JAL-1807 explicit imports (jalview.ws.*)

[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 c8f7ee7..0d61860 100644 (file)
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -20,12 +20,14 @@
  */
 package jalview.ws.dbsources;
 
-import com.stevesoft.pat.Regex;
-
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.DBRefSource;
+import jalview.io.FormatAdapter;
 import jalview.ws.seqfetcher.DbSourceProxy;
 
+import com.stevesoft.pat.Regex;
+
 /**
  * TODO: later PFAM is a complex datasource - it could return a tree in addition
  * to an alignment TODO: create interface to pass alignment properties and tree
@@ -41,8 +43,8 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
   {
     super();
     // all extensions of this PFAM source base class are DOMAINDB sources
-    addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
-    addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
+    addDbSourceProperty(DBRefSource.DOMAINDB);
+    addDbSourceProperty(DBRefSource.ALIGNMENTDB);
   }
 
   /*
@@ -74,7 +76,7 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
    * this doesn't work - DbSource is key for the hash of DbSourceProxy instances
    * - 1:many mapping for DbSource to proxy will be lost. * suggest : PFAM is an
    * 'alignment' source - means proxy is higher level than a sequence source.
-   * return jalview.datamodel.DBRefSource.PFAM; }
+   * return DBRefSource.PFAM; }
    */
 
   /*
@@ -117,16 +119,16 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
     // individual references to each sequence in each family alignment that's
     // retrieved.
     startQuery();
-    AlignmentI rcds = new jalview.io.FormatAdapter().readFile(getXFAMURL()
-            + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
+    AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL()
+            + queries.trim().toUpperCase(), FormatAdapter.URL,
             "STH");
     for (int s = 0, sNum = rcds.getHeight(); s < sNum; s++)
     {
       rcds.getSequenceAt(s).addDBRef(
-              new DBRefEntry(jalview.datamodel.DBRefSource.PFAM,
+new DBRefEntry(DBRefSource.PFAM,
               // getDbSource(),
                       getDbVersion(), queries.trim().toUpperCase()));
-      if (!getDbSource().equals(jalview.datamodel.DBRefSource.PFAM))
+      if (!getDbSource().equals(DBRefSource.PFAM))
       { // add the specific ref too
         rcds.getSequenceAt(s).addDBRef(
                 new DBRefEntry(getDbSource(), getDbVersion(), queries
@@ -153,7 +155,7 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
 
   public String getXfamSource()
   {
-    return jalview.datamodel.DBRefSource.PFAM;
+    return DBRefSource.PFAM;
   }
 
 }