Merge branch 'develop' into features/r2_11_2/JAL-3829_3dbeacons

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

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 6a6ccd0..672a59e 100755 (executable)
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -46,7 +46,39 @@ public class PDBEntry
 
   public enum Type
   {
-    PDB, MMCIF, FILE;
+    // TODO is FILE needed; if not is this enum needed, or can we
+    // use FileFormatI for PDB, MMCIF?
+    PDB("pdb", "pdb"), MMCIF("mmcif", "cif"), FILE("?", "?");
+
+    /*
+     * file extension for cached structure file; must be one that
+     * is recognised by Chimera 'open' command
+     * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
+     */
+    String ext;
+
+    /*
+     * format specifier used in dbfetch request
+     * @see http://www.ebi.ac.uk/Tools/dbfetch/dbfetch/dbfetch.databases#pdb
+     */
+    String format;
+
+    private Type(String fmt, String ex)
+    {
+      format = fmt;
+      ext = ex;
+    }
+
+    public String getFormat()
+    {
+      return format;
+    }
+
+    public String getExtension()
+    {
+      return ext;
+    }
+
     /**
      * case insensitive matching for Type enum
      * 
@@ -77,7 +109,6 @@ public class PDBEntry
     }
   }
 
-
   /**
    * Answers true if obj is a PDBEntry with the same id and chain code (both
    * ignoring case), file, type and properties
@@ -121,17 +152,6 @@ public class PDBEntry
   {
   }
 
-  /**
-   * Constructor given file path and PDB id.
-   * 
-   * @param filePath
-   */
-  // public PDBEntry(String filePath, String pdbId)
-  // {
-  // this.file = filePath;
-  // this.id = pdbId;
-  // }
-
   public PDBEntry(String pdbId, String chain, PDBEntry.Type type,
           String filePath)
   {
@@ -144,7 +164,8 @@ public class PDBEntry
    * @param entryType
    * @param filePath
    */
-  void init(String pdbId, String chain, PDBEntry.Type entryType, String filePath)
+  void init(String pdbId, String chain, PDBEntry.Type entryType,
+          String filePath)
   {
     this.id = pdbId;
     this.type = entryType == null ? null : entryType.toString();
@@ -179,8 +200,8 @@ public class PDBEntry
   {
     if (!DBRefSource.PDB.equals(dbr.getSource()))
     {
-      throw new IllegalArgumentException("Invalid source: "
-              + dbr.getSource());
+      throw new IllegalArgumentException(
+              "Invalid source: " + dbr.getSource());
     }
 
     String pdbId = dbr.getAccessionId();
@@ -439,4 +460,27 @@ public class PDBEntry
     }
     return true;
   }
+  
+
+  private static final String RETRIEVE_FROM="RETRIEVE_FROM";
+  /**
+   * Permanent URI for retrieving the original structure data
+   * @param urlStr
+   */
+  public void setRetrievalUrl(String urlStr)
+  {
+    setProperty(RETRIEVE_FROM, urlStr);
+  }
+  /**
+   * get the Permanent URI for retrieving the original structure data
+   */
+  public String getRetrievalUrl()
+  {
+    return (String) getProperty(RETRIEVE_FROM);
+  }
+
+  public boolean hasRetrievalUrl()
+  {
+    return (properties!=null && properties.containsKey(RETRIEVE_FROM));
+  }
 }