X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FPDBEntry.java;h=d0ab8bf3dc716190e94d0f727422acd05fbfddf5;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=adcefb3826530d567d1b9de69a3d7ee8a404d8b5;hpb=61ff8fb4efa315c35149c9d11850d99e3d00c441;p=jalview.git

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index adcefb3..d0ab8bf 100755
--- a/src/jalview/datamodel/PDBEntry.java
+++ b/src/jalview/datamodel/PDBEntry.java
@@ -20,12 +20,12 @@
  */
 package jalview.datamodel;
 
-import jalview.util.CaseInsensitiveString;
-
 import java.util.Collections;
 import java.util.Enumeration;
 import java.util.Hashtable;
 
+import jalview.util.CaseInsensitiveString;
+
 public class PDBEntry
 {
 
@@ -154,6 +154,32 @@ public class PDBEntry
   {
   }
 
+  /**
+   * Entry point when file is not known and fileType may be string
+   * @param pdbId
+   * @param chain may be null
+   * @param fileType "pdb", "mmcif", or "bcif"; null defaults to mmcif
+   */
+  public PDBEntry(String pdbId, String chain, String fileType) {
+    this.id = pdbId.toLowerCase();
+    setChainCode(chain); // I note that PDB Chains ARE case-sensitive now
+    if (fileType == null)
+      fileType = "mmcif";
+    switch (fileType.toLowerCase()) {
+    case "pdb":
+      this.type = Type.PDB.toString();
+      break;
+    case "mmcif":
+      this.type = Type.MMCIF.toString();
+      break;
+    default:
+    case "bcif":
+      System.out.println("format " + fileType + " has not been implemented; using mmCIF");
+      this.type = Type.MMCIF.toString();
+      break;
+    }
+  }
+  
   public PDBEntry(String pdbId, String chain, PDBEntry.Type type,
           String filePath)
   {
@@ -255,6 +281,12 @@ public class PDBEntry
     return id;
   }
 
+  /**
+   * TODO 
+   * 
+   * @param key  "protocol" 
+   * @param value
+   */
   public void setProperty(String key, Object value)
   {
     if (this.properties == null)