X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fws%2FPDBSequenceFetcherTest.java;h=ba90dd804df35b056697837db753bd1dc2072730;hb=07b7e8f1faf772c1ffa85999a09c84dce96a63b1;hp=c1d114422e775a5de98976f3106b04cd15e59ca0;hpb=dde2abe99b75477853a09b4668a6b46cc14bc3ef;p=jalview.git

diff --git a/test/jalview/ws/PDBSequenceFetcherTest.java b/test/jalview/ws/PDBSequenceFetcherTest.java
index c1d1144..ba90dd8 100644
--- a/test/jalview/ws/PDBSequenceFetcherTest.java
+++ b/test/jalview/ws/PDBSequenceFetcherTest.java
@@ -20,28 +20,42 @@
  */
 package jalview.ws;
 
+import static org.testng.Assert.assertEquals;
 import static org.testng.AssertJUnit.assertTrue;
 
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceI;
+import jalview.gui.JvOptionPane;
 import jalview.structure.StructureImportSettings;
 import jalview.structure.StructureImportSettings.StructureParser;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import java.util.Arrays;
 import java.util.List;
 
+import org.testng.Assert;
+import org.testng.annotations.BeforeClass;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
 public class PDBSequenceFetcherTest
 {
 
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
   SequenceFetcher sf;
 
   @BeforeMethod(alwaysRun = true)
   public void setUp() throws Exception
   {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
     // ensure 'add annotation from structure' is selected
     Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
             Boolean.TRUE.toString());
@@ -62,10 +76,7 @@ public class PDBSequenceFetcherTest
   @Test(groups = { "Network" }, enabled = true)
   public void testRnaSeqRetrieve() throws Exception
   {
-    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
-            Boolean.TRUE.toString());
-    Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT",
-            "PDB");
+    Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT", "PDB");
     List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
     AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
     assertTrue(response != null);
@@ -85,8 +96,6 @@ public class PDBSequenceFetcherTest
   @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);
@@ -97,29 +106,76 @@ public class PDBSequenceFetcherTest
   @Test(groups = { "Network" }, enabled = true)
   public void testmmCifSeqRetrieve() throws Exception
   {
-    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
-            Boolean.TRUE.toString());
     StructureImportSettings.setDefaultStructureFileFormat("mmCIF");
     testRetrieveProteinSeqFromPDB();
   }
 
+  private class TestRetrieveObject
+  {
+    String id;
+
+    int expectedHeight;
+
+    public TestRetrieveObject(String id, int expectedHeight)
+    {
+      super();
+      this.id = id;
+      this.expectedHeight = expectedHeight;
+    }
+
+  }
+
+  private List<TestRetrieveObject> toRetrieve = Arrays.asList(
+          new TestRetrieveObject("1QIP", 4),
+          new TestRetrieveObject("4IM2", 1));
+
   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())
+    for (TestRetrieveObject str : toRetrieve)
     {
-      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");
+      AlignmentI response = sps.get(0).getSequenceRecords(str.id);
+      assertTrue("No aligment for " + str.id, response != null);
+      assertEquals(response.getHeight(), str.expectedHeight,
+              "Number of chains for " + str.id);
+      for (SequenceI sq : response.getSequences())
+      {
+        assertTrue("No annotation transfered to sequence " + sq.getName(),
+                sq.getAnnotation().length > 0);
+        assertTrue("No PDBEntry on sequence " + sq.getName(),
+                sq.getAllPDBEntries().size() > 0);
+        // FIXME: should test that all residues extracted as sequences from
+        // chains in structure have a mapping to data in the structure
+        StringBuilder errors = new StringBuilder();
+        List<SequenceFeature> prev = null;
+        int lastp = -1;
+        for (int rs = sq.getStart(); rs < sq.getStart()
+                + sq.getLength(); rs++)
+        {
+          List<SequenceFeature> sf = sq.findFeatures(rs, rs, "RESNUM");
+          if (sf.size() != 1)
+          {
+            errors.append(
+                    "Expected feature at " + rs + ": saw " + sf.size());
+            errors.append("\n");
+            if (prev != null)
+            {
+              errors.append("Last Feature was at " + lastp + ": "
+                      + prev.get(0).toString());
+              errors.append("\n");
+            }
+          }
+          else
+          {
+            prev = sf;
+            lastp = rs;
+          }
+        }
+        if (errors.length() > 0)
+        {
+          Assert.fail(errors.toString());
+        }
+      }
     }
   }
-
 }