X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2FDBRefFetcher.java;h=95656796b40f8b432b5f0e8898dc7d4b6b318198;hb=98af16ccc5890b980f0c4f3acfb72d7128e3a6f0;hp=ad8c0f090de983a099e69c82841db784e2a7790a;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/ws/DBRefFetcher.java b/src/jalview/ws/DBRefFetcher.java
index ad8c0f0..9565679 100644
--- a/src/jalview/ws/DBRefFetcher.java
+++ b/src/jalview/ws/DBRefFetcher.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
@@ -30,6 +30,7 @@ import jalview.gui.CutAndPasteTransfer;
 import jalview.gui.Desktop;
 import jalview.gui.IProgressIndicator;
 import jalview.gui.OOMWarning;
+import jalview.ws.dbsources.das.api.jalviewSourceI;
 
 import java.lang.reflect.Array;
 import java.util.Enumeration;
@@ -37,8 +38,6 @@ import java.util.Hashtable;
 import java.util.StringTokenizer;
 import java.util.Vector;
 
-import org.biojava.dasobert.dasregistry.DasSource;
-
 import uk.ac.ebi.picr.model.UPEntry;
 
 /**
@@ -124,15 +123,15 @@ public class DBRefFetcher implements Runnable
     {
       // af.featureSettings_actionPerformed(null);
       String[] defdb = null, otherdb = sfetcher
-              .getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+              .getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
       Vector selsources = new Vector(), dasselsrc = (af.featureSettings != null) ? af.featureSettings
-              .getSelectedSources()
-              : new jalview.gui.DasSourceBrowser().getSelectedSources();
+              .getSelectedSources() : new jalview.gui.DasSourceBrowser()
+              .getSelectedSources();
       Enumeration en = dasselsrc.elements();
       while (en.hasMoreElements())
       {
-        DasSource src = (DasSource) en.nextElement();
-        selsources.addElement(src.getNickname());
+        jalviewSourceI src = (jalviewSourceI) en.nextElement();
+        selsources.addElement(src.getTitle());
       }
       int osel = 0;
       for (int o = 0; otherdb != null && o < otherdb.length; o++)
@@ -188,14 +187,12 @@ public class DBRefFetcher implements Runnable
     }
     // append additional sources
     String[] otherdb = sfetcher
-            .getDbInstances(jalview.ws.dbsources.DasSequenceSource.class);
+            .getDbInstances(jalview.ws.dbsources.das.datamodel.DasSequenceSource.class);
     if (otherdb != null && otherdb.length > 0)
     {
       String[] newsrc = new String[dbSources.length + otherdb.length];
       System.arraycopy(dbSources, 0, newsrc, 0, dbSources.length);
-      System
-              .arraycopy(otherdb, 0, newsrc, dbSources.length,
-                      otherdb.length);
+      System.arraycopy(otherdb, 0, newsrc, dbSources.length, otherdb.length);
       dbSources = newsrc;
     }
   }
@@ -387,9 +384,7 @@ public class DBRefFetcher implements Runnable
               for (int j = 0; j < uprefs.length; j++)
               {
                 addSeqId(sequence, uprefs[j].getAccessionId());
-                queries
-                        .addElement(uprefs[j].getAccessionId()
-                                .toUpperCase());
+                queries.addElement(uprefs[j].getAccessionId().toUpperCase());
               }
             }
             else
@@ -407,8 +402,9 @@ public class DBRefFetcher implements Runnable
                   try
                   {
                     presp = picrClient
-                            .getUPIForAccession(token, null, picrClient
-                                    .getMappedDatabaseNames(), null, true);
+                            .getUPIForAccession(token, null,
+                                    picrClient.getMappedDatabaseNames(),
+                                    null, true);
                   } catch (Exception e)
                   {
                     System.err.println("Exception with Picr for '" + token
@@ -447,11 +443,10 @@ public class DBRefFetcher implements Runnable
     } // all databases have been queries.
     if (sbuffer.length() > 0)
     {
-      output
-              .setText("Your sequences have been verified against known sequence databases. Some of the ids have been\n"
-                      + "altered, most likely the start/end residue will have been updated.\n"
-                      + "Save your alignment to maintain the updated id.\n\n"
-                      + sbuffer.toString());
+      output.setText("Your sequences have been verified against known sequence databases. Some of the ids have been\n"
+              + "altered, most likely the start/end residue will have been updated.\n"
+              + "Save your alignment to maintain the updated id.\n\n"
+              + sbuffer.toString());
       Desktop.addInternalFrame(output, "Sequence names updated ", 600, 300);
       // The above is the dataset, we must now find out the index
       // of the viewed sequence
@@ -496,9 +491,9 @@ public class DBRefFetcher implements Runnable
       // taking into account all accessionIds and names in the file
       Vector sequenceMatches = new Vector();
       // look for corresponding accession ids
-      DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(entry
-              .getDBRef(), new String[]
-      { dbSource });
+      DBRefEntry[] entryRefs = jalview.util.DBRefUtils.selectRefs(
+              entry.getDBRef(), new String[]
+              { dbSource });
       if (entryRefs == null)
       {
         System.err