JAL-2506 allow graduated colour as default in new Sequence Feature

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

diff --git a/src/jalview/ws/dbsources/Pfam.java b/src/jalview/ws/dbsources/Pfam.java
index 4f081ee..941bf1a 100644 (file)
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -23,6 +23,8 @@ package jalview.ws.dbsources;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
 import jalview.io.FormatAdapter;
 
 import com.stevesoft.pat.Regex;
@@ -119,14 +121,13 @@ abstract public class Pfam extends Xfam
     // retrieved.
     startQuery();
     AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL()
-            + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
-            "STH");
+            + 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()));
+      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(