X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSequenceFetcher.java;h=db15079791e57c3783f02023f6bcef717b2f9d24;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=d225e428c8ffbae5eb56fe62705ad58e79b242e9;hpb=49db0dff1da16c3355b43a41498c1fc93ef47e91;p=jalview.git

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index d225e42..db15079 100755
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -20,21 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.api.FeatureSettingsModelI;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.SequenceI;
-import jalview.fts.core.GFTSPanel;
-import jalview.fts.service.pdb.PDBFTSPanel;
-import jalview.fts.service.uniprot.UniprotFTSPanel;
-import jalview.io.FileFormatI;
-import jalview.io.gff.SequenceOntologyI;
-import jalview.util.DBRefUtils;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.seqfetcher.DbSourceProxy;
-
 import java.awt.BorderLayout;
 import java.awt.Font;
 import java.awt.event.ActionEvent;
@@ -57,6 +42,23 @@ import javax.swing.JScrollPane;
 import javax.swing.JTextArea;
 import javax.swing.SwingConstants;
 
+import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
+import jalview.fts.core.GFTSPanel;
+import jalview.fts.service.pdb.PDBFTSPanel;
+import jalview.fts.service.threedbeacons.TDBeaconsFTSPanel;
+import jalview.fts.service.uniprot.UniprotFTSPanel;
+import jalview.io.FileFormatI;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
 /**
  * A panel where the use may choose a database source, and enter one or more
  * accessions, to retrieve entries from the database.
@@ -104,6 +106,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       return other.key == this.key;
     }
   }
+
   private static jalview.ws.SequenceFetcher sfetch = null;
 
   JLabel exampleAccession;
@@ -370,6 +373,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       }
     }
   }
+
   /**
    * Answers a semi-colon-delimited string with the example query or queries for
    * the selected database
@@ -491,9 +495,9 @@ public class SequenceFetcher extends JPanel implements Runnable
       text = text.replace(",", ";");
     }
     text = text.replaceAll("(\\s|[; ])+", ";");
-    if (!t0.equals(text)) 
+    if (!t0.equals(text))
     {
-   	  textArea.setText(text);
+      textArea.setText(text);
     }
     if (text.isEmpty())
     {
@@ -808,7 +812,7 @@ public class SequenceFetcher extends JPanel implements Runnable
       }
     } catch (Exception e)
     {
-      Cache.log.info("Error retrieving " + accession + " from "
+      Console.info("Error retrieving " + accession + " from "
               + proxy.getDbName(), e);
     }
     return success;
@@ -831,12 +835,12 @@ public class SequenceFetcher extends JPanel implements Runnable
 
     for (String q : queries)
     {
-    	// BH 2019.01.25 dbr is never used.
-//      DBRefEntry dbr = new DBRefEntry();
-//      dbr.setSource(proxy.getDbSource());
-//      dbr.setVersion(null);
+      // BH 2019.01.25 dbr is never used.
+      // DBRefEntry dbr = new DBRefEntry();
+      // dbr.setSource(proxy.getDbSource());
+      // dbr.setVersion(null);
       String accId = proxy.getAccessionIdFromQuery(q);
-//      dbr.setAccessionId(accId);
+      // dbr.setAccessionId(accId);
       boolean rfound = false;
       for (int r = 0, nr = rs.length; r < nr; r++)
       {