X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FPfam.java;h=8877c34dc5e2e5c8e9511579f8fa181d2cd1d719;hb=b41bffc6a21d067bc272c1447c2f393dcf1118cf;hp=e4f24754f495c7e7db645b3156b30cc668892857;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index e4f2475..8877c34 100644
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 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.
  * 
@@ -20,10 +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.FormatAdapter;
 
 import com.stevesoft.pat.Regex;
 
@@ -37,6 +35,9 @@ import com.stevesoft.pat.Regex;
  */
 abstract public class Pfam extends Xfam
 {
+  static final String PFAM_BASEURL_KEY = "PFAM_BASEURL";
+
+  private static final String DEFAULT_PFAM_BASEURL = "https://pfam.xfam.org";
 
   public Pfam()
   {
@@ -51,7 +52,6 @@ abstract public class Pfam extends Xfam
   @Override
   public String getAccessionSeparator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -63,7 +63,6 @@ abstract public class Pfam extends Xfam
   @Override
   public Regex getAccessionValidator()
   {
-    // TODO Auto-generated method stub
     return null;
   }
 
@@ -94,47 +93,13 @@ 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(), jalview.io.FormatAdapter.URL,
-            "STH");
-    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_BASEURL_KEY, DEFAULT_PFAM_BASEURL);
   }
 
   /*