X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPfam.java;h=fb4e3960d3396674fd1e8bfa6fd4894cf379e8e8;hb=7b9c6bc2db695c996b7bd4e536a6718b22042125;hp=5b8a3aec3c87a9976a86752afa805e3d03a38b13;hpb=230fac58c5afe1843bf7177834fe1bd1d7e6f9d5;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 5b8a3ae..fb4e396 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -20,12 +20,8 @@
  */
 package jalview.ws.dbsources;
 
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
+import jalview.bin.Cache;
 import jalview.datamodel.DBRefSource;
-import jalview.io.DataSourceType;
-import jalview.io.FileFormat;
-import jalview.io.FormatAdapter;
 
 import com.stevesoft.pat.Regex;
 
@@ -39,6 +35,8 @@ import com.stevesoft.pat.Regex;
  */
 abstract public class Pfam extends Xfam
 {
+  private static final String PFAM_DOMAIN_KEY = "PFAM_DOMAIN";
+  private static final String DEFAULT_PFAM_DOMAIN = "http://pfam.xfam.org";
 
   public Pfam()
   {
@@ -53,7 +51,6 @@ abstract public class Pfam extends Xfam
   @Override
   public String getAccessionSeparator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -65,7 +62,6 @@ abstract public class Pfam extends Xfam
   @Override
   public Regex getAccessionValidator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -96,48 +92,13 @@ abstract public class Pfam extends Xfam
   @Override
   public String getDbVersion()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
-  /**
-   * Returns base URL for selected Pfam alignment type
-   * 
-   * @return PFAM URL stub for this DbSource
-   */
-  @Override
-  protected abstract String getXFAMURL();
-
-  /*
-   * (non-Javadoc)
-   * 
-   * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
-   */
   @Override
-  public AlignmentI getSequenceRecords(String queries) throws Exception
+  protected String getURLPrefix()
   {
-    // TODO: this is not a perfect implementation. We need to be able to add
-    // individual references to each sequence in each family alignment that's
-    // retrieved.
-    startQuery();
-    AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL()
-            + queries.trim().toUpperCase(), DataSourceType.URL,
-            FileFormat.Stockholm);
-    for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
-    {
-      rcds.getSequenceAt(s).addDBRef(
-new DBRefEntry(DBRefSource.PFAM,
-              // getDbSource(),
-                      getDbVersion(), queries.trim().toUpperCase()));
-      if (!getDbSource().equals(DBRefSource.PFAM))
-      { // add the specific ref too
-        rcds.getSequenceAt(s).addDBRef(
-                new DBRefEntry(getDbSource(), getDbVersion(), queries
-                        .trim().toUpperCase()));
-      }
-    }
-    stopQuery();
-    return rcds;
+    return Cache.getDefault(PFAM_DOMAIN_KEY, DEFAULT_PFAM_DOMAIN);
   }
 
   /*