Merge branch 'develop' into update_212_Dec_merge_with_21125_chamges

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

diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java
index 65ba18b..a966ca1 100755 (executable)
--- 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
 {
 
@@ -165,6 +165,32 @@ 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)
   {
@@ -266,6 +292,12 @@ public class PDBEntry
     return id;
   }
 
+  /**
+   * TODO 
+   * 
+   * @param key  "protocol" 
+   * @param value
+   */
   public void setProperty(String key, Object value)
   {
     if (this.properties == null)