number of residues in sequence");
+    }
+  }
+
 }