JAL-3615 used gzip endpoints for Pfam and Rfam

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

diff --git a/src/jalview/ws/dbsources/Rfam.java b/src/jalview/ws/dbsources/Rfam.java
index 122ff8d..dba3e31 100644 (file)
--- a/src/jalview/ws/dbsources/Rfam.java
+++ b/src/jalview/ws/dbsources/Rfam.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,24 +20,36 @@
  */
 package jalview.ws.dbsources;
 
-import com.stevesoft.pat.Regex;
+import jalview.bin.Cache;
+import jalview.datamodel.DBRefSource;
 
-import jalview.ws.seqfetcher.DbSourceProxy;
+import com.stevesoft.pat.Regex;
 
 /**
  * Contains methods for fetching sequences from Rfam database
  * 
  * @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";
+
+  /*
+   * append to URLs to retrieve as a gzipped file
+   */
+  public static final String GZIPPED = "?gz=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 +58,9 @@ 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 +69,9 @@ 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 +95,15 @@ 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 +114,10 @@ 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;
   }
 
 }