Merge branch 'develop' into trialMerge

[jalview.git] / src / jalview / ws / dbsources / Pdb.java

diff --git a/src/jalview/ws/dbsources/Pdb.java b/src/jalview/ws/dbsources/Pdb.java
index 757ab83..0aae38f 100644 (file)
--- a/src/jalview/ws/dbsources/Pdb.java
+++ b/src/jalview/ws/dbsources/Pdb.java
@@ -50,15 +50,17 @@ import com.stevesoft.pat.Regex;
  */
 public class Pdb extends EbiFileRetrievedProxy
 {
+  private static final String SEPARATOR = "|";
+
+  private static final String COLON = ":";
+
+  private static final int PDB_ID_LENGTH = 4;
+
   public Pdb()
   {
     super();
   }
 
-  public static final String FEATURE_INSERTION = "INSERTION";
-
-  public static final String FEATURE_RES_NUM = "RESNUM";
-
   /*
    * (non-Javadoc)
    * 
@@ -67,7 +69,6 @@ public class Pdb extends EbiFileRetrievedProxy
   @Override
   public String getAccessionSeparator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -113,23 +114,28 @@ public class Pdb extends EbiFileRetrievedProxy
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
     AlignmentI pdbAlignment = null;
-    Vector result = new Vector();
     String chain = null;
     String id = null;
-    if (queries.indexOf(":") > -1)
+    if (queries.indexOf(COLON) > -1)
     {
-      chain = queries.substring(queries.indexOf(":") + 1);
-      id = queries.substring(0, queries.indexOf(":"));
+      chain = queries.substring(queries.indexOf(COLON) + 1);
+      id = queries.substring(0, queries.indexOf(COLON));
     }
     else
     {
       id = queries;
     }
-    if (queries.length() > 4 && chain == null)
+
+    /*
+     * extract chain code if it is appended to the id and we
+     * don't already have one
+     */
+    if (queries.length() > PDB_ID_LENGTH && chain == null)
     {
-      chain = queries.substring(4, 5);
-      id = queries.substring(0, 4);
+      chain = queries.substring(PDB_ID_LENGTH, PDB_ID_LENGTH + 1);
+      id = queries.substring(0, PDB_ID_LENGTH);
     }
+
     if (!isValidReference(id))
     {
       System.err.println("Ignoring invalid pdb query: '" + id + "'");
@@ -168,16 +174,16 @@ public class Pdb extends EbiFileRetrievedProxy
               chid = pid.getChainCode();
 
             }
-            ;
-
           }
           if (chain == null
                   || (chid != null && (chid.equals(chain)
                           || chid.trim().equals(chain.trim()) || (chain
                           .trim().length() == 0 && chid.equals("_")))))
           {
-            pdbcs.setName(jalview.datamodel.DBRefSource.PDB + "|" + id
-                    + "|" + pdbcs.getName());
+            // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
+            // TODO: suggest simplify naming to 1qip|A as default name defined
+            pdbcs.setName(jalview.datamodel.DBRefSource.PDB + SEPARATOR
+                    + id + SEPARATOR + pdbcs.getName());
             // Might need to add more metadata to the PDBEntry object
             // like below
             /*
@@ -268,7 +274,6 @@ public class Pdb extends EbiFileRetrievedProxy
     return 0;
   }
 
-
   /**
    * Returns a descriptor for suitable feature display settings with
    * <ul>