X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FRfam.java;h=98df1662f4ac847fc332d98d818dcbd2a1ca0644;hb=1128674a17df402a2219d278ab332c291cb93443;hp=b07b8eabe5fcc773cb8c77f1c7b8d4e35c9aa463;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Rfam.java b/src/jalview/ws/dbsources/Rfam.java
index b07b8ea..98df166 100644
--- a/src/jalview/ws/dbsources/Rfam.java
+++ b/src/jalview/ws/dbsources/Rfam.java
@@ -20,7 +20,9 @@
  */
 package jalview.ws.dbsources;
 
-import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.bin.Cache;
+import jalview.datamodel.DBRefSource;
+import jalview.util.Platform;
 
 import com.stevesoft.pat.Regex;
 
@@ -29,15 +31,31 @@ import com.stevesoft.pat.Regex;
  * 
  * @author Lauren Michelle Lui
  */
-abstract public class Rfam extends Xfam implements DbSourceProxy
+abstract public class Rfam extends Xfam
 {
+  static final String RFAM_BASEURL_KEY = "RFAM_BASEURL";
+
+  private static final String DEFAULT_RFAM_BASEURL = "https://rfam.xfam.org";
+
+  static
+  {
+    Platform.addJ2SDirectDatabaseCall(DEFAULT_RFAM_BASEURL);
+  }
+
+  /*
+   * append to URLs to retrieve as a gzipped file
+   */
+  protected static final String GZIPPED = "?gzip=1&download=1";
+
+  @Override
+  protected String getURLPrefix()
+  {
+    return Cache.getDefault(RFAM_BASEURL_KEY, DEFAULT_RFAM_BASEURL);
+  }
 
   public Rfam()
   {
     super();
-    // all extensions of this RFAM source base class are DOMAINDB sources
-    addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
-    addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
   }
 
   /*
@@ -46,9 +64,9 @@ abstract public class Rfam extends Xfam implements DbSourceProxy
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator() Left here for
    * consistency with Pfam class
    */
+  @Override
   public String getAccessionSeparator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -57,9 +75,9 @@ abstract public class Rfam extends Xfam implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getAccessionValidator() * Left here for
    */
+  @Override
   public Regex getAccessionValidator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -83,23 +101,15 @@ abstract public class Rfam extends Xfam implements DbSourceProxy
   @Override
   public String getDbVersion()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
-  /**
-   * Returns base URL for selected Rfam alignment type
-   * 
-   * @return RFAM URL stub for this DbSource
-   */
-  @Override
-  protected abstract String getXFAMURL();
-
   /*
    * (non-Javadoc)
    * 
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
    */
+  @Override
   public boolean isValidReference(String accession)
   {
     return accession.indexOf("RF") == 0;
@@ -110,9 +120,10 @@ abstract public class Rfam extends Xfam implements DbSourceProxy
    * 
    * @see jalview.ws.dbsources.Xfam#getXfamSource()
    */
+  @Override
   public String getXfamSource()
   {
-    return jalview.datamodel.DBRefSource.RFAM;
+    return DBRefSource.RFAM;
   }
 
 }