Merge branch 'improvement/JAL-3830_remove_dock_icon_in_headless_mode' into develop

[jalview.git] / src / jalview / datamodel / PDBEntry.java

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 741ef07..ae8523d 100755 (executable)
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -20,12 +20,13 @@
  */
 package jalview.datamodel;
 
-import jalview.util.CaseInsensitiveString;
-
 import java.util.Collections;
 import java.util.Enumeration;
 import java.util.Hashtable;
 
+import jalview.io.StructureFile;
+import jalview.util.CaseInsensitiveString;
+
 public class PDBEntry
 {
 
@@ -39,11 +40,14 @@ public class PDBEntry
   private static final int PDB_ID_LENGTH = 4;
 
   /**
-   * property set when id is a 'manufactured' identifier from the structure data's filename
+   * property set when id is a 'manufactured' identifier from the structure
+   * data's filename
    */
   private static final String FAKED_ID = "faked_pdbid";
+
   /**
-   * property set when the id is authoritative, and should be used in preference to any identifiers in the structure data
+   * property set when the id is authoritative, and should be used in preference
+   * to any identifiers in the structure data
    */
   private static final String AUTHORITATIVE_ID = "authoritative_pdbid";
 
@@ -53,11 +57,14 @@ public class PDBEntry
 
   private String id;
 
+  private StructureFile sf = null;
+
   public enum Type
   {
     // TODO is FILE needed; if not is this enum needed, or can we
     // use FileFormatI for PDB, MMCIF?
-    PDB("pdb", "pdb"), MMCIF("mmcif", "cif"), BCIF("bcif","bcif"),FILE("?", "?");
+    PDB("pdb", "pdb"), MMCIF("mmcif", "cif"), BCIF("bcif", "bcif"),
+    FILE("?", "?");
 
     /*
      * file extension for cached structure file; must be one that
@@ -493,12 +500,12 @@ public class PDBEntry
     }
     return true;
   }
-  
+
   public void setAuthoritative(boolean isAuthoritative)
   {
     setProperty(AUTHORITATIVE_ID, Boolean.valueOf(isAuthoritative));
   }
-  
+
   /**
    * 
    * @return true if the identifier should be preferred over any identifiers
@@ -508,13 +515,14 @@ public class PDBEntry
   {
     if (_hasProperty(AUTHORITATIVE_ID))
     {
-      return ((Boolean)getProperty(AUTHORITATIVE_ID));
+      return ((Boolean) getProperty(AUTHORITATIVE_ID));
     }
     return false;
   }
 
   /**
    * set when Jalview has manufactured the ID using a local filename
+   * 
    * @return
    */
   public boolean fakedPDBId()
@@ -525,15 +533,17 @@ public class PDBEntry
     }
     return false;
   }
+
   public void setFakedPDBId(boolean faked)
   {
     if (faked)
     {
       setProperty(FAKED_ID, Boolean.TRUE);
     }
-    else 
+    else
     {
-      if (properties!=null) {
+      if (properties != null)
+      {
         properties.remove(FAKED_ID);
       }
     }
@@ -619,4 +629,19 @@ public class PDBEntry
   {
     return _hasProperty(PROVIDER);
   }
+
+  public StructureFile getStructureFile()
+  {
+    return sf;
+  }
+
+  public void setStructureFile(StructureFile f)
+  {
+    sf = f;
+  }
+
+  public boolean hasStructureFile()
+  {
+    return sf != null && sf.inFile != null && sf.inFile.exists();
+  }
 }