JAL-3438 spotless for 2.11.2.0

[jalview.git] / src / jalview / io / StructureFile.java

diff --git a/src/jalview/io/StructureFile.java b/src/jalview/io/StructureFile.java
index 3025907..6b623a1 100644 (file)
--- 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)
     {
@@ -342,7 +343,14 @@ 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()