JAL-2344 override to ignore (obsolete?) JalviewFileView

[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 0643267..5b8a3ae 100644 (file)
--- a/src/jalview/ws/dbsources/Pfam.java
+++ b/src/jalview/ws/dbsources/Pfam.java
@@ -1,29 +1,33 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * 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.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * PURPOSE.  See the GNU General Public License for more details.
  * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.ws.dbsources;
 
-
-import com.stevesoft.pat.Regex;
-
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.DBRefEntry;
-import jalview.ws.seqfetcher.DbSourceProxy;
+import jalview.datamodel.DBRefSource;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FormatAdapter;
+
+import com.stevesoft.pat.Regex;
 
 /**
  * TODO: later PFAM is a complex datasource - it could return a tree in addition
@@ -33,15 +37,12 @@ import jalview.ws.seqfetcher.DbSourceProxy;
  * @author JimP
  * 
  */
-abstract public class Pfam extends Xfam implements DbSourceProxy
+abstract public class Pfam extends Xfam
 {
 
   public Pfam()
   {
     super();
-    // all extensions of this PFAM source base class are DOMAINDB sources
-    addDbSourceProperty(jalview.datamodel.DBRefSource.DOMAINDB);
-    addDbSourceProperty(jalview.datamodel.DBRefSource.ALIGNMENTDB);
   }
 
   /*
@@ -49,6 +50,7 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getAccessionSeparator()
    */
+  @Override
   public String getAccessionSeparator()
   {
     // TODO Auto-generated method stub
@@ -60,6 +62,7 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getAccessionValidator()
    */
+  @Override
   public Regex getAccessionValidator()
   {
     // TODO Auto-generated method stub
@@ -110,22 +113,23 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#getSequenceRecords(java.lang.String[])
    */
+  @Override
   public AlignmentI getSequenceRecords(String queries) throws Exception
   {
     // 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 jalview.io.FormatAdapter().readFile(getXFAMURL()
-            + queries.trim().toUpperCase(), jalview.io.FormatAdapter.URL,
-            "STH");
+    AlignmentI rcds = new FormatAdapter().readFile(getXFAMURL()
+            + queries.trim().toUpperCase(), DataSourceType.URL,
+            FileFormat.Stockholm);
     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
@@ -141,6 +145,7 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
    * 
    * @see jalview.ws.DbSourceProxy#isValidReference(java.lang.String)
    */
+  @Override
   public boolean isValidReference(String accession)
   {
     return accession.indexOf("PF") == 0;
@@ -150,9 +155,10 @@ abstract public class Pfam extends Xfam implements DbSourceProxy
    * public String getDbName() { return "PFAM"; // getDbSource(); }
    */
 
+  @Override
   public String getXfamSource()
   {
-    return jalview.datamodel.DBRefSource.PFAM;
+    return DBRefSource.PFAM;
   }
 
 }