X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FStructureFile.java;h=94a832b2e7a6c1f29cae64c19b1ce529dbc47cf0;hb=7b23afe919f115205c95233af7f2b71c164fc95a;hp=3025907fe46adc023add9e13001dddebcf85dae2;hpb=f4766a7bbcfae845fc95923b01fa14ff83d589ff;p=jalview.git

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 3025907..94a832b 100644
--- a/src/jalview/io/StructureFile.java
+++ b/src/jalview/io/StructureFile.java
@@ -38,7 +38,7 @@ import java.lang.reflect.Constructor;
 import java.util.List;
 import java.util.Vector;
 
-import MCview.PDBChain;
+import mc_view.PDBChain;
 
 public abstract class StructureFile extends AlignFile
 {
@@ -68,7 +68,7 @@ public abstract class StructureFile extends AlignFile
 
   private boolean pdbIdAvailable;
 
-  public StructureFile(String inFile, DataSourceType sourceType)
+  public StructureFile(Object inFile, DataSourceType sourceType)
           throws IOException
   {
     super(inFile, sourceType);
@@ -98,7 +98,7 @@ public abstract class StructureFile extends AlignFile
 
   }
 
-  public StructureFile(boolean parseImmediately, String dataObject,
+  public StructureFile(boolean parseImmediately, Object dataObject,
           DataSourceType sourceType) throws IOException
   {
     super(parseImmediately, dataObject, sourceType);
@@ -119,6 +119,7 @@ public abstract class StructureFile extends AlignFile
     pdbSequence.setName(getId() + "|" + pdbSequence.getName());
     PDBEntry entry = new PDBEntry();
     entry.setId(getId());
+    entry.setFakedPDBId(!isPPDBIdAvailable());
     entry.setType(getStructureFileType());
     if (chain.id != null)
     {
@@ -341,8 +342,15 @@ public abstract class StructureFile extends AlignFile
     }
     StructureImportSettings.setShowSeqFeatures(true);
   }
-
-  public PDBChain findChain(String id) throws Exception
+  
+  /**
+   * Answers the first PDBChain found matching the given id, or null if none 
+   * is found
+   * 
+   * @param id
+   * @return
+   */
+  public PDBChain findChain(String id)
   {
     for (PDBChain chain : getChains())
     {
@@ -351,7 +359,7 @@ public abstract class StructureFile extends AlignFile
         return chain;
       }
     }
-    throw new Exception("PDB chain not Found!");
+    return null;
   }
 
   public void makeResidueList()