JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

[jalview.git] / src / jalview / io / WSWUBlastClient.java

diff --git a/src/jalview/io/WSWUBlastClient.java b/src/jalview/io/WSWUBlastClient.java
index 81b4e55..1e7cc40 100755 (executable)
--- a/src/jalview/io/WSWUBlastClient.java
+++ b/src/jalview/io/WSWUBlastClient.java
@@ -1,30 +1,48 @@
 /*
- * 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 2.9)
+ * Copyright (C) 2015 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.io;
 
-import java.util.*;
-
-import javax.swing.*;
-
-import jalview.analysis.*;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import uk.ac.ebi.www.*;
+import jalview.analysis.AlignSeq;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.Sequence;
+import jalview.gui.AlignmentPanel;
+import jalview.gui.CutAndPasteTransfer;
+import jalview.gui.Desktop;
+import jalview.util.MessageManager;
+
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.ImageIcon;
+import javax.swing.JOptionPane;
+
+import uk.ac.ebi.www.Data;
+import uk.ac.ebi.www.InputParams;
+import uk.ac.ebi.www.WSFile;
+import uk.ac.ebi.www.WSWUBlast;
+import uk.ac.ebi.www.WSWUBlastService;
+import uk.ac.ebi.www.WSWUBlastServiceLocator;
 
 /**
  * DOCUMENT ME!
@@ -56,16 +74,12 @@ public class WSWUBlastClient
   {
     this.ap = ap;
     this.al = al;
-    output
-            .setText("To display sequence features an exact Uniprot id with 100% sequence identity match must be entered."
-                    + "\nIn order to display these features, try changing the names of your sequences to the ids suggested below."
-                    + "\n\nRunning WSWUBlast at EBI."
-                    + "\nPlease quote Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R."
-                    + "\nSOAP-based services provided by the European Bioinformatics Institute."
-                    + "\nNucleic Acids Res. 33(1):W25-W28 (2005));");
+    output.setText(MessageManager
+            .getString("label.wswublast_client_credits"));
 
-    Desktop.addInternalFrame(output,
-            "BLASTing for unidentified sequences ", 800, 300);
+    Desktop.addInternalFrame(output, MessageManager
+            .getString("label.blasting_for_unidentified_sequence"), 800,
+            300);
 
     for (int i = 0; i < ids.size(); i++)
     {
@@ -122,8 +136,7 @@ public class WSWUBlastClient
             {
               maxFound = value;
               buffer.append(" " + id2 + " " + value + "%; ");
-              suggestedIds.addElement(new Object[]
-              { seq, id2 });
+              suggestedIds.addElement(new Object[] { seq, id2 });
             }
           }
         }
@@ -208,8 +221,9 @@ public class WSWUBlastClient
           imageIndex++;
           imageIndex %= 9;
           output.setFrameIcon(imageIcon[imageIndex]);
-          output.setTitle("BLASTing for unidentified sequences - "
-                  + jobsRunning + " jobs running.");
+          output.setTitle(MessageManager.formatMessage(
+                  "label.blasting_for_unidentified_sequence_jobs_running",
+                  new String[] { Integer.valueOf(jobsRunning).toString() }));
         } catch (Exception ex)
         {
         }
@@ -286,8 +300,8 @@ public class WSWUBlastClient
         Data inputs[] = new Data[1];
         Data input = new Data();
         input.setType("sequence");
-        input.setContent(AlignSeq.extractGaps("-. ", sequence
-                .getSequenceAsString()));
+        input.setContent(AlignSeq.extractGaps("-. ",
+                sequence.getSequenceAsString()));
         inputs[0] = input;
 
         WSWUBlastService service = new WSWUBlastServiceLocator();