JAL-1824 updated caching procedure for pdb entries. Also refactored getPDBEntry metho...

[jalview.git] / src / MCview / PDBfile.java

diff --git a/src/MCview/PDBfile.java b/src/MCview/PDBfile.java
index d81e734..58991f3 100755 (executable)
--- a/src/MCview/PDBfile.java
+++ b/src/MCview/PDBfile.java
@@ -20,14 +20,6 @@
  */
 package MCview;
 
-import java.awt.Color;
-import java.io.IOException;
-import java.lang.reflect.Constructor;
-import java.util.ArrayList;
-import java.util.Hashtable;
-import java.util.List;
-import java.util.Vector;
-
 import jalview.analysis.AlignSeq;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
@@ -37,6 +29,14 @@ import jalview.datamodel.SequenceI;
 import jalview.io.FileParse;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.io.IOException;
+import java.lang.reflect.Constructor;
+import java.util.ArrayList;
+import java.util.Hashtable;
+import java.util.List;
+import java.util.Vector;
+
 public class PDBfile extends jalview.io.AlignFile
 {
   private static String CALC_ID_PREFIX = "JalviewPDB";
@@ -379,7 +379,7 @@ public class PDBfile extends jalview.io.AlignFile
         final Object[] args = new Object[]
         { new FileParse(getDataName(), type) };
         Object jmf = constructor.newInstance(args);
-        Alignment al = new Alignment((SequenceI[]) cl.getMethod(
+        AlignmentI al = new Alignment((SequenceI[]) cl.getMethod(
                 "getSeqsAsArray", new Class[]
                 {}).invoke(jmf));
         cl.getMethod("addAnnotations", new Class[]
@@ -388,11 +388,11 @@ public class PDBfile extends jalview.io.AlignFile
         {
           if (sq.getDatasetSequence() != null)
           {
-            sq.getDatasetSequence().getPDBId().clear();
+            sq.getDatasetSequence().getAllPDBEntries().clear();
           }
           else
           {
-            sq.getPDBId().clear();
+            sq.getAllPDBEntries().clear();
           }
         }
         replaceAndUpdateChains(prot, al, AlignSeq.PEP, false);
@@ -456,16 +456,16 @@ public class PDBfile extends jalview.io.AlignFile
         {
           if (sq.getDatasetSequence() != null)
           {
-            if (sq.getDatasetSequence().getPDBId() != null)
+            if (sq.getDatasetSequence().getAllPDBEntries() != null)
             {
-              sq.getDatasetSequence().getPDBId().clear();
+              sq.getDatasetSequence().getAllPDBEntries().clear();
             }
           }
           else
           {
-            if (sq.getPDBId() != null)
+            if (sq.getAllPDBEntries() != null)
             {
-              sq.getPDBId().clear();
+              sq.getAllPDBEntries().clear();
             }
           }
         }