X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FPDBEntry.java;h=c1dc77c1224570f11088a283ac837c458e4ea3c2;hb=83dd6154fdf5f727bc587ef58790c08e8404b757;hp=97fb08ddae8428f89008b165fe6909ad99d369c4;hpb=7d67fb613ec026dc9a265e351e7fab542e3f1d61;p=jalview.git

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 97fb08d..c1dc77c 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -46,11 +46,21 @@ public class PDBEntry
 
   public enum Type
   {
-    // TODO is FILE needed; if not is this needed or can we
+    // TODO is FILE needed; if not is this enum needed, or can we
     // use FileFormatI for PDB, MMCIF?
-    PDB("pdb", "xml"), MMCIF("mmcif", "mmcif"), FILE("?", "?");
+    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)
@@ -63,6 +73,7 @@ public class PDBEntry
     {
       return format;
     }
+
     public String getExtension()
     {
       return ext;
@@ -141,7 +152,6 @@ public class PDBEntry
   {
   }
 
-
   public PDBEntry(String pdbId, String chain, PDBEntry.Type type,
           String filePath)
   {
@@ -154,7 +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();
@@ -189,8 +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();