X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2FMCview%2FPDBfileTest.java;h=54576c6757d5cce0cb63ab784d68bcd2ada416f7;hb=ee198b3ca3687f18a2ee186f4e7c7330f4ea30f0;hp=9d7009ff35151db08940a9bfbb03a8e699510092;hpb=52288466dd1e71946a06fd1e6ea15fa8e652c693;p=jalview.git

diff --git a/test/MCview/PDBfileTest.java b/test/MCview/PDBfileTest.java
index 9d7009f..54576c6 100644
--- a/test/MCview/PDBfileTest.java
+++ b/test/MCview/PDBfileTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package MCview;
 
 import static org.testng.AssertJUnit.assertEquals;
@@ -12,7 +32,7 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
-import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
 
 import java.io.IOException;
 import java.util.List;
@@ -50,19 +70,21 @@ public class PDBfileTest
      * Constructor with file path performs parse()
      */
     PDBfile pf = new PDBfile(false, false, false, "examples/3W5V.pdb",
-            AppletFormatAdapter.FILE);
+            DataSourceType.FILE);
 
-    assertEquals("3W5V", pf.id);
+    assertEquals("3W5V", pf.getId());
     // verify no alignment annotations created
     assertNull(getAlignmentAnnotations(pf));
 
-    assertEquals(4, pf.chains.size());
-    assertEquals("A", pf.chains.get(0).id);
-    assertEquals("B", pf.chains.get(1).id);
-    assertEquals("C", pf.chains.get(2).id);
-    assertEquals("D", pf.chains.get(3).id);
+    assertEquals(4, pf.getChains().size());
+    assertEquals("A", pf.getChains().get(0).id);
+    assertEquals("B", pf.getChains().get(1).id);
+    assertEquals("C", pf.getChains().get(2).id);
+    assertEquals("D", pf.getChains().get(3).id);
+
+    PDBChain chainA = pf.getChains().get(0);
+    SequenceI seqA = pf.getSeqs().get(0);
 
-    PDBChain chainA = pf.chains.get(0);
     assertEquals(0, chainA.seqstart); // not set
     assertEquals(0, chainA.seqend); // not set
     assertEquals(18, chainA.sequence.getStart());
@@ -71,27 +93,27 @@ public class PDBfileTest
     assertTrue(chainA.sequence.getSequenceAsString().endsWith("WNVEVY"));
     assertEquals("3W5V|A", chainA.sequence.getName());
     assertNull(chainA.sequence.getAnnotation());
-    assertEquals(1, chainA.sequence.getAllPDBEntries().size());
-    PDBEntry pdb = chainA.sequence.getAllPDBEntries().get(0);
+    assertEquals(1, seqA.getAllPDBEntries().size());
+    PDBEntry pdb = seqA.getAllPDBEntries().get(0);
     assertEquals("A", pdb.getChainCode());
     assertEquals("PDB", pdb.getType());
     assertEquals("3W5V", pdb.getId());
 
-    PDBChain chainB = pf.chains.get(1);
+    PDBChain chainB = pf.getChains().get(1);
     assertEquals(1, chainB.sequence.getStart());
     assertEquals(96, chainB.sequence.getEnd());
     assertTrue(chainB.sequence.getSequenceAsString().startsWith("ATYNVK"));
     assertTrue(chainB.sequence.getSequenceAsString().endsWith("KEEELT"));
     assertEquals("3W5V|B", chainB.sequence.getName());
 
-    PDBChain chainC = pf.chains.get(2);
+    PDBChain chainC = pf.getChains().get(2);
     assertEquals(18, chainC.sequence.getStart());
     assertEquals(314, chainC.sequence.getEnd());
     assertTrue(chainC.sequence.getSequenceAsString().startsWith("KCSKKQEE"));
     assertTrue(chainC.sequence.getSequenceAsString().endsWith("WNVEVY"));
     assertEquals("3W5V|C", chainC.sequence.getName());
 
-    PDBChain chainD = pf.chains.get(3);
+    PDBChain chainD = pf.getChains().get(3);
     assertEquals(1, chainD.sequence.getStart());
     assertEquals(96, chainD.sequence.getEnd());
     assertTrue(chainD.sequence.getSequenceAsString().startsWith("ATYNVK"));
@@ -124,7 +146,7 @@ public class PDBfileTest
   public void testParse_withAnnotations_noSS() throws IOException
   {
     PDBfile pf = new PDBfile(true, false, false, "examples/3W5V.pdb",
-            AppletFormatAdapter.FILE);
+            DataSourceType.FILE);
 
     AlignmentAnnotation[] anns = getAlignmentAnnotations(pf);
     assertEquals(4, anns.length);
@@ -182,7 +204,7 @@ public class PDBfileTest
   public void testParse_withJmol_noAnnotations() throws IOException
   {
     PDBfile pf = new PDBfile(false, true, false, "examples/3W5V.pdb",
-            AppletFormatAdapter.FILE);
+            DataSourceType.FILE);
 
     /*
      * alignment annotations _are_ created anyway (in
@@ -195,7 +217,7 @@ public class PDBfileTest
      * no sequence annotations created - tempFactor annotation is not added
      * unless the flag to 'addAlignmentAnnotations' is set true
      */
-    for (PDBChain c : pf.chains)
+    for (PDBChain c : pf.getChains())
     {
       assertNull(c.sequence.getAnnotation());
     }
@@ -212,7 +234,7 @@ public class PDBfileTest
           throws IOException
   {
     PDBfile pf = new PDBfile(true, true, false, "examples/3W5V.pdb",
-            AppletFormatAdapter.FILE);
+            DataSourceType.FILE);
 
     /*
      * Alignment annotations for TempFactor, SecStruct, per sequence (chain)
@@ -231,10 +253,10 @@ public class PDBfileTest
     /*
      * PDBFileWithJmol (unlike PDBChain!) leaves PDB id upper case
      */
-    assertEquals("Secondary Structure for 3W5VA", anns[0].description);
-    assertEquals("Secondary Structure for 3W5VB", anns[2].description);
-    assertEquals("Secondary Structure for 3W5VC", anns[4].description);
-    assertEquals("Secondary Structure for 3W5VD", anns[6].description);
+    assertEquals("Secondary Structure for 3w5vA", anns[0].description);
+    assertEquals("Secondary Structure for 3w5vB", anns[2].description);
+    assertEquals("Secondary Structure for 3w5vC", anns[4].description);
+    assertEquals("Secondary Structure for 3w5vD", anns[6].description);
 
     /*
      * Verify SS annotations are linked to respective sequences (chains)
@@ -270,7 +292,7 @@ public class PDBfileTest
     // TODO requires a mock for Annotate3D processing
     // and/or run as an integration test
     PDBfile pf = new PDBfile(true, true, true, "examples/2GIS.pdb",
-            AppletFormatAdapter.FILE);
+            DataSourceType.FILE);
   }
 
   /**