X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FXfam.java;h=3554f0177faf6efc15f549db7b1342f2a950e918;hb=36c3c5a0883c68bb8b007bb392668977331f9f1a;hp=c392ce67e341d757d812c52d6ae8460fa70241dc;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/ws/dbsources/Xfam.java b/src/jalview/ws/dbsources/Xfam.java
index c392ce6..3554f01 100644
--- a/src/jalview/ws/dbsources/Xfam.java
+++ b/src/jalview/ws/dbsources/Xfam.java
@@ -22,6 +22,9 @@ package jalview.ws.dbsources;
 
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
 import jalview.ws.seqfetcher.DbSourceProxyImpl;
 
 /**
@@ -40,10 +43,12 @@ public abstract class Xfam extends DbSourceProxyImpl
 
   protected abstract String getXFAMURL();
 
+  @Override
   public abstract String getDbVersion();
 
   abstract String getXfamSource();
 
+  @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
     // TODO: this is not a perfect implementation. We need to be able to add
@@ -51,9 +56,9 @@ public abstract class Xfam extends DbSourceProxyImpl
     // retrieved.
     startQuery();
     // TODO: trap HTTP 404 exceptions and return null
-    AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
-            + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
-            "STH");
+    AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL()
+            + queries.trim().toUpperCase() + getXFAMURLSUFFIX(),
+            DataSourceType.URL, FileFormat.Stockholm);
     for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
     {
       rcds.getSequenceAt(s).addDBRef(new DBRefEntry(getXfamSource(),
@@ -70,4 +75,23 @@ public abstract class Xfam extends DbSourceProxyImpl
     return rcds;
   }
 
+  /**
+   * Pfam and Rfam provide alignments
+   */
+  @Override
+  public boolean isAlignmentSource()
+  {
+    return true;
+  }
+
+  /**
+   * default suffix to append the retrieval URL for this source.
+   * 
+   * @return "" for most Xfam sources
+   */
+  public String getXFAMURLSUFFIX()
+  {
+    return "";
+  }
+
 }